Starting phenix.real_space_refine on Tue Jul 7 01:58:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0w_66447/07_2026/9x0w_66447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0w_66447/07_2026/9x0w_66447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0w_66447/07_2026/9x0w_66447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0w_66447/07_2026/9x0w_66447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0w_66447/07_2026/9x0w_66447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0w_66447/07_2026/9x0w_66447.map" } resolution = 3.02 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 140 5.16 5 C 26138 2.51 5 N 6916 2.21 5 O 7910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 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: 41118 Number of models: 1 Model: "" Number of chains: 41 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: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "P" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "Q" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "R" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "S" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "T" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "U" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "V" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "W" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "X" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "Y" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "Z" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "a" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "b" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.38, per 1000 atoms: 0.23 Number of scatterers: 41118 At special positions: 0 Unit cell: (172.53, 174.15, 138.51, 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 140 16.00 P 14 15.00 O 7910 8.00 N 6916 7.00 C 26138 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS S 101 " - pdb=" SG CYS S 104 " distance=2.02 Simple disulfide: pdb=" SG CYS T 101 " - pdb=" SG CYS T 104 " distance=2.02 Simple disulfide: pdb=" SG CYS U 101 " - pdb=" SG CYS U 104 " distance=2.02 Simple disulfide: pdb=" SG CYS V 101 " - pdb=" SG CYS V 104 " distance=2.02 Simple disulfide: pdb=" SG CYS W 101 " - pdb=" SG CYS W 104 " distance=2.02 Simple disulfide: pdb=" SG CYS X 101 " - pdb=" SG CYS X 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 101 " - pdb=" SG CYS Y 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 101 " - pdb=" SG CYS Z 104 " distance=2.02 Simple disulfide: pdb=" SG CYS a 101 " - pdb=" SG CYS a 104 " distance=2.02 Simple disulfide: pdb=" SG CYS b 101 " - pdb=" SG CYS b 104 " distance=2.02 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: 3.49 Conformation dependent library (CDL) restraints added in 2.0 seconds 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9744 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 58 sheets defined 25.1% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.943A pdb=" N ARG A 682 " --> pdb=" O TYR A 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 removed outlier: 3.706A 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 80 Processing helix chain 'O' and resid 81 through 90 Processing helix chain 'O' and resid 90 through 100 removed outlier: 4.043A pdb=" N ARG O 100 " --> pdb=" O GLU O 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 401 Processing helix chain 'B' and resid 430 through 444 Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'C' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'E' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'F' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'G' and resid 679 through 683 removed outlier: 3.942A 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 430 through 444 Processing helix chain 'H' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'I' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'J' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'K' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'L' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'M' and resid 679 through 683 removed outlier: 3.943A 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 430 through 444 Processing helix chain 'N' and resid 679 through 683 removed outlier: 3.943A pdb=" N ARG N 682 " --> pdb=" O TYR N 679 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'P' and resid 81 through 90 Processing helix chain 'P' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG P 100 " --> pdb=" O GLU P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.706A 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 80 Processing helix chain 'Q' and resid 81 through 90 Processing helix chain 'Q' and resid 90 through 100 removed outlier: 4.043A pdb=" N ARG Q 100 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'R' and resid 81 through 90 Processing helix chain 'R' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG R 100 " --> pdb=" O GLU R 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'S' and resid 81 through 90 Processing helix chain 'S' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG S 100 " --> pdb=" O GLU S 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'T' and resid 81 through 90 Processing helix chain 'T' and resid 90 through 100 removed outlier: 4.043A pdb=" N ARG T 100 " --> pdb=" O GLU T 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'U' and resid 81 through 90 Processing helix chain 'U' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 53 removed outlier: 3.706A 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 80 Processing helix chain 'V' and resid 81 through 90 Processing helix chain 'V' and resid 90 through 100 removed outlier: 4.043A pdb=" N ARG V 100 " --> pdb=" O GLU V 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'W' and resid 81 through 90 Processing helix chain 'W' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG W 100 " --> pdb=" O GLU W 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'X' and resid 81 through 90 Processing helix chain 'X' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG X 100 " --> pdb=" O GLU X 96 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 53 removed outlier: 3.706A 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 80 Processing helix chain 'Y' and resid 81 through 90 Processing helix chain 'Y' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG Y 100 " --> pdb=" O GLU Y 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'Z' and resid 81 through 90 Processing helix chain 'Z' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG Z 100 " --> pdb=" O GLU Z 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 53 removed outlier: 3.705A 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 80 Processing helix chain 'a' and resid 81 through 90 Processing helix chain 'a' and resid 90 through 100 removed outlier: 4.043A pdb=" N ARG a 100 " --> pdb=" O GLU a 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 53 removed outlier: 3.704A 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 80 Processing helix chain 'b' and resid 81 through 90 Processing helix chain 'b' and resid 90 through 100 removed outlier: 4.042A pdb=" N ARG b 100 " --> pdb=" O GLU b 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 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 1506 hydrogen bonds defined for protein. 4101 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: 9.10 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9027 1.33 - 1.45: 8507 1.45 - 1.57: 23962 1.57 - 1.70: 28 1.70 - 1.82: 224 Bond restraints: 41748 Sorted by residual: bond pdb=" CA GLU N 617 " pdb=" C GLU N 617 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.23e-02 6.61e+03 1.47e+01 bond pdb=" CA GLU B 617 " pdb=" C GLU B 617 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.23e-02 6.61e+03 1.46e+01 bond pdb=" CA GLU J 617 " pdb=" C GLU J 617 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.23e-02 6.61e+03 1.46e+01 bond pdb=" CA GLU K 617 " pdb=" C GLU K 617 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.23e-02 6.61e+03 1.46e+01 bond pdb=" CA GLU L 617 " pdb=" C GLU L 617 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.23e-02 6.61e+03 1.45e+01 ... (remaining 41743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 53714 1.95 - 3.91: 2168 3.91 - 5.86: 412 5.86 - 7.81: 98 7.81 - 9.76: 42 Bond angle restraints: 56434 Sorted by residual: angle pdb=" N GLU D 617 " pdb=" CA GLU D 617 " pdb=" C GLU D 617 " ideal model delta sigma weight residual 108.73 100.23 8.50 1.63e+00 3.76e-01 2.72e+01 angle pdb=" N VAL H 618 " pdb=" CA VAL H 618 " pdb=" C VAL H 618 " ideal model delta sigma weight residual 108.11 115.38 -7.27 1.40e+00 5.10e-01 2.70e+01 angle pdb=" N GLU C 617 " pdb=" CA GLU C 617 " pdb=" C GLU C 617 " ideal model delta sigma weight residual 108.73 100.27 8.46 1.63e+00 3.76e-01 2.70e+01 angle pdb=" N GLU M 617 " pdb=" CA GLU M 617 " pdb=" C GLU M 617 " ideal model delta sigma weight residual 108.73 100.27 8.46 1.63e+00 3.76e-01 2.70e+01 angle pdb=" N VAL E 618 " pdb=" CA VAL E 618 " pdb=" C VAL E 618 " ideal model delta sigma weight residual 108.11 115.37 -7.26 1.40e+00 5.10e-01 2.69e+01 ... (remaining 56429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 22680 16.56 - 33.12: 2142 33.12 - 49.68: 603 49.68 - 66.25: 237 66.25 - 82.81: 42 Dihedral angle restraints: 25704 sinusoidal: 10528 harmonic: 15176 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 -120.63 34.63 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS P 101 " pdb=" SG CYS P 101 " pdb=" SG CYS P 104 " pdb=" CB CYS P 104 " ideal model delta sinusoidal sigma weight residual -86.00 -120.63 34.63 1 1.00e+01 1.00e-02 1.70e+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 -120.62 34.62 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 25701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3901 0.037 - 0.074: 1571 0.074 - 0.112: 726 0.112 - 0.149: 281 0.149 - 0.186: 73 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA PRO N 678 " pdb=" N PRO N 678 " pdb=" C PRO N 678 " pdb=" CB PRO N 678 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA PRO D 678 " pdb=" N PRO D 678 " pdb=" C PRO D 678 " pdb=" CB PRO D 678 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA PRO G 678 " pdb=" N PRO G 678 " pdb=" C PRO G 678 " pdb=" CB PRO G 678 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 6549 not shown) Planarity restraints: 7266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 677 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO D 678 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 678 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 678 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 677 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO I 678 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO I 678 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 678 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 677 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO L 678 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO L 678 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 678 " -0.043 5.00e-02 4.00e+02 ... (remaining 7263 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 12035 2.82 - 3.34: 35895 3.34 - 3.86: 70541 3.86 - 4.38: 84163 4.38 - 4.90: 146499 Nonbonded interactions: 349133 Sorted by model distance: nonbonded pdb=" OH TYR A 483 " pdb=" OD1 ASP B 544 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR H 483 " pdb=" OD1 ASP I 544 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR L 483 " pdb=" OD1 ASP M 544 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR E 483 " pdb=" OD1 ASP F 544 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR D 483 " pdb=" OD1 ASP E 544 " model vdw 2.303 3.040 ... (remaining 349128 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 375 through 706) selection = (chain 'B' and resid 375 through 706) selection = (chain 'C' and resid 375 through 706) selection = (chain 'D' and resid 375 through 706) selection = (chain 'E' and resid 375 through 706) selection = (chain 'F' and resid 375 through 706) selection = (chain 'G' and resid 375 through 706) selection = (chain 'H' and resid 375 through 706) selection = (chain 'I' and resid 375 through 706) selection = (chain 'J' and resid 375 through 706) selection = (chain 'K' and resid 375 through 706) selection = (chain 'L' and resid 375 through 706) selection = (chain 'M' and resid 375 through 706) 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: 9.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.830 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.940 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.007 0.056 41776 Z= 0.484 Angle : 0.934 9.764 56490 Z= 0.589 Chirality : 0.054 0.186 6552 Planarity : 0.007 0.078 7266 Dihedral : 15.354 82.807 15876 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.95 % Allowed : 16.46 % Favored : 82.59 % 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: 5236 helix: 1.17 (0.14), residues: 1148 sheet: 0.56 (0.10), residues: 2240 loop : -0.48 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 682 TYR 0.011 0.001 TYR D 627 PHE 0.026 0.002 PHE O 57 TRP 0.003 0.001 TRP C 471 HIS 0.001 0.000 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.48 (41748) covalent geometry : angle 0.93413 / 0.59 (56434) SS BOND : bond 0.00616 / 0.38 ( 28) SS BOND : angle 0.84511 / 0.61 ( 56) hydrogen bonds : bond 0.15373 / 10.03 ( 1506) hydrogen bonds : angle 7.70867 / 5.39 ( 4101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 476 time to evaluate : 1.389 Fit side-chains REVERT: A 412 ARG cc_start: 0.6702 (mtt180) cc_final: 0.6390 (ttt90) REVERT: A 639 LYS cc_start: 0.8140 (tttt) cc_final: 0.7934 (ttpp) REVERT: B 412 ARG cc_start: 0.6753 (mtt180) cc_final: 0.6389 (ttt90) REVERT: B 639 LYS cc_start: 0.8204 (tttt) cc_final: 0.7953 (ttpp) REVERT: C 412 ARG cc_start: 0.6847 (mtt180) cc_final: 0.6551 (ttt90) REVERT: D 412 ARG cc_start: 0.6767 (mtt180) cc_final: 0.6451 (ttt90) REVERT: E 412 ARG cc_start: 0.6794 (mtt180) cc_final: 0.6401 (ttt90) REVERT: E 639 LYS cc_start: 0.8109 (tttt) cc_final: 0.7907 (ttpp) REVERT: F 412 ARG cc_start: 0.6746 (mtt180) cc_final: 0.6319 (ttt90) REVERT: F 557 GLU cc_start: 0.7671 (tt0) cc_final: 0.7433 (tt0) REVERT: F 639 LYS cc_start: 0.8099 (tttt) cc_final: 0.7844 (ttpp) REVERT: F 705 MET cc_start: 0.8249 (mmm) cc_final: 0.7647 (mtp) REVERT: G 412 ARG cc_start: 0.6778 (mtt180) cc_final: 0.6494 (ttt90) REVERT: H 412 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6421 (ttt90) REVERT: I 412 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6397 (ttt90) REVERT: I 639 LYS cc_start: 0.8206 (tttt) cc_final: 0.7955 (ttpp) REVERT: J 412 ARG cc_start: 0.6844 (mtt180) cc_final: 0.6547 (ttt90) REVERT: K 412 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6453 (ttt90) REVERT: L 412 ARG cc_start: 0.6791 (mtt180) cc_final: 0.6403 (ttt90) REVERT: L 639 LYS cc_start: 0.8110 (tttt) cc_final: 0.7900 (ttpp) REVERT: M 412 ARG cc_start: 0.6758 (mtt180) cc_final: 0.6331 (ttt90) REVERT: M 557 GLU cc_start: 0.7665 (tt0) cc_final: 0.7415 (tt0) REVERT: M 639 LYS cc_start: 0.8102 (tttt) cc_final: 0.7848 (ttpp) REVERT: M 705 MET cc_start: 0.8247 (mmm) cc_final: 0.7644 (mtp) REVERT: N 412 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6495 (ttt90) REVERT: Q 105 THR cc_start: 0.7488 (p) cc_final: 0.7219 (p) REVERT: X 105 THR cc_start: 0.7459 (p) cc_final: 0.7180 (p) outliers start: 42 outliers final: 40 residues processed: 518 average time/residue: 0.2701 time to fit residues: 221.9982 Evaluate side-chains 380 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 340 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 0.2980 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 GLN A 488 ASN A 629 ASN B 397 GLN B 488 ASN B 629 ASN C 397 GLN C 488 ASN C 629 ASN D 397 GLN D 488 ASN D 629 ASN E 397 GLN E 488 ASN F 397 GLN F 449 GLN F 488 ASN G 397 GLN G 488 ASN G 629 ASN H 397 GLN H 449 GLN H 488 ASN H 629 ASN I 397 GLN I 488 ASN I 629 ASN J 397 GLN J 488 ASN J 629 ASN K 397 GLN K 488 ASN K 629 ASN L 397 GLN L 488 ASN M 397 GLN M 449 GLN M 488 ASN M 629 ASN N 397 GLN N 488 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121865 restraints weight = 42552.008| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.19 r_work: 0.3338 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41776 Z= 0.140 Angle : 0.543 6.291 56490 Z= 0.282 Chirality : 0.047 0.137 6552 Planarity : 0.005 0.039 7266 Dihedral : 9.925 66.853 6340 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.32 % Allowed : 16.46 % Favored : 80.22 % 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: 0.73 (0.11), residues: 5236 helix: 2.11 (0.15), residues: 1148 sheet: 0.54 (0.10), residues: 2240 loop : -0.55 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 432 TYR 0.006 0.001 TYR H 427 PHE 0.014 0.001 PHE N 673 TRP 0.008 0.001 TRP N 471 HIS 0.001 0.000 HIS L 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (41748) covalent geometry : angle 0.54305 / 0.28 (56434) SS BOND : bond 0.00061 / 0.04 ( 28) SS BOND : angle 0.59454 / 0.43 ( 56) hydrogen bonds : bond 0.03742 / 2.51 ( 1506) hydrogen bonds : angle 5.60687 / 3.92 ( 4101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 304 time to evaluate : 1.461 Fit side-chains REVERT: A 412 ARG cc_start: 0.6931 (mtt180) cc_final: 0.6075 (ttt90) REVERT: A 639 LYS cc_start: 0.8034 (tttt) cc_final: 0.7778 (ttpp) REVERT: B 412 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6102 (ttt90) REVERT: B 629 ASN cc_start: 0.7658 (t0) cc_final: 0.7416 (t0) REVERT: B 639 LYS cc_start: 0.8111 (tttt) cc_final: 0.7841 (ttpp) REVERT: C 412 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6139 (ttt90) REVERT: D 412 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6235 (ttt90) REVERT: D 629 ASN cc_start: 0.7627 (t0) cc_final: 0.7424 (t0) REVERT: D 705 MET cc_start: 0.8609 (mmm) cc_final: 0.8223 (mtp) REVERT: E 412 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6191 (ttt90) REVERT: E 629 ASN cc_start: 0.7511 (t0) cc_final: 0.7254 (t0) REVERT: E 705 MET cc_start: 0.8431 (mmm) cc_final: 0.8133 (mtp) REVERT: F 412 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6065 (ttt90) REVERT: F 557 GLU cc_start: 0.8071 (tt0) cc_final: 0.7762 (tt0) REVERT: F 629 ASN cc_start: 0.7616 (t0) cc_final: 0.7412 (t0) REVERT: F 639 LYS cc_start: 0.7993 (tttt) cc_final: 0.7760 (ttpp) REVERT: F 705 MET cc_start: 0.8499 (mmm) cc_final: 0.8117 (mtp) REVERT: G 412 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6238 (ttt90) REVERT: G 629 ASN cc_start: 0.7674 (t0) cc_final: 0.7468 (t0) REVERT: H 412 ARG cc_start: 0.6936 (mtt180) cc_final: 0.6090 (ttt90) REVERT: I 412 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6123 (ttt90) REVERT: I 629 ASN cc_start: 0.7647 (t0) cc_final: 0.7404 (t0) REVERT: I 639 LYS cc_start: 0.8107 (tttt) cc_final: 0.7841 (ttpp) REVERT: J 412 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6139 (ttt90) REVERT: K 412 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6228 (ttt90) REVERT: K 629 ASN cc_start: 0.7627 (t0) cc_final: 0.7421 (t0) REVERT: K 705 MET cc_start: 0.8604 (mmm) cc_final: 0.8230 (mtp) REVERT: L 412 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6186 (ttt90) REVERT: L 629 ASN cc_start: 0.7515 (t0) cc_final: 0.7258 (t0) REVERT: L 639 LYS cc_start: 0.8017 (tttt) cc_final: 0.7804 (tttm) REVERT: L 705 MET cc_start: 0.8421 (mmm) cc_final: 0.8133 (mtp) REVERT: M 412 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6062 (ttt90) REVERT: M 557 GLU cc_start: 0.8046 (tt0) cc_final: 0.7737 (tt0) REVERT: M 629 ASN cc_start: 0.7690 (t0) cc_final: 0.7471 (t0) REVERT: M 639 LYS cc_start: 0.7982 (tttt) cc_final: 0.7761 (ttpp) REVERT: M 705 MET cc_start: 0.8512 (mmm) cc_final: 0.8135 (mtp) REVERT: N 412 ARG cc_start: 0.7146 (mtt180) cc_final: 0.6220 (ttt90) REVERT: Q 105 THR cc_start: 0.7075 (p) cc_final: 0.6825 (p) outliers start: 147 outliers final: 104 residues processed: 434 average time/residue: 0.2453 time to fit residues: 176.6230 Evaluate side-chains 372 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 268 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain H residue 414 SER Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 414 SER Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 690 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 505 optimal weight: 10.0000 chunk 242 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 452 optimal weight: 20.0000 chunk 459 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 395 optimal weight: 7.9990 chunk 445 optimal weight: 20.0000 chunk 529 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 ASN C 629 ASN F 449 GLN G 449 GLN H 629 ASN J 629 ASN M 449 GLN N 449 GLN N 629 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112521 restraints weight = 43611.227| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.06 r_work: 0.3269 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 41776 Z= 0.277 Angle : 0.617 6.536 56490 Z= 0.320 Chirality : 0.050 0.145 6552 Planarity : 0.005 0.035 7266 Dihedral : 10.126 59.966 6332 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.91 % Allowed : 16.18 % Favored : 79.91 % 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: 0.42 (0.11), residues: 5236 helix: 2.01 (0.15), residues: 1148 sheet: 0.26 (0.10), residues: 2240 loop : -0.71 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Y 55 TYR 0.010 0.001 TYR U 45 PHE 0.018 0.002 PHE A 673 TRP 0.009 0.002 TRP N 471 HIS 0.002 0.001 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.28 (41748) covalent geometry : angle 0.61747 / 0.32 (56434) SS BOND : bond 0.00275 / 0.18 ( 28) SS BOND : angle 0.33435 / 0.23 ( 56) hydrogen bonds : bond 0.03838 / 2.58 ( 1506) hydrogen bonds : angle 5.51734 / 3.87 ( 4101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 342 time to evaluate : 1.531 Fit side-chains REVERT: A 412 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6120 (ttt90) REVERT: A 486 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: A 639 LYS cc_start: 0.8024 (tttt) cc_final: 0.7784 (ttpp) REVERT: A 705 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8262 (mtm) REVERT: B 412 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6194 (tpt170) REVERT: B 629 ASN cc_start: 0.7644 (t0) cc_final: 0.7347 (t0) REVERT: B 639 LYS cc_start: 0.8057 (tttt) cc_final: 0.7739 (ttpp) REVERT: B 705 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8050 (mtm) REVERT: C 412 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6272 (ttt90) REVERT: C 687 ASP cc_start: 0.8495 (m-30) cc_final: 0.7729 (m-30) REVERT: C 705 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8224 (mtm) REVERT: D 412 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6306 (ttt90) REVERT: D 629 ASN cc_start: 0.7721 (t0) cc_final: 0.7482 (t0) REVERT: D 687 ASP cc_start: 0.8422 (m-30) cc_final: 0.7629 (m-30) REVERT: D 705 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: E 412 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6077 (ttt90) REVERT: E 629 ASN cc_start: 0.7428 (t0) cc_final: 0.7204 (t0) REVERT: E 687 ASP cc_start: 0.8482 (m-30) cc_final: 0.7687 (m-30) REVERT: E 705 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: F 412 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6082 (tpt170) REVERT: F 557 GLU cc_start: 0.7950 (tt0) cc_final: 0.7663 (tt0) REVERT: F 629 ASN cc_start: 0.7682 (t0) cc_final: 0.7456 (t0) REVERT: F 639 LYS cc_start: 0.7995 (tttt) cc_final: 0.7703 (ttpp) REVERT: F 641 GLU cc_start: 0.8532 (tt0) cc_final: 0.8268 (tt0) REVERT: F 687 ASP cc_start: 0.8435 (m-30) cc_final: 0.7611 (m-30) REVERT: F 705 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8300 (mtp) REVERT: G 412 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6213 (ttt90) REVERT: G 629 ASN cc_start: 0.7699 (t0) cc_final: 0.7472 (t0) REVERT: G 663 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7339 (mt-10) REVERT: G 687 ASP cc_start: 0.8467 (m-30) cc_final: 0.7701 (m-30) REVERT: H 412 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6074 (ttt90) REVERT: H 486 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: H 641 GLU cc_start: 0.8413 (tt0) cc_final: 0.8142 (tt0) REVERT: H 705 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: I 412 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6190 (tpt170) REVERT: I 629 ASN cc_start: 0.7637 (t0) cc_final: 0.7339 (t0) REVERT: I 639 LYS cc_start: 0.8051 (tttt) cc_final: 0.7736 (ttpp) REVERT: I 705 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: J 412 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6266 (ttt90) REVERT: J 687 ASP cc_start: 0.8529 (m-30) cc_final: 0.7778 (m-30) REVERT: K 412 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6306 (ttt90) REVERT: K 629 ASN cc_start: 0.7733 (t0) cc_final: 0.7493 (t0) REVERT: K 705 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8317 (mtm) REVERT: L 412 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6073 (ttt90) REVERT: L 629 ASN cc_start: 0.7401 (t0) cc_final: 0.7174 (t0) REVERT: L 639 LYS cc_start: 0.7903 (tttt) cc_final: 0.7684 (tttm) REVERT: L 663 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7588 (mt-10) REVERT: L 687 ASP cc_start: 0.8473 (m-30) cc_final: 0.7667 (m-30) REVERT: L 705 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8197 (mtp) REVERT: M 412 ARG cc_start: 0.7197 (mtt180) cc_final: 0.6088 (tpt170) REVERT: M 557 GLU cc_start: 0.7941 (tt0) cc_final: 0.7650 (tt0) REVERT: M 629 ASN cc_start: 0.7688 (t0) cc_final: 0.7443 (t0) REVERT: M 639 LYS cc_start: 0.7984 (tttt) cc_final: 0.7687 (ttpp) REVERT: M 641 GLU cc_start: 0.8528 (tt0) cc_final: 0.8263 (tt0) REVERT: M 687 ASP cc_start: 0.8452 (m-30) cc_final: 0.7638 (m-30) REVERT: M 705 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8320 (mtp) REVERT: N 412 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6215 (ttt90) REVERT: N 663 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7362 (mt-10) REVERT: N 687 ASP cc_start: 0.8434 (m-30) cc_final: 0.7663 (m-30) REVERT: P 47 MET cc_start: 0.4562 (mtt) cc_final: 0.4335 (mtt) outliers start: 173 outliers final: 128 residues processed: 483 average time/residue: 0.2286 time to fit residues: 184.7183 Evaluate side-chains 459 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 318 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 705 MET Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain F residue 705 MET Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 451 MET Chi-restraints excluded: chain H residue 486 ASP Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 705 MET Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 705 MET Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain K residue 705 MET Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain L residue 705 MET Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 486 ASP Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain M residue 705 MET Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 690 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 127 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 453 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 447 optimal weight: 8.9990 chunk 355 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 ASN C 629 ASN H 629 ASN J 629 ASN N 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115123 restraints weight = 43061.137| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.06 r_work: 0.3288 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 41776 Z= 0.155 Angle : 0.518 5.830 56490 Z= 0.266 Chirality : 0.046 0.137 6552 Planarity : 0.004 0.032 7266 Dihedral : 9.641 59.838 6332 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.02 % Allowed : 16.25 % Favored : 79.72 % 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: 0.49 (0.12), residues: 5236 helix: 2.37 (0.15), residues: 1148 sheet: 0.18 (0.10), residues: 2240 loop : -0.72 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 55 TYR 0.007 0.001 TYR A 679 PHE 0.012 0.001 PHE B 673 TRP 0.004 0.001 TRP D 471 HIS 0.000 0.000 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (41748) covalent geometry : angle 0.51779 / 0.27 (56434) SS BOND : bond 0.00135 / 0.09 ( 28) SS BOND : angle 0.24097 / 0.17 ( 56) hydrogen bonds : bond 0.03204 / 2.18 ( 1506) hydrogen bonds : angle 5.20314 / 3.65 ( 4101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 318 time to evaluate : 1.528 Fit side-chains REVERT: A 412 ARG cc_start: 0.6904 (mtt180) cc_final: 0.5956 (ttt90) REVERT: A 451 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7704 (tpp) REVERT: A 639 LYS cc_start: 0.7984 (tttt) cc_final: 0.7723 (ttpp) REVERT: B 412 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6104 (tpt170) REVERT: B 629 ASN cc_start: 0.7686 (t0) cc_final: 0.7368 (t0) REVERT: B 687 ASP cc_start: 0.8316 (m-30) cc_final: 0.7552 (m-30) REVERT: C 412 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6214 (tpt170) REVERT: C 687 ASP cc_start: 0.8434 (m-30) cc_final: 0.7644 (m-30) REVERT: D 412 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6242 (ttt90) REVERT: D 629 ASN cc_start: 0.7729 (t0) cc_final: 0.7478 (t0) REVERT: D 687 ASP cc_start: 0.8358 (m-30) cc_final: 0.7546 (m-30) REVERT: E 412 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6032 (ttt90) REVERT: E 629 ASN cc_start: 0.7496 (t0) cc_final: 0.7214 (t0) REVERT: E 663 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7525 (mt-10) REVERT: E 687 ASP cc_start: 0.8337 (m-30) cc_final: 0.7516 (m-30) REVERT: E 705 MET cc_start: 0.8485 (mmm) cc_final: 0.8187 (mtp) REVERT: F 412 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6217 (tpt170) REVERT: F 557 GLU cc_start: 0.7904 (tt0) cc_final: 0.7623 (tt0) REVERT: F 629 ASN cc_start: 0.7698 (t0) cc_final: 0.7462 (t0) REVERT: F 639 LYS cc_start: 0.7978 (tttt) cc_final: 0.7701 (ttpp) REVERT: F 641 GLU cc_start: 0.8439 (tt0) cc_final: 0.8221 (tt0) REVERT: F 687 ASP cc_start: 0.8431 (m-30) cc_final: 0.7610 (m-30) REVERT: F 705 MET cc_start: 0.8516 (mmm) cc_final: 0.8197 (mtp) REVERT: G 412 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6177 (ttt90) REVERT: G 629 ASN cc_start: 0.7712 (t0) cc_final: 0.7461 (t0) REVERT: G 663 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7408 (mt-10) REVERT: G 687 ASP cc_start: 0.8442 (m-30) cc_final: 0.7674 (m-30) REVERT: H 412 ARG cc_start: 0.6935 (mtt180) cc_final: 0.5987 (tpt170) REVERT: I 412 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6090 (tpt170) REVERT: I 629 ASN cc_start: 0.7683 (t0) cc_final: 0.7365 (t0) REVERT: J 412 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6207 (tpt170) REVERT: J 687 ASP cc_start: 0.8467 (m-30) cc_final: 0.7677 (m-30) REVERT: K 412 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6240 (ttt90) REVERT: K 629 ASN cc_start: 0.7736 (t0) cc_final: 0.7486 (t0) REVERT: K 687 ASP cc_start: 0.8497 (m-30) cc_final: 0.7681 (m-30) REVERT: L 412 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6030 (ttt90) REVERT: L 629 ASN cc_start: 0.7496 (t0) cc_final: 0.7211 (t0) REVERT: L 639 LYS cc_start: 0.7906 (tttt) cc_final: 0.7623 (tttm) REVERT: L 663 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7529 (mt-10) REVERT: L 687 ASP cc_start: 0.8328 (m-30) cc_final: 0.7508 (m-30) REVERT: L 705 MET cc_start: 0.8486 (mmm) cc_final: 0.8192 (mtp) REVERT: M 412 ARG cc_start: 0.7271 (mtt180) cc_final: 0.6205 (tpt170) REVERT: M 557 GLU cc_start: 0.7901 (tt0) cc_final: 0.7619 (tt0) REVERT: M 629 ASN cc_start: 0.7763 (t0) cc_final: 0.7512 (t0) REVERT: M 639 LYS cc_start: 0.7966 (tttt) cc_final: 0.7688 (ttpp) REVERT: M 641 GLU cc_start: 0.8426 (tt0) cc_final: 0.8210 (tt0) REVERT: M 687 ASP cc_start: 0.8455 (m-30) cc_final: 0.7623 (m-30) REVERT: M 705 MET cc_start: 0.8521 (mmm) cc_final: 0.8211 (mtp) REVERT: N 412 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6183 (ttt90) REVERT: N 663 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7390 (mt-10) REVERT: N 687 ASP cc_start: 0.8399 (m-30) cc_final: 0.7651 (m-30) REVERT: P 47 MET cc_start: 0.4612 (mtt) cc_final: 0.4398 (mtt) outliers start: 178 outliers final: 138 residues processed: 472 average time/residue: 0.2394 time to fit residues: 189.5750 Evaluate side-chains 445 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 306 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 665 SER Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 665 SER Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 419 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 232 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 472 optimal weight: 4.9990 chunk 411 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 389 optimal weight: 0.6980 chunk 521 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 ASN C 629 ASN H 629 ASN J 629 ASN N 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120101 restraints weight = 42283.879| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.08 r_work: 0.3341 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41776 Z= 0.109 Angle : 0.484 5.509 56490 Z= 0.248 Chirality : 0.046 0.136 6552 Planarity : 0.004 0.030 7266 Dihedral : 9.062 59.861 6331 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.07 % Allowed : 16.48 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.12), residues: 5236 helix: 2.56 (0.15), residues: 1162 sheet: 0.20 (0.11), residues: 2240 loop : -0.69 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 432 TYR 0.011 0.001 TYR C 483 PHE 0.008 0.001 PHE J 673 TRP 0.002 0.000 TRP N 480 HIS 0.000 0.000 HIS L 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (41748) covalent geometry : angle 0.48381 / 0.25 (56434) SS BOND : bond 0.00130 / 0.08 ( 28) SS BOND : angle 0.19822 / 0.14 ( 56) hydrogen bonds : bond 0.02910 / 1.98 ( 1506) hydrogen bonds : angle 4.99838 / 3.50 ( 4101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 309 time to evaluate : 1.628 Fit side-chains REVERT: A 412 ARG cc_start: 0.6850 (mtt180) cc_final: 0.5856 (ttt90) REVERT: A 451 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: A 639 LYS cc_start: 0.7960 (tttt) cc_final: 0.7733 (ttmm) REVERT: A 687 ASP cc_start: 0.8363 (m-30) cc_final: 0.7956 (m-30) REVERT: B 412 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6044 (tpt170) REVERT: B 629 ASN cc_start: 0.7683 (t0) cc_final: 0.7374 (t0) REVERT: C 412 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6068 (tpt170) REVERT: C 451 MET cc_start: 0.8216 (tpp) cc_final: 0.7833 (tpt) REVERT: C 687 ASP cc_start: 0.8383 (m-30) cc_final: 0.7643 (m-30) REVERT: D 412 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6175 (tpt170) REVERT: D 629 ASN cc_start: 0.7816 (t0) cc_final: 0.7577 (t0) REVERT: D 687 ASP cc_start: 0.8389 (m-30) cc_final: 0.7567 (m-30) REVERT: E 412 ARG cc_start: 0.7034 (mtt180) cc_final: 0.5892 (tpt170) REVERT: E 629 ASN cc_start: 0.7606 (t0) cc_final: 0.7357 (t0) REVERT: E 663 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7460 (mt-10) REVERT: E 687 ASP cc_start: 0.8263 (m-30) cc_final: 0.7412 (m-30) REVERT: E 705 MET cc_start: 0.8485 (mmm) cc_final: 0.8176 (mtp) REVERT: F 412 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6118 (tpt170) REVERT: F 629 ASN cc_start: 0.7711 (t0) cc_final: 0.7449 (t0) REVERT: F 639 LYS cc_start: 0.7942 (tttt) cc_final: 0.7678 (ttpp) REVERT: F 641 GLU cc_start: 0.8471 (tt0) cc_final: 0.8256 (tt0) REVERT: F 705 MET cc_start: 0.8514 (mmm) cc_final: 0.8266 (mtt) REVERT: G 412 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6043 (tpt170) REVERT: G 629 ASN cc_start: 0.7718 (t0) cc_final: 0.7463 (t0) REVERT: G 663 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7416 (mt-10) REVERT: H 412 ARG cc_start: 0.6827 (mtt180) cc_final: 0.5823 (ttt90) REVERT: H 687 ASP cc_start: 0.8386 (m-30) cc_final: 0.8004 (m-30) REVERT: I 412 ARG cc_start: 0.7157 (mtt180) cc_final: 0.6044 (tpt170) REVERT: I 629 ASN cc_start: 0.7681 (t0) cc_final: 0.7375 (t0) REVERT: I 687 ASP cc_start: 0.8287 (m-30) cc_final: 0.7478 (m-30) REVERT: J 412 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6075 (tpt170) REVERT: K 412 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6172 (tpt170) REVERT: K 629 ASN cc_start: 0.7829 (t0) cc_final: 0.7591 (t0) REVERT: L 412 ARG cc_start: 0.7049 (mtt180) cc_final: 0.5902 (tpt170) REVERT: L 629 ASN cc_start: 0.7618 (t0) cc_final: 0.7373 (t0) REVERT: L 639 LYS cc_start: 0.7843 (tttt) cc_final: 0.7485 (ttpp) REVERT: L 663 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7441 (mt-10) REVERT: L 687 ASP cc_start: 0.8263 (m-30) cc_final: 0.7415 (m-30) REVERT: L 705 MET cc_start: 0.8470 (mmm) cc_final: 0.8164 (mtp) REVERT: M 412 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6109 (tpt170) REVERT: M 557 GLU cc_start: 0.7844 (tt0) cc_final: 0.7487 (tt0) REVERT: M 629 ASN cc_start: 0.7797 (t0) cc_final: 0.7525 (t0) REVERT: M 639 LYS cc_start: 0.7946 (tttt) cc_final: 0.7676 (ttpp) REVERT: M 641 GLU cc_start: 0.8467 (tt0) cc_final: 0.8252 (tt0) REVERT: M 705 MET cc_start: 0.8527 (mmm) cc_final: 0.8287 (mtt) REVERT: N 412 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6057 (tpt170) REVERT: N 663 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7391 (mt-10) outliers start: 180 outliers final: 135 residues processed: 467 average time/residue: 0.2429 time to fit residues: 190.4276 Evaluate side-chains 439 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 303 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 656 ILE Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 258 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 530 optimal weight: 0.9980 chunk 457 optimal weight: 9.9990 chunk 385 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 375 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 ASN C 629 ASN H 629 ASN J 629 ASN N 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119597 restraints weight = 42493.644| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.08 r_work: 0.3336 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41776 Z= 0.124 Angle : 0.486 5.552 56490 Z= 0.249 Chirality : 0.046 0.135 6552 Planarity : 0.004 0.032 7266 Dihedral : 8.764 58.978 6318 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.57 % Allowed : 16.16 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.12), residues: 5236 helix: 2.60 (0.15), residues: 1162 sheet: 0.16 (0.11), residues: 2240 loop : -0.69 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 432 TYR 0.009 0.001 TYR C 679 PHE 0.010 0.001 PHE C 673 TRP 0.003 0.001 TRP J 471 HIS 0.000 0.000 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (41748) covalent geometry : angle 0.48580 / 0.25 (56434) SS BOND : bond 0.00123 / 0.08 ( 28) SS BOND : angle 0.17837 / 0.13 ( 56) hydrogen bonds : bond 0.02908 / 1.98 ( 1506) hydrogen bonds : angle 4.94881 / 3.47 ( 4101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 309 time to evaluate : 1.584 Fit side-chains REVERT: A 412 ARG cc_start: 0.6937 (mtt180) cc_final: 0.5807 (tpt170) REVERT: A 451 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7648 (tpp) REVERT: A 639 LYS cc_start: 0.7990 (tttt) cc_final: 0.7763 (ttmm) REVERT: A 687 ASP cc_start: 0.8423 (m-30) cc_final: 0.8083 (m-30) REVERT: B 412 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6019 (tpt170) REVERT: B 629 ASN cc_start: 0.7689 (t0) cc_final: 0.7361 (t0) REVERT: C 412 ARG cc_start: 0.7233 (mtt180) cc_final: 0.6123 (tpt170) REVERT: C 451 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7865 (tpt) REVERT: C 687 ASP cc_start: 0.8410 (m-30) cc_final: 0.7662 (m-30) REVERT: C 705 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8185 (mtm) REVERT: D 412 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6230 (tpt170) REVERT: D 629 ASN cc_start: 0.7862 (t0) cc_final: 0.7612 (t0) REVERT: D 687 ASP cc_start: 0.8362 (m-30) cc_final: 0.7539 (m-30) REVERT: E 412 ARG cc_start: 0.7051 (mtt180) cc_final: 0.5865 (tpt170) REVERT: E 629 ASN cc_start: 0.7635 (t0) cc_final: 0.7426 (t0) REVERT: E 663 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7491 (mt-10) REVERT: E 687 ASP cc_start: 0.8290 (m-30) cc_final: 0.7425 (m-30) REVERT: E 705 MET cc_start: 0.8508 (mmm) cc_final: 0.8201 (mtp) REVERT: F 412 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6097 (tpt170) REVERT: F 557 GLU cc_start: 0.7866 (tt0) cc_final: 0.7514 (tt0) REVERT: F 629 ASN cc_start: 0.7850 (t0) cc_final: 0.7580 (t0) REVERT: F 641 GLU cc_start: 0.8464 (tt0) cc_final: 0.8253 (tt0) REVERT: F 687 ASP cc_start: 0.8400 (m-30) cc_final: 0.7559 (m-30) REVERT: F 705 MET cc_start: 0.8528 (mmm) cc_final: 0.8281 (mtt) REVERT: G 412 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6056 (tpt170) REVERT: G 629 ASN cc_start: 0.7761 (t0) cc_final: 0.7493 (t0) REVERT: G 663 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7415 (mt-10) REVERT: G 687 ASP cc_start: 0.8415 (m-30) cc_final: 0.7631 (m-30) REVERT: H 412 ARG cc_start: 0.6922 (mtt180) cc_final: 0.5801 (tpt170) REVERT: H 687 ASP cc_start: 0.8437 (m-30) cc_final: 0.8092 (m-30) REVERT: H 705 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8183 (mtm) REVERT: I 412 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6023 (tpt170) REVERT: I 629 ASN cc_start: 0.7686 (t0) cc_final: 0.7359 (t0) REVERT: I 687 ASP cc_start: 0.8325 (m-30) cc_final: 0.7499 (m-30) REVERT: J 412 ARG cc_start: 0.7240 (mtt180) cc_final: 0.6123 (tpt170) REVERT: J 451 MET cc_start: 0.8204 (tpp) cc_final: 0.7823 (tpt) REVERT: J 687 ASP cc_start: 0.8449 (m-30) cc_final: 0.7721 (m-30) REVERT: K 412 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6222 (tpt170) REVERT: K 629 ASN cc_start: 0.7878 (t0) cc_final: 0.7629 (t0) REVERT: L 412 ARG cc_start: 0.7062 (mtt180) cc_final: 0.5869 (tpt170) REVERT: L 629 ASN cc_start: 0.7632 (t0) cc_final: 0.7420 (t0) REVERT: L 663 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7476 (mt-10) REVERT: L 687 ASP cc_start: 0.8287 (m-30) cc_final: 0.7425 (m-30) REVERT: L 705 MET cc_start: 0.8492 (mmm) cc_final: 0.8188 (mtp) REVERT: M 412 ARG cc_start: 0.7146 (mtt180) cc_final: 0.6085 (tpt170) REVERT: M 557 GLU cc_start: 0.7860 (tt0) cc_final: 0.7505 (tt0) REVERT: M 629 ASN cc_start: 0.7884 (t0) cc_final: 0.7605 (t0) REVERT: M 641 GLU cc_start: 0.8466 (tt0) cc_final: 0.8256 (tt0) REVERT: M 687 ASP cc_start: 0.8420 (m-30) cc_final: 0.7589 (m-30) REVERT: M 705 MET cc_start: 0.8541 (mmm) cc_final: 0.8300 (mtt) REVERT: N 412 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6062 (tpt170) REVERT: N 663 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7419 (mt-10) REVERT: N 687 ASP cc_start: 0.8359 (m-30) cc_final: 0.7582 (m-30) outliers start: 202 outliers final: 175 residues processed: 472 average time/residue: 0.2390 time to fit residues: 189.5614 Evaluate side-chains 483 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 304 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 597 GLU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 451 MET Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 597 GLU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 705 MET Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 656 ILE Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 451 MET Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 597 GLU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 665 SER Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 665 SER Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 656 ILE Chi-restraints excluded: chain M residue 665 SER Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 447 VAL Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 696 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 48 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 475 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 385 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 ASN C 629 ASN H 629 ASN J 629 ASN N 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119586 restraints weight = 42475.259| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.08 r_work: 0.3338 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41776 Z= 0.122 Angle : 0.482 5.619 56490 Z= 0.247 Chirality : 0.046 0.135 6552 Planarity : 0.004 0.034 7266 Dihedral : 8.563 57.747 6318 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.54 % Allowed : 16.32 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.12), residues: 5236 helix: 2.65 (0.15), residues: 1162 sheet: 0.10 (0.11), residues: 2240 loop : -0.69 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 685 TYR 0.009 0.001 TYR K 679 PHE 0.009 0.001 PHE E 673 TRP 0.003 0.001 TRP J 471 HIS 0.001 0.000 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (41748) covalent geometry : angle 0.48225 / 0.25 (56434) SS BOND : bond 0.00128 / 0.08 ( 28) SS BOND : angle 0.16865 / 0.12 ( 56) hydrogen bonds : bond 0.02878 / 1.96 ( 1506) hydrogen bonds : angle 4.90094 / 3.43 ( 4101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 317 time to evaluate : 1.598 Fit side-chains REVERT: A 412 ARG cc_start: 0.6962 (mtt180) cc_final: 0.5775 (tpt170) REVERT: A 451 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7682 (tpp) REVERT: A 639 LYS cc_start: 0.7967 (tttt) cc_final: 0.7738 (ttmm) REVERT: A 705 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8140 (mtm) REVERT: B 412 ARG cc_start: 0.7153 (mtt180) cc_final: 0.5957 (tpt170) REVERT: B 629 ASN cc_start: 0.7714 (t0) cc_final: 0.7410 (t0) REVERT: C 412 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6056 (tpt170) REVERT: C 451 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7818 (tpt) REVERT: C 687 ASP cc_start: 0.8416 (m-30) cc_final: 0.7658 (m-30) REVERT: D 412 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6158 (tpt170) REVERT: D 629 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7495 (t0) REVERT: D 687 ASP cc_start: 0.8353 (m-30) cc_final: 0.7500 (m-30) REVERT: E 412 ARG cc_start: 0.7052 (mtt180) cc_final: 0.5891 (tpt170) REVERT: E 629 ASN cc_start: 0.7634 (t0) cc_final: 0.7418 (t0) REVERT: E 663 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7479 (mt-10) REVERT: E 687 ASP cc_start: 0.8306 (m-30) cc_final: 0.7437 (m-30) REVERT: F 412 ARG cc_start: 0.7100 (mtt180) cc_final: 0.5968 (tpt170) REVERT: F 557 GLU cc_start: 0.7846 (tt0) cc_final: 0.7470 (tt0) REVERT: F 629 ASN cc_start: 0.7854 (t0) cc_final: 0.7601 (t0) REVERT: F 687 ASP cc_start: 0.8398 (m-30) cc_final: 0.7547 (m-30) REVERT: F 705 MET cc_start: 0.8546 (mmm) cc_final: 0.8299 (mtt) REVERT: G 412 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6123 (tpt170) REVERT: G 629 ASN cc_start: 0.7789 (t0) cc_final: 0.7506 (t0) REVERT: G 663 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7393 (mt-10) REVERT: G 687 ASP cc_start: 0.8404 (m-30) cc_final: 0.7600 (m-30) REVERT: H 412 ARG cc_start: 0.6931 (mtt180) cc_final: 0.5801 (tpt170) REVERT: H 705 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: I 412 ARG cc_start: 0.7156 (mtt180) cc_final: 0.5956 (tpt170) REVERT: I 629 ASN cc_start: 0.7714 (t0) cc_final: 0.7401 (t0) REVERT: I 687 ASP cc_start: 0.8341 (m-30) cc_final: 0.7503 (m-30) REVERT: J 412 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6059 (tpt170) REVERT: J 451 MET cc_start: 0.8240 (tpp) cc_final: 0.7823 (tpt) REVERT: J 687 ASP cc_start: 0.8469 (m-30) cc_final: 0.7649 (m-30) REVERT: K 412 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6144 (tpt170) REVERT: K 629 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7512 (t0) REVERT: L 412 ARG cc_start: 0.7057 (mtt180) cc_final: 0.5895 (tpt170) REVERT: L 629 ASN cc_start: 0.7629 (t0) cc_final: 0.7408 (t0) REVERT: L 639 LYS cc_start: 0.7744 (tttt) cc_final: 0.7380 (ttpp) REVERT: L 663 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7471 (mt-10) REVERT: L 687 ASP cc_start: 0.8305 (m-30) cc_final: 0.7439 (m-30) REVERT: M 412 ARG cc_start: 0.7093 (mtt180) cc_final: 0.5962 (tpt170) REVERT: M 557 GLU cc_start: 0.7838 (tt0) cc_final: 0.7457 (tt0) REVERT: M 629 ASN cc_start: 0.7810 (t0) cc_final: 0.7523 (t0) REVERT: M 687 ASP cc_start: 0.8413 (m-30) cc_final: 0.7574 (m-30) REVERT: M 705 MET cc_start: 0.8555 (mmm) cc_final: 0.8312 (mtt) REVERT: N 412 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6126 (tpt170) REVERT: N 663 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7405 (mt-10) REVERT: N 687 ASP cc_start: 0.8378 (m-30) cc_final: 0.7555 (m-30) outliers start: 201 outliers final: 174 residues processed: 475 average time/residue: 0.2413 time to fit residues: 192.4621 Evaluate side-chains 492 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 312 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 629 ASN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 451 MET Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 597 GLU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 705 MET Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 656 ILE Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 597 GLU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 629 ASN Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 665 SER Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 665 SER Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 656 ILE Chi-restraints excluded: chain M residue 665 SER Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 447 VAL Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 597 GLU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 656 ILE Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 696 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 134 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 464 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 340 optimal weight: 0.9980 chunk 495 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 331 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 345 optimal weight: 5.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 GLN B 430 GLN C 430 GLN C 629 ASN D 430 GLN E 430 GLN F 430 GLN G 430 GLN H 430 GLN H 629 ASN I 430 GLN J 430 GLN J 629 ASN K 430 GLN L 430 GLN M 430 GLN N 430 GLN N 629 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114522 restraints weight = 43264.273| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.07 r_work: 0.3284 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 41776 Z= 0.267 Angle : 0.584 6.202 56490 Z= 0.300 Chirality : 0.049 0.138 6552 Planarity : 0.005 0.039 7266 Dihedral : 9.287 59.142 6318 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.72 % Allowed : 16.57 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 5236 helix: 2.40 (0.15), residues: 1162 sheet: -0.18 (0.11), residues: 2268 loop : -0.75 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 685 TYR 0.009 0.001 TYR K 679 PHE 0.017 0.002 PHE C 673 TRP 0.009 0.001 TRP J 471 HIS 0.002 0.001 HIS H 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.27 (41748) covalent geometry : angle 0.58401 / 0.30 (56434) SS BOND : bond 0.00261 / 0.17 ( 28) SS BOND : angle 0.23020 / 0.16 ( 56) hydrogen bonds : bond 0.03459 / 2.35 ( 1506) hydrogen bonds : angle 5.17690 / 3.63 ( 4101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 329 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6054 (tpt170) REVERT: A 451 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7756 (tpp) REVERT: A 705 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: B 412 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6133 (tpt170) REVERT: B 629 ASN cc_start: 0.7763 (t0) cc_final: 0.7457 (t0) REVERT: B 687 ASP cc_start: 0.8629 (m-30) cc_final: 0.8347 (m-30) REVERT: B 705 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: C 412 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6214 (tpt170) REVERT: C 451 MET cc_start: 0.8415 (tpp) cc_final: 0.8007 (tpt) REVERT: C 687 ASP cc_start: 0.8478 (m-30) cc_final: 0.7645 (m-30) REVERT: C 705 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8282 (mtm) REVERT: D 412 ARG cc_start: 0.7367 (mtt180) cc_final: 0.6275 (tpt170) REVERT: D 629 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7594 (t0) REVERT: D 705 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8233 (mtm) REVERT: E 412 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6058 (tpt170) REVERT: E 451 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8177 (tpt) REVERT: E 629 ASN cc_start: 0.7610 (t0) cc_final: 0.7379 (t0) REVERT: E 663 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7525 (mt-10) REVERT: E 705 MET cc_start: 0.8521 (mmm) cc_final: 0.8227 (mtp) REVERT: F 412 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6084 (tpt170) REVERT: F 557 GLU cc_start: 0.7949 (tt0) cc_final: 0.7669 (tt0) REVERT: F 629 ASN cc_start: 0.7921 (t0) cc_final: 0.7691 (t0) REVERT: F 687 ASP cc_start: 0.8433 (m-30) cc_final: 0.7580 (m-30) REVERT: G 412 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6268 (tpt170) REVERT: G 629 ASN cc_start: 0.7793 (t0) cc_final: 0.7540 (t0) REVERT: G 663 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7404 (mt-10) REVERT: G 687 ASP cc_start: 0.8519 (m-30) cc_final: 0.7639 (m-30) REVERT: H 412 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6006 (tpt170) REVERT: H 641 GLU cc_start: 0.8407 (tt0) cc_final: 0.8107 (tt0) REVERT: H 705 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8249 (mtm) REVERT: I 412 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6134 (tpt170) REVERT: I 629 ASN cc_start: 0.7715 (t0) cc_final: 0.7410 (t0) REVERT: I 705 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7999 (mtm) REVERT: J 412 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6217 (tpt170) REVERT: J 451 MET cc_start: 0.8379 (tpp) cc_final: 0.7966 (tpt) REVERT: J 687 ASP cc_start: 0.8501 (m-30) cc_final: 0.7773 (m-30) REVERT: K 412 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6274 (tpt170) REVERT: K 629 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7608 (t0) REVERT: K 705 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8227 (mtm) REVERT: L 412 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6054 (tpt170) REVERT: L 629 ASN cc_start: 0.7613 (t0) cc_final: 0.7401 (t0) REVERT: L 663 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7525 (mt-10) REVERT: M 412 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6070 (tpt170) REVERT: M 557 GLU cc_start: 0.7933 (tt0) cc_final: 0.7649 (tt0) REVERT: M 629 ASN cc_start: 0.7941 (t0) cc_final: 0.7671 (t0) REVERT: M 687 ASP cc_start: 0.8443 (m-30) cc_final: 0.7569 (m-30) REVERT: N 412 ARG cc_start: 0.7415 (mtt180) cc_final: 0.6262 (tpt170) REVERT: N 687 ASP cc_start: 0.8515 (m-30) cc_final: 0.7642 (m-30) outliers start: 209 outliers final: 170 residues processed: 493 average time/residue: 0.2390 time to fit residues: 198.7543 Evaluate side-chains 498 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 317 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 629 ASN Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 597 GLU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 629 ASN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 597 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 597 GLU Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 629 ASN Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 705 MET Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 447 VAL Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 705 MET Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 597 GLU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 629 ASN Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 597 GLU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 629 ASN Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 665 SER Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain K residue 705 MET Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 665 SER Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 597 GLU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 665 SER Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 597 GLU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 696 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 174 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 507 optimal weight: 6.9990 chunk 490 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 629 ASN H 629 ASN J 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118154 restraints weight = 42781.499| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.08 r_work: 0.3336 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41776 Z= 0.126 Angle : 0.504 5.812 56490 Z= 0.258 Chirality : 0.046 0.138 6552 Planarity : 0.004 0.042 7266 Dihedral : 8.918 59.294 6314 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.07 % Allowed : 17.47 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.12), residues: 5236 helix: 2.59 (0.15), residues: 1162 sheet: -0.11 (0.11), residues: 2268 loop : -0.74 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 686 TYR 0.010 0.001 TYR I 627 PHE 0.010 0.001 PHE B 673 TRP 0.004 0.001 TRP I 480 HIS 0.001 0.000 HIS J 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (41748) covalent geometry : angle 0.50374 / 0.26 (56434) SS BOND : bond 0.00112 / 0.07 ( 28) SS BOND : angle 0.18729 / 0.13 ( 56) hydrogen bonds : bond 0.02998 / 2.05 ( 1506) hydrogen bonds : angle 4.97793 / 3.48 ( 4101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 318 time to evaluate : 1.644 Fit side-chains REVERT: A 412 ARG cc_start: 0.7069 (mtt180) cc_final: 0.5913 (tpt170) REVERT: A 451 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7660 (tpp) REVERT: A 687 ASP cc_start: 0.8435 (m-30) cc_final: 0.8154 (m-30) REVERT: B 412 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6020 (tpt170) REVERT: B 629 ASN cc_start: 0.7730 (t0) cc_final: 0.7433 (t0) REVERT: C 412 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6207 (tpt170) REVERT: C 451 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7965 (tpt) REVERT: C 687 ASP cc_start: 0.8511 (m-30) cc_final: 0.7689 (m-30) REVERT: C 705 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8209 (mtm) REVERT: D 412 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6187 (tpt170) REVERT: D 629 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7573 (t0) REVERT: D 687 ASP cc_start: 0.8481 (m-30) cc_final: 0.7789 (m-30) REVERT: E 412 ARG cc_start: 0.7103 (mtt180) cc_final: 0.5973 (tpt170) REVERT: E 451 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8033 (tpt) REVERT: E 629 ASN cc_start: 0.7617 (t0) cc_final: 0.7408 (t0) REVERT: E 663 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7501 (mt-10) REVERT: E 687 ASP cc_start: 0.8369 (m-30) cc_final: 0.7542 (m-30) REVERT: F 412 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6039 (tpt170) REVERT: F 557 GLU cc_start: 0.7887 (tt0) cc_final: 0.7539 (tt0) REVERT: F 629 ASN cc_start: 0.7953 (t0) cc_final: 0.7713 (t0) REVERT: F 687 ASP cc_start: 0.8440 (m-30) cc_final: 0.7593 (m-30) REVERT: G 412 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6159 (tpt170) REVERT: G 629 ASN cc_start: 0.7763 (t0) cc_final: 0.7518 (t0) REVERT: G 663 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7430 (mt-10) REVERT: G 687 ASP cc_start: 0.8477 (m-30) cc_final: 0.7642 (m-30) REVERT: H 412 ARG cc_start: 0.7073 (mtt180) cc_final: 0.5920 (tpt170) REVERT: H 687 ASP cc_start: 0.8441 (m-30) cc_final: 0.8163 (m-30) REVERT: I 412 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6017 (tpt170) REVERT: I 629 ASN cc_start: 0.7729 (t0) cc_final: 0.7435 (t0) REVERT: I 687 ASP cc_start: 0.8428 (m-30) cc_final: 0.7651 (m-30) REVERT: J 412 ARG cc_start: 0.7269 (mtt180) cc_final: 0.6202 (tpt170) REVERT: J 451 MET cc_start: 0.8336 (tpp) cc_final: 0.7909 (tpp) REVERT: J 687 ASP cc_start: 0.8447 (m-30) cc_final: 0.7617 (m-30) REVERT: K 412 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6180 (tpt170) REVERT: K 629 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7571 (t0) REVERT: L 412 ARG cc_start: 0.7114 (mtt180) cc_final: 0.5976 (tpt170) REVERT: L 451 MET cc_start: 0.8293 (tpt) cc_final: 0.7922 (tpt) REVERT: L 629 ASN cc_start: 0.7629 (t0) cc_final: 0.7420 (t0) REVERT: L 663 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7511 (mt-10) REVERT: L 687 ASP cc_start: 0.8372 (m-30) cc_final: 0.7545 (m-30) REVERT: M 412 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6025 (tpt170) REVERT: M 557 GLU cc_start: 0.7877 (tt0) cc_final: 0.7526 (tt0) REVERT: M 629 ASN cc_start: 0.7903 (t0) cc_final: 0.7630 (t0) REVERT: M 687 ASP cc_start: 0.8452 (m-30) cc_final: 0.7594 (m-30) REVERT: N 412 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6159 (tpt170) REVERT: N 663 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7434 (mt-10) REVERT: N 687 ASP cc_start: 0.8469 (m-30) cc_final: 0.7633 (m-30) outliers start: 180 outliers final: 163 residues processed: 461 average time/residue: 0.2413 time to fit residues: 186.6919 Evaluate side-chains 478 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 309 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 597 GLU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 629 ASN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 451 MET Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 518 SER Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 597 GLU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 597 GLU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 629 ASN Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 665 SER Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 665 SER Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 665 SER Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 597 GLU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 656 ILE Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 696 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 439 optimal weight: 2.9990 chunk 531 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 482 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 348 optimal weight: 0.9980 chunk 490 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 449 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117051 restraints weight = 42800.393| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.08 r_work: 0.3318 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 41776 Z= 0.157 Angle : 0.512 5.775 56490 Z= 0.262 Chirality : 0.047 0.137 6552 Planarity : 0.004 0.044 7266 Dihedral : 8.843 59.673 6314 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.87 % Allowed : 17.97 % Favored : 78.16 % 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: 0.34 (0.12), residues: 5236 helix: 2.60 (0.15), residues: 1162 sheet: -0.15 (0.11), residues: 2268 loop : -0.72 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 100 TYR 0.009 0.001 TYR A 679 PHE 0.012 0.001 PHE I 673 TRP 0.004 0.001 TRP D 471 HIS 0.001 0.000 HIS H 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (41748) covalent geometry : angle 0.51255 / 0.26 (56434) SS BOND : bond 0.00164 / 0.11 ( 28) SS BOND : angle 0.15701 / 0.11 ( 56) hydrogen bonds : bond 0.03061 / 2.09 ( 1506) hydrogen bonds : angle 5.00020 / 3.50 ( 4101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 302 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.7105 (mtt180) cc_final: 0.5918 (tpt170) REVERT: A 451 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: A 687 ASP cc_start: 0.8456 (m-30) cc_final: 0.8138 (m-30) REVERT: B 412 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6045 (tpt170) REVERT: B 629 ASN cc_start: 0.7743 (t0) cc_final: 0.7450 (t0) REVERT: B 687 ASP cc_start: 0.8524 (m-30) cc_final: 0.8285 (m-30) REVERT: C 412 ARG cc_start: 0.7388 (mtt180) cc_final: 0.6392 (tpt170) REVERT: C 451 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7954 (tpt) REVERT: C 687 ASP cc_start: 0.8499 (m-30) cc_final: 0.7682 (m-30) REVERT: C 705 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8283 (mtm) REVERT: D 412 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6198 (tpt170) REVERT: D 629 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7607 (t0) REVERT: D 687 ASP cc_start: 0.8475 (m-30) cc_final: 0.7730 (m-30) REVERT: E 412 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6022 (tpt170) REVERT: E 451 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8041 (tpt) REVERT: E 629 ASN cc_start: 0.7628 (t0) cc_final: 0.7408 (t0) REVERT: E 663 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7515 (mt-10) REVERT: F 412 ARG cc_start: 0.7142 (mtt180) cc_final: 0.6081 (tpt170) REVERT: F 557 GLU cc_start: 0.7909 (tt0) cc_final: 0.7627 (tt0) REVERT: F 629 ASN cc_start: 0.7946 (t0) cc_final: 0.7704 (t0) REVERT: F 687 ASP cc_start: 0.8362 (m-30) cc_final: 0.7503 (m-30) REVERT: G 412 ARG cc_start: 0.7332 (mtt180) cc_final: 0.6253 (tpt170) REVERT: G 629 ASN cc_start: 0.7785 (t0) cc_final: 0.7539 (t0) REVERT: G 663 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7450 (mt-10) REVERT: G 687 ASP cc_start: 0.8502 (m-30) cc_final: 0.7671 (m-30) REVERT: H 412 ARG cc_start: 0.7125 (mtt180) cc_final: 0.5945 (tpt170) REVERT: H 687 ASP cc_start: 0.8459 (m-30) cc_final: 0.8141 (m-30) REVERT: I 412 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6036 (tpt170) REVERT: I 629 ASN cc_start: 0.7748 (t0) cc_final: 0.7457 (t0) REVERT: I 687 ASP cc_start: 0.8440 (m-30) cc_final: 0.7643 (m-30) REVERT: J 412 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6389 (tpt170) REVERT: J 451 MET cc_start: 0.8353 (tpp) cc_final: 0.7939 (tpp) REVERT: J 687 ASP cc_start: 0.8518 (m-30) cc_final: 0.7687 (m-30) REVERT: K 412 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6189 (tpt170) REVERT: K 629 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7620 (t0) REVERT: L 412 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6025 (tpt170) REVERT: L 451 MET cc_start: 0.8341 (tpt) cc_final: 0.7945 (tpt) REVERT: L 629 ASN cc_start: 0.7623 (t0) cc_final: 0.7403 (t0) REVERT: L 663 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7523 (mt-10) REVERT: M 412 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6064 (tpt170) REVERT: M 557 GLU cc_start: 0.7899 (tt0) cc_final: 0.7611 (tt0) REVERT: M 629 ASN cc_start: 0.7939 (t0) cc_final: 0.7656 (t0) REVERT: M 687 ASP cc_start: 0.8429 (m-30) cc_final: 0.7572 (m-30) REVERT: N 412 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6251 (tpt170) REVERT: N 663 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7438 (mt-10) REVERT: N 687 ASP cc_start: 0.8485 (m-30) cc_final: 0.7632 (m-30) outliers start: 171 outliers final: 159 residues processed: 442 average time/residue: 0.2434 time to fit residues: 180.7000 Evaluate side-chains 465 residues out of total 4424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 300 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 665 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 427 TYR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 597 GLU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 629 ASN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 665 SER Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 427 TYR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 MET Chi-restraints excluded: chain E residue 493 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 427 TYR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 493 ASP Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 575 LEU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 427 TYR Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 648 VAL Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain G residue 665 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 427 TYR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 451 MET Chi-restraints excluded: chain H residue 493 ASP Chi-restraints excluded: chain H residue 518 SER Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain H residue 665 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 427 TYR Chi-restraints excluded: chain I residue 493 ASP Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 597 GLU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 427 TYR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 493 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 566 THR Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 597 GLU Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 427 TYR Chi-restraints excluded: chain K residue 493 ASP Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 597 GLU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 629 ASN Chi-restraints excluded: chain K residue 648 VAL Chi-restraints excluded: chain K residue 665 SER Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 427 TYR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 493 ASP Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 616 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 665 SER Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 427 TYR Chi-restraints excluded: chain M residue 447 VAL Chi-restraints excluded: chain M residue 493 ASP Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 575 LEU Chi-restraints excluded: chain M residue 597 GLU Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 665 SER Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 427 TYR Chi-restraints excluded: chain N residue 493 ASP Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 575 LEU Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 631 LEU Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 665 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 696 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 153 optimal weight: 1.9990 chunk 515 optimal weight: 10.0000 chunk 461 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 474 optimal weight: 0.4980 chunk 432 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 459 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118634 restraints weight = 42848.181| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.08 r_work: 0.3328 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41776 Z= 0.123 Angle : 0.491 5.640 56490 Z= 0.251 Chirality : 0.046 0.136 6552 Planarity : 0.004 0.044 7266 Dihedral : 8.584 59.377 6314 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.71 % Allowed : 18.13 % Favored : 78.16 % 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: 0.42 (0.12), residues: 5236 helix: 2.67 (0.15), residues: 1162 sheet: -0.11 (0.11), residues: 2268 loop : -0.70 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 686 TYR 0.009 0.001 TYR A 679 PHE 0.009 0.001 PHE L 673 TRP 0.002 0.000 TRP D 471 HIS 0.000 0.000 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (41748) covalent geometry : angle 0.49100 / 0.25 (56434) SS BOND : bond 0.00117 / 0.08 ( 28) SS BOND : angle 0.16960 / 0.12 ( 56) hydrogen bonds : bond 0.02876 / 1.97 ( 1506) hydrogen bonds : angle 4.90625 / 3.43 ( 4101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11056.61 seconds wall clock time: 189 minutes 59.94 seconds (11399.94 seconds total)