Starting phenix.real_space_refine on Fri Jun 5 18:15:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w5f_8767/06_2026/5w5f_8767.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w5f_8767/06_2026/5w5f_8767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2026/5w5f_8767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2026/5w5f_8767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2026/5w5f_8767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2026/5w5f_8767.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 14904 2.51 5 N 3942 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23472 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Restraints were copied for chains: R, C, B, D, E, F, G, H, I, J, K, L, M, N, O, P, Q Time building chain proxies: 2.60, per 1000 atoms: 0.11 Number of scatterers: 23472 At special positions: 0 Unit cell: (102.96, 101.64, 146.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 4554 8.00 N 3942 7.00 C 14904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.0 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5472 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 36 sheets defined 22.1% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP A 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE A 34 " --> pdb=" O ASN A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'R' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 10 " --> pdb=" O VAL R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP R 14 " --> pdb=" O GLU R 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 14' Processing helix chain 'R' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE R 34 " --> pdb=" O ASN R 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 31 through 34' Processing helix chain 'R' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE R 85 " --> pdb=" O ALA R 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP R 88 " --> pdb=" O LYS R 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA R 92 " --> pdb=" O TRP R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS R 108 " --> pdb=" O PRO R 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 103 through 108' Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 10 " --> pdb=" O VAL C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 14 removed outlier: 3.726A pdb=" N ASP C 14 " --> pdb=" O GLU C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 14' Processing helix chain 'C' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 79 through 93 removed outlier: 4.243A pdb=" N PHE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C 92 " --> pdb=" O TRP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG B 8 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP B 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE B 34 " --> pdb=" O ASN B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 34' Processing helix chain 'B' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'D' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 10 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP D 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 14' Processing helix chain 'D' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE D 34 " --> pdb=" O ASN D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 34' Processing helix chain 'D' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA D 92 " --> pdb=" O TRP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'E' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP E 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 11 through 14' Processing helix chain 'E' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE E 34 " --> pdb=" O ASN E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 34' Processing helix chain 'E' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 108 " --> pdb=" O PRO E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG F 8 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP F 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 14' Processing helix chain 'F' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE F 34 " --> pdb=" O ASN F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.511A pdb=" N TYR F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 108 " --> pdb=" O PRO F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'G' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG G 8 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP G 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 11 through 14' Processing helix chain 'G' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE G 34 " --> pdb=" O ASN G 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 31 through 34' Processing helix chain 'G' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA G 92 " --> pdb=" O TRP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 108 " --> pdb=" O PRO G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 108' Processing helix chain 'H' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 10 " --> pdb=" O VAL H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP H 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 11 through 14' Processing helix chain 'H' and resid 31 through 34 removed outlier: 3.544A pdb=" N PHE H 34 " --> pdb=" O ASN H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 34' Processing helix chain 'H' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA H 92 " --> pdb=" O TRP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR H 107 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 108' Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG I 8 " --> pdb=" O ASP I 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE I 10 " --> pdb=" O VAL I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP I 14 " --> pdb=" O GLU I 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 11 through 14' Processing helix chain 'I' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE I 34 " --> pdb=" O ASN I 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 31 through 34' Processing helix chain 'I' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA I 92 " --> pdb=" O TRP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS I 108 " --> pdb=" O PRO I 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 103 through 108' Processing helix chain 'J' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP J 14 " --> pdb=" O GLU J 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 11 through 14' Processing helix chain 'J' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE J 34 " --> pdb=" O ASN J 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 31 through 34' Processing helix chain 'J' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA J 92 " --> pdb=" O TRP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.511A pdb=" N TYR J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS J 108 " --> pdb=" O PRO J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 108' Processing helix chain 'K' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 10 " --> pdb=" O VAL K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP K 14 " --> pdb=" O GLU K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 11 through 14' Processing helix chain 'K' and resid 31 through 34 removed outlier: 3.542A pdb=" N PHE K 34 " --> pdb=" O ASN K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 31 through 34' Processing helix chain 'K' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA K 92 " --> pdb=" O TRP K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS K 108 " --> pdb=" O PRO K 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 108' Processing helix chain 'L' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE L 10 " --> pdb=" O VAL L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP L 14 " --> pdb=" O GLU L 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 11 through 14' Processing helix chain 'L' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE L 34 " --> pdb=" O ASN L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 79 through 93 removed outlier: 4.241A pdb=" N PHE L 85 " --> pdb=" O ALA L 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP L 88 " --> pdb=" O LYS L 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA L 92 " --> pdb=" O TRP L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR L 107 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS L 108 " --> pdb=" O PRO L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 103 through 108' Processing helix chain 'M' and resid 4 through 10 removed outlier: 3.643A pdb=" N ARG M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE M 10 " --> pdb=" O VAL M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP M 14 " --> pdb=" O GLU M 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 11 through 14' Processing helix chain 'M' and resid 31 through 34 removed outlier: 3.542A pdb=" N PHE M 34 " --> pdb=" O ASN M 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 31 through 34' Processing helix chain 'M' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE M 85 " --> pdb=" O ALA M 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA M 92 " --> pdb=" O TRP M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS M 108 " --> pdb=" O PRO M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 108' Processing helix chain 'N' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE N 10 " --> pdb=" O VAL N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP N 14 " --> pdb=" O GLU N 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 11 through 14' Processing helix chain 'N' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE N 34 " --> pdb=" O ASN N 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 31 through 34' Processing helix chain 'N' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE N 85 " --> pdb=" O ALA N 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA N 92 " --> pdb=" O TRP N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS N 108 " --> pdb=" O PRO N 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 103 through 108' Processing helix chain 'O' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE O 10 " --> pdb=" O VAL O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP O 14 " --> pdb=" O GLU O 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 11 through 14' Processing helix chain 'O' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE O 34 " --> pdb=" O ASN O 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 31 through 34' Processing helix chain 'O' and resid 79 through 93 removed outlier: 4.243A pdb=" N PHE O 85 " --> pdb=" O ALA O 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP O 88 " --> pdb=" O LYS O 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA O 92 " --> pdb=" O TRP O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS O 108 " --> pdb=" O PRO O 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 103 through 108' Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 10 " --> pdb=" O VAL P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 14 removed outlier: 3.726A pdb=" N ASP P 14 " --> pdb=" O GLU P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 11 through 14' Processing helix chain 'P' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE P 34 " --> pdb=" O ASN P 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 31 through 34' Processing helix chain 'P' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP P 88 " --> pdb=" O LYS P 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA P 92 " --> pdb=" O TRP P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS P 108 " --> pdb=" O PRO P 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 103 through 108' Processing helix chain 'Q' and resid 4 through 10 removed outlier: 3.641A pdb=" N ARG Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE Q 10 " --> pdb=" O VAL Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP Q 14 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE Q 34 " --> pdb=" O ASN Q 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 31 through 34' Processing helix chain 'Q' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP Q 88 " --> pdb=" O LYS Q 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA Q 92 " --> pdb=" O TRP Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS Q 108 " --> pdb=" O PRO Q 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 103 through 108' Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA A 111 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS A 130 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 113 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU A 128 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN A 115 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU A 126 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 156 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL A 137 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU A 154 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR A 70 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET A 74 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS A 36 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 142 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 140 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 163 removed outlier: 3.711A pdb=" N TYR A 161 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 128 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 22.513A pdb=" N ILE A 129 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 20.122A pdb=" N GLY P 52 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 16.307A pdb=" N GLY A 131 " --> pdb=" O PRO P 50 " (cutoff:3.500A) removed outlier: 12.473A pdb=" N TRP A 133 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS P 48 " --> pdb=" O TRP A 133 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR A 135 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 45 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP P 63 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE P 49 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL P 51 " --> pdb=" O ASN P 59 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN P 59 " --> pdb=" O VAL P 51 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE P 53 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS P 57 " --> pdb=" O PHE P 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 53 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN A 59 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 51 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA A 61 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE A 49 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 63 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 45 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR D 135 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LYS A 48 " --> pdb=" O TRP D 133 " (cutoff:3.500A) removed outlier: 12.454A pdb=" N TRP D 133 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 16.301A pdb=" N GLY D 131 " --> pdb=" O PRO A 50 " (cutoff:3.500A) removed outlier: 20.125A pdb=" N GLY A 52 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 22.526A pdb=" N ILE D 129 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU D 128 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 161 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.745A pdb=" N ALA D 111 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS D 130 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 113 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU D 128 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN D 115 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 126 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 156 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL D 137 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU D 154 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR D 70 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET D 74 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS D 36 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 142 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 140 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.723A pdb=" N LEU A 140 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 142 " --> pdb=" O THR P 39 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS P 36 " --> pdb=" O MET P 74 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET P 74 " --> pdb=" O CYS P 36 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR P 70 " --> pdb=" O ALA P 40 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU P 154 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL P 137 " --> pdb=" O GLU P 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR P 156 " --> pdb=" O THR P 135 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU P 126 " --> pdb=" O GLN P 115 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN P 115 " --> pdb=" O GLU P 126 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU P 128 " --> pdb=" O VAL P 113 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL P 113 " --> pdb=" O GLU P 128 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS P 130 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA P 111 " --> pdb=" O LYS P 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS M 57 " --> pdb=" O PHE M 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE M 53 " --> pdb=" O LYS M 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN M 59 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL M 51 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA M 61 " --> pdb=" O ILE M 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE M 49 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP M 63 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE M 45 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR P 135 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N LYS M 48 " --> pdb=" O TRP P 133 " (cutoff:3.500A) removed outlier: 12.516A pdb=" N TRP P 133 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 16.370A pdb=" N GLY P 131 " --> pdb=" O PRO M 50 " (cutoff:3.500A) removed outlier: 20.190A pdb=" N GLY M 52 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 22.579A pdb=" N ILE P 129 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU P 128 " --> pdb=" O GLU P 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR P 161 " --> pdb=" O LYS P 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA R 111 " --> pdb=" O LYS R 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS R 130 " --> pdb=" O ALA R 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL R 113 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU R 128 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN R 115 " --> pdb=" O GLU R 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU R 126 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR R 156 " --> pdb=" O THR R 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL R 137 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU R 154 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR R 70 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET R 74 " --> pdb=" O CYS R 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS R 36 " --> pdb=" O MET R 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 142 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 140 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 161 through 163 removed outlier: 3.711A pdb=" N TYR R 161 " --> pdb=" O LYS R 130 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU R 128 " --> pdb=" O GLU R 163 " (cutoff:3.500A) removed outlier: 22.580A pdb=" N ILE R 129 " --> pdb=" O GLY O 52 " (cutoff:3.500A) removed outlier: 20.181A pdb=" N GLY O 52 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 16.352A pdb=" N GLY R 131 " --> pdb=" O PRO O 50 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N TRP R 133 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS O 48 " --> pdb=" O TRP R 133 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR R 135 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE O 45 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP O 63 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE O 49 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA O 61 " --> pdb=" O ILE O 49 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL O 51 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN O 59 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE O 53 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS O 57 " --> pdb=" O PHE O 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS R 57 " --> pdb=" O PHE R 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE R 53 " --> pdb=" O LYS R 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN R 59 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL R 51 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA R 61 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE R 49 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP R 63 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE R 45 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR B 135 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LYS R 48 " --> pdb=" O TRP B 133 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N TRP B 133 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 16.326A pdb=" N GLY B 131 " --> pdb=" O PRO R 50 " (cutoff:3.500A) removed outlier: 20.156A pdb=" N GLY R 52 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 22.554A pdb=" N ILE B 129 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 128 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 161 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA B 111 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 130 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 113 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU B 128 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN B 115 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 126 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B 156 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL B 137 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU B 154 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR B 70 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET B 74 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 36 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 142 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 140 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 140 through 143 removed outlier: 3.685A pdb=" N LEU R 140 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU R 142 " --> pdb=" O THR O 39 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS O 36 " --> pdb=" O MET O 74 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET O 74 " --> pdb=" O CYS O 36 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR O 70 " --> pdb=" O ALA O 40 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU O 154 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL O 137 " --> pdb=" O GLU O 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR O 156 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU O 126 " --> pdb=" O GLN O 115 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN O 115 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU O 128 " --> pdb=" O VAL O 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL O 113 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS O 130 " --> pdb=" O ALA O 111 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA O 111 " --> pdb=" O LYS O 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS L 57 " --> pdb=" O PHE L 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE L 53 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN L 59 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL L 51 " --> pdb=" O ASN L 59 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA L 61 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE L 49 " --> pdb=" O ALA L 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP L 63 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE L 45 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR O 135 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LYS L 48 " --> pdb=" O TRP O 133 " (cutoff:3.500A) removed outlier: 12.482A pdb=" N TRP O 133 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 16.340A pdb=" N GLY O 131 " --> pdb=" O PRO L 50 " (cutoff:3.500A) removed outlier: 20.170A pdb=" N GLY L 52 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 22.568A pdb=" N ILE O 129 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU O 128 " --> pdb=" O GLU O 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR O 161 " --> pdb=" O LYS O 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA C 111 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS C 130 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 113 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU C 128 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN C 115 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU C 126 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 156 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL C 137 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU C 154 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR C 70 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET C 74 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS C 36 " --> pdb=" O MET C 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 142 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.710A pdb=" N TYR C 161 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 128 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 22.505A pdb=" N ILE C 129 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) removed outlier: 20.109A pdb=" N GLY Q 52 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 16.293A pdb=" N GLY C 131 " --> pdb=" O PRO Q 50 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N TRP C 133 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS Q 48 " --> pdb=" O TRP C 133 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR C 135 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE Q 45 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP Q 63 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE Q 49 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA Q 61 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL Q 51 " --> pdb=" O ASN Q 59 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN Q 59 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE Q 53 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS Q 57 " --> pdb=" O PHE Q 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE C 53 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN C 59 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL C 51 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA C 61 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE C 49 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP C 63 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 45 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N THR E 135 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LYS C 48 " --> pdb=" O TRP E 133 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N TRP E 133 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 16.295A pdb=" N GLY E 131 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 20.112A pdb=" N GLY C 52 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 22.508A pdb=" N ILE E 129 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU E 128 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA E 111 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 130 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL E 113 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU E 128 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN E 115 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU E 126 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR E 156 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL E 137 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU E 154 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR E 70 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET E 74 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 36 " --> pdb=" O MET E 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU H 142 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 140 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 143 removed outlier: 3.679A pdb=" N LEU C 140 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 142 " --> pdb=" O THR Q 39 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS Q 36 " --> pdb=" O MET Q 74 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET Q 74 " --> pdb=" O CYS Q 36 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR Q 70 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU Q 154 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL Q 137 " --> pdb=" O GLU Q 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR Q 156 " --> pdb=" O THR Q 135 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU Q 126 " --> pdb=" O GLN Q 115 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN Q 115 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU Q 128 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Q 113 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS Q 130 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA Q 111 " --> pdb=" O LYS Q 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS N 57 " --> pdb=" O PHE N 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE N 53 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN N 59 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL N 51 " --> pdb=" O ASN N 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA N 61 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE N 49 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP N 63 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 45 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR Q 135 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N LYS N 48 " --> pdb=" O TRP Q 133 " (cutoff:3.500A) removed outlier: 12.459A pdb=" N TRP Q 133 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 16.307A pdb=" N GLY Q 131 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 20.122A pdb=" N GLY N 52 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 22.514A pdb=" N ILE Q 129 " --> pdb=" O GLY N 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU Q 128 " --> pdb=" O GLU Q 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR Q 161 " --> pdb=" O LYS Q 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 53 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN B 59 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 51 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA B 61 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE B 49 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 63 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 45 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR F 135 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N LYS B 48 " --> pdb=" O TRP F 133 " (cutoff:3.500A) removed outlier: 12.484A pdb=" N TRP F 133 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 16.340A pdb=" N GLY F 131 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 20.170A pdb=" N GLY B 52 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 22.569A pdb=" N ILE F 129 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU F 128 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR F 161 " --> pdb=" O LYS F 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA F 111 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS F 130 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 113 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU F 128 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN F 115 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU F 126 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR F 156 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL F 137 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU F 154 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR F 70 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET F 74 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS F 36 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU I 142 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 140 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE D 53 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN D 59 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 51 " --> pdb=" O ASN D 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA D 61 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE D 49 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 63 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 45 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N THR G 135 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N LYS D 48 " --> pdb=" O TRP G 133 " (cutoff:3.500A) removed outlier: 12.472A pdb=" N TRP G 133 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 16.316A pdb=" N GLY G 131 " --> pdb=" O PRO D 50 " (cutoff:3.500A) removed outlier: 20.142A pdb=" N GLY D 52 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 22.536A pdb=" N ILE G 129 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU G 128 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR G 161 " --> pdb=" O LYS G 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA G 111 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS G 130 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL G 113 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU G 128 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN G 115 " --> pdb=" O GLU G 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU G 126 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR G 156 " --> pdb=" O THR G 135 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL G 137 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU G 154 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR G 70 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET G 74 " --> pdb=" O CYS G 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS G 36 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU J 142 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 140 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS E 57 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE E 53 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN E 59 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL E 51 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA E 61 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE E 49 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP E 63 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 45 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR H 135 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LYS E 48 " --> pdb=" O TRP H 133 " (cutoff:3.500A) removed outlier: 12.451A pdb=" N TRP H 133 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 16.299A pdb=" N GLY H 131 " --> pdb=" O PRO E 50 " (cutoff:3.500A) removed outlier: 20.117A pdb=" N GLY E 52 " --> pdb=" O ILE H 129 " (cutoff:3.500A) removed outlier: 22.513A pdb=" N ILE H 129 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU H 128 " --> pdb=" O GLU H 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR H 161 " --> pdb=" O LYS H 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA H 111 " --> pdb=" O LYS H 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS H 130 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 113 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU H 128 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN H 115 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU H 126 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR H 156 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL H 137 " --> pdb=" O GLU H 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU H 154 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR H 70 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET H 74 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS H 36 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 142 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU K 140 " --> pdb=" O LEU H 41 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS F 57 " --> pdb=" O PHE F 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE F 53 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN F 59 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL F 51 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA F 61 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE F 49 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP F 63 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 45 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR I 135 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N LYS F 48 " --> pdb=" O TRP I 133 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N TRP I 133 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 16.347A pdb=" N GLY I 131 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 20.174A pdb=" N GLY F 52 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 22.572A pdb=" N ILE I 129 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU I 128 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR I 161 " --> pdb=" O LYS I 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 21 through 24 removed outlier: 6.743A pdb=" N ALA I 111 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS I 130 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL I 113 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU I 128 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN I 115 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU I 126 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR I 156 " --> pdb=" O THR I 135 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL I 137 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU I 154 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR I 70 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET I 74 " --> pdb=" O CYS I 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS I 36 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 142 " --> pdb=" O THR I 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU L 140 " --> pdb=" O LEU I 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS G 57 " --> pdb=" O PHE G 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE G 53 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN G 59 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL G 51 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA G 61 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP G 63 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 45 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR J 135 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LYS G 48 " --> pdb=" O TRP J 133 " (cutoff:3.500A) removed outlier: 12.465A pdb=" N TRP J 133 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 16.308A pdb=" N GLY J 131 " --> pdb=" O PRO G 50 " (cutoff:3.500A) removed outlier: 20.128A pdb=" N GLY G 52 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 22.524A pdb=" N ILE J 129 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU J 128 " --> pdb=" O GLU J 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR J 161 " --> pdb=" O LYS J 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA J 111 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS J 130 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL J 113 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU J 128 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN J 115 " --> pdb=" O GLU J 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU J 126 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR J 156 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL J 137 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU J 154 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR J 70 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET J 74 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS J 36 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU M 142 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M 140 " --> pdb=" O LEU J 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS H 57 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE H 53 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN H 59 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL H 51 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA H 61 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE H 49 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP H 63 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 45 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR K 135 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LYS H 48 " --> pdb=" O TRP K 133 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N TRP K 133 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 16.291A pdb=" N GLY K 131 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 20.110A pdb=" N GLY H 52 " --> pdb=" O ILE K 129 " (cutoff:3.500A) removed outlier: 22.506A pdb=" N ILE K 129 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU K 128 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR K 161 " --> pdb=" O LYS K 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 21 through 24 removed outlier: 6.743A pdb=" N ALA K 111 " --> pdb=" O LYS K 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS K 130 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL K 113 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU K 128 " --> pdb=" O VAL K 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN K 115 " --> pdb=" O GLU K 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU K 126 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR K 156 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL K 137 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU K 154 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR K 70 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET K 74 " --> pdb=" O CYS K 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS K 36 " --> pdb=" O MET K 74 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 142 " --> pdb=" O THR K 39 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU N 140 " --> pdb=" O LEU K 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE I 53 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN I 59 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL I 51 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA I 61 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE I 49 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP I 63 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE I 45 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR L 135 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS I 48 " --> pdb=" O TRP L 133 " (cutoff:3.500A) removed outlier: 12.479A pdb=" N TRP L 133 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 16.326A pdb=" N GLY L 131 " --> pdb=" O PRO I 50 " (cutoff:3.500A) removed outlier: 20.150A pdb=" N GLY I 52 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 22.544A pdb=" N ILE L 129 " --> pdb=" O GLY I 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU L 128 " --> pdb=" O GLU L 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 161 " --> pdb=" O LYS L 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA L 111 " --> pdb=" O LYS L 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS L 130 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL L 113 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU L 128 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN L 115 " --> pdb=" O GLU L 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU L 126 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR L 156 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL L 137 " --> pdb=" O GLU L 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU L 154 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR L 70 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET L 74 " --> pdb=" O CYS L 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS L 36 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU O 142 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU O 140 " --> pdb=" O LEU L 41 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS J 57 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE J 53 " --> pdb=" O LYS J 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN J 59 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL J 51 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA J 61 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE J 49 " --> pdb=" O ALA J 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP J 63 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 45 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR M 135 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N LYS J 48 " --> pdb=" O TRP M 133 " (cutoff:3.500A) removed outlier: 12.403A pdb=" N TRP M 133 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 16.242A pdb=" N GLY M 131 " --> pdb=" O PRO J 50 " (cutoff:3.500A) removed outlier: 20.086A pdb=" N GLY J 52 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 22.485A pdb=" N ILE M 129 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU M 128 " --> pdb=" O GLU M 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR M 161 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA M 111 " --> pdb=" O LYS M 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS M 130 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL M 113 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU M 128 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN M 115 " --> pdb=" O GLU M 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU M 126 " --> pdb=" O GLN M 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR M 156 " --> pdb=" O THR M 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL M 137 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU M 154 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR M 70 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET M 74 " --> pdb=" O CYS M 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS M 36 " --> pdb=" O MET M 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU P 142 " --> pdb=" O THR M 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU P 140 " --> pdb=" O LEU M 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS K 57 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE K 53 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN K 59 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL K 51 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA K 61 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE K 49 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP K 63 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE K 45 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR N 135 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LYS K 48 " --> pdb=" O TRP N 133 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N TRP N 133 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 16.302A pdb=" N GLY N 131 " --> pdb=" O PRO K 50 " (cutoff:3.500A) removed outlier: 20.120A pdb=" N GLY K 52 " --> pdb=" O ILE N 129 " (cutoff:3.500A) removed outlier: 22.517A pdb=" N ILE N 129 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU N 128 " --> pdb=" O GLU N 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR N 161 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 21 through 24 removed outlier: 6.743A pdb=" N ALA N 111 " --> pdb=" O LYS N 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS N 130 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL N 113 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU N 128 " --> pdb=" O VAL N 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN N 115 " --> pdb=" O GLU N 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU N 126 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR N 156 " --> pdb=" O THR N 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL N 137 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU N 154 " --> pdb=" O VAL N 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR N 70 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET N 74 " --> pdb=" O CYS N 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS N 36 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Q 142 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU Q 140 " --> pdb=" O LEU N 41 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1782 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: 4.70 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7628 1.34 - 1.45: 3591 1.45 - 1.57: 12649 1.57 - 1.68: 0 1.68 - 1.80: 126 Bond restraints: 23994 Sorted by residual: bond pdb=" CA ASN G 55 " pdb=" CB ASN G 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.77e+00 bond pdb=" CA ASN Q 55 " pdb=" CB ASN Q 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.76e+00 bond pdb=" CA ASN P 55 " pdb=" CB ASN P 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.73e+00 bond pdb=" CA ASN B 55 " pdb=" CB ASN B 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.70e+00 bond pdb=" CA ASN K 55 " pdb=" CB ASN K 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.69e+00 ... (remaining 23989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 30873 1.88 - 3.75: 1527 3.75 - 5.63: 126 5.63 - 7.50: 18 7.50 - 9.38: 18 Bond angle restraints: 32562 Sorted by residual: angle pdb=" CA ASN H 55 " pdb=" CB ASN H 55 " pdb=" CG ASN H 55 " ideal model delta sigma weight residual 112.60 115.58 -2.98 1.00e+00 1.00e+00 8.88e+00 angle pdb=" CA ASN I 55 " pdb=" CB ASN I 55 " pdb=" CG ASN I 55 " ideal model delta sigma weight residual 112.60 115.57 -2.97 1.00e+00 1.00e+00 8.79e+00 angle pdb=" CA ASN F 55 " pdb=" CB ASN F 55 " pdb=" CG ASN F 55 " ideal model delta sigma weight residual 112.60 115.56 -2.96 1.00e+00 1.00e+00 8.75e+00 angle pdb=" CA ASN R 55 " pdb=" CB ASN R 55 " pdb=" CG ASN R 55 " ideal model delta sigma weight residual 112.60 115.56 -2.96 1.00e+00 1.00e+00 8.74e+00 angle pdb=" CA ASN J 55 " pdb=" CB ASN J 55 " pdb=" CG ASN J 55 " ideal model delta sigma weight residual 112.60 115.54 -2.94 1.00e+00 1.00e+00 8.66e+00 ... (remaining 32557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 13110 14.76 - 29.52: 678 29.52 - 44.28: 216 44.28 - 59.04: 36 59.04 - 73.80: 72 Dihedral angle restraints: 14112 sinusoidal: 5652 harmonic: 8460 Sorted by residual: dihedral pdb=" CA ARG G 118 " pdb=" C ARG G 118 " pdb=" N ASP G 119 " pdb=" CA ASP G 119 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG M 118 " pdb=" C ARG M 118 " pdb=" N ASP M 119 " pdb=" CA ASP M 119 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG H 118 " pdb=" C ARG H 118 " pdb=" N ASP H 119 " pdb=" CA ASP H 119 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 14109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2244 0.041 - 0.082: 691 0.082 - 0.123: 431 0.123 - 0.164: 108 0.164 - 0.205: 36 Chirality restraints: 3510 Sorted by residual: chirality pdb=" CB ILE E 99 " pdb=" CA ILE E 99 " pdb=" CG1 ILE E 99 " pdb=" CG2 ILE E 99 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE O 99 " pdb=" CA ILE O 99 " pdb=" CG1 ILE O 99 " pdb=" CG2 ILE O 99 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE R 99 " pdb=" CA ILE R 99 " pdb=" CG1 ILE R 99 " pdb=" CG2 ILE R 99 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3507 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET J 54 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C MET J 54 " -0.053 2.00e-02 2.50e+03 pdb=" O MET J 54 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN J 55 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 54 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C MET I 54 " -0.053 2.00e-02 2.50e+03 pdb=" O MET I 54 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN I 55 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 54 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C MET B 54 " 0.053 2.00e-02 2.50e+03 pdb=" O MET B 54 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN B 55 " -0.018 2.00e-02 2.50e+03 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1702 2.72 - 3.26: 21811 3.26 - 3.81: 38063 3.81 - 4.35: 46128 4.35 - 4.90: 80194 Nonbonded interactions: 187898 Sorted by model distance: nonbonded pdb=" OE1 GLN J 115 " pdb=" NE2 HIS M 79 " model vdw 2.171 3.120 nonbonded pdb=" NE2 HIS R 79 " pdb=" OE1 GLN O 115 " model vdw 2.271 3.120 nonbonded pdb=" OE1 GLN A 115 " pdb=" NE2 HIS D 79 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLN R 115 " pdb=" NE2 HIS B 79 " model vdw 2.282 3.120 nonbonded pdb=" OE1 GLN I 115 " pdb=" NE2 HIS L 79 " model vdw 2.283 3.120 ... (remaining 187893 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'R' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 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 0.040 23994 Z= 0.314 Angle : 0.913 9.378 32562 Z= 0.524 Chirality : 0.057 0.205 3510 Planarity : 0.006 0.041 4284 Dihedral : 12.301 73.804 8640 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % 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: -2.49 (0.13), residues: 2898 helix: -4.29 (0.12), residues: 288 sheet: 0.13 (0.22), residues: 666 loop : -2.01 (0.11), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 17 TYR 0.012 0.003 TYR K 161 PHE 0.021 0.004 PHE L 153 TRP 0.049 0.006 TRP O 88 HIS 0.001 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.31 (23994) covalent geometry : angle 0.91283 / 0.52 (32562) hydrogen bonds : bond 0.26903 / 17.39 ( 648) hydrogen bonds : angle 10.07962 / 6.94 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1309 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.7820 (t0) cc_final: 0.7371 (t0) REVERT: A 8 ARG cc_start: 0.8360 (tmm-80) cc_final: 0.8148 (mtp-110) REVERT: A 24 GLU cc_start: 0.7193 (pt0) cc_final: 0.6233 (pt0) REVERT: A 77 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7019 (mp0) REVERT: A 83 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8371 (tp40) REVERT: A 103 LYS cc_start: 0.8219 (mttp) cc_final: 0.7908 (mtmm) REVERT: A 112 ILE cc_start: 0.8285 (mt) cc_final: 0.7862 (mm) REVERT: A 119 ASP cc_start: 0.8415 (t0) cc_final: 0.7952 (t70) REVERT: A 121 LYS cc_start: 0.8459 (pttp) cc_final: 0.8241 (ptpp) REVERT: A 128 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8038 (tt0) REVERT: A 130 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7916 (mmmm) REVERT: A 143 ASP cc_start: 0.6512 (p0) cc_final: 0.5855 (p0) REVERT: A 160 ASP cc_start: 0.8435 (m-30) cc_final: 0.8159 (m-30) REVERT: R 2 PHE cc_start: 0.7887 (m-80) cc_final: 0.7629 (m-80) REVERT: R 23 VAL cc_start: 0.7517 (p) cc_final: 0.7038 (p) REVERT: R 24 GLU cc_start: 0.7513 (pt0) cc_final: 0.7168 (pt0) REVERT: R 30 GLN cc_start: 0.8476 (mm110) cc_final: 0.8202 (pp30) REVERT: R 37 LYS cc_start: 0.8611 (tttt) cc_final: 0.8097 (tttt) REVERT: R 74 MET cc_start: 0.8630 (mtm) cc_final: 0.8368 (mtm) REVERT: R 75 ASN cc_start: 0.9135 (t160) cc_final: 0.8901 (t0) REVERT: R 76 ASP cc_start: 0.8631 (p0) cc_final: 0.8322 (p0) REVERT: R 103 LYS cc_start: 0.8753 (mttp) cc_final: 0.8507 (mmtt) REVERT: R 116 TYR cc_start: 0.8361 (m-10) cc_final: 0.7868 (m-10) REVERT: R 119 ASP cc_start: 0.7874 (t0) cc_final: 0.7463 (t70) REVERT: R 129 ILE cc_start: 0.8399 (mp) cc_final: 0.7037 (mt) REVERT: R 130 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7810 (mmmt) REVERT: R 143 ASP cc_start: 0.7255 (p0) cc_final: 0.6804 (p0) REVERT: R 148 ASN cc_start: 0.8746 (m-40) cc_final: 0.8380 (m-40) REVERT: C 1 MET cc_start: 0.5848 (tpp) cc_final: 0.4272 (tmm) REVERT: C 58 ILE cc_start: 0.5741 (pt) cc_final: 0.5248 (pt) REVERT: C 77 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6041 (tp30) REVERT: C 113 VAL cc_start: 0.7745 (p) cc_final: 0.7364 (p) REVERT: C 118 ARG cc_start: 0.6788 (tpt170) cc_final: 0.5775 (tmm160) REVERT: C 119 ASP cc_start: 0.7392 (t0) cc_final: 0.6949 (t70) REVERT: C 150 ILE cc_start: 0.8368 (tt) cc_final: 0.8145 (tp) REVERT: B 10 PHE cc_start: 0.6732 (m-10) cc_final: 0.5912 (m-10) REVERT: B 15 PHE cc_start: 0.7868 (m-10) cc_final: 0.7128 (m-80) REVERT: B 23 VAL cc_start: 0.4995 (p) cc_final: 0.4751 (p) REVERT: B 30 GLN cc_start: 0.8213 (mm110) cc_final: 0.7582 (mm-40) REVERT: B 45 ILE cc_start: 0.8572 (mm) cc_final: 0.8357 (mm) REVERT: B 77 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6756 (mt-10) REVERT: B 112 ILE cc_start: 0.8242 (mt) cc_final: 0.7914 (pt) REVERT: B 129 ILE cc_start: 0.7609 (mp) cc_final: 0.7262 (mt) REVERT: B 146 SER cc_start: 0.8307 (m) cc_final: 0.7992 (p) REVERT: D 1 MET cc_start: 0.6723 (tpp) cc_final: 0.6506 (tpt) REVERT: D 5 ASP cc_start: 0.7454 (t0) cc_final: 0.7063 (m-30) REVERT: D 91 ILE cc_start: 0.8986 (mt) cc_final: 0.8563 (mm) REVERT: D 97 ASN cc_start: 0.7971 (t0) cc_final: 0.7732 (t0) REVERT: D 103 LYS cc_start: 0.8188 (mttp) cc_final: 0.7876 (mtmm) REVERT: D 112 ILE cc_start: 0.8464 (mt) cc_final: 0.8042 (pt) REVERT: D 127 ILE cc_start: 0.8035 (mt) cc_final: 0.7629 (mp) REVERT: D 129 ILE cc_start: 0.7877 (mp) cc_final: 0.6839 (mt) REVERT: D 147 ASN cc_start: 0.8700 (m-40) cc_final: 0.8256 (m-40) REVERT: E 1 MET cc_start: 0.6673 (tpp) cc_final: 0.6421 (tpt) REVERT: E 24 GLU cc_start: 0.6077 (pt0) cc_final: 0.5752 (tp30) REVERT: E 58 ILE cc_start: 0.6165 (pt) cc_final: 0.5952 (pt) REVERT: E 76 ASP cc_start: 0.7618 (p0) cc_final: 0.7234 (p0) REVERT: E 109 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7352 (mmtt) REVERT: E 119 ASP cc_start: 0.8010 (t0) cc_final: 0.7626 (t70) REVERT: E 159 LEU cc_start: 0.8090 (pp) cc_final: 0.7698 (pp) REVERT: F 10 PHE cc_start: 0.5705 (m-10) cc_final: 0.4993 (m-10) REVERT: F 14 ASP cc_start: 0.7698 (t0) cc_final: 0.6107 (p0) REVERT: F 67 ASP cc_start: 0.7342 (t70) cc_final: 0.6385 (p0) REVERT: F 76 ASP cc_start: 0.7388 (p0) cc_final: 0.7080 (p0) REVERT: F 98 GLU cc_start: 0.8166 (pm20) cc_final: 0.7872 (tp30) REVERT: F 106 GLU cc_start: 0.7205 (tt0) cc_final: 0.6872 (mp0) REVERT: F 112 ILE cc_start: 0.7848 (mt) cc_final: 0.7474 (mp) REVERT: F 130 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8034 (mmmt) REVERT: F 146 SER cc_start: 0.8480 (m) cc_final: 0.7630 (m) REVERT: G 14 ASP cc_start: 0.7326 (t0) cc_final: 0.6359 (p0) REVERT: G 20 LEU cc_start: 0.6808 (mp) cc_final: 0.6585 (mt) REVERT: G 53 PHE cc_start: 0.7599 (t80) cc_final: 0.7384 (t80) REVERT: G 76 ASP cc_start: 0.7117 (p0) cc_final: 0.6804 (p0) REVERT: G 98 GLU cc_start: 0.7486 (pm20) cc_final: 0.6682 (pp20) REVERT: G 127 ILE cc_start: 0.6744 (mt) cc_final: 0.6118 (mp) REVERT: G 130 LYS cc_start: 0.8096 (mmtp) cc_final: 0.7224 (mmmm) REVERT: H 39 THR cc_start: 0.6739 (t) cc_final: 0.6496 (t) REVERT: H 73 VAL cc_start: 0.4171 (m) cc_final: 0.3907 (p) REVERT: H 91 ILE cc_start: 0.8484 (mt) cc_final: 0.8226 (tt) REVERT: H 118 ARG cc_start: 0.4865 (tpt170) cc_final: 0.3666 (ttm170) REVERT: H 127 ILE cc_start: 0.5865 (mt) cc_final: 0.5615 (mp) REVERT: I 1 MET cc_start: 0.8114 (tpp) cc_final: 0.7280 (tpt) REVERT: I 14 ASP cc_start: 0.7286 (t0) cc_final: 0.6887 (p0) REVERT: I 97 ASN cc_start: 0.7391 (t0) cc_final: 0.6696 (t0) REVERT: I 106 GLU cc_start: 0.7571 (tt0) cc_final: 0.7113 (mm-30) REVERT: I 112 ILE cc_start: 0.7687 (mt) cc_final: 0.7484 (mt) REVERT: J 1 MET cc_start: 0.7720 (tpp) cc_final: 0.7472 (tpp) REVERT: J 14 ASP cc_start: 0.6100 (t0) cc_final: 0.5503 (p0) REVERT: J 66 PHE cc_start: 0.7500 (m-80) cc_final: 0.7099 (m-80) REVERT: J 73 VAL cc_start: 0.7254 (m) cc_final: 0.6973 (p) REVERT: J 84 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7659 (ptmt) REVERT: J 140 LEU cc_start: 0.8790 (tt) cc_final: 0.8565 (tt) REVERT: J 142 LEU cc_start: 0.5190 (pp) cc_final: 0.4789 (pp) REVERT: J 152 THR cc_start: 0.5088 (t) cc_final: 0.4756 (t) REVERT: K 1 MET cc_start: 0.7651 (tpp) cc_final: 0.7307 (tpt) REVERT: K 82 ARG cc_start: 0.6571 (ttt-90) cc_final: 0.5271 (ttt-90) REVERT: K 118 ARG cc_start: 0.5498 (tpt170) cc_final: 0.4272 (ttp-170) REVERT: L 1 MET cc_start: 0.8605 (tpp) cc_final: 0.7142 (tpt) REVERT: L 12 SER cc_start: 0.8433 (m) cc_final: 0.7758 (p) REVERT: L 14 ASP cc_start: 0.7664 (t0) cc_final: 0.6997 (t70) REVERT: L 22 GLN cc_start: 0.7257 (tt0) cc_final: 0.6872 (tt0) REVERT: L 24 GLU cc_start: 0.7314 (pt0) cc_final: 0.7055 (pt0) REVERT: L 35 GLN cc_start: 0.8273 (mt0) cc_final: 0.7957 (mt0) REVERT: L 57 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8583 (mmmt) REVERT: L 87 ASP cc_start: 0.7610 (t0) cc_final: 0.7355 (t0) REVERT: L 106 GLU cc_start: 0.7955 (tt0) cc_final: 0.7622 (mm-30) REVERT: L 114 ARG cc_start: 0.7999 (ptt-90) cc_final: 0.7626 (mtm-85) REVERT: L 119 ASP cc_start: 0.7482 (t0) cc_final: 0.6799 (t70) REVERT: L 126 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7733 (pp20) REVERT: L 161 TYR cc_start: 0.7888 (p90) cc_final: 0.7521 (p90) REVERT: L 163 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7618 (mm-30) REVERT: M 1 MET cc_start: 0.8417 (tpp) cc_final: 0.7420 (tpp) REVERT: M 5 ASP cc_start: 0.6581 (t0) cc_final: 0.6297 (t0) REVERT: M 39 THR cc_start: 0.8364 (t) cc_final: 0.8160 (t) REVERT: M 83 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7954 (tp-100) REVERT: M 84 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7924 (ptmt) REVERT: M 109 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7899 (mmtp) REVERT: M 140 LEU cc_start: 0.8088 (tt) cc_final: 0.7788 (tp) REVERT: N 73 VAL cc_start: 0.6765 (m) cc_final: 0.6480 (p) REVERT: N 142 LEU cc_start: 0.5164 (pp) cc_final: 0.4931 (pp) REVERT: N 150 ILE cc_start: 0.7524 (tt) cc_final: 0.7268 (tp) REVERT: N 161 TYR cc_start: 0.5422 (p90) cc_final: 0.3716 (p90) REVERT: O 1 MET cc_start: 0.8703 (tpp) cc_final: 0.7118 (tpp) REVERT: O 3 VAL cc_start: 0.8508 (m) cc_final: 0.8210 (m) REVERT: O 5 ASP cc_start: 0.8276 (t0) cc_final: 0.7975 (t0) REVERT: O 20 LEU cc_start: 0.8312 (mp) cc_final: 0.7947 (mt) REVERT: O 22 GLN cc_start: 0.8290 (tt0) cc_final: 0.7645 (tt0) REVERT: O 30 GLN cc_start: 0.8542 (mm110) cc_final: 0.7828 (tp40) REVERT: O 34 PHE cc_start: 0.8927 (m-10) cc_final: 0.8672 (m-10) REVERT: O 37 LYS cc_start: 0.7918 (tttt) cc_final: 0.7676 (tttp) REVERT: O 54 MET cc_start: 0.7324 (tpp) cc_final: 0.7044 (mmt) REVERT: O 74 MET cc_start: 0.8809 (mtm) cc_final: 0.8601 (mtt) REVERT: O 75 ASN cc_start: 0.8780 (t160) cc_final: 0.8571 (t0) REVERT: O 83 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7961 (tm-30) REVERT: O 103 LYS cc_start: 0.8879 (mttp) cc_final: 0.8427 (tptt) REVERT: O 112 ILE cc_start: 0.8581 (mt) cc_final: 0.8261 (tt) REVERT: O 114 ARG cc_start: 0.7944 (ptt-90) cc_final: 0.7273 (ptt-90) REVERT: O 119 ASP cc_start: 0.7549 (t0) cc_final: 0.7037 (t70) REVERT: O 160 ASP cc_start: 0.8317 (m-30) cc_final: 0.7879 (m-30) REVERT: O 163 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7761 (mm-30) REVERT: P 5 ASP cc_start: 0.7964 (t0) cc_final: 0.7592 (t0) REVERT: P 20 LEU cc_start: 0.7681 (mp) cc_final: 0.7289 (mp) REVERT: P 22 GLN cc_start: 0.8164 (tt0) cc_final: 0.7695 (tt0) REVERT: P 76 ASP cc_start: 0.7587 (p0) cc_final: 0.6389 (p0) REVERT: P 87 ASP cc_start: 0.8311 (t0) cc_final: 0.8007 (t0) REVERT: P 112 ILE cc_start: 0.8076 (mt) cc_final: 0.7744 (mm) REVERT: P 116 TYR cc_start: 0.7494 (m-10) cc_final: 0.6887 (m-80) REVERT: P 119 ASP cc_start: 0.7805 (t0) cc_final: 0.7355 (t70) REVERT: P 143 ASP cc_start: 0.6933 (p0) cc_final: 0.6509 (p0) REVERT: Q 19 ASN cc_start: 0.5741 (p0) cc_final: 0.5421 (t0) REVERT: Q 48 LYS cc_start: 0.7807 (ttpm) cc_final: 0.7553 (ttpt) REVERT: Q 58 ILE cc_start: 0.6867 (pt) cc_final: 0.6546 (pt) REVERT: Q 118 ARG cc_start: 0.6190 (tpt170) cc_final: 0.5770 (tmm160) REVERT: Q 124 THR cc_start: 0.7977 (t) cc_final: 0.6951 (m) outliers start: 0 outliers final: 0 residues processed: 1309 average time/residue: 0.1792 time to fit residues: 358.6889 Evaluate side-chains 913 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 913 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN R 147 ASN C 75 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 147 ASN E 19 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN G 148 ASN H 35 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 GLN L 89 GLN ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 35 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 147 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN Q 75 ASN Q 89 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100291 restraints weight = 48011.706| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.29 r_work: 0.3290 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23994 Z= 0.201 Angle : 0.691 8.480 32562 Z= 0.371 Chirality : 0.051 0.193 3510 Planarity : 0.005 0.038 4284 Dihedral : 7.037 74.003 3132 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.29 % Allowed : 18.29 % Favored : 75.43 % 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: -2.13 (0.14), residues: 2898 helix: -3.56 (0.18), residues: 306 sheet: -0.27 (0.19), residues: 756 loop : -1.58 (0.12), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 56 TYR 0.031 0.002 TYR G 107 PHE 0.018 0.002 PHE L 34 TRP 0.029 0.002 TRP G 88 HIS 0.004 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (23994) covalent geometry : angle 0.69135 / 0.37 (32562) hydrogen bonds : bond 0.03894 / 2.56 ( 648) hydrogen bonds : angle 6.68031 / 4.61 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1188 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8298 (tpt) cc_final: 0.7196 (tpt) REVERT: A 14 ASP cc_start: 0.7266 (t70) cc_final: 0.7033 (t70) REVERT: A 17 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7870 (mmt-90) REVERT: A 24 GLU cc_start: 0.7777 (pt0) cc_final: 0.7517 (pt0) REVERT: A 39 THR cc_start: 0.8438 (t) cc_final: 0.8127 (t) REVERT: A 70 THR cc_start: 0.8402 (p) cc_final: 0.8006 (t) REVERT: A 98 GLU cc_start: 0.8601 (tp30) cc_final: 0.8378 (tp30) REVERT: A 112 ILE cc_start: 0.8773 (mt) cc_final: 0.8470 (mm) REVERT: A 119 ASP cc_start: 0.8663 (t0) cc_final: 0.8304 (t0) REVERT: A 127 ILE cc_start: 0.8813 (mp) cc_final: 0.8379 (mt) REVERT: A 130 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8556 (mmmm) REVERT: A 148 ASN cc_start: 0.8558 (m-40) cc_final: 0.8333 (m110) REVERT: R 22 GLN cc_start: 0.8056 (tt0) cc_final: 0.7744 (tt0) REVERT: R 23 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8358 (p) REVERT: R 24 GLU cc_start: 0.7940 (pt0) cc_final: 0.7562 (pt0) REVERT: R 30 GLN cc_start: 0.8464 (mm110) cc_final: 0.8247 (tm-30) REVERT: R 31 ASN cc_start: 0.8458 (p0) cc_final: 0.8164 (t0) REVERT: R 74 MET cc_start: 0.8768 (mtm) cc_final: 0.8506 (mtm) REVERT: R 91 ILE cc_start: 0.9377 (mm) cc_final: 0.9133 (mm) REVERT: R 112 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8908 (pt) REVERT: R 116 TYR cc_start: 0.8753 (m-10) cc_final: 0.8110 (m-10) REVERT: R 119 ASP cc_start: 0.8418 (t0) cc_final: 0.7878 (t70) REVERT: R 139 GLU cc_start: 0.8158 (tp30) cc_final: 0.7739 (tp30) REVERT: R 148 ASN cc_start: 0.8300 (m-40) cc_final: 0.8039 (m110) REVERT: C 48 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8215 (ttpp) REVERT: C 118 ARG cc_start: 0.7002 (tpt170) cc_final: 0.5274 (ptt180) REVERT: B 116 TYR cc_start: 0.8724 (m-10) cc_final: 0.8455 (m-10) REVERT: B 139 GLU cc_start: 0.7955 (tp30) cc_final: 0.6787 (pt0) REVERT: B 160 ASP cc_start: 0.8152 (m-30) cc_final: 0.7939 (m-30) REVERT: D 1 MET cc_start: 0.7235 (tpp) cc_final: 0.6338 (tpt) REVERT: D 14 ASP cc_start: 0.6880 (p0) cc_final: 0.6127 (p0) REVERT: D 31 ASN cc_start: 0.8592 (p0) cc_final: 0.7593 (t0) REVERT: D 80 ASP cc_start: 0.8094 (p0) cc_final: 0.7890 (p0) REVERT: D 83 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8708 (tp-100) REVERT: D 112 ILE cc_start: 0.8566 (mt) cc_final: 0.7729 (mm) REVERT: D 127 ILE cc_start: 0.8511 (mt) cc_final: 0.8184 (mp) REVERT: D 129 ILE cc_start: 0.8028 (mp) cc_final: 0.7556 (mt) REVERT: D 130 LYS cc_start: 0.8346 (mmmm) cc_final: 0.7884 (mmmt) REVERT: E 37 LYS cc_start: 0.8696 (tttt) cc_final: 0.8429 (tttp) REVERT: E 76 ASP cc_start: 0.8662 (p0) cc_final: 0.8276 (p0) REVERT: E 77 GLU cc_start: 0.8333 (mp0) cc_final: 0.7790 (mp0) REVERT: E 90 SER cc_start: 0.8812 (t) cc_final: 0.8132 (p) REVERT: E 119 ASP cc_start: 0.8498 (t0) cc_final: 0.8152 (t0) REVERT: E 127 ILE cc_start: 0.7884 (mp) cc_final: 0.7514 (mp) REVERT: F 2 PHE cc_start: 0.7665 (m-80) cc_final: 0.7441 (m-80) REVERT: F 47 GLU cc_start: 0.4233 (pt0) cc_final: 0.3471 (pt0) REVERT: F 69 TRP cc_start: 0.8683 (t60) cc_final: 0.8290 (t60) REVERT: F 76 ASP cc_start: 0.8082 (p0) cc_final: 0.7590 (p0) REVERT: F 83 GLN cc_start: 0.8262 (tp40) cc_final: 0.8024 (tp40) REVERT: F 112 ILE cc_start: 0.8633 (mt) cc_final: 0.8278 (tt) REVERT: F 119 ASP cc_start: 0.7623 (t0) cc_final: 0.7163 (t70) REVERT: F 142 LEU cc_start: 0.8612 (pt) cc_final: 0.8410 (pt) REVERT: F 154 GLU cc_start: 0.8413 (pt0) cc_final: 0.8126 (tt0) REVERT: G 1 MET cc_start: 0.7604 (tpp) cc_final: 0.7359 (tpt) REVERT: G 2 PHE cc_start: 0.7418 (m-80) cc_final: 0.7171 (m-80) REVERT: G 27 TYR cc_start: 0.7559 (t80) cc_final: 0.7275 (t80) REVERT: G 49 ILE cc_start: 0.8912 (mt) cc_final: 0.8686 (mt) REVERT: G 63 ASP cc_start: 0.7638 (p0) cc_final: 0.7432 (p0) REVERT: G 71 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8594 (m) REVERT: G 76 ASP cc_start: 0.8577 (p0) cc_final: 0.8168 (p0) REVERT: G 87 ASP cc_start: 0.8037 (t0) cc_final: 0.7821 (t0) REVERT: G 98 GLU cc_start: 0.8100 (pm20) cc_final: 0.7319 (pp20) REVERT: G 103 LYS cc_start: 0.8676 (mttp) cc_final: 0.8325 (mmtp) REVERT: G 135 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8582 (p) REVERT: G 139 GLU cc_start: 0.7842 (tp30) cc_final: 0.7586 (mm-30) REVERT: G 157 LEU cc_start: 0.8603 (mp) cc_final: 0.8213 (mp) REVERT: G 161 TYR cc_start: 0.8555 (p90) cc_final: 0.8261 (p90) REVERT: H 1 MET cc_start: 0.7101 (tpt) cc_final: 0.6463 (tpt) REVERT: H 2 PHE cc_start: 0.6914 (m-80) cc_final: 0.6558 (t80) REVERT: H 5 ASP cc_start: 0.7534 (p0) cc_final: 0.7321 (p0) REVERT: H 17 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7001 (mpp80) REVERT: H 39 THR cc_start: 0.8396 (t) cc_final: 0.8125 (t) REVERT: H 99 ILE cc_start: 0.6854 (tt) cc_final: 0.6417 (tp) REVERT: H 118 ARG cc_start: 0.6980 (tpt170) cc_final: 0.5580 (ttm170) REVERT: H 119 ASP cc_start: 0.8036 (t0) cc_final: 0.7737 (t70) REVERT: H 146 SER cc_start: 0.8603 (m) cc_final: 0.8327 (p) REVERT: I 2 PHE cc_start: 0.8282 (m-80) cc_final: 0.7913 (m-80) REVERT: I 34 PHE cc_start: 0.8352 (m-80) cc_final: 0.7767 (m-80) REVERT: I 77 GLU cc_start: 0.8237 (mp0) cc_final: 0.8001 (mp0) REVERT: I 80 ASP cc_start: 0.8092 (p0) cc_final: 0.7776 (p0) REVERT: I 91 ILE cc_start: 0.8888 (mt) cc_final: 0.8497 (mm) REVERT: I 97 ASN cc_start: 0.7712 (t0) cc_final: 0.7415 (t0) REVERT: I 142 LEU cc_start: 0.8913 (pt) cc_final: 0.8646 (pt) REVERT: I 148 ASN cc_start: 0.8595 (p0) cc_final: 0.8233 (m-40) REVERT: I 149 GLU cc_start: 0.8181 (mp0) cc_final: 0.7731 (mp0) REVERT: J 1 MET cc_start: 0.7978 (tpp) cc_final: 0.7463 (tpt) REVERT: J 4 ASP cc_start: 0.7708 (m-30) cc_final: 0.7373 (m-30) REVERT: J 11 GLU cc_start: 0.7312 (mp0) cc_final: 0.7074 (mp0) REVERT: J 14 ASP cc_start: 0.7163 (t0) cc_final: 0.6876 (t70) REVERT: J 54 MET cc_start: 0.7423 (mmm) cc_final: 0.6989 (tpp) REVERT: J 73 VAL cc_start: 0.7809 (m) cc_final: 0.7566 (p) REVERT: J 77 GLU cc_start: 0.6880 (mp0) cc_final: 0.6653 (mp0) REVERT: J 79 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7005 (t-90) REVERT: J 80 ASP cc_start: 0.7968 (p0) cc_final: 0.7741 (p0) REVERT: J 91 ILE cc_start: 0.8906 (tt) cc_final: 0.8644 (tp) REVERT: J 145 ASP cc_start: 0.8818 (t0) cc_final: 0.8560 (m-30) REVERT: K 1 MET cc_start: 0.7254 (tpp) cc_final: 0.6577 (tpt) REVERT: K 22 GLN cc_start: 0.6752 (tt0) cc_final: 0.6408 (tt0) REVERT: K 118 ARG cc_start: 0.6408 (tpt170) cc_final: 0.4547 (ttp-170) REVERT: L 1 MET cc_start: 0.8337 (tpp) cc_final: 0.8028 (tpt) REVERT: L 83 GLN cc_start: 0.8725 (tp40) cc_final: 0.8177 (tp40) REVERT: L 161 TYR cc_start: 0.8533 (p90) cc_final: 0.8301 (p90) REVERT: M 14 ASP cc_start: 0.6863 (t0) cc_final: 0.6643 (t0) REVERT: M 30 GLN cc_start: 0.7837 (mm110) cc_final: 0.7320 (tm-30) REVERT: M 35 GLN cc_start: 0.8423 (mt0) cc_final: 0.8149 (mt0) REVERT: M 48 LYS cc_start: 0.8240 (ttpm) cc_final: 0.7361 (ttpp) REVERT: M 77 GLU cc_start: 0.7799 (mp0) cc_final: 0.6980 (mp0) REVERT: M 79 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7864 (t-90) REVERT: M 145 ASP cc_start: 0.8295 (p0) cc_final: 0.8031 (t0) REVERT: N 2 PHE cc_start: 0.7037 (m-80) cc_final: 0.6806 (t80) REVERT: N 31 ASN cc_start: 0.7383 (p0) cc_final: 0.6824 (t0) REVERT: N 123 VAL cc_start: 0.7867 (t) cc_final: 0.7586 (p) REVERT: N 154 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7731 (tt0) REVERT: O 4 ASP cc_start: 0.8285 (m-30) cc_final: 0.7924 (p0) REVERT: O 11 GLU cc_start: 0.8252 (tp30) cc_final: 0.7938 (tp30) REVERT: O 14 ASP cc_start: 0.7693 (t0) cc_final: 0.7452 (t70) REVERT: O 21 PHE cc_start: 0.8915 (p90) cc_final: 0.8637 (p90) REVERT: O 22 GLN cc_start: 0.8173 (tt0) cc_final: 0.7958 (tt0) REVERT: O 24 GLU cc_start: 0.8155 (pt0) cc_final: 0.7909 (pt0) REVERT: O 35 GLN cc_start: 0.8315 (mt0) cc_final: 0.8095 (mt0) REVERT: O 51 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8517 (p) REVERT: O 54 MET cc_start: 0.7801 (tpp) cc_final: 0.7387 (mmt) REVERT: O 83 GLN cc_start: 0.8447 (tp-100) cc_final: 0.8049 (tm-30) REVERT: O 112 ILE cc_start: 0.8893 (mt) cc_final: 0.8682 (tt) REVERT: O 119 ASP cc_start: 0.8227 (t0) cc_final: 0.7773 (t70) REVERT: P 1 MET cc_start: 0.8565 (tpt) cc_final: 0.8097 (tpt) REVERT: P 8 ARG cc_start: 0.8237 (ptp-110) cc_final: 0.7853 (ptm160) REVERT: P 76 ASP cc_start: 0.7661 (p0) cc_final: 0.7399 (p0) REVERT: P 83 GLN cc_start: 0.8673 (tp40) cc_final: 0.8363 (tp40) REVERT: P 119 ASP cc_start: 0.8281 (t0) cc_final: 0.7851 (t0) REVERT: P 128 GLU cc_start: 0.7803 (pm20) cc_final: 0.7600 (pm20) REVERT: Q 2 PHE cc_start: 0.6886 (m-80) cc_final: 0.6173 (t80) REVERT: Q 8 ARG cc_start: 0.8149 (ptm160) cc_final: 0.7917 (ptm160) REVERT: Q 27 TYR cc_start: 0.7683 (t80) cc_final: 0.7375 (t80) REVERT: Q 48 LYS cc_start: 0.7947 (ttpm) cc_final: 0.7641 (ttpt) REVERT: Q 55 ASN cc_start: 0.6731 (t160) cc_final: 0.6358 (t0) REVERT: Q 118 ARG cc_start: 0.7107 (tpt170) cc_final: 0.5512 (tmm160) REVERT: Q 144 TRP cc_start: 0.8848 (m-10) cc_final: 0.6616 (m100) REVERT: Q 163 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7214 (mm-30) outliers start: 155 outliers final: 94 residues processed: 1280 average time/residue: 0.1696 time to fit residues: 334.1720 Evaluate side-chains 1059 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 957 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 145 ASP Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 112 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 148 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN I 55 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN K 75 ASN K 79 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 147 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN P 147 ASN P 148 ASN ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088869 restraints weight = 49070.988| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.27 r_work: 0.3107 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.8873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23994 Z= 0.219 Angle : 0.679 10.068 32562 Z= 0.361 Chirality : 0.050 0.185 3510 Planarity : 0.004 0.058 4284 Dihedral : 7.079 81.898 3132 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 8.07 % Allowed : 20.56 % Favored : 71.37 % 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: -2.10 (0.14), residues: 2898 helix: -3.30 (0.17), residues: 360 sheet: -0.20 (0.19), residues: 756 loop : -1.56 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 64 TYR 0.023 0.002 TYR D 27 PHE 0.023 0.002 PHE P 2 TRP 0.023 0.002 TRP G 88 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (23994) covalent geometry : angle 0.67883 / 0.36 (32562) hydrogen bonds : bond 0.04114 / 2.66 ( 648) hydrogen bonds : angle 6.47888 / 4.45 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1104 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.8393 (t0) cc_final: 0.8190 (t0) REVERT: A 14 ASP cc_start: 0.7374 (t70) cc_final: 0.7151 (t70) REVERT: A 20 LEU cc_start: 0.9075 (mp) cc_final: 0.8855 (mt) REVERT: A 24 GLU cc_start: 0.7931 (pt0) cc_final: 0.7499 (pt0) REVERT: A 57 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8327 (mmtt) REVERT: A 75 ASN cc_start: 0.8668 (t160) cc_final: 0.7593 (t0) REVERT: A 76 ASP cc_start: 0.8606 (p0) cc_final: 0.7671 (p0) REVERT: A 77 GLU cc_start: 0.8341 (mp0) cc_final: 0.7774 (mp0) REVERT: A 112 ILE cc_start: 0.8900 (mt) cc_final: 0.8639 (mm) REVERT: A 119 ASP cc_start: 0.8730 (t0) cc_final: 0.8298 (t70) REVERT: A 126 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7710 (tm-30) REVERT: R 23 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8276 (m) REVERT: R 34 PHE cc_start: 0.8839 (m-10) cc_final: 0.8021 (m-10) REVERT: R 74 MET cc_start: 0.8907 (mtm) cc_final: 0.8648 (mtm) REVERT: R 75 ASN cc_start: 0.9119 (t0) cc_final: 0.8900 (t0) REVERT: R 116 TYR cc_start: 0.8794 (m-10) cc_final: 0.8020 (m-10) REVERT: R 119 ASP cc_start: 0.8512 (t0) cc_final: 0.8070 (t70) REVERT: R 126 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7280 (tm-30) REVERT: R 128 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7362 (tm-30) REVERT: R 148 ASN cc_start: 0.8425 (m-40) cc_final: 0.8194 (m110) REVERT: C 76 ASP cc_start: 0.8230 (p0) cc_final: 0.7906 (p0) REVERT: C 77 GLU cc_start: 0.8023 (pm20) cc_final: 0.7591 (mp0) REVERT: C 80 ASP cc_start: 0.8857 (p0) cc_final: 0.8648 (p0) REVERT: C 95 GLN cc_start: 0.8459 (tt0) cc_final: 0.8210 (tt0) REVERT: B 27 TYR cc_start: 0.9026 (t80) cc_final: 0.8787 (t80) REVERT: B 106 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7787 (tp30) REVERT: B 116 TYR cc_start: 0.9034 (m-10) cc_final: 0.8764 (m-10) REVERT: B 139 GLU cc_start: 0.8360 (tp30) cc_final: 0.7240 (pt0) REVERT: D 5 ASP cc_start: 0.8406 (t70) cc_final: 0.8131 (t70) REVERT: D 8 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7481 (ptm-80) REVERT: D 31 ASN cc_start: 0.8731 (p0) cc_final: 0.7891 (t0) REVERT: D 70 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8067 (t) REVERT: D 83 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8894 (tp-100) REVERT: D 129 ILE cc_start: 0.8474 (mp) cc_final: 0.8179 (mt) REVERT: D 130 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8255 (mmmt) REVERT: D 161 TYR cc_start: 0.8622 (p90) cc_final: 0.8332 (p90) REVERT: E 2 PHE cc_start: 0.8269 (m-80) cc_final: 0.6057 (t80) REVERT: E 15 PHE cc_start: 0.7617 (m-10) cc_final: 0.7347 (m-80) REVERT: E 22 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7297 (tm-30) REVERT: E 37 LYS cc_start: 0.8799 (tttt) cc_final: 0.8420 (tttp) REVERT: E 45 ILE cc_start: 0.9020 (tp) cc_final: 0.8766 (tt) REVERT: E 76 ASP cc_start: 0.8784 (p0) cc_final: 0.8540 (p0) REVERT: E 77 GLU cc_start: 0.8535 (mp0) cc_final: 0.8255 (mp0) REVERT: E 90 SER cc_start: 0.9207 (t) cc_final: 0.8718 (p) REVERT: E 142 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7610 (pt) REVERT: E 161 TYR cc_start: 0.8970 (p90) cc_final: 0.8722 (p90) REVERT: F 1 MET cc_start: 0.8455 (tpp) cc_final: 0.8178 (tpp) REVERT: F 14 ASP cc_start: 0.7863 (t0) cc_final: 0.7558 (t0) REVERT: F 15 PHE cc_start: 0.7853 (m-80) cc_final: 0.7375 (m-80) REVERT: F 22 GLN cc_start: 0.8100 (tp40) cc_final: 0.7627 (tt0) REVERT: F 24 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 30 GLN cc_start: 0.8099 (mm110) cc_final: 0.7882 (pp30) REVERT: F 47 GLU cc_start: 0.4636 (pt0) cc_final: 0.4217 (pt0) REVERT: F 69 TRP cc_start: 0.9029 (t60) cc_final: 0.8779 (t60) REVERT: F 119 ASP cc_start: 0.7780 (t0) cc_final: 0.7412 (t70) REVERT: F 135 THR cc_start: 0.8602 (m) cc_final: 0.8206 (m) REVERT: F 137 VAL cc_start: 0.9031 (t) cc_final: 0.8756 (p) REVERT: F 142 LEU cc_start: 0.8739 (pt) cc_final: 0.8488 (pt) REVERT: F 154 GLU cc_start: 0.8419 (pt0) cc_final: 0.7998 (tt0) REVERT: F 161 TYR cc_start: 0.8569 (p90) cc_final: 0.8260 (p90) REVERT: G 2 PHE cc_start: 0.7946 (m-80) cc_final: 0.7732 (m-10) REVERT: G 24 GLU cc_start: 0.7607 (pt0) cc_final: 0.7273 (pt0) REVERT: G 31 ASN cc_start: 0.8330 (p0) cc_final: 0.7586 (t0) REVERT: G 47 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7813 (tt0) REVERT: G 54 MET cc_start: 0.7395 (mmm) cc_final: 0.6974 (tpp) REVERT: G 70 THR cc_start: 0.8355 (p) cc_final: 0.8069 (t) REVERT: G 76 ASP cc_start: 0.8678 (p0) cc_final: 0.8424 (p0) REVERT: G 97 ASN cc_start: 0.8694 (t0) cc_final: 0.8214 (t0) REVERT: G 98 GLU cc_start: 0.8309 (pm20) cc_final: 0.7701 (pp20) REVERT: G 103 LYS cc_start: 0.8688 (mttp) cc_final: 0.8417 (mtmm) REVERT: G 114 ARG cc_start: 0.8505 (mtm180) cc_final: 0.8099 (mtm180) REVERT: G 127 ILE cc_start: 0.8528 (mp) cc_final: 0.8107 (mp) REVERT: G 143 ASP cc_start: 0.8283 (t70) cc_final: 0.8078 (t70) REVERT: G 146 SER cc_start: 0.8782 (m) cc_final: 0.8342 (p) REVERT: G 161 TYR cc_start: 0.8661 (p90) cc_final: 0.8372 (p90) REVERT: H 2 PHE cc_start: 0.7862 (m-80) cc_final: 0.6875 (t80) REVERT: H 70 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8216 (t) REVERT: H 76 ASP cc_start: 0.8409 (p0) cc_final: 0.8184 (p0) REVERT: H 77 GLU cc_start: 0.7999 (mp0) cc_final: 0.7398 (mp0) REVERT: H 128 GLU cc_start: 0.7212 (tp30) cc_final: 0.7001 (tp30) REVERT: H 145 ASP cc_start: 0.7685 (t0) cc_final: 0.7399 (m-30) REVERT: H 160 ASP cc_start: 0.8657 (m-30) cc_final: 0.8436 (m-30) REVERT: I 2 PHE cc_start: 0.8271 (m-80) cc_final: 0.7901 (m-80) REVERT: I 77 GLU cc_start: 0.8142 (mp0) cc_final: 0.7565 (mp0) REVERT: I 97 ASN cc_start: 0.7408 (t0) cc_final: 0.7155 (t0) REVERT: I 130 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8418 (mmmm) REVERT: I 146 SER cc_start: 0.8766 (m) cc_final: 0.8447 (p) REVERT: I 148 ASN cc_start: 0.8535 (p0) cc_final: 0.8136 (m-40) REVERT: J 1 MET cc_start: 0.8224 (tpp) cc_final: 0.7857 (tpt) REVERT: J 8 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7835 (ptp-110) REVERT: J 14 ASP cc_start: 0.7661 (t0) cc_final: 0.7375 (t70) REVERT: J 28 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7648 (mt) REVERT: J 54 MET cc_start: 0.7847 (mmm) cc_final: 0.7622 (tpp) REVERT: J 79 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: J 91 ILE cc_start: 0.9177 (tt) cc_final: 0.8899 (tp) REVERT: J 145 ASP cc_start: 0.8930 (t0) cc_final: 0.8703 (m-30) REVERT: K 1 MET cc_start: 0.7673 (tpp) cc_final: 0.7163 (tpp) REVERT: K 2 PHE cc_start: 0.8162 (m-80) cc_final: 0.6626 (t80) REVERT: K 103 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7300 (mmtt) REVERT: K 128 GLU cc_start: 0.7465 (pm20) cc_final: 0.7136 (pm20) REVERT: L 1 MET cc_start: 0.8161 (tpp) cc_final: 0.7910 (tpt) REVERT: L 28 LEU cc_start: 0.8836 (mm) cc_final: 0.8465 (mp) REVERT: L 34 PHE cc_start: 0.9231 (m-80) cc_final: 0.8917 (m-80) REVERT: L 83 GLN cc_start: 0.8796 (tp40) cc_final: 0.8594 (tp40) REVERT: L 141 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7752 (mm110) REVERT: L 147 ASN cc_start: 0.8094 (m110) cc_final: 0.7861 (m-40) REVERT: M 14 ASP cc_start: 0.7650 (t0) cc_final: 0.7442 (t0) REVERT: M 30 GLN cc_start: 0.8359 (mm110) cc_final: 0.7967 (pp30) REVERT: M 34 PHE cc_start: 0.8929 (m-80) cc_final: 0.8685 (m-80) REVERT: M 76 ASP cc_start: 0.7455 (p0) cc_final: 0.6323 (p0) REVERT: M 77 GLU cc_start: 0.8208 (mp0) cc_final: 0.7994 (mp0) REVERT: M 79 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.7982 (t-90) REVERT: M 126 GLU cc_start: 0.8225 (pp20) cc_final: 0.7952 (pp20) REVERT: M 128 GLU cc_start: 0.7835 (pm20) cc_final: 0.7312 (pm20) REVERT: M 146 SER cc_start: 0.8516 (m) cc_final: 0.8126 (p) REVERT: N 2 PHE cc_start: 0.7860 (m-80) cc_final: 0.7446 (m-10) REVERT: N 11 GLU cc_start: 0.7874 (mp0) cc_final: 0.7635 (mp0) REVERT: N 14 ASP cc_start: 0.7116 (t0) cc_final: 0.6817 (t0) REVERT: N 22 GLN cc_start: 0.8303 (tt0) cc_final: 0.8094 (tt0) REVERT: N 24 GLU cc_start: 0.7690 (pt0) cc_final: 0.7102 (pt0) REVERT: N 31 ASN cc_start: 0.8357 (p0) cc_final: 0.7833 (t0) REVERT: N 35 GLN cc_start: 0.8510 (tt0) cc_final: 0.8199 (tt0) REVERT: N 39 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8392 (t) REVERT: N 80 ASP cc_start: 0.8551 (p0) cc_final: 0.8224 (p0) REVERT: N 95 GLN cc_start: 0.8235 (tt0) cc_final: 0.7910 (tt0) REVERT: N 98 GLU cc_start: 0.8360 (tp30) cc_final: 0.8019 (tp30) REVERT: N 116 TYR cc_start: 0.6877 (m-10) cc_final: 0.6423 (m-10) REVERT: N 119 ASP cc_start: 0.7443 (p0) cc_final: 0.7122 (p0) REVERT: N 122 THR cc_start: 0.8027 (m) cc_final: 0.7667 (m) REVERT: N 123 VAL cc_start: 0.8073 (t) cc_final: 0.7830 (p) REVERT: N 160 ASP cc_start: 0.8277 (m-30) cc_final: 0.8064 (m-30) REVERT: O 11 GLU cc_start: 0.8283 (tp30) cc_final: 0.7984 (tp30) REVERT: O 54 MET cc_start: 0.7511 (tpp) cc_final: 0.7111 (mmt) REVERT: O 163 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7953 (mm-30) REVERT: P 8 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7980 (ptm160) REVERT: P 76 ASP cc_start: 0.8321 (p0) cc_final: 0.7857 (p0) REVERT: P 119 ASP cc_start: 0.8380 (t0) cc_final: 0.8044 (t0) REVERT: P 132 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8252 (tp) REVERT: Q 14 ASP cc_start: 0.7823 (t0) cc_final: 0.7592 (t0) REVERT: Q 15 PHE cc_start: 0.8164 (m-10) cc_final: 0.7815 (m-80) REVERT: Q 76 ASP cc_start: 0.8099 (p0) cc_final: 0.7752 (p0) REVERT: Q 77 GLU cc_start: 0.8325 (mp0) cc_final: 0.7863 (mp0) REVERT: Q 112 ILE cc_start: 0.8967 (mt) cc_final: 0.8543 (mt) REVERT: Q 145 ASP cc_start: 0.7628 (t0) cc_final: 0.7385 (t0) REVERT: Q 159 LEU cc_start: 0.8664 (pt) cc_final: 0.8460 (pp) REVERT: Q 163 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7538 (mm-30) outliers start: 199 outliers final: 126 residues processed: 1238 average time/residue: 0.1650 time to fit residues: 318.1751 Evaluate side-chains 1056 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 921 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 25 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 chunk 26 optimal weight: 0.0270 chunk 225 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 277 optimal weight: 5.9990 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 ASN I 35 GLN I 136 ASN I 147 ASN J 35 GLN ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN P 148 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.085128 restraints weight = 50414.619| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.29 r_work: 0.3027 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.9639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23994 Z= 0.173 Angle : 0.631 10.118 32562 Z= 0.333 Chirality : 0.049 0.174 3510 Planarity : 0.004 0.039 4284 Dihedral : 6.921 81.892 3132 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 7.95 % Allowed : 23.11 % Favored : 68.94 % 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: -1.88 (0.14), residues: 2898 helix: -2.72 (0.20), residues: 360 sheet: -0.05 (0.20), residues: 756 loop : -1.51 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 64 TYR 0.017 0.002 TYR B 161 PHE 0.016 0.001 PHE R 53 TRP 0.018 0.001 TRP F 88 HIS 0.003 0.001 HIS K 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (23994) covalent geometry : angle 0.63096 / 0.33 (32562) hydrogen bonds : bond 0.03481 / 2.29 ( 648) hydrogen bonds : angle 6.12685 / 4.22 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1030 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8043 (pt0) cc_final: 0.7630 (pt0) REVERT: A 76 ASP cc_start: 0.8433 (p0) cc_final: 0.7847 (p0) REVERT: A 112 ILE cc_start: 0.8821 (mt) cc_final: 0.8578 (mm) REVERT: A 119 ASP cc_start: 0.8740 (t0) cc_final: 0.8158 (t0) REVERT: A 121 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8491 (ptpp) REVERT: R 2 PHE cc_start: 0.8112 (m-80) cc_final: 0.7160 (m-10) REVERT: R 23 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8287 (m) REVERT: R 24 GLU cc_start: 0.8084 (pt0) cc_final: 0.7229 (pt0) REVERT: R 31 ASN cc_start: 0.8606 (p0) cc_final: 0.8402 (t0) REVERT: R 34 PHE cc_start: 0.8954 (m-10) cc_final: 0.7965 (m-10) REVERT: R 75 ASN cc_start: 0.9139 (t0) cc_final: 0.8901 (t0) REVERT: R 114 ARG cc_start: 0.8345 (mtm180) cc_final: 0.8139 (ptp90) REVERT: R 116 TYR cc_start: 0.8639 (m-10) cc_final: 0.7875 (m-10) REVERT: R 126 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7380 (tm-30) REVERT: R 141 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: C 77 GLU cc_start: 0.8111 (pm20) cc_final: 0.7597 (mp0) REVERT: C 95 GLN cc_start: 0.8477 (tt0) cc_final: 0.8259 (tt0) REVERT: B 34 PHE cc_start: 0.8762 (m-80) cc_final: 0.8397 (m-10) REVERT: B 83 GLN cc_start: 0.8849 (tp40) cc_final: 0.7650 (tp-100) REVERT: B 106 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7738 (tp30) REVERT: B 139 GLU cc_start: 0.8438 (tp30) cc_final: 0.7005 (pt0) REVERT: B 141 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: D 31 ASN cc_start: 0.8587 (p0) cc_final: 0.7772 (t0) REVERT: D 47 GLU cc_start: 0.8241 (tp30) cc_final: 0.7847 (tp30) REVERT: D 48 LYS cc_start: 0.8633 (ttpt) cc_final: 0.7594 (ttmt) REVERT: D 70 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7951 (t) REVERT: D 83 GLN cc_start: 0.9240 (tp-100) cc_final: 0.8971 (tp-100) REVERT: D 112 ILE cc_start: 0.8575 (mm) cc_final: 0.8350 (mm) REVERT: D 139 GLU cc_start: 0.8252 (tp30) cc_final: 0.7864 (tp30) REVERT: D 161 TYR cc_start: 0.8742 (p90) cc_final: 0.8520 (p90) REVERT: E 2 PHE cc_start: 0.8272 (m-80) cc_final: 0.5903 (t80) REVERT: E 5 ASP cc_start: 0.8015 (t0) cc_final: 0.7747 (t0) REVERT: E 37 LYS cc_start: 0.8821 (tttt) cc_final: 0.8575 (tttp) REVERT: E 45 ILE cc_start: 0.8983 (tp) cc_final: 0.8728 (tt) REVERT: E 76 ASP cc_start: 0.8717 (p0) cc_final: 0.8071 (p0) REVERT: E 77 GLU cc_start: 0.8782 (mp0) cc_final: 0.8570 (mp0) REVERT: E 83 GLN cc_start: 0.8921 (tp40) cc_final: 0.8420 (tm-30) REVERT: E 90 SER cc_start: 0.9104 (t) cc_final: 0.8699 (p) REVERT: E 160 ASP cc_start: 0.8053 (m-30) cc_final: 0.7763 (m-30) REVERT: E 161 TYR cc_start: 0.9000 (p90) cc_final: 0.8749 (p90) REVERT: F 1 MET cc_start: 0.8670 (tpp) cc_final: 0.8408 (tpp) REVERT: F 22 GLN cc_start: 0.8250 (tp40) cc_final: 0.7882 (tt0) REVERT: F 24 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7554 (tm-30) REVERT: F 30 GLN cc_start: 0.8376 (mm110) cc_final: 0.8079 (pp30) REVERT: F 47 GLU cc_start: 0.4647 (pt0) cc_final: 0.3209 (tt0) REVERT: F 76 ASP cc_start: 0.8181 (p0) cc_final: 0.7711 (p0) REVERT: F 112 ILE cc_start: 0.9092 (mt) cc_final: 0.8738 (tt) REVERT: F 128 GLU cc_start: 0.8134 (pm20) cc_final: 0.7934 (pm20) REVERT: F 135 THR cc_start: 0.8649 (m) cc_final: 0.8320 (m) REVERT: F 137 VAL cc_start: 0.8941 (t) cc_final: 0.8716 (p) REVERT: F 154 GLU cc_start: 0.8443 (pt0) cc_final: 0.8061 (tt0) REVERT: F 161 TYR cc_start: 0.8861 (p90) cc_final: 0.8577 (p90) REVERT: G 1 MET cc_start: 0.7736 (tpt) cc_final: 0.7350 (tpt) REVERT: G 2 PHE cc_start: 0.8269 (m-80) cc_final: 0.7895 (m-10) REVERT: G 14 ASP cc_start: 0.7416 (t0) cc_final: 0.7168 (p0) REVERT: G 27 TYR cc_start: 0.8381 (t80) cc_final: 0.8102 (t80) REVERT: G 31 ASN cc_start: 0.8338 (p0) cc_final: 0.7635 (t0) REVERT: G 37 LYS cc_start: 0.8504 (tttt) cc_final: 0.8152 (tttt) REVERT: G 54 MET cc_start: 0.7619 (mmm) cc_final: 0.7113 (tpp) REVERT: G 98 GLU cc_start: 0.8603 (pm20) cc_final: 0.8016 (pp20) REVERT: G 103 LYS cc_start: 0.8741 (mttp) cc_final: 0.8442 (mtmm) REVERT: G 114 ARG cc_start: 0.8545 (mtm180) cc_final: 0.8215 (mtm180) REVERT: G 130 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8499 (mmmm) REVERT: G 146 SER cc_start: 0.8682 (m) cc_final: 0.8154 (p) REVERT: G 161 TYR cc_start: 0.8713 (p90) cc_final: 0.8350 (p90) REVERT: H 2 PHE cc_start: 0.8106 (m-80) cc_final: 0.6842 (t80) REVERT: H 35 GLN cc_start: 0.8565 (tt0) cc_final: 0.8081 (mt0) REVERT: H 39 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8082 (t) REVERT: H 70 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8256 (t) REVERT: H 140 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8265 (mt) REVERT: H 160 ASP cc_start: 0.8593 (m-30) cc_final: 0.8355 (m-30) REVERT: I 22 GLN cc_start: 0.8072 (mt0) cc_final: 0.7701 (mt0) REVERT: I 139 GLU cc_start: 0.8649 (tp30) cc_final: 0.7904 (pt0) REVERT: I 146 SER cc_start: 0.8668 (m) cc_final: 0.8273 (p) REVERT: I 154 GLU cc_start: 0.8426 (pt0) cc_final: 0.7985 (tt0) REVERT: J 15 PHE cc_start: 0.7865 (m-80) cc_final: 0.7503 (m-80) REVERT: J 27 TYR cc_start: 0.7941 (t80) cc_final: 0.7619 (t80) REVERT: J 28 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7883 (mt) REVERT: J 45 ILE cc_start: 0.8665 (mt) cc_final: 0.8240 (tt) REVERT: J 79 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7232 (t-90) REVERT: J 91 ILE cc_start: 0.9183 (tt) cc_final: 0.8556 (tp) REVERT: J 109 LYS cc_start: 0.8744 (mttt) cc_final: 0.8159 (mmtp) REVERT: J 145 ASP cc_start: 0.8924 (t0) cc_final: 0.8508 (m-30) REVERT: J 161 TYR cc_start: 0.8500 (p90) cc_final: 0.7943 (p90) REVERT: K 1 MET cc_start: 0.8059 (tpp) cc_final: 0.7523 (tpp) REVERT: K 2 PHE cc_start: 0.7730 (m-80) cc_final: 0.6318 (t80) REVERT: K 7 THR cc_start: 0.8062 (p) cc_final: 0.7480 (t) REVERT: K 22 GLN cc_start: 0.8142 (tt0) cc_final: 0.7942 (tt0) REVERT: K 77 GLU cc_start: 0.7535 (pm20) cc_final: 0.7313 (pm20) REVERT: K 79 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.6039 (t-90) REVERT: K 103 LYS cc_start: 0.8086 (mmtt) cc_final: 0.6853 (mmtp) REVERT: K 128 GLU cc_start: 0.7537 (pm20) cc_final: 0.7322 (pm20) REVERT: L 1 MET cc_start: 0.8355 (tpp) cc_final: 0.8122 (tpt) REVERT: L 28 LEU cc_start: 0.8864 (mm) cc_final: 0.8560 (mp) REVERT: L 34 PHE cc_start: 0.9256 (m-80) cc_final: 0.8420 (m-80) REVERT: L 141 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7878 (mm110) REVERT: M 2 PHE cc_start: 0.8615 (m-10) cc_final: 0.8219 (m-10) REVERT: M 30 GLN cc_start: 0.8398 (mm110) cc_final: 0.8084 (pp30) REVERT: M 80 ASP cc_start: 0.8373 (p0) cc_final: 0.8147 (p0) REVERT: M 114 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8073 (mtm180) REVERT: M 126 GLU cc_start: 0.8385 (pp20) cc_final: 0.8019 (pp20) REVERT: M 128 GLU cc_start: 0.7717 (pm20) cc_final: 0.7148 (pm20) REVERT: M 146 SER cc_start: 0.8379 (m) cc_final: 0.7673 (p) REVERT: N 4 ASP cc_start: 0.7576 (m-30) cc_final: 0.7279 (m-30) REVERT: N 30 GLN cc_start: 0.8402 (mm110) cc_final: 0.8081 (mm-40) REVERT: N 31 ASN cc_start: 0.8541 (p0) cc_final: 0.8081 (t0) REVERT: N 35 GLN cc_start: 0.8679 (tt0) cc_final: 0.8442 (mt0) REVERT: N 80 ASP cc_start: 0.8587 (p0) cc_final: 0.8232 (p0) REVERT: N 91 ILE cc_start: 0.9161 (mt) cc_final: 0.8837 (mt) REVERT: N 95 GLN cc_start: 0.8223 (tt0) cc_final: 0.7961 (tt0) REVERT: N 98 GLU cc_start: 0.8388 (tp30) cc_final: 0.8158 (tp30) REVERT: N 145 ASP cc_start: 0.7768 (p0) cc_final: 0.7056 (t0) REVERT: N 163 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7585 (mm-30) REVERT: O 2 PHE cc_start: 0.8324 (m-80) cc_final: 0.7857 (m-80) REVERT: O 4 ASP cc_start: 0.8423 (m-30) cc_final: 0.8076 (p0) REVERT: O 11 GLU cc_start: 0.8401 (tp30) cc_final: 0.8166 (tp30) REVERT: O 14 ASP cc_start: 0.7943 (t0) cc_final: 0.7535 (t70) REVERT: O 54 MET cc_start: 0.7555 (tpp) cc_final: 0.7171 (mmt) REVERT: O 83 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8128 (tm-30) REVERT: O 119 ASP cc_start: 0.8507 (t0) cc_final: 0.8022 (t70) REVERT: O 160 ASP cc_start: 0.8485 (m-30) cc_final: 0.7705 (m-30) REVERT: O 163 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7909 (mm-30) REVERT: P 5 ASP cc_start: 0.8428 (t70) cc_final: 0.8206 (t0) REVERT: P 8 ARG cc_start: 0.8349 (ptp-110) cc_final: 0.8009 (ptm160) REVERT: P 73 VAL cc_start: 0.8403 (m) cc_final: 0.7962 (p) REVERT: P 76 ASP cc_start: 0.8264 (p0) cc_final: 0.7855 (p0) REVERT: P 98 GLU cc_start: 0.8489 (tp30) cc_final: 0.8227 (tp30) REVERT: P 103 LYS cc_start: 0.8979 (mptt) cc_final: 0.8535 (mtmm) REVERT: P 112 ILE cc_start: 0.9060 (mt) cc_final: 0.8593 (tt) REVERT: P 119 ASP cc_start: 0.8690 (t0) cc_final: 0.7930 (t0) REVERT: P 121 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8069 (ptpp) REVERT: Q 8 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7586 (mtp-110) REVERT: Q 14 ASP cc_start: 0.7922 (t0) cc_final: 0.7502 (t0) REVERT: Q 15 PHE cc_start: 0.8247 (m-10) cc_final: 0.7757 (m-80) REVERT: Q 24 GLU cc_start: 0.8159 (pp20) cc_final: 0.7892 (pp20) REVERT: Q 76 ASP cc_start: 0.8229 (p0) cc_final: 0.8001 (p0) REVERT: Q 77 GLU cc_start: 0.8452 (mp0) cc_final: 0.7842 (mp0) REVERT: Q 118 ARG cc_start: 0.7585 (tpt170) cc_final: 0.5532 (ttm170) REVERT: Q 148 ASN cc_start: 0.8263 (m-40) cc_final: 0.8032 (m-40) outliers start: 196 outliers final: 146 residues processed: 1164 average time/residue: 0.1674 time to fit residues: 302.2458 Evaluate side-chains 1077 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 921 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 141 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 147 ASN Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 19 ASN Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 96 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN C 79 HIS C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN D 22 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 136 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 95 GLN N 83 GLN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082318 restraints weight = 50491.112| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.20 r_work: 0.2973 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 1.0315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23994 Z= 0.215 Angle : 0.656 9.614 32562 Z= 0.346 Chirality : 0.049 0.173 3510 Planarity : 0.004 0.033 4284 Dihedral : 7.117 82.447 3132 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 9.37 % Allowed : 23.20 % Favored : 67.44 % 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: -1.79 (0.14), residues: 2898 helix: -2.30 (0.22), residues: 360 sheet: -0.02 (0.20), residues: 756 loop : -1.53 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 64 TYR 0.017 0.002 TYR A 107 PHE 0.017 0.002 PHE I 66 TRP 0.018 0.002 TRP K 88 HIS 0.004 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (23994) covalent geometry : angle 0.65569 / 0.35 (32562) hydrogen bonds : bond 0.03682 / 2.41 ( 648) hydrogen bonds : angle 6.17462 / 4.23 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 965 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8035 (pt0) cc_final: 0.7600 (pt0) REVERT: A 54 MET cc_start: 0.8016 (mmm) cc_final: 0.7559 (tpp) REVERT: A 57 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8076 (mmtt) REVERT: A 112 ILE cc_start: 0.8797 (mt) cc_final: 0.8576 (mm) REVERT: A 119 ASP cc_start: 0.8764 (t0) cc_final: 0.8154 (t0) REVERT: A 121 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8466 (ptpp) REVERT: A 161 TYR cc_start: 0.8615 (p90) cc_final: 0.8272 (p90) REVERT: R 2 PHE cc_start: 0.8218 (m-80) cc_final: 0.7500 (m-10) REVERT: R 31 ASN cc_start: 0.8677 (p0) cc_final: 0.8474 (t0) REVERT: R 34 PHE cc_start: 0.8972 (m-10) cc_final: 0.7916 (m-10) REVERT: R 39 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7851 (t) REVERT: R 75 ASN cc_start: 0.9124 (t0) cc_final: 0.8824 (t0) REVERT: R 126 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7399 (tm-30) REVERT: R 128 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 8 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7791 (mtp-110) REVERT: C 24 GLU cc_start: 0.8422 (pp20) cc_final: 0.8181 (pp20) REVERT: C 54 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7979 (tpp) REVERT: C 77 GLU cc_start: 0.8420 (pm20) cc_final: 0.7654 (mp0) REVERT: C 112 ILE cc_start: 0.9095 (mt) cc_final: 0.8598 (tt) REVERT: B 1 MET cc_start: 0.8326 (tpp) cc_final: 0.8074 (tpp) REVERT: B 34 PHE cc_start: 0.8949 (m-80) cc_final: 0.8701 (m-10) REVERT: B 83 GLN cc_start: 0.8861 (tp40) cc_final: 0.8168 (tp-100) REVERT: B 106 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7968 (tp30) REVERT: B 141 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: D 31 ASN cc_start: 0.8673 (p0) cc_final: 0.7894 (t0) REVERT: D 47 GLU cc_start: 0.8322 (tp30) cc_final: 0.7870 (tp30) REVERT: D 54 MET cc_start: 0.7736 (mmm) cc_final: 0.7347 (tpp) REVERT: D 88 TRP cc_start: 0.9372 (t60) cc_final: 0.9168 (t60) REVERT: D 97 ASN cc_start: 0.7989 (t0) cc_final: 0.7421 (t0) REVERT: D 126 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7631 (tm-30) REVERT: D 161 TYR cc_start: 0.8661 (p90) cc_final: 0.8286 (p90) REVERT: E 2 PHE cc_start: 0.8440 (m-80) cc_final: 0.5853 (t80) REVERT: E 4 ASP cc_start: 0.8195 (m-30) cc_final: 0.7860 (p0) REVERT: E 30 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7822 (tp40) REVERT: E 45 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8740 (tt) REVERT: E 83 GLN cc_start: 0.8914 (tp40) cc_final: 0.8489 (tm-30) REVERT: E 90 SER cc_start: 0.9134 (t) cc_final: 0.8718 (p) REVERT: E 126 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7910 (pp20) REVERT: E 142 LEU cc_start: 0.8307 (pt) cc_final: 0.7914 (pt) REVERT: E 160 ASP cc_start: 0.8004 (m-30) cc_final: 0.7657 (m-30) REVERT: E 161 TYR cc_start: 0.8948 (p90) cc_final: 0.8444 (p90) REVERT: F 1 MET cc_start: 0.8663 (tpp) cc_final: 0.8256 (tpp) REVERT: F 22 GLN cc_start: 0.8566 (tp40) cc_final: 0.8106 (tt0) REVERT: F 24 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7385 (tm-30) REVERT: F 30 GLN cc_start: 0.8624 (mm110) cc_final: 0.8259 (pp30) REVERT: F 47 GLU cc_start: 0.4607 (pt0) cc_final: 0.3878 (pt0) REVERT: F 112 ILE cc_start: 0.8950 (mt) cc_final: 0.8627 (tt) REVERT: F 135 THR cc_start: 0.8645 (m) cc_final: 0.8302 (m) REVERT: F 137 VAL cc_start: 0.9180 (t) cc_final: 0.8975 (p) REVERT: F 141 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8464 (mm-40) REVERT: F 154 GLU cc_start: 0.8349 (pt0) cc_final: 0.7923 (tt0) REVERT: G 1 MET cc_start: 0.7968 (tpt) cc_final: 0.7554 (tpt) REVERT: G 2 PHE cc_start: 0.8153 (m-80) cc_final: 0.7868 (m-80) REVERT: G 31 ASN cc_start: 0.8326 (p0) cc_final: 0.7743 (t0) REVERT: G 54 MET cc_start: 0.7706 (mmm) cc_final: 0.7323 (tpp) REVERT: G 98 GLU cc_start: 0.8551 (pm20) cc_final: 0.7935 (pp20) REVERT: G 99 ILE cc_start: 0.8545 (mt) cc_final: 0.8094 (mt) REVERT: G 100 THR cc_start: 0.7594 (t) cc_final: 0.7175 (m) REVERT: G 103 LYS cc_start: 0.8906 (mttp) cc_final: 0.8695 (mtmm) REVERT: G 130 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8497 (mmmm) REVERT: G 146 SER cc_start: 0.8268 (m) cc_final: 0.7844 (p) REVERT: G 161 TYR cc_start: 0.8851 (p90) cc_final: 0.8458 (p90) REVERT: H 2 PHE cc_start: 0.8089 (m-80) cc_final: 0.6687 (t80) REVERT: H 14 ASP cc_start: 0.7079 (t70) cc_final: 0.6539 (t70) REVERT: H 35 GLN cc_start: 0.8455 (tt0) cc_final: 0.8011 (tt0) REVERT: H 39 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7466 (t) REVERT: H 70 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8247 (t) REVERT: H 74 MET cc_start: 0.8813 (mtt) cc_final: 0.8417 (mtm) REVERT: H 77 GLU cc_start: 0.8295 (mp0) cc_final: 0.7861 (mp0) REVERT: H 121 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8359 (ptpp) REVERT: H 130 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8216 (mmmm) REVERT: H 140 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8261 (mt) REVERT: I 1 MET cc_start: 0.8446 (tpp) cc_final: 0.8230 (tpp) REVERT: I 22 GLN cc_start: 0.8157 (mt0) cc_final: 0.7933 (mt0) REVERT: I 139 GLU cc_start: 0.8601 (tp30) cc_final: 0.7978 (tp30) REVERT: I 143 ASP cc_start: 0.8719 (t0) cc_final: 0.8474 (t70) REVERT: I 146 SER cc_start: 0.8837 (m) cc_final: 0.8155 (p) REVERT: I 154 GLU cc_start: 0.8571 (pt0) cc_final: 0.8138 (tt0) REVERT: J 8 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7866 (ptp-110) REVERT: J 28 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8173 (mt) REVERT: J 30 GLN cc_start: 0.8682 (mm110) cc_final: 0.8318 (pp30) REVERT: J 37 LYS cc_start: 0.8716 (tttt) cc_final: 0.8514 (tttm) REVERT: J 79 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7500 (t-90) REVERT: J 126 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7940 (mt-10) REVERT: J 161 TYR cc_start: 0.8603 (p90) cc_final: 0.8152 (p90) REVERT: K 77 GLU cc_start: 0.7966 (pm20) cc_final: 0.7443 (mp0) REVERT: K 79 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.6138 (t-90) REVERT: K 103 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7548 (mmtt) REVERT: K 106 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7865 (mt-10) REVERT: K 121 LYS cc_start: 0.8118 (pttp) cc_final: 0.7902 (ptpt) REVERT: K 128 GLU cc_start: 0.7737 (pm20) cc_final: 0.7530 (pm20) REVERT: L 28 LEU cc_start: 0.8991 (mm) cc_final: 0.8671 (mp) REVERT: L 141 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7869 (mm110) REVERT: M 2 PHE cc_start: 0.8603 (m-10) cc_final: 0.8260 (m-10) REVERT: M 30 GLN cc_start: 0.8325 (mm110) cc_final: 0.8094 (pp30) REVERT: M 103 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8620 (mtmm) REVERT: M 114 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: M 126 GLU cc_start: 0.8506 (pp20) cc_final: 0.8073 (pp20) REVERT: M 128 GLU cc_start: 0.7844 (pm20) cc_final: 0.6874 (pm20) REVERT: M 146 SER cc_start: 0.8873 (m) cc_final: 0.8460 (p) REVERT: N 30 GLN cc_start: 0.8587 (mm110) cc_final: 0.8379 (mm-40) REVERT: N 31 ASN cc_start: 0.8707 (p0) cc_final: 0.8311 (t0) REVERT: N 80 ASP cc_start: 0.8644 (p0) cc_final: 0.8196 (p0) REVERT: N 91 ILE cc_start: 0.9353 (mt) cc_final: 0.9024 (mm) REVERT: N 95 GLN cc_start: 0.8260 (tt0) cc_final: 0.7940 (tt0) REVERT: N 109 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8767 (mmtt) REVERT: N 127 ILE cc_start: 0.8518 (mt) cc_final: 0.8316 (mp) REVERT: N 160 ASP cc_start: 0.8371 (m-30) cc_final: 0.7558 (m-30) REVERT: O 8 ARG cc_start: 0.8404 (ptm160) cc_final: 0.7744 (ptm160) REVERT: O 11 GLU cc_start: 0.8465 (tp30) cc_final: 0.8221 (tp30) REVERT: O 24 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: O 83 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8121 (tm-30) REVERT: P 20 LEU cc_start: 0.9114 (mt) cc_final: 0.8898 (mt) REVERT: P 76 ASP cc_start: 0.8251 (p0) cc_final: 0.7925 (p0) REVERT: P 98 GLU cc_start: 0.8473 (tp30) cc_final: 0.8151 (tp30) REVERT: P 112 ILE cc_start: 0.9112 (mt) cc_final: 0.8658 (tt) REVERT: P 119 ASP cc_start: 0.8741 (t0) cc_final: 0.8117 (t0) REVERT: P 121 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8092 (ptpp) REVERT: Q 1 MET cc_start: 0.8624 (mmt) cc_final: 0.8151 (mmm) REVERT: Q 8 ARG cc_start: 0.8191 (mtm110) cc_final: 0.7968 (mtp-110) REVERT: Q 14 ASP cc_start: 0.7948 (t0) cc_final: 0.7600 (t0) REVERT: Q 15 PHE cc_start: 0.8274 (m-10) cc_final: 0.7742 (m-80) REVERT: Q 31 ASN cc_start: 0.7996 (p0) cc_final: 0.7340 (t0) REVERT: Q 37 LYS cc_start: 0.8919 (tttp) cc_final: 0.8693 (tttp) REVERT: Q 39 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8311 (t) REVERT: Q 77 GLU cc_start: 0.8664 (mp0) cc_final: 0.8298 (mp0) REVERT: Q 154 GLU cc_start: 0.8334 (tt0) cc_final: 0.7874 (tt0) outliers start: 231 outliers final: 171 residues processed: 1123 average time/residue: 0.1662 time to fit residues: 288.6311 Evaluate side-chains 1088 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 904 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 147 ASN Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 19 ASN Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 GLU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 99 ILE Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 115 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN K 22 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082959 restraints weight = 50877.317| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.22 r_work: 0.2989 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 1.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23994 Z= 0.176 Angle : 0.635 10.237 32562 Z= 0.334 Chirality : 0.049 0.191 3510 Planarity : 0.004 0.037 4284 Dihedral : 6.922 78.966 3132 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 8.68 % Allowed : 24.74 % Favored : 66.59 % 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: -1.74 (0.14), residues: 2898 helix: -2.10 (0.23), residues: 360 sheet: -0.01 (0.20), residues: 756 loop : -1.51 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 64 TYR 0.017 0.002 TYR A 107 PHE 0.013 0.001 PHE Q 21 TRP 0.016 0.001 TRP I 88 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (23994) covalent geometry : angle 0.63518 / 0.33 (32562) hydrogen bonds : bond 0.03470 / 2.28 ( 648) hydrogen bonds : angle 5.99595 / 4.11 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 962 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8721 (ptm-80) cc_final: 0.8329 (ptm-80) REVERT: A 24 GLU cc_start: 0.8086 (pt0) cc_final: 0.7629 (pt0) REVERT: A 54 MET cc_start: 0.8072 (mmm) cc_final: 0.7581 (tpp) REVERT: A 57 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8180 (mmtt) REVERT: A 112 ILE cc_start: 0.8763 (mt) cc_final: 0.8298 (mm) REVERT: A 119 ASP cc_start: 0.8675 (t0) cc_final: 0.8249 (t70) REVERT: A 121 LYS cc_start: 0.8712 (ptpt) cc_final: 0.8366 (ptpp) REVERT: A 126 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 151 GLN cc_start: 0.8065 (tt0) cc_final: 0.7797 (tt0) REVERT: A 161 TYR cc_start: 0.8659 (p90) cc_final: 0.8306 (p90) REVERT: R 2 PHE cc_start: 0.8236 (m-80) cc_final: 0.7543 (m-10) REVERT: R 31 ASN cc_start: 0.8602 (p0) cc_final: 0.8352 (t0) REVERT: R 34 PHE cc_start: 0.9015 (m-10) cc_final: 0.7945 (m-10) REVERT: R 39 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7809 (t) REVERT: R 75 ASN cc_start: 0.9134 (t0) cc_final: 0.8900 (t0) REVERT: R 126 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7473 (tm-30) REVERT: R 128 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7438 (tm-30) REVERT: R 130 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8679 (mmmt) REVERT: C 57 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8529 (mmtp) REVERT: C 112 ILE cc_start: 0.9014 (mt) cc_final: 0.8699 (tt) REVERT: B 1 MET cc_start: 0.8390 (tpp) cc_final: 0.8142 (tpp) REVERT: B 34 PHE cc_start: 0.8946 (m-80) cc_final: 0.8689 (m-10) REVERT: B 83 GLN cc_start: 0.8927 (tp40) cc_final: 0.8256 (tp-100) REVERT: B 106 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7944 (tp30) REVERT: B 112 ILE cc_start: 0.9118 (mt) cc_final: 0.8752 (tt) REVERT: B 141 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: B 161 TYR cc_start: 0.8928 (p90) cc_final: 0.8636 (p90) REVERT: D 1 MET cc_start: 0.7966 (tpt) cc_final: 0.7649 (tpp) REVERT: D 8 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.6990 (ptm160) REVERT: D 31 ASN cc_start: 0.8669 (p0) cc_final: 0.7932 (t0) REVERT: D 47 GLU cc_start: 0.8330 (tp30) cc_final: 0.8024 (tp30) REVERT: D 54 MET cc_start: 0.7679 (mmm) cc_final: 0.7362 (tpp) REVERT: D 83 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8244 (tp-100) REVERT: D 97 ASN cc_start: 0.8031 (t0) cc_final: 0.7613 (t0) REVERT: D 139 GLU cc_start: 0.8432 (tp30) cc_final: 0.7546 (pt0) REVERT: D 161 TYR cc_start: 0.8590 (p90) cc_final: 0.8159 (p90) REVERT: E 2 PHE cc_start: 0.8451 (m-80) cc_final: 0.5809 (t80) REVERT: E 4 ASP cc_start: 0.8184 (m-30) cc_final: 0.7866 (p0) REVERT: E 14 ASP cc_start: 0.7172 (t0) cc_final: 0.6971 (t0) REVERT: E 30 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7942 (tp40) REVERT: E 45 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (tt) REVERT: E 83 GLN cc_start: 0.8891 (tp40) cc_final: 0.8470 (tm-30) REVERT: E 90 SER cc_start: 0.9109 (t) cc_final: 0.8741 (p) REVERT: E 126 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7718 (pp20) REVERT: E 142 LEU cc_start: 0.8347 (pt) cc_final: 0.7996 (pt) REVERT: E 160 ASP cc_start: 0.7934 (m-30) cc_final: 0.7570 (m-30) REVERT: E 161 TYR cc_start: 0.8947 (p90) cc_final: 0.8454 (p90) REVERT: F 1 MET cc_start: 0.8580 (tpp) cc_final: 0.8171 (tpp) REVERT: F 2 PHE cc_start: 0.7767 (m-80) cc_final: 0.7350 (m-80) REVERT: F 22 GLN cc_start: 0.8454 (tp40) cc_final: 0.8181 (tt0) REVERT: F 24 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7275 (tm-30) REVERT: F 27 TYR cc_start: 0.8766 (t80) cc_final: 0.8556 (t80) REVERT: F 36 CYS cc_start: 0.8621 (t) cc_final: 0.8086 (t) REVERT: F 47 GLU cc_start: 0.4582 (pt0) cc_final: 0.4268 (pt0) REVERT: F 112 ILE cc_start: 0.9030 (mt) cc_final: 0.8730 (tt) REVERT: F 135 THR cc_start: 0.8713 (m) cc_final: 0.8437 (p) REVERT: F 139 GLU cc_start: 0.8718 (tp30) cc_final: 0.7409 (pt0) REVERT: F 154 GLU cc_start: 0.8444 (pt0) cc_final: 0.8053 (tt0) REVERT: G 1 MET cc_start: 0.7991 (tpt) cc_final: 0.7773 (tpt) REVERT: G 2 PHE cc_start: 0.8212 (m-80) cc_final: 0.7958 (m-80) REVERT: G 31 ASN cc_start: 0.8375 (p0) cc_final: 0.7820 (t0) REVERT: G 35 GLN cc_start: 0.8090 (mt0) cc_final: 0.7758 (mt0) REVERT: G 54 MET cc_start: 0.7769 (mmm) cc_final: 0.7378 (tpp) REVERT: G 98 GLU cc_start: 0.8572 (pm20) cc_final: 0.7999 (pp20) REVERT: G 99 ILE cc_start: 0.8486 (mt) cc_final: 0.8229 (mt) REVERT: G 103 LYS cc_start: 0.8932 (mttp) cc_final: 0.8665 (mtmm) REVERT: G 106 GLU cc_start: 0.8026 (pm20) cc_final: 0.7758 (pm20) REVERT: G 130 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8499 (mmmm) REVERT: G 146 SER cc_start: 0.8247 (m) cc_final: 0.7953 (p) REVERT: G 161 TYR cc_start: 0.8811 (p90) cc_final: 0.8460 (p90) REVERT: H 2 PHE cc_start: 0.8103 (m-80) cc_final: 0.6612 (t80) REVERT: H 10 PHE cc_start: 0.5484 (m-10) cc_final: 0.5272 (m-10) REVERT: H 30 GLN cc_start: 0.8431 (pp30) cc_final: 0.8219 (pp30) REVERT: H 35 GLN cc_start: 0.8348 (tt0) cc_final: 0.7830 (mt0) REVERT: H 39 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7451 (t) REVERT: H 70 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8269 (t) REVERT: H 76 ASP cc_start: 0.8463 (p0) cc_final: 0.8238 (p0) REVERT: H 115 GLN cc_start: 0.7877 (tt0) cc_final: 0.7555 (tt0) REVERT: H 130 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8149 (mmmm) REVERT: H 140 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8252 (mt) REVERT: H 161 TYR cc_start: 0.8795 (p90) cc_final: 0.8536 (p90) REVERT: I 36 CYS cc_start: 0.9138 (t) cc_final: 0.8637 (t) REVERT: I 139 GLU cc_start: 0.8537 (tp30) cc_final: 0.7753 (pt0) REVERT: I 146 SER cc_start: 0.8813 (m) cc_final: 0.8213 (p) REVERT: I 154 GLU cc_start: 0.8593 (pt0) cc_final: 0.8106 (tt0) REVERT: J 8 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7997 (ptp-110) REVERT: J 28 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8301 (mt) REVERT: J 30 GLN cc_start: 0.8523 (mm110) cc_final: 0.8304 (pp30) REVERT: J 77 GLU cc_start: 0.8248 (mp0) cc_final: 0.7996 (mp0) REVERT: J 79 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7520 (t-90) REVERT: J 109 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8748 (mmtp) REVERT: J 145 ASP cc_start: 0.8954 (t0) cc_final: 0.8573 (m-30) REVERT: K 31 ASN cc_start: 0.8493 (p0) cc_final: 0.7988 (t0) REVERT: K 77 GLU cc_start: 0.7904 (pm20) cc_final: 0.7505 (mp0) REVERT: K 79 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.6928 (t-90) REVERT: K 103 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7717 (mmtt) REVERT: K 121 LYS cc_start: 0.8157 (pttp) cc_final: 0.7845 (ptpp) REVERT: L 28 LEU cc_start: 0.9006 (mm) cc_final: 0.8632 (mp) REVERT: L 98 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6235 (mm-30) REVERT: L 114 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8419 (mtm110) REVERT: M 2 PHE cc_start: 0.8567 (m-10) cc_final: 0.8220 (m-10) REVERT: M 47 GLU cc_start: 0.7997 (tp30) cc_final: 0.7523 (tp30) REVERT: M 48 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7777 (ttmt) REVERT: M 103 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8604 (mtmm) REVERT: M 146 SER cc_start: 0.8714 (m) cc_final: 0.8290 (p) REVERT: N 30 GLN cc_start: 0.8622 (mm110) cc_final: 0.8236 (mm-40) REVERT: N 31 ASN cc_start: 0.8710 (p0) cc_final: 0.8414 (t0) REVERT: N 76 ASP cc_start: 0.8049 (p0) cc_final: 0.7726 (p0) REVERT: N 80 ASP cc_start: 0.8862 (p0) cc_final: 0.8345 (p0) REVERT: N 91 ILE cc_start: 0.9443 (mt) cc_final: 0.9151 (mm) REVERT: N 95 GLN cc_start: 0.8308 (tt0) cc_final: 0.7993 (tt0) REVERT: N 116 TYR cc_start: 0.8859 (m-10) cc_final: 0.8586 (m-10) REVERT: N 155 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8175 (p) REVERT: N 160 ASP cc_start: 0.8425 (m-30) cc_final: 0.7636 (m-30) REVERT: O 4 ASP cc_start: 0.8436 (m-30) cc_final: 0.8049 (p0) REVERT: O 8 ARG cc_start: 0.8381 (ptm160) cc_final: 0.7785 (ptm160) REVERT: O 11 GLU cc_start: 0.8468 (tp30) cc_final: 0.8195 (tp30) REVERT: O 24 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: O 83 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8210 (tm-30) REVERT: O 119 ASP cc_start: 0.8444 (t0) cc_final: 0.7916 (t70) REVERT: O 160 ASP cc_start: 0.8234 (m-30) cc_final: 0.7775 (m-30) REVERT: P 1 MET cc_start: 0.8649 (tpt) cc_final: 0.8377 (tpp) REVERT: P 8 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8041 (ptm160) REVERT: P 70 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7584 (t) REVERT: P 76 ASP cc_start: 0.8367 (p0) cc_final: 0.7920 (p0) REVERT: P 112 ILE cc_start: 0.9090 (mt) cc_final: 0.8650 (tt) REVERT: P 119 ASP cc_start: 0.8695 (t0) cc_final: 0.8102 (t0) REVERT: P 121 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8174 (ptpp) REVERT: P 141 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8507 (mm110) REVERT: Q 1 MET cc_start: 0.8591 (mmt) cc_final: 0.8244 (mmm) REVERT: Q 8 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7950 (mtp-110) REVERT: Q 24 GLU cc_start: 0.8160 (pp20) cc_final: 0.7803 (pp20) REVERT: Q 31 ASN cc_start: 0.7959 (p0) cc_final: 0.7576 (t0) REVERT: Q 37 LYS cc_start: 0.8909 (tttp) cc_final: 0.8545 (tmmt) REVERT: Q 47 GLU cc_start: 0.8515 (tp30) cc_final: 0.8232 (tp30) REVERT: Q 77 GLU cc_start: 0.8545 (mp0) cc_final: 0.8249 (mp0) REVERT: Q 103 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8764 (mtmt) REVERT: Q 115 GLN cc_start: 0.7809 (pt0) cc_final: 0.7470 (pt0) REVERT: Q 142 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7611 (pt) REVERT: Q 154 GLU cc_start: 0.8302 (tt0) cc_final: 0.7851 (tt0) outliers start: 214 outliers final: 170 residues processed: 1104 average time/residue: 0.1706 time to fit residues: 291.1481 Evaluate side-chains 1096 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 912 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 GLN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 147 ASN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 19 ASN Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 GLU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN G 30 GLN ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN M 147 ASN N 83 GLN O 55 ASN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083863 restraints weight = 50564.826| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.24 r_work: 0.3003 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 1.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23994 Z= 0.154 Angle : 0.636 11.136 32562 Z= 0.332 Chirality : 0.048 0.208 3510 Planarity : 0.004 0.035 4284 Dihedral : 6.720 76.281 3132 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 8.76 % Allowed : 25.22 % Favored : 66.02 % 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: -1.71 (0.14), residues: 2898 helix: -2.01 (0.24), residues: 360 sheet: -0.03 (0.20), residues: 756 loop : -1.49 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 64 TYR 0.029 0.002 TYR J 27 PHE 0.011 0.001 PHE O 10 TRP 0.013 0.001 TRP I 88 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (23994) covalent geometry : angle 0.63634 / 0.33 (32562) hydrogen bonds : bond 0.03354 / 2.20 ( 648) hydrogen bonds : angle 5.89293 / 4.03 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 966 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8186 (pt0) cc_final: 0.7685 (pt0) REVERT: A 54 MET cc_start: 0.8101 (mmm) cc_final: 0.7729 (tpp) REVERT: A 112 ILE cc_start: 0.8728 (mt) cc_final: 0.8523 (mm) REVERT: A 119 ASP cc_start: 0.8804 (t0) cc_final: 0.8366 (t70) REVERT: A 121 LYS cc_start: 0.8686 (ptpt) cc_final: 0.8367 (ptpp) REVERT: A 161 TYR cc_start: 0.8682 (p90) cc_final: 0.8306 (p90) REVERT: R 2 PHE cc_start: 0.8219 (m-80) cc_final: 0.7550 (m-10) REVERT: R 21 PHE cc_start: 0.8848 (p90) cc_final: 0.8527 (p90) REVERT: R 34 PHE cc_start: 0.8985 (m-10) cc_final: 0.7944 (m-10) REVERT: R 39 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7814 (t) REVERT: R 75 ASN cc_start: 0.9161 (t0) cc_final: 0.8913 (t0) REVERT: R 126 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7481 (tm-30) REVERT: R 128 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7517 (tm-30) REVERT: R 130 LYS cc_start: 0.8996 (mmtp) cc_final: 0.8668 (mmmt) REVERT: R 141 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: C 24 GLU cc_start: 0.8335 (pp20) cc_final: 0.7990 (tm-30) REVERT: C 57 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8454 (mmtp) REVERT: C 77 GLU cc_start: 0.8340 (pm20) cc_final: 0.7560 (mp0) REVERT: C 112 ILE cc_start: 0.9001 (mt) cc_final: 0.8703 (tt) REVERT: C 160 ASP cc_start: 0.7776 (m-30) cc_final: 0.7469 (m-30) REVERT: B 1 MET cc_start: 0.8458 (tpp) cc_final: 0.8219 (tpp) REVERT: B 34 PHE cc_start: 0.8964 (m-80) cc_final: 0.8703 (m-10) REVERT: B 83 GLN cc_start: 0.8884 (tp40) cc_final: 0.8043 (tp-100) REVERT: B 106 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8079 (tp30) REVERT: B 112 ILE cc_start: 0.9115 (mt) cc_final: 0.8735 (tt) REVERT: B 121 LYS cc_start: 0.8591 (mttp) cc_final: 0.8281 (mptt) REVERT: B 141 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8049 (mm-40) REVERT: B 161 TYR cc_start: 0.8928 (p90) cc_final: 0.8721 (p90) REVERT: D 1 MET cc_start: 0.7981 (tpt) cc_final: 0.7737 (tpp) REVERT: D 8 ARG cc_start: 0.7558 (mtp-110) cc_final: 0.6989 (ptm160) REVERT: D 30 GLN cc_start: 0.8577 (mm110) cc_final: 0.8000 (pp30) REVERT: D 31 ASN cc_start: 0.8560 (p0) cc_final: 0.8183 (t0) REVERT: D 54 MET cc_start: 0.7740 (mmm) cc_final: 0.7463 (tpp) REVERT: D 83 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8225 (tp-100) REVERT: D 88 TRP cc_start: 0.9392 (t60) cc_final: 0.8981 (t60) REVERT: D 97 ASN cc_start: 0.7942 (t0) cc_final: 0.7369 (t0) REVERT: D 139 GLU cc_start: 0.8326 (tp30) cc_final: 0.7457 (pt0) REVERT: D 161 TYR cc_start: 0.8431 (p90) cc_final: 0.8014 (p90) REVERT: E 2 PHE cc_start: 0.8355 (m-80) cc_final: 0.5809 (t80) REVERT: E 4 ASP cc_start: 0.8213 (m-30) cc_final: 0.7898 (p0) REVERT: E 23 VAL cc_start: 0.7982 (p) cc_final: 0.7740 (p) REVERT: E 28 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8371 (mt) REVERT: E 30 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7810 (tp40) REVERT: E 45 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8681 (tt) REVERT: E 83 GLN cc_start: 0.8892 (tp40) cc_final: 0.8452 (tm-30) REVERT: E 90 SER cc_start: 0.9091 (t) cc_final: 0.8735 (p) REVERT: E 126 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (pp20) REVERT: E 142 LEU cc_start: 0.8359 (pt) cc_final: 0.7986 (pt) REVERT: E 160 ASP cc_start: 0.7975 (m-30) cc_final: 0.7665 (m-30) REVERT: E 161 TYR cc_start: 0.8933 (p90) cc_final: 0.8430 (p90) REVERT: F 1 MET cc_start: 0.8416 (tpp) cc_final: 0.8115 (tpp) REVERT: F 2 PHE cc_start: 0.7838 (m-80) cc_final: 0.7536 (m-80) REVERT: F 22 GLN cc_start: 0.8417 (tp40) cc_final: 0.8190 (tt0) REVERT: F 24 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7227 (tm-30) REVERT: F 35 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: F 36 CYS cc_start: 0.8618 (t) cc_final: 0.8058 (t) REVERT: F 47 GLU cc_start: 0.4737 (pt0) cc_final: 0.4429 (pt0) REVERT: F 112 ILE cc_start: 0.9013 (mt) cc_final: 0.8741 (tt) REVERT: F 116 TYR cc_start: 0.8552 (m-80) cc_final: 0.8228 (m-80) REVERT: F 135 THR cc_start: 0.8717 (m) cc_final: 0.8444 (p) REVERT: F 154 GLU cc_start: 0.8428 (pt0) cc_final: 0.8057 (tt0) REVERT: G 1 MET cc_start: 0.7985 (tpt) cc_final: 0.7753 (tpt) REVERT: G 2 PHE cc_start: 0.8133 (m-80) cc_final: 0.7852 (m-80) REVERT: G 28 LEU cc_start: 0.9018 (mm) cc_final: 0.8721 (mt) REVERT: G 35 GLN cc_start: 0.8187 (mt0) cc_final: 0.7958 (mt0) REVERT: G 54 MET cc_start: 0.7773 (mmm) cc_final: 0.7401 (tpp) REVERT: G 98 GLU cc_start: 0.8543 (pm20) cc_final: 0.7987 (pp20) REVERT: G 99 ILE cc_start: 0.8537 (mt) cc_final: 0.8258 (mt) REVERT: G 106 GLU cc_start: 0.8039 (pm20) cc_final: 0.7762 (pm20) REVERT: G 112 ILE cc_start: 0.8815 (mt) cc_final: 0.8266 (tt) REVERT: G 146 SER cc_start: 0.8050 (m) cc_final: 0.7704 (p) REVERT: G 161 TYR cc_start: 0.8848 (p90) cc_final: 0.8498 (p90) REVERT: H 2 PHE cc_start: 0.8213 (m-80) cc_final: 0.6528 (t80) REVERT: H 11 GLU cc_start: 0.7264 (mp0) cc_final: 0.6850 (mp0) REVERT: H 14 ASP cc_start: 0.7129 (t70) cc_final: 0.6319 (t70) REVERT: H 35 GLN cc_start: 0.8183 (tt0) cc_final: 0.7681 (mt0) REVERT: H 39 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7411 (t) REVERT: H 70 THR cc_start: 0.8539 (p) cc_final: 0.8283 (t) REVERT: H 115 GLN cc_start: 0.7860 (tt0) cc_final: 0.7600 (tt0) REVERT: H 121 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8639 (ptpp) REVERT: H 130 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8173 (mmmm) REVERT: H 140 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8282 (mt) REVERT: H 161 TYR cc_start: 0.8832 (p90) cc_final: 0.8520 (p90) REVERT: I 4 ASP cc_start: 0.8058 (m-30) cc_final: 0.7708 (p0) REVERT: I 14 ASP cc_start: 0.8219 (t0) cc_final: 0.7791 (t0) REVERT: I 15 PHE cc_start: 0.8057 (m-80) cc_final: 0.7746 (m-10) REVERT: I 36 CYS cc_start: 0.9095 (t) cc_final: 0.8741 (t) REVERT: I 139 GLU cc_start: 0.8513 (tp30) cc_final: 0.7746 (pt0) REVERT: I 146 SER cc_start: 0.8822 (m) cc_final: 0.7540 (p) REVERT: I 154 GLU cc_start: 0.8581 (pt0) cc_final: 0.8090 (tt0) REVERT: J 8 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7982 (ptp-110) REVERT: J 28 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8237 (mt) REVERT: J 37 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8592 (tttm) REVERT: J 75 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7824 (t0) REVERT: J 79 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.7664 (t-90) REVERT: K 31 ASN cc_start: 0.8503 (p0) cc_final: 0.8006 (t0) REVERT: K 48 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8420 (ttpt) REVERT: K 77 GLU cc_start: 0.7864 (pm20) cc_final: 0.7349 (mp0) REVERT: K 79 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7180 (t-90) REVERT: K 103 LYS cc_start: 0.8440 (mmtt) cc_final: 0.7757 (mmtt) REVERT: K 121 LYS cc_start: 0.8217 (pttp) cc_final: 0.7884 (ptpp) REVERT: K 128 GLU cc_start: 0.7407 (pm20) cc_final: 0.7203 (pm20) REVERT: L 28 LEU cc_start: 0.8941 (mm) cc_final: 0.8627 (mp) REVERT: L 30 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8256 (pp30) REVERT: M 2 PHE cc_start: 0.8528 (m-10) cc_final: 0.8161 (m-10) REVERT: M 15 PHE cc_start: 0.7800 (m-80) cc_final: 0.7439 (m-10) REVERT: M 17 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7127 (mpt180) REVERT: M 103 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8593 (mtmm) REVERT: M 106 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7899 (tp30) REVERT: M 146 SER cc_start: 0.8806 (m) cc_final: 0.8393 (p) REVERT: N 30 GLN cc_start: 0.8553 (mm110) cc_final: 0.8242 (mm-40) REVERT: N 76 ASP cc_start: 0.8102 (p0) cc_final: 0.7672 (p0) REVERT: N 79 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7113 (t70) REVERT: N 80 ASP cc_start: 0.8863 (p0) cc_final: 0.8425 (p0) REVERT: N 91 ILE cc_start: 0.9438 (mt) cc_final: 0.9162 (mm) REVERT: N 95 GLN cc_start: 0.8215 (tt0) cc_final: 0.7940 (tt0) REVERT: N 112 ILE cc_start: 0.8851 (mt) cc_final: 0.8239 (tt) REVERT: N 136 ASN cc_start: 0.8831 (p0) cc_final: 0.8435 (p0) REVERT: N 155 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8273 (p) REVERT: N 160 ASP cc_start: 0.8438 (m-30) cc_final: 0.7677 (m-30) REVERT: O 4 ASP cc_start: 0.8435 (m-30) cc_final: 0.8050 (p0) REVERT: O 8 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7881 (ptm160) REVERT: O 11 GLU cc_start: 0.8355 (tp30) cc_final: 0.8015 (tp30) REVERT: O 14 ASP cc_start: 0.7705 (t0) cc_final: 0.7315 (t70) REVERT: O 83 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8210 (tm-30) REVERT: O 119 ASP cc_start: 0.8486 (t0) cc_final: 0.7952 (t70) REVERT: O 145 ASP cc_start: 0.8447 (t0) cc_final: 0.8094 (m-30) REVERT: O 160 ASP cc_start: 0.8287 (m-30) cc_final: 0.7864 (m-30) REVERT: P 1 MET cc_start: 0.8562 (tpt) cc_final: 0.8335 (tpp) REVERT: P 8 ARG cc_start: 0.8509 (ptp-110) cc_final: 0.8057 (ptm160) REVERT: P 54 MET cc_start: 0.7473 (tpp) cc_final: 0.7187 (tpp) REVERT: P 70 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7569 (t) REVERT: P 112 ILE cc_start: 0.9086 (mt) cc_final: 0.8616 (tt) REVERT: P 119 ASP cc_start: 0.8723 (t0) cc_final: 0.8022 (t0) REVERT: P 121 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8221 (ptpp) REVERT: Q 1 MET cc_start: 0.8593 (mmt) cc_final: 0.8251 (mmm) REVERT: Q 8 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7921 (mtp-110) REVERT: Q 15 PHE cc_start: 0.8539 (m-10) cc_final: 0.8055 (m-80) REVERT: Q 24 GLU cc_start: 0.8086 (pp20) cc_final: 0.7884 (pt0) REVERT: Q 37 LYS cc_start: 0.8831 (tttp) cc_final: 0.8453 (tmmt) REVERT: Q 47 GLU cc_start: 0.8551 (tp30) cc_final: 0.8277 (tp30) REVERT: Q 103 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8794 (mtmt) outliers start: 216 outliers final: 175 residues processed: 1111 average time/residue: 0.1705 time to fit residues: 291.5896 Evaluate side-chains 1121 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 929 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 141 GLN Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 GLN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 34 PHE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 147 ASN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 HIS Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 156 THR Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 99 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN M 147 ASN N 83 GLN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082318 restraints weight = 50787.321| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.21 r_work: 0.2971 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 1.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23994 Z= 0.198 Angle : 0.670 10.332 32562 Z= 0.352 Chirality : 0.049 0.210 3510 Planarity : 0.004 0.036 4284 Dihedral : 6.926 79.506 3132 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 9.12 % Allowed : 25.22 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.71 (0.14), residues: 2898 helix: -1.86 (0.24), residues: 360 sheet: -0.09 (0.20), residues: 756 loop : -1.49 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 64 TYR 0.029 0.002 TYR C 107 PHE 0.014 0.001 PHE F 53 TRP 0.015 0.001 TRP I 88 HIS 0.003 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (23994) covalent geometry : angle 0.67015 / 0.35 (32562) hydrogen bonds : bond 0.03524 / 2.32 ( 648) hydrogen bonds : angle 5.96611 / 4.08 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 927 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8063 (pt0) cc_final: 0.7542 (pt0) REVERT: A 54 MET cc_start: 0.8189 (mmm) cc_final: 0.7933 (tpp) REVERT: A 112 ILE cc_start: 0.8784 (mt) cc_final: 0.8550 (mm) REVERT: A 119 ASP cc_start: 0.8777 (t0) cc_final: 0.8458 (t70) REVERT: A 126 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 161 TYR cc_start: 0.8720 (p90) cc_final: 0.8363 (p90) REVERT: R 2 PHE cc_start: 0.8251 (m-80) cc_final: 0.7612 (m-10) REVERT: R 34 PHE cc_start: 0.9042 (m-10) cc_final: 0.7988 (m-10) REVERT: R 39 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7756 (t) REVERT: R 126 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7431 (tm-30) REVERT: R 130 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8723 (mmmt) REVERT: R 141 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: C 24 GLU cc_start: 0.8390 (pp20) cc_final: 0.8029 (tm-30) REVERT: C 57 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8485 (mmtp) REVERT: C 112 ILE cc_start: 0.9017 (mt) cc_final: 0.8768 (tt) REVERT: B 1 MET cc_start: 0.8446 (tpp) cc_final: 0.8218 (tpp) REVERT: B 34 PHE cc_start: 0.9032 (m-80) cc_final: 0.8704 (m-10) REVERT: B 83 GLN cc_start: 0.8871 (tp40) cc_final: 0.7912 (tp-100) REVERT: B 112 ILE cc_start: 0.9110 (mt) cc_final: 0.8685 (tt) REVERT: B 116 TYR cc_start: 0.8890 (m-10) cc_final: 0.8651 (m-10) REVERT: B 141 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: D 1 MET cc_start: 0.7986 (tpt) cc_final: 0.7731 (tpp) REVERT: D 8 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.6983 (ptm160) REVERT: D 31 ASN cc_start: 0.8550 (p0) cc_final: 0.8141 (t0) REVERT: D 47 GLU cc_start: 0.8356 (tp30) cc_final: 0.8144 (tp30) REVERT: D 54 MET cc_start: 0.7767 (mmm) cc_final: 0.7539 (tpp) REVERT: D 88 TRP cc_start: 0.9386 (t60) cc_final: 0.8975 (t60) REVERT: D 97 ASN cc_start: 0.7997 (t0) cc_final: 0.7649 (t0) REVERT: D 161 TYR cc_start: 0.8433 (p90) cc_final: 0.7947 (p90) REVERT: E 2 PHE cc_start: 0.8392 (m-80) cc_final: 0.5888 (t80) REVERT: E 28 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8285 (mt) REVERT: E 30 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7747 (tp40) REVERT: E 45 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8751 (tt) REVERT: E 83 GLN cc_start: 0.8897 (tp40) cc_final: 0.8485 (tm-30) REVERT: E 90 SER cc_start: 0.9100 (t) cc_final: 0.8727 (p) REVERT: E 116 TYR cc_start: 0.9034 (m-10) cc_final: 0.8824 (m-10) REVERT: E 126 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7621 (pp20) REVERT: E 142 LEU cc_start: 0.8451 (pt) cc_final: 0.8114 (pt) REVERT: E 161 TYR cc_start: 0.8935 (p90) cc_final: 0.8359 (p90) REVERT: F 1 MET cc_start: 0.8537 (tpp) cc_final: 0.8250 (tpp) REVERT: F 2 PHE cc_start: 0.7860 (m-80) cc_final: 0.7563 (m-80) REVERT: F 22 GLN cc_start: 0.8497 (tp40) cc_final: 0.8270 (tt0) REVERT: F 24 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7292 (tm-30) REVERT: F 35 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: F 36 CYS cc_start: 0.8629 (t) cc_final: 0.8039 (t) REVERT: F 47 GLU cc_start: 0.4780 (pt0) cc_final: 0.4432 (pt0) REVERT: F 112 ILE cc_start: 0.8976 (mt) cc_final: 0.8722 (tt) REVERT: F 116 TYR cc_start: 0.8573 (m-80) cc_final: 0.8292 (m-80) REVERT: F 128 GLU cc_start: 0.8342 (pm20) cc_final: 0.8039 (pm20) REVERT: F 135 THR cc_start: 0.8731 (m) cc_final: 0.8439 (p) REVERT: F 139 GLU cc_start: 0.8685 (tp30) cc_final: 0.7435 (pt0) REVERT: F 154 GLU cc_start: 0.8396 (pt0) cc_final: 0.8036 (tt0) REVERT: G 2 PHE cc_start: 0.8193 (m-80) cc_final: 0.7794 (m-10) REVERT: G 28 LEU cc_start: 0.9050 (mm) cc_final: 0.8748 (mt) REVERT: G 54 MET cc_start: 0.7846 (mmm) cc_final: 0.7598 (tpp) REVERT: G 98 GLU cc_start: 0.8546 (pm20) cc_final: 0.8007 (pp20) REVERT: G 99 ILE cc_start: 0.8556 (mt) cc_final: 0.8339 (mt) REVERT: G 112 ILE cc_start: 0.8782 (mt) cc_final: 0.8406 (tt) REVERT: G 146 SER cc_start: 0.8027 (m) cc_final: 0.7655 (p) REVERT: G 161 TYR cc_start: 0.8858 (p90) cc_final: 0.8655 (p90) REVERT: H 4 ASP cc_start: 0.8495 (m-30) cc_final: 0.8183 (m-30) REVERT: H 11 GLU cc_start: 0.7237 (mp0) cc_final: 0.6959 (mp0) REVERT: H 14 ASP cc_start: 0.7294 (t70) cc_final: 0.6966 (t70) REVERT: H 30 GLN cc_start: 0.8397 (pp30) cc_final: 0.7922 (pp30) REVERT: H 35 GLN cc_start: 0.8307 (tt0) cc_final: 0.7822 (mt0) REVERT: H 39 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7450 (t) REVERT: H 70 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8323 (t) REVERT: H 115 GLN cc_start: 0.7839 (tt0) cc_final: 0.7561 (tt0) REVERT: H 140 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8315 (mt) REVERT: H 161 TYR cc_start: 0.8876 (p90) cc_final: 0.8579 (p90) REVERT: I 36 CYS cc_start: 0.9173 (t) cc_final: 0.8842 (t) REVERT: I 139 GLU cc_start: 0.8505 (tp30) cc_final: 0.7730 (pt0) REVERT: I 154 GLU cc_start: 0.8619 (pt0) cc_final: 0.8124 (tt0) REVERT: I 163 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8063 (mm-30) REVERT: J 8 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8026 (ptp-110) REVERT: J 28 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8367 (mt) REVERT: J 37 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8659 (tttm) REVERT: J 75 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.7823 (t0) REVERT: J 79 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7668 (t-90) REVERT: J 126 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6637 (tm-30) REVERT: J 128 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: K 31 ASN cc_start: 0.8511 (p0) cc_final: 0.8086 (t0) REVERT: K 77 GLU cc_start: 0.7992 (pm20) cc_final: 0.7427 (mp0) REVERT: K 79 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7406 (t-90) REVERT: K 103 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7639 (mmtt) REVERT: K 121 LYS cc_start: 0.8373 (pttp) cc_final: 0.8067 (ptpp) REVERT: K 149 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: L 22 GLN cc_start: 0.8029 (tt0) cc_final: 0.7820 (tt0) REVERT: L 28 LEU cc_start: 0.9017 (mm) cc_final: 0.8669 (mp) REVERT: L 30 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8284 (pp30) REVERT: M 2 PHE cc_start: 0.8579 (m-10) cc_final: 0.8240 (m-10) REVERT: M 5 ASP cc_start: 0.8141 (t0) cc_final: 0.7634 (t0) REVERT: M 15 PHE cc_start: 0.7821 (m-80) cc_final: 0.7459 (m-10) REVERT: M 17 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7176 (mpt180) REVERT: M 47 GLU cc_start: 0.7964 (tp30) cc_final: 0.7479 (tp30) REVERT: M 103 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8638 (mtmm) REVERT: M 146 SER cc_start: 0.8811 (m) cc_final: 0.8359 (p) REVERT: N 5 ASP cc_start: 0.8280 (t0) cc_final: 0.7795 (t0) REVERT: N 45 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8989 (tt) REVERT: N 76 ASP cc_start: 0.8047 (p0) cc_final: 0.7636 (p0) REVERT: N 79 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7298 (t70) REVERT: N 80 ASP cc_start: 0.8849 (p0) cc_final: 0.8566 (p0) REVERT: N 91 ILE cc_start: 0.9457 (mt) cc_final: 0.9208 (mm) REVERT: N 95 GLN cc_start: 0.8235 (tt0) cc_final: 0.7985 (tt0) REVERT: N 109 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8442 (mmtt) REVERT: N 139 GLU cc_start: 0.8725 (mm-30) cc_final: 0.7812 (tp30) REVERT: N 160 ASP cc_start: 0.8492 (m-30) cc_final: 0.7819 (m-30) REVERT: O 2 PHE cc_start: 0.8534 (m-80) cc_final: 0.8273 (m-10) REVERT: O 4 ASP cc_start: 0.8565 (m-30) cc_final: 0.8171 (p0) REVERT: O 8 ARG cc_start: 0.8348 (ptm160) cc_final: 0.7875 (ptm160) REVERT: O 83 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8224 (tm-30) REVERT: O 119 ASP cc_start: 0.8516 (t0) cc_final: 0.8032 (t70) REVERT: O 145 ASP cc_start: 0.8346 (t0) cc_final: 0.8059 (m-30) REVERT: O 160 ASP cc_start: 0.8260 (m-30) cc_final: 0.7793 (m-30) REVERT: P 1 MET cc_start: 0.8621 (tpt) cc_final: 0.8385 (tpp) REVERT: P 8 ARG cc_start: 0.8506 (ptp-110) cc_final: 0.8086 (ptm160) REVERT: P 21 PHE cc_start: 0.8954 (p90) cc_final: 0.8690 (p90) REVERT: P 54 MET cc_start: 0.7599 (tpp) cc_final: 0.7297 (tpp) REVERT: P 70 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7576 (t) REVERT: P 76 ASP cc_start: 0.8304 (p0) cc_final: 0.7819 (p0) REVERT: P 112 ILE cc_start: 0.9091 (mt) cc_final: 0.8602 (tt) REVERT: P 119 ASP cc_start: 0.8742 (t0) cc_final: 0.8111 (t0) REVERT: P 121 LYS cc_start: 0.8431 (ptpp) cc_final: 0.8101 (ptpp) REVERT: Q 1 MET cc_start: 0.8529 (mmt) cc_final: 0.8245 (mmm) REVERT: Q 24 GLU cc_start: 0.8115 (pp20) cc_final: 0.7887 (tm-30) REVERT: Q 34 PHE cc_start: 0.8872 (m-80) cc_final: 0.8354 (m-10) REVERT: Q 37 LYS cc_start: 0.8841 (tttp) cc_final: 0.8315 (tmmt) REVERT: Q 47 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: Q 48 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8467 (ttpt) REVERT: Q 77 GLU cc_start: 0.8521 (mp0) cc_final: 0.8230 (mp0) REVERT: Q 103 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8814 (mtmt) REVERT: Q 130 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8434 (mmmm) REVERT: Q 154 GLU cc_start: 0.8338 (tt0) cc_final: 0.7856 (tt0) outliers start: 225 outliers final: 184 residues processed: 1075 average time/residue: 0.1684 time to fit residues: 279.7106 Evaluate side-chains 1111 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 906 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 141 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 GLN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 147 ASN Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 HIS Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 99 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 190 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 249 optimal weight: 30.0000 chunk 208 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 31 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 GLN ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN N 75 ASN N 83 GLN O 55 ASN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083098 restraints weight = 50983.841| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.24 r_work: 0.2980 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 1.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23994 Z= 0.173 Angle : 0.679 10.455 32562 Z= 0.355 Chirality : 0.049 0.201 3510 Planarity : 0.004 0.035 4284 Dihedral : 6.837 76.915 3132 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.43 % Allowed : 26.36 % Favored : 65.21 % 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: -1.71 (0.14), residues: 2898 helix: -1.81 (0.24), residues: 360 sheet: -0.14 (0.20), residues: 756 loop : -1.47 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 8 TYR 0.023 0.002 TYR C 107 PHE 0.014 0.001 PHE F 53 TRP 0.014 0.001 TRP I 88 HIS 0.002 0.001 HIS Q 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (23994) covalent geometry : angle 0.67917 / 0.35 (32562) hydrogen bonds : bond 0.03424 / 2.26 ( 648) hydrogen bonds : angle 5.92936 / 4.06 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 947 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8072 (pt0) cc_final: 0.7602 (pt0) REVERT: A 112 ILE cc_start: 0.8747 (mt) cc_final: 0.8523 (mm) REVERT: A 128 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6535 (tm-30) REVERT: A 130 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8677 (mmtp) REVERT: R 2 PHE cc_start: 0.8244 (m-80) cc_final: 0.7599 (m-10) REVERT: R 8 ARG cc_start: 0.8750 (ptm160) cc_final: 0.8393 (ptm160) REVERT: R 34 PHE cc_start: 0.9029 (m-10) cc_final: 0.7974 (m-10) REVERT: R 39 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7765 (t) REVERT: R 126 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7245 (tm-30) REVERT: R 141 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: C 24 GLU cc_start: 0.8375 (pp20) cc_final: 0.7998 (tm-30) REVERT: C 57 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8401 (mmtp) REVERT: C 77 GLU cc_start: 0.8229 (pm20) cc_final: 0.7595 (mp0) REVERT: C 97 ASN cc_start: 0.8533 (t0) cc_final: 0.7917 (t0) REVERT: C 112 ILE cc_start: 0.8996 (mt) cc_final: 0.8759 (tt) REVERT: B 1 MET cc_start: 0.8407 (tpp) cc_final: 0.8164 (tpp) REVERT: B 34 PHE cc_start: 0.8976 (m-80) cc_final: 0.8701 (m-10) REVERT: B 83 GLN cc_start: 0.8837 (tp40) cc_final: 0.8074 (tp-100) REVERT: B 112 ILE cc_start: 0.9105 (mt) cc_final: 0.8669 (tt) REVERT: B 116 TYR cc_start: 0.8852 (m-10) cc_final: 0.8629 (m-10) REVERT: B 141 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: D 5 ASP cc_start: 0.8203 (t70) cc_final: 0.7932 (t0) REVERT: D 8 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7070 (ptm160) REVERT: D 28 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8763 (mt) REVERT: D 30 GLN cc_start: 0.8620 (mm110) cc_final: 0.8116 (pp30) REVERT: D 31 ASN cc_start: 0.8529 (p0) cc_final: 0.8244 (t0) REVERT: D 54 MET cc_start: 0.7876 (mmm) cc_final: 0.7616 (tpp) REVERT: D 82 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8619 (ttt90) REVERT: D 83 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8247 (tp-100) REVERT: D 88 TRP cc_start: 0.9368 (t60) cc_final: 0.8968 (t60) REVERT: D 97 ASN cc_start: 0.8051 (t0) cc_final: 0.7442 (t0) REVERT: D 130 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8558 (mmmt) REVERT: D 161 TYR cc_start: 0.8429 (p90) cc_final: 0.7873 (p90) REVERT: E 2 PHE cc_start: 0.8415 (m-80) cc_final: 0.5922 (t80) REVERT: E 4 ASP cc_start: 0.8300 (m-30) cc_final: 0.7968 (p0) REVERT: E 23 VAL cc_start: 0.8102 (p) cc_final: 0.7839 (p) REVERT: E 28 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8383 (mp) REVERT: E 30 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7795 (tp40) REVERT: E 45 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8707 (tt) REVERT: E 83 GLN cc_start: 0.8894 (tp40) cc_final: 0.8475 (tm-30) REVERT: E 90 SER cc_start: 0.9105 (t) cc_final: 0.8737 (p) REVERT: E 130 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8776 (mmmt) REVERT: E 142 LEU cc_start: 0.8416 (pt) cc_final: 0.8100 (pt) REVERT: E 161 TYR cc_start: 0.8928 (p90) cc_final: 0.8331 (p90) REVERT: F 1 MET cc_start: 0.8463 (tpp) cc_final: 0.8187 (tpp) REVERT: F 2 PHE cc_start: 0.7875 (m-80) cc_final: 0.7519 (m-80) REVERT: F 24 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7309 (tm-30) REVERT: F 35 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: F 36 CYS cc_start: 0.8630 (t) cc_final: 0.8034 (t) REVERT: F 47 GLU cc_start: 0.4797 (pt0) cc_final: 0.4463 (pt0) REVERT: F 112 ILE cc_start: 0.8974 (mt) cc_final: 0.8757 (tt) REVERT: F 116 TYR cc_start: 0.8530 (m-80) cc_final: 0.8287 (m-80) REVERT: F 128 GLU cc_start: 0.8329 (pm20) cc_final: 0.7993 (pm20) REVERT: F 135 THR cc_start: 0.8740 (m) cc_final: 0.8480 (p) REVERT: F 141 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8219 (mm-40) REVERT: F 154 GLU cc_start: 0.8394 (pt0) cc_final: 0.8075 (tt0) REVERT: G 2 PHE cc_start: 0.8574 (m-80) cc_final: 0.8017 (m-80) REVERT: G 28 LEU cc_start: 0.9039 (mm) cc_final: 0.8746 (mt) REVERT: G 54 MET cc_start: 0.7849 (mmm) cc_final: 0.7631 (tpp) REVERT: G 75 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8533 (t0) REVERT: G 98 GLU cc_start: 0.8564 (pm20) cc_final: 0.8023 (pp20) REVERT: G 99 ILE cc_start: 0.8447 (mt) cc_final: 0.8199 (mt) REVERT: G 112 ILE cc_start: 0.8773 (mt) cc_final: 0.8338 (tt) REVERT: G 146 SER cc_start: 0.7942 (m) cc_final: 0.7556 (p) REVERT: H 4 ASP cc_start: 0.8553 (m-30) cc_final: 0.8251 (m-30) REVERT: H 14 ASP cc_start: 0.7247 (t70) cc_final: 0.6410 (t70) REVERT: H 30 GLN cc_start: 0.8370 (pp30) cc_final: 0.7934 (pp30) REVERT: H 35 GLN cc_start: 0.8296 (tt0) cc_final: 0.7795 (mt0) REVERT: H 39 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7400 (t) REVERT: H 54 MET cc_start: 0.8216 (mmm) cc_final: 0.7741 (tpp) REVERT: H 115 GLN cc_start: 0.7842 (tt0) cc_final: 0.7575 (tt0) REVERT: H 140 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8311 (mt) REVERT: H 161 TYR cc_start: 0.8833 (p90) cc_final: 0.8580 (p90) REVERT: I 4 ASP cc_start: 0.8145 (m-30) cc_final: 0.7855 (p0) REVERT: I 14 ASP cc_start: 0.8152 (t0) cc_final: 0.7778 (t0) REVERT: I 15 PHE cc_start: 0.8072 (m-10) cc_final: 0.7678 (m-10) REVERT: I 36 CYS cc_start: 0.9248 (t) cc_final: 0.8752 (m) REVERT: I 139 GLU cc_start: 0.8530 (tp30) cc_final: 0.7923 (tp30) REVERT: I 154 GLU cc_start: 0.8620 (pt0) cc_final: 0.8152 (tt0) REVERT: I 163 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8006 (mm-30) REVERT: J 8 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.8014 (ptp-110) REVERT: J 28 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8498 (mt) REVERT: J 37 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8524 (tttm) REVERT: J 75 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.7808 (t0) REVERT: J 79 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7617 (t-90) REVERT: J 128 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: J 149 GLU cc_start: 0.6987 (mp0) cc_final: 0.6702 (mp0) REVERT: K 1 MET cc_start: 0.8394 (tpt) cc_final: 0.8000 (tpp) REVERT: K 30 GLN cc_start: 0.8396 (mm110) cc_final: 0.8145 (pp30) REVERT: K 31 ASN cc_start: 0.8456 (p0) cc_final: 0.7920 (t0) REVERT: K 77 GLU cc_start: 0.8006 (pm20) cc_final: 0.7519 (mp0) REVERT: K 79 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7398 (t-90) REVERT: K 103 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7698 (mmtt) REVERT: L 22 GLN cc_start: 0.7877 (tt0) cc_final: 0.7260 (mt0) REVERT: L 28 LEU cc_start: 0.9001 (mm) cc_final: 0.8776 (mp) REVERT: M 4 ASP cc_start: 0.8539 (m-30) cc_final: 0.7842 (p0) REVERT: M 14 ASP cc_start: 0.7565 (t0) cc_final: 0.7329 (t0) REVERT: M 15 PHE cc_start: 0.7806 (m-80) cc_final: 0.7428 (m-10) REVERT: M 17 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7120 (mpt180) REVERT: M 47 GLU cc_start: 0.7975 (tp30) cc_final: 0.7450 (tp30) REVERT: M 103 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8598 (mtmm) REVERT: M 146 SER cc_start: 0.8778 (m) cc_final: 0.8332 (p) REVERT: N 5 ASP cc_start: 0.8251 (t0) cc_final: 0.7727 (t0) REVERT: N 31 ASN cc_start: 0.9106 (m-40) cc_final: 0.8700 (p0) REVERT: N 45 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8915 (tt) REVERT: N 76 ASP cc_start: 0.8105 (p0) cc_final: 0.7643 (p0) REVERT: N 79 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7227 (t70) REVERT: N 80 ASP cc_start: 0.8844 (p0) cc_final: 0.8511 (p0) REVERT: N 91 ILE cc_start: 0.9456 (mt) cc_final: 0.9199 (mm) REVERT: N 95 GLN cc_start: 0.8226 (tt0) cc_final: 0.7882 (tt0) REVERT: N 109 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8589 (mmtt) REVERT: N 139 GLU cc_start: 0.8742 (mm-30) cc_final: 0.7831 (tp30) REVERT: N 142 LEU cc_start: 0.8636 (pt) cc_final: 0.8237 (pt) REVERT: N 160 ASP cc_start: 0.8570 (m-30) cc_final: 0.7943 (m-30) REVERT: O 8 ARG cc_start: 0.8337 (ptm160) cc_final: 0.7839 (ptm160) REVERT: O 83 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8180 (tm-30) REVERT: O 145 ASP cc_start: 0.8500 (t0) cc_final: 0.8199 (m-30) REVERT: O 160 ASP cc_start: 0.8292 (m-30) cc_final: 0.7844 (m-30) REVERT: P 8 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.8049 (ptm160) REVERT: P 21 PHE cc_start: 0.8892 (p90) cc_final: 0.8638 (p90) REVERT: P 54 MET cc_start: 0.7558 (tpp) cc_final: 0.7290 (tpp) REVERT: P 70 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7549 (t) REVERT: P 76 ASP cc_start: 0.8352 (p0) cc_final: 0.7898 (p0) REVERT: P 79 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8611 (m-70) REVERT: P 98 GLU cc_start: 0.8588 (tp30) cc_final: 0.8271 (tp30) REVERT: P 112 ILE cc_start: 0.9078 (mt) cc_final: 0.8591 (tt) REVERT: P 119 ASP cc_start: 0.8699 (t0) cc_final: 0.8144 (t0) REVERT: P 121 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8139 (ptpp) REVERT: P 139 GLU cc_start: 0.8510 (tp30) cc_final: 0.8220 (tp30) REVERT: Q 1 MET cc_start: 0.8542 (mmt) cc_final: 0.8284 (mmm) REVERT: Q 24 GLU cc_start: 0.8108 (pp20) cc_final: 0.7878 (tm-30) REVERT: Q 34 PHE cc_start: 0.8881 (m-80) cc_final: 0.8372 (m-10) REVERT: Q 37 LYS cc_start: 0.8878 (tttp) cc_final: 0.8451 (tmmt) REVERT: Q 77 GLU cc_start: 0.8525 (mp0) cc_final: 0.8239 (mp0) REVERT: Q 130 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8395 (mmmm) REVERT: Q 142 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7863 (pt) REVERT: Q 154 GLU cc_start: 0.8342 (tt0) cc_final: 0.7867 (tt0) outliers start: 208 outliers final: 174 residues processed: 1083 average time/residue: 0.1728 time to fit residues: 288.3562 Evaluate side-chains 1114 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 919 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 141 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 GLN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 147 ASN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 HIS Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 99 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 52 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 149 optimal weight: 0.0170 chunk 95 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 169 optimal weight: 0.0970 chunk 185 optimal weight: 6.9990 overall best weight: 3.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 31 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN N 83 GLN O 55 ASN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084441 restraints weight = 50730.932| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.24 r_work: 0.3017 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 1.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23994 Z= 0.154 Angle : 0.697 10.602 32562 Z= 0.363 Chirality : 0.049 0.211 3510 Planarity : 0.004 0.036 4284 Dihedral : 6.640 74.374 3132 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 7.66 % Allowed : 27.17 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 2898 helix: -1.73 (0.24), residues: 360 sheet: -0.15 (0.20), residues: 756 loop : -1.45 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 56 TYR 0.023 0.002 TYR C 107 PHE 0.015 0.001 PHE F 53 TRP 0.012 0.001 TRP I 88 HIS 0.002 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (23994) covalent geometry : angle 0.69726 / 0.36 (32562) hydrogen bonds : bond 0.03353 / 2.22 ( 648) hydrogen bonds : angle 5.78265 / 3.95 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 949 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8170 (pt0) cc_final: 0.7606 (pt0) REVERT: A 30 GLN cc_start: 0.8228 (mm110) cc_final: 0.8011 (pp30) REVERT: A 112 ILE cc_start: 0.8807 (mt) cc_final: 0.8567 (mm) REVERT: A 119 ASP cc_start: 0.8768 (t0) cc_final: 0.8416 (t70) REVERT: A 126 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 128 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6414 (tm-30) REVERT: A 130 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8704 (mmtp) REVERT: R 2 PHE cc_start: 0.8247 (m-80) cc_final: 0.7651 (m-10) REVERT: R 8 ARG cc_start: 0.8752 (ptm160) cc_final: 0.8345 (ptm160) REVERT: R 34 PHE cc_start: 0.9005 (m-10) cc_final: 0.8008 (m-10) REVERT: R 39 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7788 (t) REVERT: R 126 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7310 (tm-30) REVERT: R 141 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: R 148 ASN cc_start: 0.8133 (m110) cc_final: 0.7546 (m110) REVERT: C 24 GLU cc_start: 0.8429 (pp20) cc_final: 0.8154 (tm-30) REVERT: C 57 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8379 (mmtp) REVERT: C 109 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8714 (mmtp) REVERT: C 160 ASP cc_start: 0.7633 (m-30) cc_final: 0.7407 (m-30) REVERT: B 1 MET cc_start: 0.8278 (tpp) cc_final: 0.8075 (tpp) REVERT: B 34 PHE cc_start: 0.8948 (m-80) cc_final: 0.8661 (m-10) REVERT: B 83 GLN cc_start: 0.8840 (tp40) cc_final: 0.8065 (tp-100) REVERT: B 112 ILE cc_start: 0.9070 (mt) cc_final: 0.8640 (tt) REVERT: B 141 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8027 (mm-40) REVERT: D 8 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.6924 (ptm160) REVERT: D 28 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8756 (mt) REVERT: D 30 GLN cc_start: 0.8399 (mm110) cc_final: 0.7910 (pp30) REVERT: D 31 ASN cc_start: 0.8457 (p0) cc_final: 0.8250 (t0) REVERT: D 54 MET cc_start: 0.7866 (mmm) cc_final: 0.7551 (tpp) REVERT: D 57 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8522 (mmtt) REVERT: D 82 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8546 (ttt90) REVERT: D 83 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8262 (tp-100) REVERT: D 88 TRP cc_start: 0.9370 (t60) cc_final: 0.8978 (t60) REVERT: D 125 LYS cc_start: 0.8405 (tptm) cc_final: 0.8172 (tmtt) REVERT: D 130 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8513 (mmmt) REVERT: D 139 GLU cc_start: 0.8361 (tp30) cc_final: 0.7422 (pt0) REVERT: D 145 ASP cc_start: 0.8628 (t0) cc_final: 0.8299 (m-30) REVERT: D 161 TYR cc_start: 0.8478 (p90) cc_final: 0.8080 (p90) REVERT: E 2 PHE cc_start: 0.8407 (m-80) cc_final: 0.5940 (t80) REVERT: E 28 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8368 (mp) REVERT: E 30 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7794 (tp40) REVERT: E 45 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8702 (tt) REVERT: E 83 GLN cc_start: 0.8867 (tp40) cc_final: 0.8437 (tm-30) REVERT: E 90 SER cc_start: 0.9075 (t) cc_final: 0.8727 (p) REVERT: E 130 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8818 (mmmt) REVERT: E 142 LEU cc_start: 0.8417 (pt) cc_final: 0.8077 (pt) REVERT: E 161 TYR cc_start: 0.8964 (p90) cc_final: 0.8404 (p90) REVERT: F 1 MET cc_start: 0.8416 (tpp) cc_final: 0.8200 (tpp) REVERT: F 2 PHE cc_start: 0.7843 (m-80) cc_final: 0.7488 (m-80) REVERT: F 22 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: F 24 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7305 (tm-30) REVERT: F 35 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: F 36 CYS cc_start: 0.8731 (t) cc_final: 0.8127 (t) REVERT: F 47 GLU cc_start: 0.4690 (pt0) cc_final: 0.4339 (pt0) REVERT: F 128 GLU cc_start: 0.8334 (pm20) cc_final: 0.7984 (pm20) REVERT: F 135 THR cc_start: 0.8707 (m) cc_final: 0.8459 (p) REVERT: F 141 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8346 (mm-40) REVERT: F 154 GLU cc_start: 0.8317 (pt0) cc_final: 0.8018 (tt0) REVERT: G 2 PHE cc_start: 0.8572 (m-80) cc_final: 0.8208 (m-10) REVERT: G 28 LEU cc_start: 0.9097 (mm) cc_final: 0.8830 (mt) REVERT: G 54 MET cc_start: 0.7818 (mmm) cc_final: 0.7604 (tpp) REVERT: G 112 ILE cc_start: 0.8767 (mt) cc_final: 0.8314 (tt) REVERT: G 125 LYS cc_start: 0.8117 (tptp) cc_final: 0.7843 (tmtt) REVERT: G 146 SER cc_start: 0.7953 (m) cc_final: 0.7449 (p) REVERT: H 4 ASP cc_start: 0.8569 (m-30) cc_final: 0.8266 (m-30) REVERT: H 30 GLN cc_start: 0.8384 (pp30) cc_final: 0.7899 (pp30) REVERT: H 31 ASN cc_start: 0.8697 (p0) cc_final: 0.8244 (t0) REVERT: H 35 GLN cc_start: 0.8312 (tt0) cc_final: 0.7785 (mt0) REVERT: H 39 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7392 (t) REVERT: H 54 MET cc_start: 0.8180 (mmm) cc_final: 0.7738 (tpp) REVERT: H 115 GLN cc_start: 0.7873 (tt0) cc_final: 0.7662 (tt0) REVERT: H 140 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8349 (mt) REVERT: H 161 TYR cc_start: 0.8836 (p90) cc_final: 0.8615 (p90) REVERT: I 36 CYS cc_start: 0.9194 (t) cc_final: 0.8884 (m) REVERT: I 103 LYS cc_start: 0.6512 (mmtt) cc_final: 0.6234 (tptt) REVERT: I 139 GLU cc_start: 0.8528 (tp30) cc_final: 0.7694 (pt0) REVERT: I 154 GLU cc_start: 0.8618 (pt0) cc_final: 0.8110 (tt0) REVERT: J 8 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8039 (ptp-110) REVERT: J 28 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8521 (mt) REVERT: J 37 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8559 (tttm) REVERT: J 75 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7881 (t0) REVERT: J 103 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8382 (mtmm) REVERT: J 125 LYS cc_start: 0.8710 (tptm) cc_final: 0.8421 (tttt) REVERT: J 128 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: J 147 ASN cc_start: 0.8318 (m-40) cc_final: 0.8107 (m110) REVERT: J 149 GLU cc_start: 0.6899 (mp0) cc_final: 0.6592 (mp0) REVERT: K 1 MET cc_start: 0.8421 (tpt) cc_final: 0.8045 (tpp) REVERT: K 24 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7528 (tp30) REVERT: K 30 GLN cc_start: 0.8573 (mm110) cc_final: 0.8225 (pp30) REVERT: K 31 ASN cc_start: 0.8464 (p0) cc_final: 0.7940 (t0) REVERT: K 48 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8440 (ttpt) REVERT: K 79 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: K 103 LYS cc_start: 0.8485 (mmtt) cc_final: 0.7773 (mmtt) REVERT: K 141 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8333 (mm110) REVERT: L 22 GLN cc_start: 0.7890 (tt0) cc_final: 0.7422 (mt0) REVERT: L 28 LEU cc_start: 0.9059 (mm) cc_final: 0.8829 (mp) REVERT: L 37 LYS cc_start: 0.8996 (tttp) cc_final: 0.8753 (tttp) REVERT: M 4 ASP cc_start: 0.8543 (m-30) cc_final: 0.7917 (p0) REVERT: M 15 PHE cc_start: 0.7756 (m-80) cc_final: 0.7395 (m-10) REVERT: M 17 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7109 (mpt180) REVERT: M 70 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8029 (t) REVERT: M 103 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8597 (mtmm) REVERT: M 109 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8441 (mmmt) REVERT: M 146 SER cc_start: 0.8749 (m) cc_final: 0.8258 (p) REVERT: N 5 ASP cc_start: 0.8256 (t0) cc_final: 0.7714 (t0) REVERT: N 31 ASN cc_start: 0.9196 (m-40) cc_final: 0.8607 (p0) REVERT: N 45 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8893 (tt) REVERT: N 54 MET cc_start: 0.8284 (mmm) cc_final: 0.8029 (tpp) REVERT: N 76 ASP cc_start: 0.8083 (p0) cc_final: 0.7609 (p0) REVERT: N 79 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7025 (t70) REVERT: N 80 ASP cc_start: 0.8774 (p0) cc_final: 0.8431 (p0) REVERT: N 91 ILE cc_start: 0.9434 (mt) cc_final: 0.9173 (mm) REVERT: N 95 GLN cc_start: 0.8255 (tt0) cc_final: 0.7939 (tt0) REVERT: N 109 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8470 (mmtt) REVERT: N 139 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7754 (tp30) REVERT: N 142 LEU cc_start: 0.8621 (pt) cc_final: 0.8204 (pt) REVERT: N 145 ASP cc_start: 0.8568 (t0) cc_final: 0.8228 (p0) REVERT: N 160 ASP cc_start: 0.8554 (m-30) cc_final: 0.7785 (m-30) REVERT: N 161 TYR cc_start: 0.9104 (p90) cc_final: 0.8549 (p90) REVERT: O 4 ASP cc_start: 0.8441 (m-30) cc_final: 0.8072 (p0) REVERT: O 8 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7804 (ptm160) REVERT: O 83 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8205 (tm-30) REVERT: O 119 ASP cc_start: 0.8455 (t0) cc_final: 0.8232 (t70) REVERT: O 145 ASP cc_start: 0.8589 (t0) cc_final: 0.8383 (m-30) REVERT: O 160 ASP cc_start: 0.8280 (m-30) cc_final: 0.7905 (m-30) REVERT: P 8 ARG cc_start: 0.8492 (ptp-110) cc_final: 0.8057 (ptm160) REVERT: P 21 PHE cc_start: 0.8963 (p90) cc_final: 0.8693 (p90) REVERT: P 70 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (t) REVERT: P 76 ASP cc_start: 0.8341 (p0) cc_final: 0.7876 (p0) REVERT: P 98 GLU cc_start: 0.8575 (tp30) cc_final: 0.8263 (tp30) REVERT: P 112 ILE cc_start: 0.9052 (mt) cc_final: 0.8574 (tt) REVERT: P 119 ASP cc_start: 0.8717 (t0) cc_final: 0.7995 (t0) REVERT: P 121 LYS cc_start: 0.8423 (ptpp) cc_final: 0.8141 (ptpp) REVERT: P 139 GLU cc_start: 0.8609 (tp30) cc_final: 0.8374 (tp30) REVERT: Q 1 MET cc_start: 0.8570 (mmt) cc_final: 0.8330 (mmm) REVERT: Q 15 PHE cc_start: 0.8423 (m-80) cc_final: 0.8203 (m-80) REVERT: Q 24 GLU cc_start: 0.8109 (pp20) cc_final: 0.7846 (tm-30) REVERT: Q 34 PHE cc_start: 0.8881 (m-80) cc_final: 0.8357 (m-10) REVERT: Q 37 LYS cc_start: 0.8844 (tttp) cc_final: 0.8409 (tmmt) REVERT: Q 77 GLU cc_start: 0.8527 (mp0) cc_final: 0.8238 (mp0) REVERT: Q 112 ILE cc_start: 0.9151 (mt) cc_final: 0.8744 (tt) REVERT: Q 130 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8438 (mmmm) REVERT: Q 142 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7774 (pt) REVERT: Q 154 GLU cc_start: 0.8346 (tt0) cc_final: 0.7890 (tt0) outliers start: 189 outliers final: 156 residues processed: 1070 average time/residue: 0.1696 time to fit residues: 279.3208 Evaluate side-chains 1107 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 931 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 141 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 19 ASN Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 HIS Chi-restraints excluded: chain N residue 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 99 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 186 optimal weight: 0.0370 chunk 117 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 ASN R 148 ASN B 22 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN O 55 ASN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083444 restraints weight = 50888.816| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.27 r_work: 0.2997 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 1.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23994 Z= 0.173 Angle : 0.705 10.578 32562 Z= 0.367 Chirality : 0.049 0.237 3510 Planarity : 0.004 0.038 4284 Dihedral : 6.686 74.944 3132 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.58 % Allowed : 27.53 % Favored : 64.88 % 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: -1.69 (0.14), residues: 2898 helix: -1.64 (0.24), residues: 360 sheet: -0.19 (0.20), residues: 756 loop : -1.47 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 56 TYR 0.022 0.002 TYR B 161 PHE 0.027 0.001 PHE A 53 TRP 0.012 0.001 TRP I 88 HIS 0.003 0.001 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (23994) covalent geometry : angle 0.70501 / 0.37 (32562) hydrogen bonds : bond 0.03447 / 2.27 ( 648) hydrogen bonds : angle 5.81056 / 3.97 ( 1782) =============================================================================== Job complete usr+sys time: 5832.12 seconds wall clock time: 100 minutes 44.92 seconds (6044.92 seconds total)