Starting phenix.real_space_refine on Thu Jun 19 19:38:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w5f_8767/06_2025/5w5f_8767.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w5f_8767/06_2025/5w5f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2025/5w5f_8767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2025/5w5f_8767.map" model { file = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2025/5w5f_8767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w5f_8767/06_2025/5w5f_8767.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 5.74, per 1000 atoms: 0.24 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: 5.11 Conformation dependent library (CDL) restraints added in 3.1 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: 3.16 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: 7.90 Time building geometry restraints manager: 6.06 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 43.050 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.049 0.006 TRP O 88 HIS 0.001 0.001 HIS R 79 PHE 0.021 0.004 PHE L 153 TYR 0.012 0.003 TYR K 161 ARG 0.006 0.001 ARG E 17 Details of bonding type rmsd hydrogen bonds : bond 0.26903 ( 648) hydrogen bonds : angle 10.07962 ( 1782) covalent geometry : bond 0.00699 (23994) covalent geometry : angle 0.91283 (32562) *********************** 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 : 2.801 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: 0.3536 time to fit residues: 701.1446 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 : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 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** L 55 ASN 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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 147 ASN ** P 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN Q 75 ASN Q 89 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099933 restraints weight = 47815.939| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.30 r_work: 0.3285 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23994 Z= 0.204 Angle : 0.699 8.307 32562 Z= 0.375 Chirality : 0.052 0.192 3510 Planarity : 0.005 0.042 4284 Dihedral : 7.122 74.580 3132 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.37 % Allowed : 18.05 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.14), residues: 2898 helix: -3.57 (0.18), residues: 306 sheet: -0.22 (0.19), residues: 756 loop : -1.59 (0.12), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 88 HIS 0.005 0.002 HIS E 79 PHE 0.019 0.002 PHE L 34 TYR 0.028 0.002 TYR G 107 ARG 0.008 0.001 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 648) hydrogen bonds : angle 6.71651 ( 1782) covalent geometry : bond 0.00461 (23994) covalent geometry : angle 0.69919 (32562) *********************** 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 1348 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1191 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8283 (tpt) cc_final: 0.7199 (tpt) REVERT: A 14 ASP cc_start: 0.7286 (t70) cc_final: 0.7041 (t70) REVERT: A 17 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7870 (mmt-90) REVERT: A 24 GLU cc_start: 0.7694 (pt0) cc_final: 0.7441 (pt0) REVERT: A 39 THR cc_start: 0.8438 (t) cc_final: 0.8130 (t) REVERT: A 70 THR cc_start: 0.8402 (p) cc_final: 0.8010 (t) REVERT: A 98 GLU cc_start: 0.8587 (tp30) cc_final: 0.8360 (tp30) REVERT: A 112 ILE cc_start: 0.8797 (mt) cc_final: 0.8506 (mm) REVERT: A 119 ASP cc_start: 0.8652 (t0) cc_final: 0.8377 (t0) REVERT: A 127 ILE cc_start: 0.8817 (mp) cc_final: 0.8375 (mt) REVERT: A 130 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8630 (mmmm) REVERT: A 148 ASN cc_start: 0.8592 (m-40) cc_final: 0.8374 (m110) REVERT: R 22 GLN cc_start: 0.8078 (tt0) cc_final: 0.7777 (tt0) REVERT: R 23 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8378 (p) REVERT: R 24 GLU cc_start: 0.7988 (pt0) cc_final: 0.7642 (pt0) REVERT: R 31 ASN cc_start: 0.8433 (p0) cc_final: 0.8159 (t0) REVERT: R 74 MET cc_start: 0.8794 (mtm) cc_final: 0.8527 (mtm) REVERT: R 91 ILE cc_start: 0.9372 (mm) cc_final: 0.9132 (mm) REVERT: R 112 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8922 (pt) REVERT: R 116 TYR cc_start: 0.8753 (m-10) cc_final: 0.8114 (m-10) REVERT: R 119 ASP cc_start: 0.8376 (t0) cc_final: 0.7868 (t70) REVERT: R 129 ILE cc_start: 0.8570 (mp) cc_final: 0.8259 (mt) REVERT: R 139 GLU cc_start: 0.8169 (tp30) cc_final: 0.7741 (tp30) REVERT: R 148 ASN cc_start: 0.8330 (m-40) cc_final: 0.8069 (m110) REVERT: C 48 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8226 (ttpp) REVERT: B 74 MET cc_start: 0.8690 (mtm) cc_final: 0.8300 (mtm) REVERT: B 91 ILE cc_start: 0.9197 (mt) cc_final: 0.8948 (mm) REVERT: B 115 GLN cc_start: 0.7724 (tt0) cc_final: 0.7517 (tt0) REVERT: B 116 TYR cc_start: 0.8740 (m-10) cc_final: 0.8461 (m-10) REVERT: B 129 ILE cc_start: 0.8676 (mp) cc_final: 0.8093 (mt) REVERT: B 139 GLU cc_start: 0.7955 (tp30) cc_final: 0.6796 (pt0) REVERT: B 160 ASP cc_start: 0.8101 (m-30) cc_final: 0.7888 (m-30) REVERT: D 1 MET cc_start: 0.7228 (tpp) cc_final: 0.6342 (tpt) REVERT: D 14 ASP cc_start: 0.6886 (p0) cc_final: 0.6154 (p0) REVERT: D 31 ASN cc_start: 0.8576 (p0) cc_final: 0.7604 (t0) REVERT: D 76 ASP cc_start: 0.8767 (p0) cc_final: 0.8190 (p0) REVERT: D 83 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8714 (tp-100) REVERT: D 88 TRP cc_start: 0.9220 (t60) cc_final: 0.8919 (t60) REVERT: D 112 ILE cc_start: 0.8636 (mt) cc_final: 0.7793 (mm) REVERT: D 127 ILE cc_start: 0.8457 (mt) cc_final: 0.8123 (mp) REVERT: D 129 ILE cc_start: 0.8104 (mp) cc_final: 0.7604 (mt) REVERT: D 130 LYS cc_start: 0.8394 (mmmm) cc_final: 0.7886 (mmmt) REVERT: E 37 LYS cc_start: 0.8717 (tttt) cc_final: 0.8404 (tttp) REVERT: E 76 ASP cc_start: 0.8615 (p0) cc_final: 0.8210 (p0) REVERT: E 77 GLU cc_start: 0.8320 (mp0) cc_final: 0.7993 (mp0) REVERT: E 90 SER cc_start: 0.8822 (t) cc_final: 0.8136 (p) REVERT: E 97 ASN cc_start: 0.8332 (t0) cc_final: 0.8112 (t0) REVERT: E 119 ASP cc_start: 0.8494 (t0) cc_final: 0.8156 (t0) REVERT: E 127 ILE cc_start: 0.7972 (mp) cc_final: 0.7642 (mp) REVERT: F 2 PHE cc_start: 0.7673 (m-80) cc_final: 0.7441 (m-80) REVERT: F 47 GLU cc_start: 0.4218 (pt0) cc_final: 0.3453 (pt0) REVERT: F 69 TRP cc_start: 0.8694 (t60) cc_final: 0.8301 (t60) REVERT: F 76 ASP cc_start: 0.8065 (p0) cc_final: 0.7522 (p0) REVERT: F 83 GLN cc_start: 0.8278 (tp40) cc_final: 0.8042 (tp40) REVERT: F 112 ILE cc_start: 0.8555 (mt) cc_final: 0.8252 (tt) REVERT: F 119 ASP cc_start: 0.7611 (t0) cc_final: 0.7163 (t70) REVERT: F 154 GLU cc_start: 0.8376 (pt0) cc_final: 0.8043 (tt0) REVERT: G 1 MET cc_start: 0.7505 (tpp) cc_final: 0.7239 (tpt) REVERT: G 2 PHE cc_start: 0.7435 (m-80) cc_final: 0.7180 (m-80) REVERT: G 27 TYR cc_start: 0.7503 (t80) cc_final: 0.7267 (t80) REVERT: G 49 ILE cc_start: 0.8904 (mt) cc_final: 0.8683 (mt) REVERT: G 63 ASP cc_start: 0.7660 (p0) cc_final: 0.7455 (p0) REVERT: G 71 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8633 (m) REVERT: G 76 ASP cc_start: 0.8561 (p0) cc_final: 0.8128 (p0) REVERT: G 87 ASP cc_start: 0.8081 (t0) cc_final: 0.7871 (t0) REVERT: G 98 GLU cc_start: 0.8107 (pm20) cc_final: 0.7332 (pp20) REVERT: G 103 LYS cc_start: 0.8688 (mttp) cc_final: 0.8268 (mmtp) REVERT: G 157 LEU cc_start: 0.8615 (mp) cc_final: 0.8222 (mp) REVERT: G 161 TYR cc_start: 0.8559 (p90) cc_final: 0.8310 (p90) REVERT: H 1 MET cc_start: 0.7105 (tpt) cc_final: 0.6459 (tpt) REVERT: H 2 PHE cc_start: 0.6939 (m-80) cc_final: 0.6574 (t80) REVERT: H 5 ASP cc_start: 0.7518 (p0) cc_final: 0.7295 (p0) REVERT: H 17 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7041 (mpp80) REVERT: H 39 THR cc_start: 0.8422 (t) cc_final: 0.8147 (t) REVERT: H 77 GLU cc_start: 0.7577 (mp0) cc_final: 0.7366 (mp0) REVERT: H 99 ILE cc_start: 0.6876 (tt) cc_final: 0.6448 (tp) REVERT: H 118 ARG cc_start: 0.6887 (tpt170) cc_final: 0.5462 (ttm170) REVERT: H 119 ASP cc_start: 0.8029 (t0) cc_final: 0.7739 (t70) REVERT: H 146 SER cc_start: 0.8616 (m) cc_final: 0.8153 (p) REVERT: I 2 PHE cc_start: 0.8302 (m-80) cc_final: 0.7914 (m-80) REVERT: I 34 PHE cc_start: 0.8359 (m-80) cc_final: 0.7776 (m-80) REVERT: I 77 GLU cc_start: 0.8242 (mp0) cc_final: 0.8016 (mp0) REVERT: I 80 ASP cc_start: 0.8099 (p0) cc_final: 0.7796 (p0) REVERT: I 91 ILE cc_start: 0.8886 (mt) cc_final: 0.8500 (mm) REVERT: I 97 ASN cc_start: 0.7709 (t0) cc_final: 0.7412 (t0) REVERT: I 135 THR cc_start: 0.8854 (m) cc_final: 0.8650 (p) REVERT: I 142 LEU cc_start: 0.8926 (pt) cc_final: 0.8643 (pt) REVERT: I 148 ASN cc_start: 0.8647 (p0) cc_final: 0.8393 (m-40) REVERT: I 149 GLU cc_start: 0.8158 (mp0) cc_final: 0.7876 (mp0) REVERT: J 1 MET cc_start: 0.7983 (tpp) cc_final: 0.7477 (tpt) REVERT: J 4 ASP cc_start: 0.7684 (m-30) cc_final: 0.7355 (m-30) REVERT: J 11 GLU cc_start: 0.7326 (mp0) cc_final: 0.7097 (mp0) REVERT: J 14 ASP cc_start: 0.7164 (t0) cc_final: 0.6916 (t70) REVERT: J 27 TYR cc_start: 0.5990 (t80) cc_final: 0.5134 (t80) REVERT: J 54 MET cc_start: 0.7512 (mmm) cc_final: 0.7106 (tpp) REVERT: J 77 GLU cc_start: 0.6960 (mp0) cc_final: 0.6749 (mp0) REVERT: J 79 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7061 (t-90) REVERT: J 80 ASP cc_start: 0.7985 (p0) cc_final: 0.7661 (p0) REVERT: J 91 ILE cc_start: 0.8897 (tt) cc_final: 0.8639 (tp) REVERT: J 98 GLU cc_start: 0.7653 (tp30) cc_final: 0.7423 (pm20) REVERT: J 109 LYS cc_start: 0.8264 (mttm) cc_final: 0.7942 (mmtp) REVERT: J 145 ASP cc_start: 0.8817 (t0) cc_final: 0.8549 (m-30) REVERT: K 1 MET cc_start: 0.7255 (tpp) cc_final: 0.6576 (tpt) REVERT: K 22 GLN cc_start: 0.6745 (tt0) cc_final: 0.6397 (tt0) REVERT: K 55 ASN cc_start: 0.5783 (t160) cc_final: 0.5565 (t0) REVERT: K 74 MET cc_start: 0.8361 (mmm) cc_final: 0.8127 (mpp) REVERT: K 103 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8172 (mmtt) REVERT: K 118 ARG cc_start: 0.6517 (tpt170) cc_final: 0.4449 (ttp-170) REVERT: L 1 MET cc_start: 0.8327 (tpp) cc_final: 0.8014 (tpt) REVERT: L 2 PHE cc_start: 0.8463 (m-80) cc_final: 0.8240 (m-10) REVERT: L 83 GLN cc_start: 0.8724 (tp40) cc_final: 0.8173 (tp40) REVERT: M 14 ASP cc_start: 0.6952 (t0) cc_final: 0.6716 (t0) REVERT: M 30 GLN cc_start: 0.7827 (mm110) cc_final: 0.7293 (tm-30) REVERT: M 35 GLN cc_start: 0.8422 (mt0) cc_final: 0.8152 (mt0) REVERT: M 48 LYS cc_start: 0.8172 (ttpm) cc_final: 0.7298 (ttpp) REVERT: M 77 GLU cc_start: 0.7796 (mp0) cc_final: 0.6982 (mp0) REVERT: M 79 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7866 (t-90) REVERT: M 145 ASP cc_start: 0.8314 (p0) cc_final: 0.8034 (t0) REVERT: N 31 ASN cc_start: 0.7394 (p0) cc_final: 0.6833 (t0) REVERT: N 123 VAL cc_start: 0.7875 (t) cc_final: 0.7595 (p) REVERT: N 154 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7679 (tt0) REVERT: O 4 ASP cc_start: 0.8269 (m-30) cc_final: 0.7926 (p0) REVERT: O 11 GLU cc_start: 0.8255 (tp30) cc_final: 0.7938 (tp30) REVERT: O 14 ASP cc_start: 0.7690 (t0) cc_final: 0.7416 (t70) REVERT: O 21 PHE cc_start: 0.8925 (p90) cc_final: 0.8638 (p90) REVERT: O 22 GLN cc_start: 0.8153 (tt0) cc_final: 0.7938 (tt0) REVERT: O 24 GLU cc_start: 0.8127 (pt0) cc_final: 0.7876 (pt0) REVERT: O 35 GLN cc_start: 0.8320 (mt0) cc_final: 0.8093 (mt0) REVERT: O 51 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (p) REVERT: O 54 MET cc_start: 0.7815 (tpp) cc_final: 0.7390 (mmt) REVERT: O 83 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8055 (tm-30) REVERT: O 112 ILE cc_start: 0.8899 (mt) cc_final: 0.8696 (tt) REVERT: O 119 ASP cc_start: 0.8231 (t0) cc_final: 0.7790 (t70) REVERT: O 160 ASP cc_start: 0.8078 (m-30) cc_final: 0.7491 (m-30) REVERT: P 2 PHE cc_start: 0.8627 (m-10) cc_final: 0.8322 (m-10) REVERT: P 8 ARG cc_start: 0.8190 (ptp-110) cc_final: 0.7812 (ptm160) REVERT: P 76 ASP cc_start: 0.7720 (p0) cc_final: 0.7486 (p0) REVERT: P 83 GLN cc_start: 0.8672 (tp40) cc_final: 0.8383 (tp40) REVERT: P 119 ASP cc_start: 0.8292 (t0) cc_final: 0.7862 (t0) REVERT: Q 2 PHE cc_start: 0.6911 (m-80) cc_final: 0.6190 (t80) REVERT: Q 22 GLN cc_start: 0.8067 (tt0) cc_final: 0.7862 (tt0) REVERT: Q 27 TYR cc_start: 0.7733 (t80) cc_final: 0.7449 (t80) REVERT: Q 48 LYS cc_start: 0.7978 (ttpm) cc_final: 0.7682 (ttpt) REVERT: Q 55 ASN cc_start: 0.7176 (t160) cc_final: 0.6744 (t0) REVERT: Q 118 ARG cc_start: 0.7127 (tpt170) cc_final: 0.5536 (tmm160) REVERT: Q 144 TRP cc_start: 0.8865 (m-10) cc_final: 0.6603 (m100) REVERT: Q 160 ASP cc_start: 0.7650 (m-30) cc_final: 0.7298 (m-30) REVERT: Q 163 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7263 (mm-30) outliers start: 157 outliers final: 95 residues processed: 1282 average time/residue: 0.3659 time to fit residues: 714.5046 Evaluate side-chains 1078 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 976 time to evaluate : 2.846 ------------------------------------------------------------------------------- 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 23 VAL 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 7 THR 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 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 19 ASN Chi-restraints excluded: chain F residue 51 VAL 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 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 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 23 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 72 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 3 VAL 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 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 11 GLU 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 74 MET 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 162 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 149 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 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 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** F 35 GLN ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN K 79 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 115 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 89 GLN Q 115 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088065 restraints weight = 48794.159| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.26 r_work: 0.3088 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.9013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23994 Z= 0.228 Angle : 0.687 10.004 32562 Z= 0.366 Chirality : 0.050 0.183 3510 Planarity : 0.004 0.056 4284 Dihedral : 7.268 83.227 3132 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 8.23 % Allowed : 20.92 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 2898 helix: -3.38 (0.16), residues: 360 sheet: -0.22 (0.19), residues: 756 loop : -1.56 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 88 HIS 0.004 0.001 HIS A 79 PHE 0.020 0.002 PHE H 34 TYR 0.021 0.002 TYR M 107 ARG 0.008 0.001 ARG J 64 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 648) hydrogen bonds : angle 6.50543 ( 1782) covalent geometry : bond 0.00525 (23994) covalent geometry : angle 0.68694 (32562) *********************** 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 1289 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 1086 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.8404 (t0) cc_final: 0.8202 (t0) REVERT: A 24 GLU cc_start: 0.7950 (pt0) cc_final: 0.7540 (pt0) REVERT: A 57 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8353 (mmtt) REVERT: A 75 ASN cc_start: 0.8681 (t160) cc_final: 0.7576 (t0) REVERT: A 76 ASP cc_start: 0.8580 (p0) cc_final: 0.7668 (p0) REVERT: A 77 GLU cc_start: 0.8346 (mp0) cc_final: 0.7669 (mp0) REVERT: A 83 GLN cc_start: 0.8850 (tp40) cc_final: 0.8544 (tm-30) REVERT: A 112 ILE cc_start: 0.8902 (mt) cc_final: 0.8634 (mm) REVERT: A 119 ASP cc_start: 0.8793 (t0) cc_final: 0.8291 (t70) REVERT: A 121 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8473 (ptpp) REVERT: A 126 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7734 (tm-30) REVERT: R 14 ASP cc_start: 0.7238 (t70) cc_final: 0.6809 (t0) REVERT: R 23 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8255 (p) REVERT: R 34 PHE cc_start: 0.8953 (m-10) cc_final: 0.8039 (m-10) REVERT: R 74 MET cc_start: 0.8909 (mtm) cc_final: 0.8648 (mtm) REVERT: R 75 ASN cc_start: 0.9090 (t0) cc_final: 0.8883 (t0) REVERT: R 114 ARG cc_start: 0.8434 (ptt-90) cc_final: 0.8193 (mtm180) REVERT: R 119 ASP cc_start: 0.8521 (t0) cc_final: 0.8078 (t70) REVERT: R 126 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 76 ASP cc_start: 0.8241 (p0) cc_final: 0.7898 (p0) REVERT: C 77 GLU cc_start: 0.8029 (pm20) cc_final: 0.7586 (mp0) REVERT: C 80 ASP cc_start: 0.8868 (p0) cc_final: 0.8656 (p0) REVERT: B 27 TYR cc_start: 0.9042 (t80) cc_final: 0.8824 (t80) REVERT: B 76 ASP cc_start: 0.8125 (p0) cc_final: 0.7907 (p0) REVERT: B 83 GLN cc_start: 0.8834 (tp40) cc_final: 0.7658 (tp-100) REVERT: B 106 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7725 (tp30) REVERT: B 128 GLU cc_start: 0.7648 (tp30) cc_final: 0.7446 (mm-30) REVERT: B 130 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8644 (mmmm) REVERT: B 139 GLU cc_start: 0.8363 (tp30) cc_final: 0.7218 (pt0) REVERT: D 1 MET cc_start: 0.7798 (tpp) cc_final: 0.7590 (tpt) REVERT: D 31 ASN cc_start: 0.8680 (p0) cc_final: 0.7823 (t0) REVERT: D 76 ASP cc_start: 0.8777 (p0) cc_final: 0.8446 (p0) REVERT: D 77 GLU cc_start: 0.7853 (mp0) cc_final: 0.7591 (mp0) REVERT: D 129 ILE cc_start: 0.8514 (mp) cc_final: 0.8215 (mt) REVERT: D 130 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8224 (mmmt) REVERT: D 161 TYR cc_start: 0.8604 (p90) cc_final: 0.8343 (p90) REVERT: E 1 MET cc_start: 0.8187 (tpp) cc_final: 0.7983 (tpp) REVERT: E 2 PHE cc_start: 0.8313 (m-80) cc_final: 0.6043 (t80) REVERT: E 5 ASP cc_start: 0.8177 (t0) cc_final: 0.7936 (t0) REVERT: E 15 PHE cc_start: 0.8080 (m-10) cc_final: 0.7627 (m-80) REVERT: E 22 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7352 (tm-30) REVERT: E 37 LYS cc_start: 0.8774 (tttt) cc_final: 0.8543 (tttp) REVERT: E 76 ASP cc_start: 0.8757 (p0) cc_final: 0.8519 (p0) REVERT: E 77 GLU cc_start: 0.8725 (mp0) cc_final: 0.8463 (mp0) REVERT: E 90 SER cc_start: 0.9149 (t) cc_final: 0.8657 (p) REVERT: E 112 ILE cc_start: 0.8740 (mt) cc_final: 0.8328 (mt) REVERT: E 119 ASP cc_start: 0.8667 (t0) cc_final: 0.8392 (t0) REVERT: E 142 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7714 (pt) REVERT: E 161 TYR cc_start: 0.8971 (p90) cc_final: 0.8736 (p90) REVERT: F 1 MET cc_start: 0.8475 (tpp) cc_final: 0.8199 (tpp) REVERT: F 22 GLN cc_start: 0.8138 (tp40) cc_final: 0.7626 (tt0) REVERT: F 24 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7674 (tm-30) REVERT: F 30 GLN cc_start: 0.8242 (mm110) cc_final: 0.7969 (pp30) REVERT: F 47 GLU cc_start: 0.4644 (pt0) cc_final: 0.4235 (pt0) REVERT: F 69 TRP cc_start: 0.9030 (t60) cc_final: 0.8766 (t60) REVERT: F 112 ILE cc_start: 0.8951 (mt) cc_final: 0.8723 (tt) REVERT: F 126 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 135 THR cc_start: 0.8599 (m) cc_final: 0.8201 (m) REVERT: F 154 GLU cc_start: 0.8476 (pt0) cc_final: 0.8096 (tt0) REVERT: F 161 TYR cc_start: 0.8575 (p90) cc_final: 0.8324 (p90) REVERT: G 1 MET cc_start: 0.7563 (tpp) cc_final: 0.7179 (tpt) REVERT: G 2 PHE cc_start: 0.8015 (m-80) cc_final: 0.7699 (m-10) REVERT: G 24 GLU cc_start: 0.7583 (pt0) cc_final: 0.7221 (pt0) REVERT: G 31 ASN cc_start: 0.8318 (p0) cc_final: 0.7601 (t0) REVERT: G 37 LYS cc_start: 0.8625 (tttt) cc_final: 0.8269 (tttt) REVERT: G 47 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7859 (tt0) REVERT: G 54 MET cc_start: 0.7502 (mmm) cc_final: 0.7097 (tpp) REVERT: G 70 THR cc_start: 0.8396 (p) cc_final: 0.8100 (t) REVERT: G 76 ASP cc_start: 0.8821 (p0) cc_final: 0.8587 (p0) REVERT: G 97 ASN cc_start: 0.8669 (t0) cc_final: 0.8151 (t0) REVERT: G 98 GLU cc_start: 0.8359 (pm20) cc_final: 0.7809 (pp20) REVERT: G 114 ARG cc_start: 0.8479 (mtm180) cc_final: 0.8045 (mtm180) REVERT: G 146 SER cc_start: 0.8837 (m) cc_final: 0.8407 (p) REVERT: G 161 TYR cc_start: 0.8696 (p90) cc_final: 0.8394 (p90) REVERT: H 2 PHE cc_start: 0.7979 (m-80) cc_final: 0.6673 (t80) REVERT: H 70 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (t) REVERT: H 76 ASP cc_start: 0.8509 (p0) cc_final: 0.8243 (p0) REVERT: H 145 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: H 146 SER cc_start: 0.8278 (m) cc_final: 0.8006 (p) REVERT: H 160 ASP cc_start: 0.8680 (m-30) cc_final: 0.8445 (m-30) REVERT: I 2 PHE cc_start: 0.8268 (m-80) cc_final: 0.7894 (m-80) REVERT: I 97 ASN cc_start: 0.7445 (t0) cc_final: 0.7189 (t0) REVERT: I 108 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8840 (mtpp) REVERT: I 135 THR cc_start: 0.8957 (m) cc_final: 0.8687 (p) REVERT: I 146 SER cc_start: 0.8875 (m) cc_final: 0.8487 (p) REVERT: I 148 ASN cc_start: 0.8551 (p0) cc_final: 0.8144 (m-40) REVERT: J 1 MET cc_start: 0.8271 (tpp) cc_final: 0.7935 (tpt) REVERT: J 14 ASP cc_start: 0.7732 (t0) cc_final: 0.7460 (t70) REVERT: J 24 GLU cc_start: 0.7340 (pt0) cc_final: 0.6753 (pt0) REVERT: J 28 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7722 (mt) REVERT: J 31 ASN cc_start: 0.8628 (p0) cc_final: 0.7773 (t0) REVERT: J 45 ILE cc_start: 0.8581 (mt) cc_final: 0.8146 (tt) REVERT: J 79 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7181 (t-90) REVERT: J 91 ILE cc_start: 0.9179 (tt) cc_final: 0.8901 (tp) REVERT: J 109 LYS cc_start: 0.8557 (mttm) cc_final: 0.8313 (mmtp) REVERT: J 145 ASP cc_start: 0.8934 (t0) cc_final: 0.8531 (m-30) REVERT: K 1 MET cc_start: 0.7735 (tpp) cc_final: 0.7206 (tpp) REVERT: K 2 PHE cc_start: 0.7761 (m-80) cc_final: 0.6469 (t80) REVERT: K 103 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8430 (mptt) REVERT: L 28 LEU cc_start: 0.8882 (mm) cc_final: 0.8506 (mp) REVERT: L 34 PHE cc_start: 0.9227 (m-80) cc_final: 0.8836 (m-80) REVERT: L 147 ASN cc_start: 0.8106 (m110) cc_final: 0.7863 (m110) REVERT: M 14 ASP cc_start: 0.7791 (t0) cc_final: 0.7577 (t0) REVERT: M 19 ASN cc_start: 0.8697 (p0) cc_final: 0.8462 (p0) REVERT: M 30 GLN cc_start: 0.8349 (mm110) cc_final: 0.8000 (pp30) REVERT: M 47 GLU cc_start: 0.7673 (tp30) cc_final: 0.7341 (tp30) REVERT: M 48 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7511 (ttmt) REVERT: M 76 ASP cc_start: 0.7549 (p0) cc_final: 0.6418 (p0) REVERT: M 79 HIS cc_start: 0.8623 (OUTLIER) cc_final: 0.7971 (t-90) REVERT: M 97 ASN cc_start: 0.8271 (t0) cc_final: 0.8046 (t0) REVERT: M 126 GLU cc_start: 0.8260 (pp20) cc_final: 0.7952 (pp20) REVERT: M 128 GLU cc_start: 0.7856 (pm20) cc_final: 0.7338 (pm20) REVERT: M 146 SER cc_start: 0.8534 (m) cc_final: 0.8201 (p) REVERT: N 11 GLU cc_start: 0.7935 (mp0) cc_final: 0.7686 (mp0) REVERT: N 14 ASP cc_start: 0.7050 (t0) cc_final: 0.6779 (t0) REVERT: N 22 GLN cc_start: 0.8276 (tt0) cc_final: 0.8049 (tt0) REVERT: N 24 GLU cc_start: 0.7726 (pt0) cc_final: 0.7145 (pt0) REVERT: N 31 ASN cc_start: 0.8395 (p0) cc_final: 0.7863 (t0) REVERT: N 35 GLN cc_start: 0.8469 (tt0) cc_final: 0.8162 (tt0) REVERT: N 39 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8373 (t) REVERT: N 87 ASP cc_start: 0.8547 (t0) cc_final: 0.8343 (t0) REVERT: N 91 ILE cc_start: 0.9151 (mt) cc_final: 0.8881 (mt) REVERT: N 98 GLU cc_start: 0.8366 (tp30) cc_final: 0.8072 (tp30) REVERT: N 116 TYR cc_start: 0.7059 (m-10) cc_final: 0.6751 (m-10) REVERT: N 160 ASP cc_start: 0.8309 (m-30) cc_final: 0.8013 (m-30) REVERT: O 11 GLU cc_start: 0.8185 (tp30) cc_final: 0.7870 (tp30) REVERT: O 54 MET cc_start: 0.7575 (tpp) cc_final: 0.7162 (mmt) REVERT: O 163 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7902 (mm-30) REVERT: P 8 ARG cc_start: 0.8291 (ptp-110) cc_final: 0.7965 (ptm160) REVERT: P 76 ASP cc_start: 0.8345 (p0) cc_final: 0.7903 (p0) REVERT: P 119 ASP cc_start: 0.8412 (t0) cc_final: 0.8050 (t0) REVERT: P 132 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8223 (tp) REVERT: Q 5 ASP cc_start: 0.8072 (t0) cc_final: 0.7867 (t0) REVERT: Q 8 ARG cc_start: 0.8543 (ptm160) cc_final: 0.8286 (ptm160) REVERT: Q 15 PHE cc_start: 0.8221 (m-10) cc_final: 0.7947 (m-80) REVERT: Q 39 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8215 (t) REVERT: Q 55 ASN cc_start: 0.8068 (t160) cc_final: 0.7806 (t0) REVERT: Q 77 GLU cc_start: 0.8348 (mp0) cc_final: 0.7846 (mp0) REVERT: Q 112 ILE cc_start: 0.9046 (mt) cc_final: 0.8788 (mt) REVERT: Q 145 ASP cc_start: 0.7589 (t0) cc_final: 0.7377 (t0) REVERT: Q 163 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7570 (mm-30) outliers start: 203 outliers final: 131 residues processed: 1222 average time/residue: 0.3640 time to fit residues: 686.5091 Evaluate side-chains 1062 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 920 time to evaluate : 3.339 ------------------------------------------------------------------------------- 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 90 SER 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 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 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 124 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 33 THR 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 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 45 ILE 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 142 LEU 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 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 145 ASP 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 145 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 70 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 142 LEU Chi-restraints excluded: chain H residue 145 ASP 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 72 THR Chi-restraints excluded: chain J residue 73 VAL 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 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 39 THR Chi-restraints excluded: chain M residue 48 LYS 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 132 LEU Chi-restraints excluded: chain M residue 150 ILE Chi-restraints excluded: chain N residue 23 VAL 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 142 LEU Chi-restraints excluded: chain N residue 152 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 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 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 114 ARG Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 192 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 257 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 247 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 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 136 ASN I 147 ASN J 35 GLN ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 148 ASN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 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 89 GLN Q 115 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086094 restraints weight = 49901.157| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.17 r_work: 0.3057 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.9880 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= 0.194 Angle : 0.645 9.848 32562 Z= 0.341 Chirality : 0.049 0.172 3510 Planarity : 0.004 0.046 4284 Dihedral : 7.182 83.074 3132 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 8.15 % Allowed : 22.71 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 2898 helix: -2.81 (0.20), residues: 360 sheet: -0.12 (0.19), residues: 756 loop : -1.53 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 88 HIS 0.004 0.001 HIS A 79 PHE 0.018 0.002 PHE I 66 TYR 0.021 0.002 TYR G 27 ARG 0.006 0.001 ARG N 56 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 648) hydrogen bonds : angle 6.21184 ( 1782) covalent geometry : bond 0.00451 (23994) covalent geometry : angle 0.64468 (32562) *********************** 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 1234 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1033 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7350 (t70) cc_final: 0.7114 (t70) REVERT: A 24 GLU cc_start: 0.7909 (pt0) cc_final: 0.7575 (pt0) REVERT: A 27 TYR cc_start: 0.8728 (t80) cc_final: 0.8506 (t80) REVERT: A 54 MET cc_start: 0.7948 (mmm) cc_final: 0.7587 (tpp) REVERT: A 76 ASP cc_start: 0.8429 (p0) cc_final: 0.7793 (p0) REVERT: A 83 GLN cc_start: 0.8799 (tp40) cc_final: 0.8521 (tm-30) REVERT: A 112 ILE cc_start: 0.8882 (mt) cc_final: 0.8310 (mm) REVERT: A 119 ASP cc_start: 0.8689 (t0) cc_final: 0.8233 (t70) REVERT: A 121 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8478 (ptpp) REVERT: A 126 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: R 2 PHE cc_start: 0.8178 (m-80) cc_final: 0.7291 (m-10) REVERT: R 23 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8222 (p) REVERT: R 24 GLU cc_start: 0.8025 (pt0) cc_final: 0.7543 (pt0) REVERT: R 34 PHE cc_start: 0.8926 (m-10) cc_final: 0.7908 (m-10) REVERT: R 75 ASN cc_start: 0.9064 (t0) cc_final: 0.8837 (t0) REVERT: R 126 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7396 (tm-30) REVERT: R 128 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 112 ILE cc_start: 0.9005 (mt) cc_final: 0.8533 (tt) REVERT: C 126 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 24 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 28 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8671 (mp) REVERT: B 83 GLN cc_start: 0.8784 (tp40) cc_final: 0.7729 (tp-100) REVERT: B 106 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7646 (tp30) REVERT: B 112 ILE cc_start: 0.8958 (mt) cc_final: 0.8590 (tt) REVERT: B 125 LYS cc_start: 0.8632 (tptt) cc_final: 0.8380 (tptt) REVERT: B 139 GLU cc_start: 0.8454 (tp30) cc_final: 0.7236 (pt0) REVERT: B 141 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: D 5 ASP cc_start: 0.8225 (t70) cc_final: 0.7917 (t0) REVERT: D 8 ARG cc_start: 0.7548 (mtp-110) cc_final: 0.7071 (ptm-80) REVERT: D 30 GLN cc_start: 0.8362 (mm110) cc_final: 0.7721 (pp30) REVERT: D 31 ASN cc_start: 0.8507 (p0) cc_final: 0.7866 (t0) REVERT: D 54 MET cc_start: 0.7559 (mmm) cc_final: 0.7206 (tpp) REVERT: D 77 GLU cc_start: 0.7971 (mp0) cc_final: 0.7723 (mp0) REVERT: D 88 TRP cc_start: 0.9378 (t60) cc_final: 0.9132 (t60) REVERT: D 128 GLU cc_start: 0.7514 (tp30) cc_final: 0.7304 (tp30) REVERT: D 130 LYS cc_start: 0.8465 (mmmm) cc_final: 0.7638 (mmmt) REVERT: D 136 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7754 (p0) REVERT: D 139 GLU cc_start: 0.8337 (tp30) cc_final: 0.7882 (tp30) REVERT: D 161 TYR cc_start: 0.8710 (p90) cc_final: 0.8487 (p90) REVERT: E 2 PHE cc_start: 0.8404 (m-80) cc_final: 0.5919 (t80) REVERT: E 15 PHE cc_start: 0.7893 (m-10) cc_final: 0.7585 (m-80) REVERT: E 37 LYS cc_start: 0.8858 (tttt) cc_final: 0.8652 (tttp) REVERT: E 83 GLN cc_start: 0.8850 (tp40) cc_final: 0.8360 (tm-30) REVERT: E 90 SER cc_start: 0.9073 (t) cc_final: 0.8677 (p) REVERT: E 160 ASP cc_start: 0.8003 (m-30) cc_final: 0.7698 (m-30) REVERT: E 161 TYR cc_start: 0.8955 (p90) cc_final: 0.8690 (p90) REVERT: F 1 MET cc_start: 0.8616 (tpp) cc_final: 0.8348 (tpp) REVERT: F 24 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7645 (tm-30) REVERT: F 30 GLN cc_start: 0.8366 (mm110) cc_final: 0.8148 (pp30) REVERT: F 112 ILE cc_start: 0.9065 (mt) cc_final: 0.8798 (tt) REVERT: F 128 GLU cc_start: 0.8167 (pm20) cc_final: 0.7943 (pm20) REVERT: F 135 THR cc_start: 0.8698 (m) cc_final: 0.8377 (m) REVERT: F 137 VAL cc_start: 0.9090 (t) cc_final: 0.8845 (p) REVERT: F 154 GLU cc_start: 0.8562 (pt0) cc_final: 0.8161 (tt0) REVERT: F 161 TYR cc_start: 0.8850 (p90) cc_final: 0.8576 (p90) REVERT: G 1 MET cc_start: 0.7788 (tpp) cc_final: 0.7462 (tpt) REVERT: G 2 PHE cc_start: 0.8294 (m-80) cc_final: 0.7948 (m-10) REVERT: G 28 LEU cc_start: 0.8570 (mm) cc_final: 0.8210 (mp) REVERT: G 31 ASN cc_start: 0.8350 (p0) cc_final: 0.7656 (t0) REVERT: G 54 MET cc_start: 0.7557 (mmm) cc_final: 0.6964 (tpp) REVERT: G 95 GLN cc_start: 0.8777 (tt0) cc_final: 0.8557 (tt0) REVERT: G 98 GLU cc_start: 0.8440 (pm20) cc_final: 0.7990 (pp20) REVERT: G 114 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8040 (mtm180) REVERT: G 139 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7263 (tm-30) REVERT: G 146 SER cc_start: 0.8594 (m) cc_final: 0.8197 (p) REVERT: G 161 TYR cc_start: 0.8700 (p90) cc_final: 0.8369 (p90) REVERT: H 2 PHE cc_start: 0.8106 (m-80) cc_final: 0.6837 (t80) REVERT: H 35 GLN cc_start: 0.8642 (tt0) cc_final: 0.8206 (mt0) REVERT: H 39 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7706 (t) REVERT: H 64 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (ttm-80) REVERT: H 70 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8260 (t) REVERT: H 77 GLU cc_start: 0.8148 (mp0) cc_final: 0.7821 (mp0) REVERT: H 115 GLN cc_start: 0.8091 (tt0) cc_final: 0.7774 (tt0) REVERT: H 130 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8176 (mmmm) REVERT: H 140 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8286 (mt) REVERT: H 146 SER cc_start: 0.8480 (m) cc_final: 0.8068 (p) REVERT: H 160 ASP cc_start: 0.8565 (m-30) cc_final: 0.8329 (m-30) REVERT: I 14 ASP cc_start: 0.7886 (t0) cc_final: 0.7569 (t0) REVERT: I 22 GLN cc_start: 0.8120 (mt0) cc_final: 0.7756 (mt0) REVERT: I 30 GLN cc_start: 0.8282 (mm110) cc_final: 0.8010 (tm-30) REVERT: I 87 ASP cc_start: 0.8749 (p0) cc_final: 0.8524 (p0) REVERT: I 146 SER cc_start: 0.8701 (m) cc_final: 0.8290 (p) REVERT: I 154 GLU cc_start: 0.8471 (pt0) cc_final: 0.8057 (tt0) REVERT: J 27 TYR cc_start: 0.7818 (t80) cc_final: 0.7520 (t80) REVERT: J 28 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8001 (mt) REVERT: J 31 ASN cc_start: 0.8636 (p0) cc_final: 0.8032 (t0) REVERT: J 45 ILE cc_start: 0.8799 (mt) cc_final: 0.8299 (tt) REVERT: J 79 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7324 (t-90) REVERT: J 126 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7834 (mt-10) REVERT: J 139 GLU cc_start: 0.8696 (tp30) cc_final: 0.7994 (pt0) REVERT: J 161 TYR cc_start: 0.8569 (p90) cc_final: 0.8053 (p90) REVERT: K 2 PHE cc_start: 0.7696 (m-80) cc_final: 0.6180 (t80) REVERT: K 7 THR cc_start: 0.8231 (p) cc_final: 0.7686 (t) REVERT: K 79 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.6142 (t-90) REVERT: L 28 LEU cc_start: 0.8890 (mm) cc_final: 0.8453 (mp) REVERT: L 34 PHE cc_start: 0.9176 (m-80) cc_final: 0.8253 (m-80) REVERT: L 77 GLU cc_start: 0.8371 (mp0) cc_final: 0.7997 (mp0) REVERT: M 2 PHE cc_start: 0.8633 (m-10) cc_final: 0.8304 (m-10) REVERT: M 24 GLU cc_start: 0.7968 (pt0) cc_final: 0.7377 (pt0) REVERT: M 47 GLU cc_start: 0.7527 (tp30) cc_final: 0.7225 (tp30) REVERT: M 48 LYS cc_start: 0.8486 (ttpm) cc_final: 0.7777 (ttmt) REVERT: M 80 ASP cc_start: 0.8375 (p0) cc_final: 0.8114 (p0) REVERT: M 103 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8610 (mtpt) REVERT: M 114 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7848 (mtm180) REVERT: M 126 GLU cc_start: 0.8322 (pp20) cc_final: 0.7964 (pp20) REVERT: M 128 GLU cc_start: 0.7586 (pm20) cc_final: 0.6979 (pm20) REVERT: M 139 GLU cc_start: 0.8895 (tp30) cc_final: 0.8564 (tp30) REVERT: M 146 SER cc_start: 0.8469 (m) cc_final: 0.7909 (p) REVERT: N 4 ASP cc_start: 0.7488 (m-30) cc_final: 0.7270 (m-30) REVERT: N 30 GLN cc_start: 0.8308 (mm110) cc_final: 0.8032 (mm-40) REVERT: N 31 ASN cc_start: 0.8520 (p0) cc_final: 0.8187 (t0) REVERT: N 80 ASP cc_start: 0.8620 (p0) cc_final: 0.8409 (p0) REVERT: N 91 ILE cc_start: 0.9340 (mt) cc_final: 0.9059 (mt) REVERT: N 160 ASP cc_start: 0.8244 (m-30) cc_final: 0.8024 (m-30) REVERT: N 163 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7780 (mm-30) REVERT: O 11 GLU cc_start: 0.8365 (tp30) cc_final: 0.8131 (tp30) REVERT: O 83 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8099 (tm-30) REVERT: O 112 ILE cc_start: 0.9012 (mt) cc_final: 0.8705 (tt) REVERT: P 76 ASP cc_start: 0.8345 (p0) cc_final: 0.7901 (p0) REVERT: P 98 GLU cc_start: 0.8451 (tp30) cc_final: 0.8235 (tp30) REVERT: P 106 GLU cc_start: 0.7718 (mp0) cc_final: 0.7487 (mp0) REVERT: P 112 ILE cc_start: 0.9084 (mt) cc_final: 0.8603 (tt) REVERT: P 115 GLN cc_start: 0.7900 (tt0) cc_final: 0.7658 (tt0) REVERT: P 119 ASP cc_start: 0.8682 (t0) cc_final: 0.8183 (t0) REVERT: P 121 LYS cc_start: 0.8328 (ptpp) cc_final: 0.8083 (ptpp) REVERT: P 132 LEU cc_start: 0.8621 (mp) cc_final: 0.8384 (tp) REVERT: Q 14 ASP cc_start: 0.8012 (t0) cc_final: 0.7791 (t0) REVERT: Q 15 PHE cc_start: 0.8362 (m-10) cc_final: 0.8136 (m-80) REVERT: Q 39 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8147 (t) REVERT: Q 77 GLU cc_start: 0.8426 (mp0) cc_final: 0.7982 (mp0) REVERT: Q 118 ARG cc_start: 0.7570 (tpt170) cc_final: 0.5488 (ttm170) REVERT: Q 148 ASN cc_start: 0.8191 (m-40) cc_final: 0.7971 (m-40) REVERT: Q 160 ASP cc_start: 0.8029 (m-30) cc_final: 0.7402 (m-30) outliers start: 201 outliers final: 148 residues processed: 1177 average time/residue: 0.3887 time to fit residues: 713.8675 Evaluate side-chains 1076 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 915 time to evaluate : 2.915 ------------------------------------------------------------------------------- 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 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 99 ILE Chi-restraints excluded: chain A residue 126 GLU 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 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 79 HIS 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 23 VAL Chi-restraints excluded: chain B residue 28 LEU 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 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 110 SER 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 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 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 110 SER Chi-restraints excluded: chain F residue 145 ASP 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 152 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 64 ARG 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 113 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 142 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 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 73 VAL Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 90 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 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 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 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 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 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 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 73 VAL 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 123 VAL Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 49 optimal weight: 6.9990 chunk 164 optimal weight: 0.0970 chunk 62 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 234 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 overall best weight: 4.4184 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 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** H 22 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 136 ASN 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 95 GLN M 147 ASN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086911 restraints weight = 49732.401| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.12 r_work: 0.3066 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 1.0196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23994 Z= 0.153 Angle : 0.619 9.618 32562 Z= 0.326 Chirality : 0.048 0.177 3510 Planarity : 0.004 0.035 4284 Dihedral : 6.883 80.177 3132 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 8.11 % Allowed : 24.09 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 2898 helix: -2.41 (0.22), residues: 360 sheet: -0.00 (0.20), residues: 756 loop : -1.50 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 88 HIS 0.003 0.001 HIS A 79 PHE 0.024 0.001 PHE O 21 TYR 0.019 0.002 TYR G 27 ARG 0.006 0.001 ARG H 8 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 648) hydrogen bonds : angle 5.99194 ( 1782) covalent geometry : bond 0.00358 (23994) covalent geometry : angle 0.61898 (32562) *********************** 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 1206 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 1006 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7953 (pt0) cc_final: 0.7590 (pt0) REVERT: A 27 TYR cc_start: 0.8663 (t80) cc_final: 0.8403 (t80) REVERT: A 54 MET cc_start: 0.8022 (mmm) cc_final: 0.7591 (tpp) REVERT: A 95 GLN cc_start: 0.8589 (tt0) cc_final: 0.8265 (tt0) REVERT: A 112 ILE cc_start: 0.8886 (mt) cc_final: 0.8399 (mm) REVERT: A 119 ASP cc_start: 0.8535 (t0) cc_final: 0.8014 (t70) REVERT: A 121 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8422 (ptpp) REVERT: A 161 TYR cc_start: 0.8587 (p90) cc_final: 0.8283 (p90) REVERT: R 2 PHE cc_start: 0.8193 (m-80) cc_final: 0.7109 (m-10) REVERT: R 23 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8043 (p) REVERT: R 24 GLU cc_start: 0.8071 (pt0) cc_final: 0.7653 (pt0) REVERT: R 34 PHE cc_start: 0.8934 (m-10) cc_final: 0.7850 (m-10) REVERT: R 39 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7760 (t) REVERT: R 75 ASN cc_start: 0.9064 (t0) cc_final: 0.8838 (t0) REVERT: R 114 ARG cc_start: 0.8495 (ptp90) cc_final: 0.7856 (ptp90) REVERT: R 126 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7264 (tm-30) REVERT: R 128 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7421 (tm-30) REVERT: C 24 GLU cc_start: 0.8459 (pp20) cc_final: 0.8215 (pp20) REVERT: C 112 ILE cc_start: 0.8978 (mt) cc_final: 0.8600 (tt) REVERT: C 126 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 28 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 37 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8623 (mtpp) REVERT: B 83 GLN cc_start: 0.8793 (tp40) cc_final: 0.7697 (tp-100) REVERT: B 106 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7742 (tp30) REVERT: B 112 ILE cc_start: 0.9076 (mt) cc_final: 0.8685 (tt) REVERT: B 139 GLU cc_start: 0.8496 (tp30) cc_final: 0.7428 (pt0) REVERT: B 141 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: B 161 TYR cc_start: 0.8977 (p90) cc_final: 0.8748 (p90) REVERT: D 8 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7146 (ptm-80) REVERT: D 31 ASN cc_start: 0.8451 (p0) cc_final: 0.7892 (t0) REVERT: D 48 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7580 (ttmt) REVERT: D 54 MET cc_start: 0.7699 (mmm) cc_final: 0.7378 (tpp) REVERT: D 97 ASN cc_start: 0.7937 (t0) cc_final: 0.7438 (t0) REVERT: D 127 ILE cc_start: 0.8666 (mp) cc_final: 0.8443 (mt) REVERT: D 128 GLU cc_start: 0.7651 (tp30) cc_final: 0.7268 (tp30) REVERT: D 130 LYS cc_start: 0.8569 (mmmm) cc_final: 0.7852 (mmmt) REVERT: D 136 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7834 (p0) REVERT: E 2 PHE cc_start: 0.8421 (m-80) cc_final: 0.5974 (t80) REVERT: E 30 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7745 (tp40) REVERT: E 83 GLN cc_start: 0.8866 (tp40) cc_final: 0.8431 (tm-30) REVERT: E 90 SER cc_start: 0.9082 (t) cc_final: 0.8716 (p) REVERT: E 142 LEU cc_start: 0.8279 (pt) cc_final: 0.7866 (pt) REVERT: E 161 TYR cc_start: 0.8921 (p90) cc_final: 0.8563 (p90) REVERT: F 1 MET cc_start: 0.8504 (tpp) cc_final: 0.8191 (tpp) REVERT: F 2 PHE cc_start: 0.7846 (m-80) cc_final: 0.7436 (m-80) REVERT: F 14 ASP cc_start: 0.7836 (t0) cc_final: 0.7591 (t0) REVERT: F 15 PHE cc_start: 0.8046 (m-80) cc_final: 0.7630 (m-80) REVERT: F 24 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7405 (tm-30) REVERT: F 30 GLN cc_start: 0.8386 (mm110) cc_final: 0.8174 (pp30) REVERT: F 47 GLU cc_start: 0.4571 (pt0) cc_final: 0.3874 (pt0) REVERT: F 112 ILE cc_start: 0.9015 (mt) cc_final: 0.8769 (tt) REVERT: F 119 ASP cc_start: 0.7971 (t0) cc_final: 0.7716 (t70) REVERT: F 135 THR cc_start: 0.8657 (m) cc_final: 0.8360 (m) REVERT: F 139 GLU cc_start: 0.8637 (tp30) cc_final: 0.7447 (pt0) REVERT: F 141 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8368 (mm-40) REVERT: F 154 GLU cc_start: 0.8519 (pt0) cc_final: 0.8136 (tt0) REVERT: G 1 MET cc_start: 0.7840 (tpp) cc_final: 0.7626 (tpt) REVERT: G 2 PHE cc_start: 0.8205 (m-80) cc_final: 0.7808 (m-10) REVERT: G 31 ASN cc_start: 0.8320 (p0) cc_final: 0.7738 (t0) REVERT: G 35 GLN cc_start: 0.7968 (mt0) cc_final: 0.7683 (mt0) REVERT: G 54 MET cc_start: 0.7589 (mmm) cc_final: 0.7087 (tpp) REVERT: G 76 ASP cc_start: 0.8537 (p0) cc_final: 0.8227 (p0) REVERT: G 97 ASN cc_start: 0.8542 (t0) cc_final: 0.7900 (t0) REVERT: G 98 GLU cc_start: 0.8550 (pm20) cc_final: 0.8067 (pp20) REVERT: G 99 ILE cc_start: 0.8548 (mt) cc_final: 0.8116 (mt) REVERT: G 139 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7091 (tm-30) REVERT: G 146 SER cc_start: 0.8313 (m) cc_final: 0.8104 (p) REVERT: H 2 PHE cc_start: 0.8001 (m-80) cc_final: 0.6812 (t80) REVERT: H 35 GLN cc_start: 0.8561 (tt0) cc_final: 0.8142 (mt0) REVERT: H 103 LYS cc_start: 0.8732 (mptt) cc_final: 0.8298 (mmtm) REVERT: H 121 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8335 (ptpp) REVERT: H 130 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8117 (mmmm) REVERT: H 140 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8282 (mt) REVERT: H 146 SER cc_start: 0.8406 (m) cc_final: 0.7967 (p) REVERT: H 160 ASP cc_start: 0.8486 (m-30) cc_final: 0.8271 (m-30) REVERT: I 5 ASP cc_start: 0.7716 (p0) cc_final: 0.7237 (p0) REVERT: I 22 GLN cc_start: 0.8059 (mt0) cc_final: 0.7840 (mt0) REVERT: I 30 GLN cc_start: 0.8267 (mm110) cc_final: 0.7991 (tm-30) REVERT: I 37 LYS cc_start: 0.9031 (tttm) cc_final: 0.8582 (tttp) REVERT: I 77 GLU cc_start: 0.8403 (mp0) cc_final: 0.8093 (mp0) REVERT: I 128 GLU cc_start: 0.7635 (pm20) cc_final: 0.7432 (pm20) REVERT: I 146 SER cc_start: 0.8779 (m) cc_final: 0.8389 (p) REVERT: I 154 GLU cc_start: 0.8607 (pt0) cc_final: 0.8201 (tt0) REVERT: I 161 TYR cc_start: 0.8638 (p90) cc_final: 0.8379 (p90) REVERT: J 14 ASP cc_start: 0.7553 (t0) cc_final: 0.7244 (t0) REVERT: J 15 PHE cc_start: 0.7886 (m-80) cc_final: 0.7613 (m-80) REVERT: J 31 ASN cc_start: 0.8711 (p0) cc_final: 0.7962 (t0) REVERT: J 45 ILE cc_start: 0.8816 (mt) cc_final: 0.8309 (tt) REVERT: J 76 ASP cc_start: 0.8920 (p0) cc_final: 0.8669 (p0) REVERT: J 114 ARG cc_start: 0.8721 (mpp80) cc_final: 0.8502 (mpp80) REVERT: J 139 GLU cc_start: 0.8708 (tp30) cc_final: 0.8261 (mm-30) REVERT: K 2 PHE cc_start: 0.7633 (m-80) cc_final: 0.5920 (t80) REVERT: K 7 THR cc_start: 0.8395 (p) cc_final: 0.7847 (t) REVERT: K 24 GLU cc_start: 0.6970 (tp30) cc_final: 0.6745 (tp30) REVERT: K 30 GLN cc_start: 0.8371 (mm110) cc_final: 0.8165 (mm-40) REVERT: K 79 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.6193 (t-90) REVERT: K 95 GLN cc_start: 0.8195 (tp40) cc_final: 0.7725 (tp40) REVERT: L 34 PHE cc_start: 0.9099 (m-80) cc_final: 0.8265 (m-80) REVERT: L 77 GLU cc_start: 0.8430 (mp0) cc_final: 0.8056 (mp0) REVERT: M 2 PHE cc_start: 0.8592 (m-10) cc_final: 0.8270 (m-10) REVERT: M 103 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8562 (mtmm) REVERT: M 109 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8439 (mmmt) REVERT: M 114 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8013 (mtm180) REVERT: M 146 SER cc_start: 0.8838 (m) cc_final: 0.7799 (p) REVERT: N 4 ASP cc_start: 0.7579 (m-30) cc_final: 0.7329 (m-30) REVERT: N 30 GLN cc_start: 0.8385 (mm110) cc_final: 0.8171 (mm-40) REVERT: N 31 ASN cc_start: 0.8551 (p0) cc_final: 0.8288 (t0) REVERT: N 80 ASP cc_start: 0.8616 (p0) cc_final: 0.8379 (p0) REVERT: N 91 ILE cc_start: 0.9380 (mt) cc_final: 0.9122 (mt) REVERT: N 109 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8453 (mmtp) REVERT: N 160 ASP cc_start: 0.8213 (m-30) cc_final: 0.7674 (m-30) REVERT: O 2 PHE cc_start: 0.8490 (m-80) cc_final: 0.7921 (m-80) REVERT: O 4 ASP cc_start: 0.8404 (m-30) cc_final: 0.8032 (p0) REVERT: O 8 ARG cc_start: 0.8183 (ptm160) cc_final: 0.7674 (ptm160) REVERT: O 11 GLU cc_start: 0.8299 (tp30) cc_final: 0.8070 (tp30) REVERT: O 54 MET cc_start: 0.6733 (tpt) cc_final: 0.6199 (mmt) REVERT: O 83 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8121 (tm-30) REVERT: P 8 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.8062 (ptm160) REVERT: P 76 ASP cc_start: 0.8241 (p0) cc_final: 0.7811 (p0) REVERT: P 112 ILE cc_start: 0.9070 (mt) cc_final: 0.8615 (tt) REVERT: P 115 GLN cc_start: 0.7940 (tt0) cc_final: 0.7650 (tt0) REVERT: P 119 ASP cc_start: 0.8674 (t0) cc_final: 0.7997 (t0) REVERT: P 121 LYS cc_start: 0.8331 (ptpp) cc_final: 0.8063 (ptpp) REVERT: P 132 LEU cc_start: 0.8544 (mp) cc_final: 0.8278 (tp) REVERT: Q 1 MET cc_start: 0.8477 (mmt) cc_final: 0.8099 (mmm) REVERT: Q 14 ASP cc_start: 0.8012 (t0) cc_final: 0.7596 (p0) REVERT: Q 24 GLU cc_start: 0.8138 (pp20) cc_final: 0.7717 (pp20) REVERT: Q 31 ASN cc_start: 0.8059 (p0) cc_final: 0.7348 (t0) REVERT: Q 39 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8097 (t) REVERT: Q 77 GLU cc_start: 0.8725 (mp0) cc_final: 0.8298 (mp0) REVERT: Q 118 ARG cc_start: 0.7584 (tpt170) cc_final: 0.5599 (ttm170) REVERT: Q 142 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7629 (pt) outliers start: 200 outliers final: 151 residues processed: 1138 average time/residue: 0.3546 time to fit residues: 619.4430 Evaluate side-chains 1096 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 936 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 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 99 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 23 VAL 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 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 77 GLU Chi-restraints excluded: chain C residue 79 HIS 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 23 VAL Chi-restraints excluded: chain B residue 28 LEU 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 B residue 150 ILE 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 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 28 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 113 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 23 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 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 3 VAL Chi-restraints excluded: chain H residue 23 VAL 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 140 LEU Chi-restraints excluded: chain H residue 142 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 151 GLN Chi-restraints excluded: chain J residue 23 VAL 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 73 VAL Chi-restraints excluded: chain J residue 79 HIS 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 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 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 L residue 150 ILE 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 70 THR 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 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 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 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 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 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 73 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 115 GLN Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 43 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 177 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 148 ASN D 22 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN J 19 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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 35 GLN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084837 restraints weight = 49893.830| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.16 r_work: 0.3035 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 1.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23994 Z= 0.194 Angle : 0.648 9.889 32562 Z= 0.342 Chirality : 0.049 0.184 3510 Planarity : 0.004 0.043 4284 Dihedral : 7.024 81.243 3132 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 9.33 % Allowed : 23.48 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 2898 helix: -2.08 (0.24), residues: 360 sheet: -0.01 (0.20), residues: 756 loop : -1.50 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 88 HIS 0.003 0.001 HIS J 79 PHE 0.017 0.002 PHE F 53 TYR 0.020 0.002 TYR G 27 ARG 0.008 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 648) hydrogen bonds : angle 6.02901 ( 1782) covalent geometry : bond 0.00454 (23994) covalent geometry : angle 0.64804 (32562) *********************** 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 1188 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 958 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7919 (pt0) cc_final: 0.7518 (pt0) REVERT: A 54 MET cc_start: 0.8070 (mmm) cc_final: 0.7655 (tpp) REVERT: A 57 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8032 (mmtt) REVERT: A 76 ASP cc_start: 0.8245 (p0) cc_final: 0.8034 (p0) REVERT: A 112 ILE cc_start: 0.8740 (mt) cc_final: 0.8392 (mm) REVERT: A 119 ASP cc_start: 0.8578 (t0) cc_final: 0.8309 (t70) REVERT: A 126 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7118 (tm-30) REVERT: A 161 TYR cc_start: 0.8680 (p90) cc_final: 0.8348 (p90) REVERT: R 2 PHE cc_start: 0.8222 (m-80) cc_final: 0.7502 (m-10) REVERT: R 23 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8206 (m) REVERT: R 24 GLU cc_start: 0.8080 (pt0) cc_final: 0.7678 (pt0) REVERT: R 34 PHE cc_start: 0.8976 (m-10) cc_final: 0.7974 (m-10) REVERT: R 39 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7710 (t) REVERT: R 75 ASN cc_start: 0.9087 (t0) cc_final: 0.8848 (t0) REVERT: R 114 ARG cc_start: 0.8581 (ptp90) cc_final: 0.8060 (ptp90) REVERT: R 126 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 112 ILE cc_start: 0.9096 (mt) cc_final: 0.8742 (tt) REVERT: B 24 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 28 LEU cc_start: 0.9107 (mm) cc_final: 0.8885 (mp) REVERT: B 83 GLN cc_start: 0.8766 (tp40) cc_final: 0.8048 (tp-100) REVERT: B 106 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7798 (tp30) REVERT: B 112 ILE cc_start: 0.9092 (mt) cc_final: 0.8727 (tt) REVERT: B 141 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: D 28 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8772 (mm) REVERT: D 30 GLN cc_start: 0.8494 (mm110) cc_final: 0.8012 (pp30) REVERT: D 31 ASN cc_start: 0.8406 (p0) cc_final: 0.8090 (t0) REVERT: D 54 MET cc_start: 0.7868 (mmm) cc_final: 0.7623 (tpp) REVERT: D 97 ASN cc_start: 0.8003 (t0) cc_final: 0.7385 (t0) REVERT: D 109 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8663 (mmtp) REVERT: D 130 LYS cc_start: 0.8621 (mmmm) cc_final: 0.7660 (mmmt) REVERT: D 136 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7845 (p0) REVERT: E 2 PHE cc_start: 0.8506 (m-80) cc_final: 0.5927 (t80) REVERT: E 4 ASP cc_start: 0.8182 (m-30) cc_final: 0.7915 (p0) REVERT: E 30 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7785 (tp40) REVERT: E 31 ASN cc_start: 0.8392 (p0) cc_final: 0.8101 (t0) REVERT: E 83 GLN cc_start: 0.8883 (tp40) cc_final: 0.8467 (tm-30) REVERT: E 90 SER cc_start: 0.9097 (t) cc_final: 0.8717 (p) REVERT: E 116 TYR cc_start: 0.8980 (m-10) cc_final: 0.8396 (m-10) REVERT: E 142 LEU cc_start: 0.8405 (pt) cc_final: 0.8057 (pt) REVERT: E 154 GLU cc_start: 0.8286 (tt0) cc_final: 0.8031 (tt0) REVERT: E 161 TYR cc_start: 0.8930 (p90) cc_final: 0.8485 (p90) REVERT: F 1 MET cc_start: 0.8483 (tpp) cc_final: 0.8073 (tpp) REVERT: F 2 PHE cc_start: 0.7896 (m-80) cc_final: 0.7412 (m-80) REVERT: F 24 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7622 (tm-30) REVERT: F 47 GLU cc_start: 0.4630 (pt0) cc_final: 0.4126 (pt0) REVERT: F 112 ILE cc_start: 0.9016 (mt) cc_final: 0.8803 (tt) REVERT: F 135 THR cc_start: 0.8675 (m) cc_final: 0.8404 (p) REVERT: F 139 GLU cc_start: 0.8705 (tp30) cc_final: 0.7501 (pt0) REVERT: F 154 GLU cc_start: 0.8501 (pt0) cc_final: 0.8110 (tt0) REVERT: G 2 PHE cc_start: 0.8348 (m-80) cc_final: 0.7599 (m-80) REVERT: G 28 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8621 (mp) REVERT: G 31 ASN cc_start: 0.8498 (p0) cc_final: 0.7958 (t0) REVERT: G 35 GLN cc_start: 0.8159 (mt0) cc_final: 0.7850 (mt0) REVERT: G 54 MET cc_start: 0.7673 (mmm) cc_final: 0.7272 (tpp) REVERT: G 95 GLN cc_start: 0.8804 (tt0) cc_final: 0.8582 (tt0) REVERT: G 112 ILE cc_start: 0.8818 (mt) cc_final: 0.8262 (tt) REVERT: G 139 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7034 (tm-30) REVERT: G 146 SER cc_start: 0.8348 (m) cc_final: 0.8017 (p) REVERT: H 2 PHE cc_start: 0.8214 (m-80) cc_final: 0.6645 (t80) REVERT: H 35 GLN cc_start: 0.8441 (tt0) cc_final: 0.7948 (mt0) REVERT: H 39 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7546 (t) REVERT: H 115 GLN cc_start: 0.7800 (tt0) cc_final: 0.7567 (tt0) REVERT: H 119 ASP cc_start: 0.8365 (t70) cc_final: 0.8136 (t70) REVERT: H 130 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8080 (mmmm) REVERT: H 140 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8316 (mt) REVERT: H 160 ASP cc_start: 0.8440 (m-30) cc_final: 0.8214 (m-30) REVERT: I 30 GLN cc_start: 0.8363 (mm110) cc_final: 0.8107 (tm-30) REVERT: I 36 CYS cc_start: 0.8951 (t) cc_final: 0.8743 (t) REVERT: I 37 LYS cc_start: 0.8928 (tttm) cc_final: 0.8723 (tttp) REVERT: I 154 GLU cc_start: 0.8661 (pt0) cc_final: 0.8218 (tt0) REVERT: J 45 ILE cc_start: 0.8945 (mt) cc_final: 0.8422 (tt) REVERT: J 114 ARG cc_start: 0.8800 (mpp80) cc_final: 0.8548 (mpp80) REVERT: J 126 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7742 (mt-10) REVERT: J 139 GLU cc_start: 0.8759 (tp30) cc_final: 0.7777 (pt0) REVERT: J 145 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: K 22 GLN cc_start: 0.8370 (tt0) cc_final: 0.8149 (tt0) REVERT: K 31 ASN cc_start: 0.8343 (p0) cc_final: 0.7873 (t0) REVERT: K 79 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.6659 (t-90) REVERT: K 121 LYS cc_start: 0.8125 (pttp) cc_final: 0.7826 (ptpp) REVERT: L 28 LEU cc_start: 0.8910 (mm) cc_final: 0.8621 (mp) REVERT: L 114 ARG cc_start: 0.8633 (mtm110) cc_final: 0.8431 (mtm110) REVERT: M 2 PHE cc_start: 0.8595 (m-10) cc_final: 0.8258 (m-10) REVERT: M 103 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8595 (mtmm) REVERT: M 146 SER cc_start: 0.8428 (m) cc_final: 0.8056 (p) REVERT: M 163 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7673 (mm-30) REVERT: N 30 GLN cc_start: 0.8516 (mm110) cc_final: 0.8145 (mm-40) REVERT: N 80 ASP cc_start: 0.8626 (p0) cc_final: 0.8316 (p0) REVERT: N 91 ILE cc_start: 0.9426 (mt) cc_final: 0.9071 (mm) REVERT: N 98 GLU cc_start: 0.8695 (tp30) cc_final: 0.8492 (tp30) REVERT: N 103 LYS cc_start: 0.8740 (tppt) cc_final: 0.8494 (tppt) REVERT: N 139 GLU cc_start: 0.8586 (mm-30) cc_final: 0.7670 (tp30) REVERT: N 155 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8167 (p) REVERT: N 160 ASP cc_start: 0.8298 (m-30) cc_final: 0.7795 (m-30) REVERT: O 4 ASP cc_start: 0.8450 (m-30) cc_final: 0.8043 (p0) REVERT: O 8 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7709 (ptm160) REVERT: O 11 GLU cc_start: 0.8472 (tp30) cc_final: 0.8185 (tp30) REVERT: O 14 ASP cc_start: 0.7857 (t0) cc_final: 0.7452 (t70) REVERT: O 15 PHE cc_start: 0.7807 (m-10) cc_final: 0.7437 (m-10) REVERT: O 54 MET cc_start: 0.6789 (tpt) cc_final: 0.6255 (mmt) REVERT: O 83 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8064 (tm-30) REVERT: O 119 ASP cc_start: 0.8367 (t0) cc_final: 0.7885 (t70) REVERT: O 160 ASP cc_start: 0.8274 (m-30) cc_final: 0.7809 (m-30) REVERT: P 8 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8118 (ptm160) REVERT: P 70 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7630 (t) REVERT: P 76 ASP cc_start: 0.8241 (p0) cc_final: 0.7777 (p0) REVERT: P 112 ILE cc_start: 0.9099 (mt) cc_final: 0.8608 (tt) REVERT: P 115 GLN cc_start: 0.7929 (tt0) cc_final: 0.7659 (tt0) REVERT: P 119 ASP cc_start: 0.8631 (t0) cc_final: 0.8112 (t0) REVERT: P 121 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8154 (ptpp) REVERT: Q 1 MET cc_start: 0.8452 (mmt) cc_final: 0.8073 (mmm) REVERT: Q 24 GLU cc_start: 0.8108 (pp20) cc_final: 0.7892 (tm-30) REVERT: Q 31 ASN cc_start: 0.8035 (p0) cc_final: 0.7611 (t0) REVERT: Q 39 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8215 (t) REVERT: Q 77 GLU cc_start: 0.8611 (mp0) cc_final: 0.8253 (mp0) REVERT: Q 109 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8649 (mmtp) REVERT: Q 126 GLU cc_start: 0.8556 (pt0) cc_final: 0.7985 (pp20) REVERT: Q 128 GLU cc_start: 0.8366 (pm20) cc_final: 0.8075 (pm20) REVERT: Q 154 GLU cc_start: 0.8064 (tt0) cc_final: 0.7742 (tt0) outliers start: 230 outliers final: 179 residues processed: 1109 average time/residue: 0.3733 time to fit residues: 640.7357 Evaluate side-chains 1091 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 899 time to evaluate : 2.499 ------------------------------------------------------------------------------- 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 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 A residue 159 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 23 VAL 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 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 49 ILE 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 77 GLU Chi-restraints excluded: chain C residue 79 HIS 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 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 B residue 150 ILE 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 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 149 GLU 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 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 F residue 19 ASN Chi-restraints excluded: chain F residue 23 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 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 28 LEU 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 90 SER 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 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 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 142 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 151 GLN Chi-restraints excluded: chain J residue 23 VAL 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 73 VAL Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 145 ASP 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 99 ILE 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 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 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 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 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 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 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 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 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 112 ILE 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 132 LEU Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 0 optimal weight: 30.0000 chunk 256 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN N 35 GLN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 55 ASN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084966 restraints weight = 50196.580| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.20 r_work: 0.3036 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 1.0742 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= 0.173 Angle : 0.654 10.379 32562 Z= 0.343 Chirality : 0.049 0.174 3510 Planarity : 0.004 0.034 4284 Dihedral : 6.916 79.559 3132 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 8.92 % Allowed : 24.57 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 2898 helix: -1.91 (0.24), residues: 360 sheet: -0.02 (0.20), residues: 756 loop : -1.49 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 88 HIS 0.003 0.001 HIS A 79 PHE 0.016 0.001 PHE F 53 TYR 0.023 0.002 TYR G 27 ARG 0.006 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 648) hydrogen bonds : angle 5.97133 ( 1782) covalent geometry : bond 0.00405 (23994) covalent geometry : angle 0.65400 (32562) *********************** 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 1184 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 964 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8439 (ptm-80) REVERT: A 24 GLU cc_start: 0.7972 (pt0) cc_final: 0.7544 (pt0) REVERT: A 112 ILE cc_start: 0.8763 (mt) cc_final: 0.8491 (mm) REVERT: A 119 ASP cc_start: 0.8603 (t0) cc_final: 0.7998 (t70) REVERT: A 121 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8359 (ptpp) REVERT: A 126 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 161 TYR cc_start: 0.8663 (p90) cc_final: 0.8336 (p90) REVERT: R 2 PHE cc_start: 0.8227 (m-80) cc_final: 0.6993 (m-10) REVERT: R 23 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8198 (m) REVERT: R 24 GLU cc_start: 0.8124 (pt0) cc_final: 0.7609 (pt0) REVERT: R 34 PHE cc_start: 0.8947 (m-10) cc_final: 0.7975 (m-10) REVERT: R 114 ARG cc_start: 0.8605 (ptp90) cc_final: 0.7957 (ptp90) REVERT: R 126 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7515 (tm-30) REVERT: R 128 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: R 130 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8778 (mmtp) REVERT: C 103 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8503 (mtpt) REVERT: C 112 ILE cc_start: 0.9066 (mt) cc_final: 0.8639 (tt) REVERT: C 160 ASP cc_start: 0.7724 (m-30) cc_final: 0.7467 (m-30) REVERT: B 24 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 83 GLN cc_start: 0.8790 (tp40) cc_final: 0.7974 (tp-100) REVERT: B 106 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7775 (tp30) REVERT: B 112 ILE cc_start: 0.9075 (mt) cc_final: 0.8672 (tt) REVERT: B 121 LYS cc_start: 0.8730 (mttp) cc_final: 0.8437 (mptt) REVERT: B 141 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: D 30 GLN cc_start: 0.8436 (mm110) cc_final: 0.7946 (pp30) REVERT: D 31 ASN cc_start: 0.8385 (p0) cc_final: 0.8055 (t0) REVERT: D 54 MET cc_start: 0.7890 (mmm) cc_final: 0.7567 (tpp) REVERT: D 97 ASN cc_start: 0.7935 (t0) cc_final: 0.7417 (t0) REVERT: D 112 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8107 (mm) REVERT: D 136 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7830 (p0) REVERT: E 2 PHE cc_start: 0.8436 (m-80) cc_final: 0.5936 (t80) REVERT: E 4 ASP cc_start: 0.8246 (m-30) cc_final: 0.7956 (p0) REVERT: E 30 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7774 (tp40) REVERT: E 83 GLN cc_start: 0.8867 (tp40) cc_final: 0.8457 (tm-30) REVERT: E 90 SER cc_start: 0.9079 (t) cc_final: 0.8700 (p) REVERT: E 142 LEU cc_start: 0.8415 (pt) cc_final: 0.8080 (pt) REVERT: E 154 GLU cc_start: 0.8342 (tt0) cc_final: 0.8092 (tt0) REVERT: E 160 ASP cc_start: 0.7974 (m-30) cc_final: 0.7674 (m-30) REVERT: E 161 TYR cc_start: 0.8945 (p90) cc_final: 0.8494 (p90) REVERT: F 1 MET cc_start: 0.8371 (tpp) cc_final: 0.8043 (tpp) REVERT: F 2 PHE cc_start: 0.7781 (m-80) cc_final: 0.7581 (m-80) REVERT: F 14 ASP cc_start: 0.7938 (t0) cc_final: 0.7703 (t0) REVERT: F 24 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7348 (tm-30) REVERT: F 36 CYS cc_start: 0.8503 (t) cc_final: 0.7982 (t) REVERT: F 47 GLU cc_start: 0.4616 (pt0) cc_final: 0.4262 (pt0) REVERT: F 119 ASP cc_start: 0.8051 (t0) cc_final: 0.7837 (t70) REVERT: F 135 THR cc_start: 0.8737 (m) cc_final: 0.8468 (p) REVERT: F 154 GLU cc_start: 0.8547 (pt0) cc_final: 0.8182 (tt0) REVERT: G 2 PHE cc_start: 0.8432 (m-80) cc_final: 0.7683 (m-80) REVERT: G 28 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8633 (mp) REVERT: G 31 ASN cc_start: 0.8373 (p0) cc_final: 0.8107 (t0) REVERT: G 35 GLN cc_start: 0.8222 (mt0) cc_final: 0.7938 (mt0) REVERT: G 54 MET cc_start: 0.7687 (mmm) cc_final: 0.7395 (tpp) REVERT: G 112 ILE cc_start: 0.8782 (mt) cc_final: 0.8308 (tt) REVERT: G 119 ASP cc_start: 0.8606 (t0) cc_final: 0.8388 (t0) REVERT: G 121 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8564 (ptpp) REVERT: G 139 GLU cc_start: 0.7968 (mm-30) cc_final: 0.6943 (tm-30) REVERT: G 146 SER cc_start: 0.8094 (m) cc_final: 0.7711 (p) REVERT: H 2 PHE cc_start: 0.8203 (m-80) cc_final: 0.6529 (t80) REVERT: H 28 LEU cc_start: 0.9027 (mt) cc_final: 0.8748 (mp) REVERT: H 35 GLN cc_start: 0.8349 (tt0) cc_final: 0.7836 (mt0) REVERT: H 39 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7426 (t) REVERT: H 115 GLN cc_start: 0.7794 (tt0) cc_final: 0.7492 (tt0) REVERT: H 140 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8326 (mt) REVERT: I 30 GLN cc_start: 0.8376 (mm110) cc_final: 0.8112 (tm-30) REVERT: I 36 CYS cc_start: 0.9097 (t) cc_final: 0.8804 (t) REVERT: I 154 GLU cc_start: 0.8757 (pt0) cc_final: 0.8302 (tt0) REVERT: J 14 ASP cc_start: 0.7607 (t0) cc_final: 0.7335 (t0) REVERT: J 37 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8491 (tttt) REVERT: J 45 ILE cc_start: 0.8908 (mt) cc_final: 0.8433 (tt) REVERT: J 76 ASP cc_start: 0.8887 (p0) cc_final: 0.8390 (p0) REVERT: J 112 ILE cc_start: 0.8791 (mm) cc_final: 0.8507 (mt) REVERT: J 128 GLU cc_start: 0.8138 (pm20) cc_final: 0.7322 (pm20) REVERT: J 139 GLU cc_start: 0.8704 (tp30) cc_final: 0.8232 (mm-30) REVERT: J 145 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: K 24 GLU cc_start: 0.7118 (tp30) cc_final: 0.6893 (tp30) REVERT: K 31 ASN cc_start: 0.8470 (p0) cc_final: 0.7985 (t0) REVERT: K 79 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: K 95 GLN cc_start: 0.7997 (tp40) cc_final: 0.7540 (tp-100) REVERT: K 121 LYS cc_start: 0.8112 (pttp) cc_final: 0.7806 (ptpp) REVERT: K 125 LYS cc_start: 0.8593 (tptm) cc_final: 0.8286 (tptm) REVERT: K 127 ILE cc_start: 0.8352 (mp) cc_final: 0.8101 (mm) REVERT: L 28 LEU cc_start: 0.8863 (mm) cc_final: 0.8583 (mp) REVERT: L 114 ARG cc_start: 0.8670 (mtm110) cc_final: 0.8362 (mtm110) REVERT: L 141 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: M 2 PHE cc_start: 0.8568 (m-10) cc_final: 0.8255 (m-10) REVERT: M 17 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7029 (mpt180) REVERT: M 103 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8602 (mtmm) REVERT: M 109 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8394 (mmmt) REVERT: M 146 SER cc_start: 0.8634 (m) cc_final: 0.8340 (p) REVERT: N 4 ASP cc_start: 0.7667 (p0) cc_final: 0.7139 (m-30) REVERT: N 5 ASP cc_start: 0.8313 (t0) cc_final: 0.7285 (t0) REVERT: N 80 ASP cc_start: 0.8577 (p0) cc_final: 0.8238 (p0) REVERT: N 91 ILE cc_start: 0.9441 (mt) cc_final: 0.9098 (mm) REVERT: N 98 GLU cc_start: 0.8799 (tp30) cc_final: 0.8595 (tp30) REVERT: N 103 LYS cc_start: 0.8646 (tppt) cc_final: 0.8410 (tppt) REVERT: N 139 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7623 (tp30) REVERT: N 160 ASP cc_start: 0.8340 (m-30) cc_final: 0.7844 (m-30) REVERT: O 4 ASP cc_start: 0.8451 (m-30) cc_final: 0.8052 (p0) REVERT: O 8 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7790 (ptm160) REVERT: O 11 GLU cc_start: 0.8634 (tp30) cc_final: 0.8311 (tp30) REVERT: O 14 ASP cc_start: 0.7818 (t0) cc_final: 0.7414 (t70) REVERT: O 15 PHE cc_start: 0.7734 (m-10) cc_final: 0.7366 (m-10) REVERT: O 54 MET cc_start: 0.6698 (tpt) cc_final: 0.6188 (mmt) REVERT: O 83 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8196 (tm-30) REVERT: O 98 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5895 (mm-30) REVERT: O 119 ASP cc_start: 0.8382 (t0) cc_final: 0.7888 (t70) REVERT: O 160 ASP cc_start: 0.8255 (m-30) cc_final: 0.7844 (m-30) REVERT: P 8 ARG cc_start: 0.8537 (ptp-110) cc_final: 0.8117 (ptm160) REVERT: P 70 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7610 (t) REVERT: Q 1 MET cc_start: 0.8429 (mmt) cc_final: 0.8079 (mmm) REVERT: Q 31 ASN cc_start: 0.7994 (p0) cc_final: 0.7605 (t0) REVERT: Q 34 PHE cc_start: 0.8859 (m-80) cc_final: 0.8317 (m-10) REVERT: Q 37 LYS cc_start: 0.8486 (tttp) cc_final: 0.8030 (tmmt) REVERT: Q 39 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8011 (t) REVERT: Q 77 GLU cc_start: 0.8609 (mp0) cc_final: 0.8241 (mp0) REVERT: Q 112 ILE cc_start: 0.9175 (mt) cc_final: 0.8820 (tt) REVERT: Q 154 GLU cc_start: 0.8117 (tt0) cc_final: 0.7729 (tt0) outliers start: 220 outliers final: 181 residues processed: 1110 average time/residue: 0.3574 time to fit residues: 608.6066 Evaluate side-chains 1088 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 893 time to evaluate : 2.696 ------------------------------------------------------------------------------- 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 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 23 VAL 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 128 GLU Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 49 ILE 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 77 GLU Chi-restraints excluded: chain C residue 79 HIS 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 6 VAL 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 B residue 150 ILE 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 112 ILE 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 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 113 VAL Chi-restraints excluded: chain F residue 19 ASN 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 152 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 28 LEU 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 90 SER 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 20 LEU 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 142 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 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 73 VAL Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 145 ASP 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 99 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 112 ILE 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 123 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 L residue 141 GLN Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 17 ARG 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 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 85 PHE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 152 THR 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 136 ASN 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 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 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 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 132 LEU Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 157 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 236 optimal weight: 8.9990 chunk 94 optimal weight: 0.0570 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 177 optimal weight: 30.0000 chunk 69 optimal weight: 0.1980 chunk 191 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 overall best weight: 3.8504 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086485 restraints weight = 49596.798| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.10 r_work: 0.3062 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 1.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23994 Z= 0.149 Angle : 0.659 10.395 32562 Z= 0.345 Chirality : 0.048 0.179 3510 Planarity : 0.004 0.034 4284 Dihedral : 6.715 77.666 3132 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.27 % Allowed : 25.39 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 2898 helix: -1.87 (0.24), residues: 360 sheet: -0.04 (0.20), residues: 756 loop : -1.47 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 88 HIS 0.002 0.001 HIS Q 79 PHE 0.016 0.001 PHE F 53 TYR 0.025 0.002 TYR G 27 ARG 0.006 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 648) hydrogen bonds : angle 5.85486 ( 1782) covalent geometry : bond 0.00352 (23994) covalent geometry : angle 0.65919 (32562) *********************** 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 1156 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 952 time to evaluate : 3.239 Fit side-chains REVERT: A 24 GLU cc_start: 0.7980 (pt0) cc_final: 0.7530 (pt0) REVERT: A 112 ILE cc_start: 0.8704 (mt) cc_final: 0.8477 (mm) REVERT: A 119 ASP cc_start: 0.8545 (t0) cc_final: 0.8292 (t70) REVERT: A 126 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 128 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 161 TYR cc_start: 0.8618 (p90) cc_final: 0.8364 (p90) REVERT: R 2 PHE cc_start: 0.8271 (m-80) cc_final: 0.7950 (m-10) REVERT: R 8 ARG cc_start: 0.8704 (ptm160) cc_final: 0.8323 (ptm160) REVERT: R 23 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (m) REVERT: R 24 GLU cc_start: 0.8039 (pt0) cc_final: 0.7534 (pt0) REVERT: R 34 PHE cc_start: 0.8914 (m-10) cc_final: 0.7941 (m-10) REVERT: R 39 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7699 (t) REVERT: R 114 ARG cc_start: 0.8604 (ptp90) cc_final: 0.7883 (ptp90) REVERT: R 116 TYR cc_start: 0.8609 (m-10) cc_final: 0.7778 (m-10) REVERT: R 126 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7462 (tm-30) REVERT: R 128 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: R 130 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8715 (mmtp) REVERT: C 97 ASN cc_start: 0.8383 (t0) cc_final: 0.7768 (t0) REVERT: C 103 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8537 (mtpt) REVERT: C 112 ILE cc_start: 0.9014 (mt) cc_final: 0.8575 (tt) REVERT: C 126 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7431 (tm-30) REVERT: C 160 ASP cc_start: 0.7621 (m-30) cc_final: 0.7380 (m-30) REVERT: B 24 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 83 GLN cc_start: 0.8771 (tp40) cc_final: 0.7980 (tp-100) REVERT: B 112 ILE cc_start: 0.9092 (mt) cc_final: 0.8720 (tt) REVERT: B 121 LYS cc_start: 0.8680 (mttp) cc_final: 0.8415 (mptt) REVERT: B 141 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: D 31 ASN cc_start: 0.8435 (p0) cc_final: 0.8116 (t0) REVERT: D 97 ASN cc_start: 0.7894 (t0) cc_final: 0.7537 (t0) REVERT: D 112 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7970 (tt) REVERT: D 136 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7804 (p0) REVERT: D 145 ASP cc_start: 0.8636 (t0) cc_final: 0.8346 (m-30) REVERT: E 2 PHE cc_start: 0.8427 (m-80) cc_final: 0.5956 (t80) REVERT: E 4 ASP cc_start: 0.8201 (m-30) cc_final: 0.7938 (p0) REVERT: E 28 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8319 (mt) REVERT: E 30 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7779 (tp40) REVERT: E 83 GLN cc_start: 0.8844 (tp40) cc_final: 0.8429 (tm-30) REVERT: E 90 SER cc_start: 0.9057 (t) cc_final: 0.8711 (p) REVERT: E 142 LEU cc_start: 0.8410 (pt) cc_final: 0.8025 (pt) REVERT: E 154 GLU cc_start: 0.8235 (tt0) cc_final: 0.7980 (tt0) REVERT: E 161 TYR cc_start: 0.8942 (p90) cc_final: 0.8495 (p90) REVERT: F 1 MET cc_start: 0.8339 (tpp) cc_final: 0.8100 (tpp) REVERT: F 2 PHE cc_start: 0.7973 (m-80) cc_final: 0.7562 (m-80) REVERT: F 24 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7598 (tm-30) REVERT: F 36 CYS cc_start: 0.8492 (t) cc_final: 0.8020 (t) REVERT: F 47 GLU cc_start: 0.4779 (pt0) cc_final: 0.4447 (pt0) REVERT: F 128 GLU cc_start: 0.8215 (pm20) cc_final: 0.7957 (pm20) REVERT: F 135 THR cc_start: 0.8708 (m) cc_final: 0.8487 (p) REVERT: F 154 GLU cc_start: 0.8471 (pt0) cc_final: 0.8130 (tt0) REVERT: G 2 PHE cc_start: 0.8556 (m-80) cc_final: 0.7876 (m-80) REVERT: G 37 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8080 (tttp) REVERT: G 54 MET cc_start: 0.7684 (mmm) cc_final: 0.7390 (tpp) REVERT: G 112 ILE cc_start: 0.8710 (mt) cc_final: 0.8244 (tt) REVERT: G 139 GLU cc_start: 0.7948 (mm-30) cc_final: 0.6938 (tm-30) REVERT: G 146 SER cc_start: 0.8041 (m) cc_final: 0.7660 (p) REVERT: H 2 PHE cc_start: 0.8216 (m-80) cc_final: 0.6503 (t80) REVERT: H 4 ASP cc_start: 0.8514 (m-30) cc_final: 0.8265 (m-30) REVERT: H 28 LEU cc_start: 0.9016 (mt) cc_final: 0.8805 (mp) REVERT: H 30 GLN cc_start: 0.8304 (pp30) cc_final: 0.8076 (pp30) REVERT: H 35 GLN cc_start: 0.8528 (tt0) cc_final: 0.8049 (mt0) REVERT: H 54 MET cc_start: 0.8264 (mmm) cc_final: 0.7755 (tpp) REVERT: H 115 GLN cc_start: 0.7763 (tt0) cc_final: 0.7482 (tt0) REVERT: H 130 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8345 (mmmm) REVERT: H 140 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8403 (mt) REVERT: I 14 ASP cc_start: 0.7327 (t0) cc_final: 0.7102 (t70) REVERT: I 36 CYS cc_start: 0.9164 (t) cc_final: 0.8856 (t) REVERT: I 130 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8573 (mmmm) REVERT: I 154 GLU cc_start: 0.8674 (pt0) cc_final: 0.8228 (tt0) REVERT: I 163 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8027 (mm-30) REVERT: J 7 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8045 (p) REVERT: J 24 GLU cc_start: 0.7223 (pt0) cc_final: 0.6927 (pt0) REVERT: J 45 ILE cc_start: 0.8873 (mt) cc_final: 0.8422 (tt) REVERT: J 57 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8526 (mmtp) REVERT: J 128 GLU cc_start: 0.7845 (pm20) cc_final: 0.7584 (pm20) REVERT: J 139 GLU cc_start: 0.8698 (tp30) cc_final: 0.7653 (pt0) REVERT: J 145 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: K 5 ASP cc_start: 0.7126 (t70) cc_final: 0.6750 (t0) REVERT: K 30 GLN cc_start: 0.8504 (mm110) cc_final: 0.8096 (pp30) REVERT: K 31 ASN cc_start: 0.8345 (p0) cc_final: 0.7763 (t0) REVERT: K 77 GLU cc_start: 0.7866 (pm20) cc_final: 0.7393 (mp0) REVERT: K 79 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.6939 (t-90) REVERT: K 112 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8435 (tt) REVERT: K 121 LYS cc_start: 0.8171 (pttp) cc_final: 0.7895 (ptpp) REVERT: K 149 GLU cc_start: 0.8488 (tp30) cc_final: 0.8252 (tp30) REVERT: L 28 LEU cc_start: 0.8939 (mm) cc_final: 0.8708 (mt) REVERT: L 30 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8137 (pp30) REVERT: L 141 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: L 143 ASP cc_start: 0.7704 (p0) cc_final: 0.7295 (p0) REVERT: L 145 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8055 (p0) REVERT: M 4 ASP cc_start: 0.8482 (m-30) cc_final: 0.7922 (p0) REVERT: M 15 PHE cc_start: 0.7688 (m-80) cc_final: 0.7302 (m-80) REVERT: M 17 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7117 (mpt180) REVERT: M 70 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8015 (t) REVERT: M 103 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8553 (mtmm) REVERT: M 109 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8475 (mmmt) REVERT: M 116 TYR cc_start: 0.8479 (m-10) cc_final: 0.8227 (m-80) REVERT: M 146 SER cc_start: 0.8648 (m) cc_final: 0.8137 (p) REVERT: N 4 ASP cc_start: 0.7543 (p0) cc_final: 0.7093 (m-30) REVERT: N 5 ASP cc_start: 0.8423 (t0) cc_final: 0.7328 (t0) REVERT: N 34 PHE cc_start: 0.8322 (m-80) cc_final: 0.8069 (m-80) REVERT: N 76 ASP cc_start: 0.7870 (p0) cc_final: 0.7492 (p0) REVERT: N 80 ASP cc_start: 0.8609 (p0) cc_final: 0.8256 (p0) REVERT: N 91 ILE cc_start: 0.9427 (mt) cc_final: 0.9080 (mm) REVERT: N 99 ILE cc_start: 0.8252 (tt) cc_final: 0.7878 (tt) REVERT: N 103 LYS cc_start: 0.8606 (tppt) cc_final: 0.8374 (tppt) REVERT: N 139 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7645 (tp30) REVERT: N 145 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8062 (p0) REVERT: N 160 ASP cc_start: 0.8312 (m-30) cc_final: 0.7858 (m-30) REVERT: O 2 PHE cc_start: 0.8328 (m-80) cc_final: 0.8082 (m-10) REVERT: O 4 ASP cc_start: 0.8400 (m-30) cc_final: 0.8024 (p0) REVERT: O 8 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7747 (ptm160) REVERT: O 11 GLU cc_start: 0.8587 (tp30) cc_final: 0.8253 (tp30) REVERT: O 14 ASP cc_start: 0.7729 (t0) cc_final: 0.7356 (t70) REVERT: O 15 PHE cc_start: 0.7798 (m-10) cc_final: 0.7464 (m-10) REVERT: O 54 MET cc_start: 0.6755 (tpt) cc_final: 0.6223 (mmt) REVERT: O 83 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8172 (tm-30) REVERT: O 98 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5910 (mm-30) REVERT: O 119 ASP cc_start: 0.8394 (t0) cc_final: 0.7960 (t70) REVERT: O 160 ASP cc_start: 0.8264 (m-30) cc_final: 0.7881 (m-30) REVERT: P 8 ARG cc_start: 0.8545 (ptp-110) cc_final: 0.8123 (ptm160) REVERT: P 21 PHE cc_start: 0.8901 (p90) cc_final: 0.8646 (p90) REVERT: P 63 ASP cc_start: 0.7192 (m-30) cc_final: 0.6954 (m-30) REVERT: P 70 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7628 (t) REVERT: P 112 ILE cc_start: 0.9079 (mt) cc_final: 0.8621 (tt) REVERT: P 119 ASP cc_start: 0.8573 (t0) cc_final: 0.8190 (t0) REVERT: P 160 ASP cc_start: 0.8144 (m-30) cc_final: 0.7908 (m-30) REVERT: Q 1 MET cc_start: 0.8472 (mmt) cc_final: 0.8136 (mmm) REVERT: Q 34 PHE cc_start: 0.8883 (m-80) cc_final: 0.8296 (m-10) REVERT: Q 39 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7999 (t) REVERT: Q 112 ILE cc_start: 0.9163 (mt) cc_final: 0.8816 (tt) outliers start: 204 outliers final: 164 residues processed: 1083 average time/residue: 0.3700 time to fit residues: 611.1242 Evaluate side-chains 1074 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 891 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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 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 159 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 23 VAL 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 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 49 ILE 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 77 GLU Chi-restraints excluded: chain C residue 79 HIS 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 6 VAL 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 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 112 ILE 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 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 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 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 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 90 SER 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 20 LEU Chi-restraints excluded: chain H residue 34 PHE Chi-restraints excluded: chain H residue 58 ILE 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 142 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 48 LYS 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 151 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 23 VAL 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 73 VAL Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 145 ASP 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 99 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 112 ILE 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 141 GLN Chi-restraints excluded: chain L residue 145 ASP 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 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 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 145 ASP 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 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 136 ASN Chi-restraints excluded: chain O residue 145 ASP 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 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 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR 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 132 LEU Chi-restraints excluded: chain Q residue 142 LEU 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 76 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 169 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** 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** ** G 79 HIS ** 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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085910 restraints weight = 49922.573| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.16 r_work: 0.3053 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 1.0968 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= 0.167 Angle : 0.686 11.012 32562 Z= 0.358 Chirality : 0.049 0.192 3510 Planarity : 0.004 0.035 4284 Dihedral : 6.748 79.727 3132 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 8.11 % Allowed : 26.40 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 2898 helix: -1.78 (0.24), residues: 360 sheet: -0.12 (0.19), residues: 756 loop : -1.48 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 88 HIS 0.003 0.001 HIS F 79 PHE 0.026 0.001 PHE O 21 TYR 0.023 0.002 TYR G 27 ARG 0.005 0.000 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 648) hydrogen bonds : angle 5.86182 ( 1782) covalent geometry : bond 0.00394 (23994) covalent geometry : angle 0.68570 (32562) *********************** 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 1143 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 943 time to evaluate : 2.713 Fit side-chains REVERT: A 24 GLU cc_start: 0.8012 (pt0) cc_final: 0.7527 (pt0) REVERT: A 112 ILE cc_start: 0.8725 (mt) cc_final: 0.8474 (mm) REVERT: A 126 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 128 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7252 (tm-30) REVERT: R 8 ARG cc_start: 0.8749 (ptm160) cc_final: 0.8350 (ptm160) REVERT: R 23 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8186 (m) REVERT: R 24 GLU cc_start: 0.8104 (pt0) cc_final: 0.7607 (pt0) REVERT: R 34 PHE cc_start: 0.8814 (m-10) cc_final: 0.7961 (m-10) REVERT: R 114 ARG cc_start: 0.8621 (ptp90) cc_final: 0.8036 (ptp90) REVERT: R 128 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: R 130 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8721 (mmtp) REVERT: C 97 ASN cc_start: 0.8369 (t0) cc_final: 0.7746 (t0) REVERT: C 103 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8590 (mtpt) REVERT: C 109 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8851 (mmtp) REVERT: C 112 ILE cc_start: 0.9024 (mt) cc_final: 0.8580 (tt) REVERT: C 126 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 83 GLN cc_start: 0.8754 (tp40) cc_final: 0.7987 (tp-100) REVERT: B 112 ILE cc_start: 0.9067 (mt) cc_final: 0.8669 (tt) REVERT: B 121 LYS cc_start: 0.8703 (mttp) cc_final: 0.8399 (mptt) REVERT: B 141 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: D 14 ASP cc_start: 0.7360 (p0) cc_final: 0.7138 (p0) REVERT: D 30 GLN cc_start: 0.8430 (mm110) cc_final: 0.8033 (pp30) REVERT: D 31 ASN cc_start: 0.8386 (p0) cc_final: 0.8149 (t0) REVERT: D 97 ASN cc_start: 0.7991 (t0) cc_final: 0.7653 (t0) REVERT: D 112 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8051 (tt) REVERT: D 130 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8546 (mmmt) REVERT: D 136 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7778 (p0) REVERT: D 145 ASP cc_start: 0.8693 (t0) cc_final: 0.8427 (m-30) REVERT: E 2 PHE cc_start: 0.8431 (m-80) cc_final: 0.5951 (t80) REVERT: E 4 ASP cc_start: 0.8227 (m-30) cc_final: 0.7958 (p0) REVERT: E 28 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 30 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7858 (tp40) REVERT: E 83 GLN cc_start: 0.8876 (tp40) cc_final: 0.8463 (tm-30) REVERT: E 90 SER cc_start: 0.9050 (t) cc_final: 0.8696 (p) REVERT: E 142 LEU cc_start: 0.8482 (pt) cc_final: 0.8134 (pt) REVERT: E 154 GLU cc_start: 0.8248 (tt0) cc_final: 0.8001 (tt0) REVERT: E 160 ASP cc_start: 0.8010 (m-30) cc_final: 0.7621 (m-30) REVERT: E 161 TYR cc_start: 0.8961 (p90) cc_final: 0.8468 (p90) REVERT: F 1 MET cc_start: 0.8239 (tpp) cc_final: 0.8024 (tpp) REVERT: F 2 PHE cc_start: 0.7941 (m-80) cc_final: 0.7533 (m-80) REVERT: F 24 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 36 CYS cc_start: 0.8683 (t) cc_final: 0.8238 (t) REVERT: F 128 GLU cc_start: 0.8280 (pm20) cc_final: 0.7995 (pm20) REVERT: F 135 THR cc_start: 0.8719 (m) cc_final: 0.8502 (p) REVERT: F 141 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8267 (mm-40) REVERT: F 151 GLN cc_start: 0.7807 (mt0) cc_final: 0.7577 (mt0) REVERT: F 154 GLU cc_start: 0.8489 (pt0) cc_final: 0.8164 (tt0) REVERT: G 2 PHE cc_start: 0.8571 (m-80) cc_final: 0.7801 (m-80) REVERT: G 37 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8451 (tttt) REVERT: G 54 MET cc_start: 0.7681 (mmm) cc_final: 0.7457 (tpp) REVERT: G 112 ILE cc_start: 0.8683 (mt) cc_final: 0.8215 (tt) REVERT: G 139 GLU cc_start: 0.7952 (mm-30) cc_final: 0.6922 (tm-30) REVERT: G 146 SER cc_start: 0.8060 (m) cc_final: 0.7659 (p) REVERT: H 4 ASP cc_start: 0.8573 (m-30) cc_final: 0.8352 (m-30) REVERT: H 30 GLN cc_start: 0.8338 (pp30) cc_final: 0.7860 (pp30) REVERT: H 35 GLN cc_start: 0.8427 (tt0) cc_final: 0.7975 (mt0) REVERT: H 54 MET cc_start: 0.8259 (mmm) cc_final: 0.7719 (tpp) REVERT: H 115 GLN cc_start: 0.7758 (tt0) cc_final: 0.7455 (tt0) REVERT: H 130 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8409 (mmmm) REVERT: H 139 GLU cc_start: 0.8810 (tp30) cc_final: 0.8362 (pt0) REVERT: H 140 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8412 (mt) REVERT: I 36 CYS cc_start: 0.9167 (t) cc_final: 0.8811 (t) REVERT: I 139 GLU cc_start: 0.8462 (tp30) cc_final: 0.7716 (pt0) REVERT: I 154 GLU cc_start: 0.8727 (pt0) cc_final: 0.8237 (tt0) REVERT: I 163 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7996 (mm-30) REVERT: J 1 MET cc_start: 0.8105 (tpt) cc_final: 0.7895 (tpt) REVERT: J 14 ASP cc_start: 0.7543 (t0) cc_final: 0.7261 (t0) REVERT: J 15 PHE cc_start: 0.7928 (m-80) cc_final: 0.7678 (m-80) REVERT: J 30 GLN cc_start: 0.7818 (pp30) cc_final: 0.7290 (tm-30) REVERT: J 45 ILE cc_start: 0.8932 (mt) cc_final: 0.8470 (tt) REVERT: J 57 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8438 (mmtp) REVERT: J 76 ASP cc_start: 0.8725 (p0) cc_final: 0.8332 (p0) REVERT: J 139 GLU cc_start: 0.8695 (tp30) cc_final: 0.7686 (pt0) REVERT: J 145 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: J 149 GLU cc_start: 0.7235 (mp0) cc_final: 0.6861 (mp0) REVERT: K 1 MET cc_start: 0.8344 (tpt) cc_final: 0.7966 (tpp) REVERT: K 5 ASP cc_start: 0.7329 (t70) cc_final: 0.6989 (t0) REVERT: K 30 GLN cc_start: 0.8583 (mm110) cc_final: 0.8129 (pp30) REVERT: K 31 ASN cc_start: 0.8371 (p0) cc_final: 0.7797 (t0) REVERT: K 77 GLU cc_start: 0.7929 (pm20) cc_final: 0.7562 (mp0) REVERT: K 79 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: K 121 LYS cc_start: 0.8256 (pttp) cc_final: 0.8044 (ptpp) REVERT: K 149 GLU cc_start: 0.8438 (tp30) cc_final: 0.8204 (tp30) REVERT: L 1 MET cc_start: 0.8282 (tpp) cc_final: 0.8003 (tpt) REVERT: L 28 LEU cc_start: 0.8977 (mm) cc_final: 0.8740 (mt) REVERT: L 30 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8219 (pp30) REVERT: L 141 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: L 143 ASP cc_start: 0.7637 (p0) cc_final: 0.7264 (p0) REVERT: L 145 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8158 (p0) REVERT: M 4 ASP cc_start: 0.8479 (m-30) cc_final: 0.7915 (p0) REVERT: M 15 PHE cc_start: 0.7714 (m-80) cc_final: 0.7473 (m-10) REVERT: M 17 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7104 (mpt180) REVERT: M 103 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8593 (mtmm) REVERT: M 109 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8465 (mmmt) REVERT: M 146 SER cc_start: 0.8679 (m) cc_final: 0.7960 (p) REVERT: N 4 ASP cc_start: 0.7484 (p0) cc_final: 0.7041 (m-30) REVERT: N 5 ASP cc_start: 0.8478 (t0) cc_final: 0.7326 (t0) REVERT: N 34 PHE cc_start: 0.8306 (m-80) cc_final: 0.8011 (m-80) REVERT: N 45 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8969 (tt) REVERT: N 76 ASP cc_start: 0.7921 (p0) cc_final: 0.7472 (p0) REVERT: N 80 ASP cc_start: 0.8651 (p0) cc_final: 0.8431 (p0) REVERT: N 91 ILE cc_start: 0.9438 (mt) cc_final: 0.9089 (mm) REVERT: N 103 LYS cc_start: 0.8647 (tppt) cc_final: 0.8406 (tppt) REVERT: N 139 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7599 (tp30) REVERT: N 160 ASP cc_start: 0.8206 (m-30) cc_final: 0.7800 (m-30) REVERT: O 1 MET cc_start: 0.8758 (tpp) cc_final: 0.8538 (mmm) REVERT: O 2 PHE cc_start: 0.8423 (m-80) cc_final: 0.8154 (m-10) REVERT: O 4 ASP cc_start: 0.8397 (m-30) cc_final: 0.8036 (p0) REVERT: O 8 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7734 (ptm160) REVERT: O 11 GLU cc_start: 0.8628 (tp30) cc_final: 0.8250 (tp30) REVERT: O 14 ASP cc_start: 0.7772 (t0) cc_final: 0.7383 (t70) REVERT: O 15 PHE cc_start: 0.7770 (m-10) cc_final: 0.7432 (m-10) REVERT: O 54 MET cc_start: 0.6667 (tpt) cc_final: 0.6143 (mmt) REVERT: O 83 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8158 (tm-30) REVERT: O 119 ASP cc_start: 0.8422 (t0) cc_final: 0.7954 (t70) REVERT: O 160 ASP cc_start: 0.8271 (m-30) cc_final: 0.7801 (m-30) REVERT: P 8 ARG cc_start: 0.8525 (ptp-110) cc_final: 0.8156 (ptm160) REVERT: P 21 PHE cc_start: 0.8894 (p90) cc_final: 0.8609 (p90) REVERT: P 70 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7611 (t) REVERT: P 76 ASP cc_start: 0.8302 (p0) cc_final: 0.7753 (p0) REVERT: P 112 ILE cc_start: 0.9075 (mt) cc_final: 0.8637 (tt) REVERT: P 119 ASP cc_start: 0.8629 (t0) cc_final: 0.8333 (t0) REVERT: Q 1 MET cc_start: 0.8412 (mmt) cc_final: 0.8103 (mmm) REVERT: Q 24 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7544 (tp30) REVERT: Q 34 PHE cc_start: 0.8877 (m-80) cc_final: 0.8266 (m-10) REVERT: Q 39 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7990 (t) REVERT: Q 77 GLU cc_start: 0.8603 (mp0) cc_final: 0.8242 (mp0) REVERT: Q 112 ILE cc_start: 0.9153 (mt) cc_final: 0.8822 (tt) outliers start: 200 outliers final: 173 residues processed: 1071 average time/residue: 0.3602 time to fit residues: 590.5477 Evaluate side-chains 1098 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 910 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 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 159 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 23 VAL 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 72 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 49 ILE 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 77 GLU Chi-restraints excluded: chain C residue 79 HIS 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 6 VAL 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 B residue 150 ILE 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 112 ILE 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 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 F residue 19 ASN 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 150 ILE 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 90 SER 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 45 ILE Chi-restraints excluded: chain H residue 58 ILE 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 142 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 48 LYS 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 J residue 23 VAL 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 73 VAL Chi-restraints excluded: chain J residue 79 HIS Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 145 ASP 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 99 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 113 VAL 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 L residue 141 GLN Chi-restraints excluded: chain L residue 145 ASP 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 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 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 O residue 19 ASN Chi-restraints excluded: chain O residue 23 VAL 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 136 ASN 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 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 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 45 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR 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 132 LEU Chi-restraints excluded: chain Q residue 142 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084956 restraints weight = 50257.153| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.16 r_work: 0.3038 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 1.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23994 Z= 0.197 Angle : 0.717 10.368 32562 Z= 0.375 Chirality : 0.050 0.242 3510 Planarity : 0.004 0.035 4284 Dihedral : 6.891 79.343 3132 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 7.99 % Allowed : 27.25 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 2898 helix: -1.72 (0.24), residues: 360 sheet: -0.21 (0.20), residues: 720 loop : -1.55 (0.12), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 88 HIS 0.003 0.001 HIS J 79 PHE 0.022 0.002 PHE O 21 TYR 0.022 0.002 TYR B 161 ARG 0.006 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 648) hydrogen bonds : angle 5.94293 ( 1782) covalent geometry : bond 0.00466 (23994) covalent geometry : angle 0.71674 (32562) ********************** 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 1115 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 918 time to evaluate : 3.211 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7959 (pt0) cc_final: 0.7489 (pt0) REVERT: A 112 ILE cc_start: 0.8732 (mt) cc_final: 0.8488 (mm) REVERT: A 119 ASP cc_start: 0.8554 (t0) cc_final: 0.8294 (t70) REVERT: A 126 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7282 (tm-30) REVERT: R 24 GLU cc_start: 0.8006 (pt0) cc_final: 0.7617 (pt0) REVERT: R 34 PHE cc_start: 0.8849 (m-10) cc_final: 0.7964 (m-10) REVERT: R 114 ARG cc_start: 0.8610 (ptp90) cc_final: 0.8060 (ptp90) REVERT: R 128 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: R 130 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8716 (mmtp) REVERT: C 103 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8590 (mtmt) REVERT: C 109 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8849 (mmtp) REVERT: C 112 ILE cc_start: 0.9025 (mt) cc_final: 0.8587 (tt) REVERT: C 126 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 24 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 74 MET cc_start: 0.8523 (mtm) cc_final: 0.8051 (mtm) REVERT: B 83 GLN cc_start: 0.8801 (tp40) cc_final: 0.8015 (tp-100) REVERT: B 112 ILE cc_start: 0.9092 (mt) cc_final: 0.8683 (tt) REVERT: B 141 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: D 20 LEU cc_start: 0.8802 (mt) cc_final: 0.8556 (mt) REVERT: D 30 GLN cc_start: 0.8456 (mm110) cc_final: 0.8049 (pp30) REVERT: D 83 GLN cc_start: 0.9085 (tp40) cc_final: 0.8093 (tp-100) REVERT: D 97 ASN cc_start: 0.7998 (t0) cc_final: 0.7679 (t0) REVERT: D 112 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8151 (tt) REVERT: D 136 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7843 (p0) REVERT: D 145 ASP cc_start: 0.8770 (t0) cc_final: 0.8560 (m-30) REVERT: E 2 PHE cc_start: 0.8437 (m-80) cc_final: 0.6147 (t80) REVERT: E 4 ASP cc_start: 0.8227 (m-30) cc_final: 0.7968 (p0) REVERT: E 28 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8179 (mt) REVERT: E 30 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7803 (tp40) REVERT: E 76 ASP cc_start: 0.8625 (p0) cc_final: 0.8424 (p0) REVERT: E 83 GLN cc_start: 0.8897 (tp40) cc_final: 0.8509 (tm-30) REVERT: E 90 SER cc_start: 0.9071 (t) cc_final: 0.8702 (p) REVERT: E 142 LEU cc_start: 0.8510 (pt) cc_final: 0.8164 (pt) REVERT: E 154 GLU cc_start: 0.8264 (tt0) cc_final: 0.8025 (tt0) REVERT: E 161 TYR cc_start: 0.8944 (p90) cc_final: 0.8394 (p90) REVERT: F 1 MET cc_start: 0.8283 (tpp) cc_final: 0.8059 (tpp) REVERT: F 2 PHE cc_start: 0.7947 (m-80) cc_final: 0.7528 (m-80) REVERT: F 24 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7577 (tm-30) REVERT: F 36 CYS cc_start: 0.8698 (t) cc_final: 0.8251 (t) REVERT: F 128 GLU cc_start: 0.8300 (pm20) cc_final: 0.8018 (pm20) REVERT: F 135 THR cc_start: 0.8730 (m) cc_final: 0.8494 (p) REVERT: F 141 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8284 (mm-40) REVERT: F 148 ASN cc_start: 0.6877 (m110) cc_final: 0.6650 (m-40) REVERT: F 154 GLU cc_start: 0.8496 (pt0) cc_final: 0.8166 (tt0) REVERT: G 2 PHE cc_start: 0.8559 (m-80) cc_final: 0.8147 (m-10) REVERT: G 37 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8518 (tttt) REVERT: G 54 MET cc_start: 0.7726 (mmm) cc_final: 0.7517 (tpp) REVERT: G 112 ILE cc_start: 0.8653 (mt) cc_final: 0.8247 (tt) REVERT: G 139 GLU cc_start: 0.7871 (mm-30) cc_final: 0.6848 (tm-30) REVERT: G 146 SER cc_start: 0.8038 (m) cc_final: 0.7637 (p) REVERT: H 30 GLN cc_start: 0.8296 (pp30) cc_final: 0.7839 (pp30) REVERT: H 31 ASN cc_start: 0.8752 (p0) cc_final: 0.8343 (t0) REVERT: H 35 GLN cc_start: 0.8475 (tt0) cc_final: 0.7959 (mt0) REVERT: H 54 MET cc_start: 0.8302 (mmm) cc_final: 0.7749 (tpp) REVERT: H 115 GLN cc_start: 0.7747 (tt0) cc_final: 0.7442 (tt0) REVERT: H 130 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8406 (mmmm) REVERT: H 139 GLU cc_start: 0.8782 (tp30) cc_final: 0.8538 (pt0) REVERT: H 140 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8403 (mt) REVERT: I 36 CYS cc_start: 0.9293 (t) cc_final: 0.8846 (t) REVERT: I 139 GLU cc_start: 0.8423 (tp30) cc_final: 0.7693 (pt0) REVERT: I 154 GLU cc_start: 0.8736 (pt0) cc_final: 0.8246 (tt0) REVERT: J 1 MET cc_start: 0.8080 (tpt) cc_final: 0.7734 (tpt) REVERT: J 30 GLN cc_start: 0.7938 (pp30) cc_final: 0.7409 (tm-30) REVERT: J 45 ILE cc_start: 0.8908 (mt) cc_final: 0.8487 (tt) REVERT: J 57 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8398 (mmtp) REVERT: J 76 ASP cc_start: 0.8733 (p0) cc_final: 0.8389 (p0) REVERT: J 103 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8423 (mtmm) REVERT: J 126 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6292 (tm-30) REVERT: J 128 GLU cc_start: 0.7852 (pm20) cc_final: 0.7250 (pm20) REVERT: J 139 GLU cc_start: 0.8683 (tp30) cc_final: 0.7684 (pt0) REVERT: J 145 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: J 149 GLU cc_start: 0.7262 (mp0) cc_final: 0.6884 (mp0) REVERT: K 1 MET cc_start: 0.8442 (tpt) cc_final: 0.8110 (tpp) REVERT: K 30 GLN cc_start: 0.8565 (mm110) cc_final: 0.8221 (pp30) REVERT: K 31 ASN cc_start: 0.8390 (p0) cc_final: 0.7846 (t0) REVERT: K 77 GLU cc_start: 0.7995 (pm20) cc_final: 0.7524 (mp0) REVERT: K 79 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7109 (t-90) REVERT: K 112 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8406 (tt) REVERT: K 149 GLU cc_start: 0.8441 (tp30) cc_final: 0.8216 (tp30) REVERT: L 28 LEU cc_start: 0.8997 (mm) cc_final: 0.8708 (mp) REVERT: L 30 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8251 (pp30) REVERT: L 141 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: M 4 ASP cc_start: 0.8475 (m-30) cc_final: 0.8014 (p0) REVERT: M 17 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7094 (mpt180) REVERT: M 47 GLU cc_start: 0.7989 (tp30) cc_final: 0.7736 (tp30) REVERT: M 103 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8605 (mtmm) REVERT: M 109 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8470 (mmmt) REVERT: M 146 SER cc_start: 0.8562 (m) cc_final: 0.7772 (p) REVERT: N 4 ASP cc_start: 0.7455 (p0) cc_final: 0.7028 (m-30) REVERT: N 5 ASP cc_start: 0.8481 (t0) cc_final: 0.7305 (t0) REVERT: N 45 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.9002 (tt) REVERT: N 76 ASP cc_start: 0.7957 (p0) cc_final: 0.7525 (p0) REVERT: N 91 ILE cc_start: 0.9453 (mt) cc_final: 0.9121 (mm) REVERT: N 103 LYS cc_start: 0.8667 (tppt) cc_final: 0.8390 (tppt) REVERT: N 112 ILE cc_start: 0.8924 (mt) cc_final: 0.8376 (tt) REVERT: N 139 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8210 (tm-30) REVERT: N 160 ASP cc_start: 0.8223 (m-30) cc_final: 0.7724 (m-30) REVERT: N 161 TYR cc_start: 0.8990 (p90) cc_final: 0.8489 (p90) REVERT: O 1 MET cc_start: 0.8724 (tpp) cc_final: 0.8517 (mmm) REVERT: O 2 PHE cc_start: 0.8436 (m-80) cc_final: 0.8174 (m-10) REVERT: O 4 ASP cc_start: 0.8437 (m-30) cc_final: 0.8071 (p0) REVERT: O 8 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7750 (ptm160) REVERT: O 11 GLU cc_start: 0.8639 (tp30) cc_final: 0.8239 (tp30) REVERT: O 14 ASP cc_start: 0.7834 (t0) cc_final: 0.7398 (t70) REVERT: O 15 PHE cc_start: 0.7826 (m-10) cc_final: 0.7421 (m-80) REVERT: O 54 MET cc_start: 0.6696 (tpt) cc_final: 0.6155 (mmt) REVERT: O 83 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8158 (tm-30) REVERT: O 119 ASP cc_start: 0.8394 (t0) cc_final: 0.7895 (t70) REVERT: O 160 ASP cc_start: 0.8293 (m-30) cc_final: 0.7871 (m-30) REVERT: P 8 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8102 (ptm160) REVERT: P 21 PHE cc_start: 0.8863 (p90) cc_final: 0.8602 (p90) REVERT: P 54 MET cc_start: 0.7469 (tpp) cc_final: 0.7223 (tpp) REVERT: P 63 ASP cc_start: 0.7416 (m-30) cc_final: 0.7148 (m-30) REVERT: P 70 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7659 (t) REVERT: P 76 ASP cc_start: 0.8323 (p0) cc_final: 0.7754 (p0) REVERT: P 119 ASP cc_start: 0.8575 (t0) cc_final: 0.8351 (t0) REVERT: Q 1 MET cc_start: 0.8522 (mmt) cc_final: 0.8210 (mmm) REVERT: Q 24 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7718 (tp30) REVERT: Q 34 PHE cc_start: 0.8858 (m-80) cc_final: 0.8247 (m-10) REVERT: Q 37 LYS cc_start: 0.8709 (tptp) cc_final: 0.8478 (tptt) REVERT: Q 39 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8015 (t) REVERT: Q 77 GLU cc_start: 0.8530 (mp0) cc_final: 0.8255 (mp0) REVERT: Q 112 ILE cc_start: 0.9150 (mt) cc_final: 0.8832 (tt) outliers start: 197 outliers final: 172 residues processed: 1048 average time/residue: 0.3939 time to fit residues: 638.9073 Evaluate side-chains 1059 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 873 time to evaluate : 4.173 ------------------------------------------------------------------------------- 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 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 55 ASN 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 128 GLU Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 49 ILE 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 77 GLU Chi-restraints excluded: chain C residue 79 HIS 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 6 VAL 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 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 112 ILE 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 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 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 150 ILE 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 90 SER 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 45 ILE Chi-restraints excluded: chain H residue 58 ILE 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 142 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 48 LYS 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 J residue 23 VAL 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 79 HIS Chi-restraints excluded: chain J residue 99 ILE Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 145 ASP 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 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 99 ILE Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 112 ILE 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 L residue 141 GLN Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 30 GLN 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 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 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 O residue 19 ASN Chi-restraints excluded: chain O residue 23 VAL 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 136 ASN 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 142 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 3 VAL 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 79 HIS Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 142 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 166 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 147 ASN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 ASN ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.085277 restraints weight = 50108.533| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.13 r_work: 0.3039 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 1.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23994 Z= 0.193 Angle : 0.717 11.074 32562 Z= 0.374 Chirality : 0.050 0.199 3510 Planarity : 0.004 0.034 4284 Dihedral : 6.932 79.228 3132 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 8.03 % Allowed : 27.13 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 2898 helix: -2.04 (0.21), residues: 450 sheet: -0.26 (0.20), residues: 720 loop : -1.71 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 88 HIS 0.003 0.001 HIS J 79 PHE 0.020 0.002 PHE O 34 TYR 0.022 0.002 TYR B 161 ARG 0.006 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 648) hydrogen bonds : angle 5.93573 ( 1782) covalent geometry : bond 0.00457 (23994) covalent geometry : angle 0.71653 (32562) =============================================================================== Job complete usr+sys time: 12654.65 seconds wall clock time: 220 minutes 9.81 seconds (13209.81 seconds total)