Starting phenix.real_space_refine on Thu Mar 5 22:08:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nht_9373/03_2026/6nht_9373.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nht_9373/03_2026/6nht_9373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nht_9373/03_2026/6nht_9373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nht_9373/03_2026/6nht_9373.map" model { file = "/net/cci-nas-00/data/ceres_data/6nht_9373/03_2026/6nht_9373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nht_9373/03_2026/6nht_9373.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.205 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 108 5.16 5 C 16476 2.51 5 N 4524 2.21 5 O 5028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26136 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Restraints were copied for chains: B, C, D, I, J, K, L, Q, R, S, T, F, G, H, M, N, O, P, U, V, W, X Time building chain proxies: 2.34, per 1000 atoms: 0.09 Number of scatterers: 26136 At special positions: 0 Unit cell: (153.7, 152.64, 147.34, 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 108 16.00 O 5028 8.00 N 4524 7.00 C 16476 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 58.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 removed outlier: 3.540A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 72 removed outlier: 3.759A pdb=" N GLY A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'B' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 72 removed outlier: 3.759A pdb=" N GLY B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'C' and resid 24 through 45 removed outlier: 3.540A pdb=" N GLU C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 137 removed outlier: 3.511A pdb=" N LYS C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'D' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 72 removed outlier: 3.759A pdb=" N GLY D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 137 removed outlier: 3.509A pdb=" N LYS D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'E' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU E 22 " --> pdb=" O PRO E 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU F 22 " --> pdb=" O PRO F 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU G 22 " --> pdb=" O PRO G 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU H 22 " --> pdb=" O PRO H 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU I 58 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER I 72 " --> pdb=" O GLY I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET I 97 " --> pdb=" O ARG I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS I 114 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 150 removed outlier: 3.512A pdb=" N ALA I 148 " --> pdb=" O ALA I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 169 " --> pdb=" O GLY I 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 170 " --> pdb=" O LYS I 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA I 171 " --> pdb=" O LYS I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'J' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU J 29 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER J 39 " --> pdb=" O ASP J 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.761A pdb=" N GLY J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE J 55 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU J 58 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER J 72 " --> pdb=" O GLY J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS J 89 " --> pdb=" O ALA J 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 137 removed outlier: 3.511A pdb=" N LYS J 114 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP J 116 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS J 118 " --> pdb=" O LYS J 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 161 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE J 162 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 169 " --> pdb=" O GLY J 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU J 170 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA J 171 " --> pdb=" O LYS J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'K' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU K 29 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 55 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER K 72 " --> pdb=" O GLY K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS K 114 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA K 148 " --> pdb=" O ALA K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 174 removed outlier: 3.564A pdb=" N LEU K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU K 168 " --> pdb=" O GLN K 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 169 " --> pdb=" O GLY K 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU K 170 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'L' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 39 " --> pdb=" O ASP L 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER L 72 " --> pdb=" O GLY L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS L 89 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET L 97 " --> pdb=" O ARG L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS L 114 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP L 116 " --> pdb=" O SER L 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS L 118 " --> pdb=" O LYS L 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE L 162 " --> pdb=" O ARG L 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU L 168 " --> pdb=" O GLN L 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 169 " --> pdb=" O GLY L 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU L 170 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 171 " --> pdb=" O LYS L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'M' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU M 22 " --> pdb=" O PRO M 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL M 87 " --> pdb=" O SER M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU N 22 " --> pdb=" O PRO N 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU O 22 " --> pdb=" O PRO O 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 31 removed outlier: 3.859A pdb=" N LEU P 22 " --> pdb=" O PRO P 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL P 87 " --> pdb=" O SER P 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 45 removed outlier: 3.542A pdb=" N GLU Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY Q 42 " --> pdb=" O THR Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY Q 54 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 58 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN Q 61 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER Q 72 " --> pdb=" O GLY Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS Q 89 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG Q 93 " --> pdb=" O LYS Q 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP Q 116 " --> pdb=" O SER Q 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR Q 120 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR Q 131 " --> pdb=" O ARG Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA Q 148 " --> pdb=" O ALA Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU Q 155 " --> pdb=" O ASP Q 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Q 162 " --> pdb=" O ARG Q 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU Q 168 " --> pdb=" O GLN Q 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU Q 169 " --> pdb=" O GLY Q 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU Q 170 " --> pdb=" O LYS Q 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Q 171 " --> pdb=" O LYS Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 185 Processing helix chain 'R' and resid 24 through 45 removed outlier: 3.542A pdb=" N GLU R 29 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY R 42 " --> pdb=" O THR R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY R 54 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER R 72 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 98 removed outlier: 4.079A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 137 removed outlier: 3.511A pdb=" N LYS R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS R 118 " --> pdb=" O LYS R 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR R 131 " --> pdb=" O ARG R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA R 148 " --> pdb=" O ALA R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE R 162 " --> pdb=" O ARG R 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 168 " --> pdb=" O GLN R 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA R 171 " --> pdb=" O LYS R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'S' and resid 24 through 45 removed outlier: 3.542A pdb=" N GLU S 29 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY S 42 " --> pdb=" O THR S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 72 removed outlier: 3.761A pdb=" N GLY S 54 " --> pdb=" O GLU S 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE S 55 " --> pdb=" O GLU S 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN S 61 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER S 72 " --> pdb=" O GLY S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS S 89 " --> pdb=" O ALA S 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG S 93 " --> pdb=" O LYS S 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS S 114 " --> pdb=" O LEU S 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP S 116 " --> pdb=" O SER S 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR S 120 " --> pdb=" O ASP S 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR S 131 " --> pdb=" O ARG S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA S 148 " --> pdb=" O ALA S 144 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU S 155 " --> pdb=" O ASP S 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE S 160 " --> pdb=" O LEU S 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU S 161 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE S 162 " --> pdb=" O ARG S 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU S 168 " --> pdb=" O GLN S 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 169 " --> pdb=" O GLY S 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU S 170 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA S 171 " --> pdb=" O LYS S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 185 Processing helix chain 'T' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU T 29 " --> pdb=" O SER T 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY T 42 " --> pdb=" O THR T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.761A pdb=" N GLY T 54 " --> pdb=" O GLU T 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE T 55 " --> pdb=" O GLU T 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN T 61 " --> pdb=" O GLU T 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER T 72 " --> pdb=" O GLY T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 98 removed outlier: 4.079A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET T 97 " --> pdb=" O ARG T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS T 114 " --> pdb=" O LEU T 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS T 118 " --> pdb=" O LYS T 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR T 120 " --> pdb=" O ASP T 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR T 131 " --> pdb=" O ARG T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 150 removed outlier: 3.514A pdb=" N ALA T 148 " --> pdb=" O ALA T 144 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU T 161 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE T 162 " --> pdb=" O ARG T 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 168 " --> pdb=" O GLN T 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU T 169 " --> pdb=" O GLY T 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU T 170 " --> pdb=" O LYS T 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA T 171 " --> pdb=" O LYS T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 185 Processing helix chain 'U' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU U 22 " --> pdb=" O PRO U 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL U 87 " --> pdb=" O SER U 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 31 removed outlier: 3.861A pdb=" N LEU V 22 " --> pdb=" O PRO V 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN V 24 " --> pdb=" O GLU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA V 86 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL V 87 " --> pdb=" O SER V 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 31 removed outlier: 3.859A pdb=" N LEU W 22 " --> pdb=" O PRO W 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN W 24 " --> pdb=" O GLU W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA W 86 " --> pdb=" O ALA W 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 31 removed outlier: 3.861A pdb=" N LEU X 22 " --> pdb=" O PRO X 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN X 24 " --> pdb=" O GLU X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL X 87 " --> pdb=" O SER X 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.426A pdb=" N ALA M 49 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 62 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU E 105 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA E 64 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG E 107 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 66 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET E 109 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 68 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 100 " --> pdb=" O VAL U 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG E 13 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.429A pdb=" N ALA E 49 " --> pdb=" O PHE U 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU U 62 " --> pdb=" O SER U 103 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU U 105 " --> pdb=" O LEU U 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA U 64 " --> pdb=" O GLU U 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG U 107 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU U 66 " --> pdb=" O ARG U 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET U 109 " --> pdb=" O LEU U 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE U 68 " --> pdb=" O MET U 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL U 100 " --> pdb=" O VAL M 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.577A pdb=" N VAL M 100 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 62 " --> pdb=" O SER M 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU M 105 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA M 64 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG M 107 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU M 66 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET M 109 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE M 68 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA U 49 " --> pdb=" O PHE M 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 49 through 52 removed outlier: 4.431A pdb=" N ALA G 49 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 62 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU F 105 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA F 64 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG F 107 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU F 66 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET F 109 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE F 68 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 100 " --> pdb=" O VAL P 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG F 13 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 52 removed outlier: 4.425A pdb=" N ALA F 49 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU P 62 " --> pdb=" O SER P 103 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU P 105 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA P 64 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG P 107 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU P 66 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET P 109 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE P 68 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL P 100 " --> pdb=" O VAL G 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.592A pdb=" N VAL G 100 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU G 62 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU G 105 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA G 64 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG G 107 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU G 66 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET G 109 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE G 68 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA P 49 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG G 13 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 49 through 52 removed outlier: 4.415A pdb=" N ALA V 49 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 62 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU H 105 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA H 64 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG H 107 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU H 66 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET H 109 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE H 68 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 100 " --> pdb=" O VAL W 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG H 13 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.431A pdb=" N ALA H 49 " --> pdb=" O PHE W 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU W 62 " --> pdb=" O SER W 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU W 105 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA W 64 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ARG W 107 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU W 66 " --> pdb=" O ARG W 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET W 109 " --> pdb=" O LEU W 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE W 68 " --> pdb=" O MET W 109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL W 100 " --> pdb=" O VAL V 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 3.597A pdb=" N VAL V 100 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU V 62 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU V 105 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA V 64 " --> pdb=" O GLU V 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG V 107 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU V 66 " --> pdb=" O ARG V 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET V 109 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE V 68 " --> pdb=" O MET V 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA W 49 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG M 13 " --> pdb=" O ALA M 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.394A pdb=" N ALA O 49 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU N 62 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU N 105 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA N 64 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG N 107 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU N 66 " --> pdb=" O ARG N 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET N 109 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE N 68 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 100 " --> pdb=" O VAL X 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG N 13 " --> pdb=" O ALA N 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.434A pdb=" N ALA N 49 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU X 62 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU X 105 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA X 64 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG X 107 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU X 66 " --> pdb=" O ARG X 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET X 109 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE X 68 " --> pdb=" O MET X 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL X 100 " --> pdb=" O VAL O 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.637A pdb=" N VAL O 100 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU O 62 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU O 105 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA O 64 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG O 107 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU O 66 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET O 109 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE O 68 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA X 49 " --> pdb=" O PHE O 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG O 13 " --> pdb=" O ALA O 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG P 13 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 removed outlier: 6.831A pdb=" N ARG U 13 " --> pdb=" O ALA U 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG V 13 " --> pdb=" O ALA V 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG W 13 " --> pdb=" O ALA W 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG X 13 " --> pdb=" O ALA X 93 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.82 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: 8941 1.34 - 1.46: 2966 1.46 - 1.57: 14277 1.57 - 1.69: 12 1.69 - 1.80: 180 Bond restraints: 26376 Sorted by residual: bond pdb=" CB GLU O 48 " pdb=" CG GLU O 48 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.23e+00 bond pdb=" CB GLU W 48 " pdb=" CG GLU W 48 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" CB GLU G 48 " pdb=" CG GLU G 48 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.17e+00 bond pdb=" CB GLU F 48 " pdb=" CG GLU F 48 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.16e+00 bond pdb=" CB GLU X 48 " pdb=" CG GLU X 48 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 26371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34232 1.64 - 3.27: 1050 3.27 - 4.91: 166 4.91 - 6.54: 48 6.54 - 8.18: 24 Bond angle restraints: 35520 Sorted by residual: angle pdb=" CA GLU K 77 " pdb=" CB GLU K 77 " pdb=" CG GLU K 77 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU D 77 " pdb=" CB GLU D 77 " pdb=" CG GLU D 77 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU A 77 " pdb=" CB GLU A 77 " pdb=" CG GLU A 77 " ideal model delta sigma weight residual 114.10 122.26 -8.16 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU C 77 " pdb=" CB GLU C 77 " pdb=" CG GLU C 77 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU Q 77 " pdb=" CB GLU Q 77 " pdb=" CG GLU Q 77 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 ... (remaining 35515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14736 17.88 - 35.77: 1140 35.77 - 53.65: 168 53.65 - 71.54: 48 71.54 - 89.42: 96 Dihedral angle restraints: 16188 sinusoidal: 6408 harmonic: 9780 Sorted by residual: dihedral pdb=" CB GLU X 98 " pdb=" CG GLU X 98 " pdb=" CD GLU X 98 " pdb=" OE1 GLU X 98 " ideal model delta sinusoidal sigma weight residual 0.00 -89.42 89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU M 98 " pdb=" CG GLU M 98 " pdb=" CD GLU M 98 " pdb=" OE1 GLU M 98 " ideal model delta sinusoidal sigma weight residual 0.00 -89.42 89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU O 98 " pdb=" CG GLU O 98 " pdb=" CD GLU O 98 " pdb=" OE1 GLU O 98 " ideal model delta sinusoidal sigma weight residual 0.00 -89.40 89.40 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2298 0.031 - 0.063: 1364 0.063 - 0.094: 353 0.094 - 0.125: 184 0.125 - 0.156: 37 Chirality restraints: 4236 Sorted by residual: chirality pdb=" CB VAL E 57 " pdb=" CA VAL E 57 " pdb=" CG1 VAL E 57 " pdb=" CG2 VAL E 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CB VAL O 57 " pdb=" CA VAL O 57 " pdb=" CG1 VAL O 57 " pdb=" CG2 VAL O 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB VAL V 57 " pdb=" CA VAL V 57 " pdb=" CG1 VAL V 57 " pdb=" CG2 VAL V 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 4233 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU V 48 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" CD GLU V 48 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU V 48 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU V 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU P 48 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" CD GLU P 48 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU P 48 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU P 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU N 48 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" CD GLU N 48 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU N 48 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU N 48 " 0.013 2.00e-02 2.50e+03 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 9189 2.90 - 3.40: 22824 3.40 - 3.90: 40203 3.90 - 4.40: 48940 4.40 - 4.90: 83327 Nonbonded interactions: 204483 Sorted by model distance: nonbonded pdb=" O ILE N 74 " pdb=" OG1 THR N 78 " model vdw 2.394 3.040 nonbonded pdb=" O ILE W 74 " pdb=" OG1 THR W 78 " model vdw 2.394 3.040 nonbonded pdb=" O ILE G 74 " pdb=" OG1 THR G 78 " model vdw 2.394 3.040 nonbonded pdb=" O ILE P 74 " pdb=" OG1 THR P 78 " model vdw 2.395 3.040 nonbonded pdb=" O ILE V 74 " pdb=" OG1 THR V 78 " model vdw 2.395 3.040 ... (remaining 204478 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 2.230 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 19.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.006 0.054 26376 Z= 0.265 Angle : 0.747 8.176 35520 Z= 0.429 Chirality : 0.045 0.156 4236 Planarity : 0.005 0.049 4560 Dihedral : 15.208 89.423 9900 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.45 % Allowed : 4.99 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.86 (0.09), residues: 3384 helix: -5.04 (0.03), residues: 2004 sheet: 0.27 (0.26), residues: 420 loop : -2.46 (0.13), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 43 TYR 0.014 0.002 TYR F 61 PHE 0.006 0.001 PHE W 44 TRP 0.004 0.002 TRP C 86 HIS 0.003 0.001 HIS P 63 Details of bonding type rmsd covalent geometry : bond 0.00632 (26376) covalent geometry : angle 0.74674 (35520) hydrogen bonds : bond 0.32648 ( 1368) hydrogen bonds : angle 10.44201 ( 4032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 704 time to evaluate : 0.776 Fit side-chains REVERT: A 51 GLU cc_start: 0.7791 (tp30) cc_final: 0.7514 (tp30) REVERT: A 75 LYS cc_start: 0.8285 (mttt) cc_final: 0.8025 (mttt) REVERT: C 51 GLU cc_start: 0.7785 (tp30) cc_final: 0.7501 (tp30) REVERT: C 53 LYS cc_start: 0.8965 (tttt) cc_final: 0.8656 (tttt) REVERT: D 65 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8004 (mtpt) REVERT: H 70 ASP cc_start: 0.7936 (p0) cc_final: 0.7670 (p0) REVERT: I 67 MET cc_start: 0.8939 (mtp) cc_final: 0.8683 (mtm) REVERT: J 67 MET cc_start: 0.8998 (mtp) cc_final: 0.8724 (mtp) REVERT: J 158 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7968 (mmt180) REVERT: L 151 ASP cc_start: 0.7493 (m-30) cc_final: 0.7204 (m-30) REVERT: M 37 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7436 (tm-30) REVERT: R 123 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7897 (mmm160) REVERT: S 75 LYS cc_start: 0.8243 (mttt) cc_final: 0.7983 (mttt) REVERT: S 92 LEU cc_start: 0.8815 (mt) cc_final: 0.8602 (mm) REVERT: S 96 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7301 (mt-10) REVERT: S 97 MET cc_start: 0.8427 (mtp) cc_final: 0.8118 (mtp) REVERT: W 15 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7813 (mt-10) REVERT: W 24 GLN cc_start: 0.8053 (mt0) cc_final: 0.7792 (mt0) REVERT: X 37 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7542 (tm-30) outliers start: 12 outliers final: 2 residues processed: 704 average time/residue: 0.9258 time to fit residues: 719.5790 Evaluate side-chains 460 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 458 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 34 GLN M 34 GLN O 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103150 restraints weight = 28827.329| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.30 r_work: 0.3017 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26376 Z= 0.113 Angle : 0.471 6.010 35520 Z= 0.259 Chirality : 0.038 0.118 4236 Planarity : 0.004 0.036 4560 Dihedral : 4.042 18.387 3724 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.53 % Allowed : 15.70 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.11), residues: 3384 helix: -2.77 (0.08), residues: 2016 sheet: 1.08 (0.25), residues: 420 loop : -1.87 (0.14), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 59 TYR 0.014 0.001 TYR O 61 PHE 0.004 0.001 PHE A 40 TRP 0.012 0.003 TRP I 86 HIS 0.002 0.000 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00254 (26376) covalent geometry : angle 0.47128 (35520) hydrogen bonds : bond 0.04594 ( 1368) hydrogen bonds : angle 4.77104 ( 4032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 536 time to evaluate : 1.089 Fit side-chains REVERT: A 36 GLU cc_start: 0.8264 (tt0) cc_final: 0.8047 (tt0) REVERT: A 51 GLU cc_start: 0.8289 (tp30) cc_final: 0.7846 (tp30) REVERT: A 92 LEU cc_start: 0.8276 (mp) cc_final: 0.8054 (mm) REVERT: B 61 ASN cc_start: 0.8384 (m-40) cc_final: 0.7982 (m110) REVERT: C 36 GLU cc_start: 0.8349 (tt0) cc_final: 0.8110 (tt0) REVERT: C 51 GLU cc_start: 0.7934 (tp30) cc_final: 0.7484 (tp30) REVERT: C 67 MET cc_start: 0.8351 (mtp) cc_final: 0.8039 (mtm) REVERT: C 89 LYS cc_start: 0.8481 (ttpt) cc_final: 0.7945 (ttmp) REVERT: C 158 ARG cc_start: 0.7513 (mmp80) cc_final: 0.7309 (mmp80) REVERT: F 45 VAL cc_start: 0.8617 (t) cc_final: 0.8324 (m) REVERT: G 20 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8072 (mt-10) REVERT: G 45 VAL cc_start: 0.8471 (t) cc_final: 0.8249 (m) REVERT: H 51 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.8353 (ttm110) REVERT: I 67 MET cc_start: 0.8099 (mtp) cc_final: 0.7805 (mtm) REVERT: I 92 LEU cc_start: 0.8354 (mt) cc_final: 0.8117 (mm) REVERT: J 158 ARG cc_start: 0.7609 (mmt-90) cc_final: 0.7256 (mmt180) REVERT: J 167 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6495 (mttm) REVERT: K 36 GLU cc_start: 0.8355 (tt0) cc_final: 0.8082 (tt0) REVERT: K 51 GLU cc_start: 0.7966 (tp30) cc_final: 0.7764 (tp30) REVERT: K 151 ASP cc_start: 0.7987 (m-30) cc_final: 0.7662 (m-30) REVERT: L 76 ILE cc_start: 0.8131 (mt) cc_final: 0.7791 (mp) REVERT: L 184 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6626 (mmt) REVERT: N 20 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7485 (mp0) REVERT: N 51 ARG cc_start: 0.8503 (tpp-160) cc_final: 0.8282 (tpp-160) REVERT: N 70 ASP cc_start: 0.8590 (p0) cc_final: 0.8188 (p0) REVERT: O 116 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8409 (ttmt) REVERT: P 27 LYS cc_start: 0.7738 (mttt) cc_final: 0.7528 (mttp) REVERT: P 37 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8045 (tm-30) REVERT: Q 62 ASP cc_start: 0.8558 (m-30) cc_final: 0.8335 (m-30) REVERT: R 93 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.8062 (ttt180) REVERT: R 184 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7337 (mmm) REVERT: S 92 LEU cc_start: 0.8185 (mt) cc_final: 0.7942 (mm) REVERT: S 96 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7581 (mt-10) REVERT: V 20 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8018 (mt-10) REVERT: W 51 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8009 (ttm110) outliers start: 41 outliers final: 14 residues processed: 551 average time/residue: 0.7728 time to fit residues: 479.5918 Evaluate side-chains 483 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 466 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 83 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 0.0670 chunk 275 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 224 optimal weight: 0.0980 chunk 314 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 GLN W 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104011 restraints weight = 28593.913| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.30 r_work: 0.3020 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26376 Z= 0.089 Angle : 0.407 5.008 35520 Z= 0.220 Chirality : 0.037 0.116 4236 Planarity : 0.002 0.030 4560 Dihedral : 3.496 11.688 3720 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.05 % Allowed : 19.42 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 3384 helix: -0.83 (0.11), residues: 2004 sheet: 1.67 (0.25), residues: 420 loop : -1.37 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 158 TYR 0.014 0.001 TYR O 61 PHE 0.004 0.000 PHE S 154 TRP 0.012 0.002 TRP Q 86 HIS 0.001 0.000 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00199 (26376) covalent geometry : angle 0.40701 (35520) hydrogen bonds : bond 0.03508 ( 1368) hydrogen bonds : angle 3.96030 ( 4032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 523 time to evaluate : 0.867 Fit side-chains REVERT: A 92 LEU cc_start: 0.8020 (mp) cc_final: 0.7787 (mm) REVERT: B 61 ASN cc_start: 0.8331 (m-40) cc_final: 0.7917 (m110) REVERT: C 36 GLU cc_start: 0.8244 (tt0) cc_final: 0.7980 (tt0) REVERT: C 51 GLU cc_start: 0.7798 (tp30) cc_final: 0.7397 (tp30) REVERT: C 67 MET cc_start: 0.8225 (mtp) cc_final: 0.8019 (mtm) REVERT: C 184 MET cc_start: 0.7088 (mmm) cc_final: 0.6849 (mmm) REVERT: D 65 LYS cc_start: 0.7559 (mtpt) cc_final: 0.6942 (mtpt) REVERT: E 20 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7430 (mp0) REVERT: E 51 ARG cc_start: 0.8569 (tpp-160) cc_final: 0.8311 (ttm110) REVERT: E 97 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7469 (mm-30) REVERT: F 45 VAL cc_start: 0.8653 (t) cc_final: 0.8431 (m) REVERT: F 51 ARG cc_start: 0.8427 (tpp-160) cc_final: 0.8157 (tpp-160) REVERT: G 20 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7925 (mp0) REVERT: G 48 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7718 (mp0) REVERT: G 51 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8393 (ttm170) REVERT: H 20 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7898 (mp0) REVERT: H 51 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8286 (ttm110) REVERT: I 67 MET cc_start: 0.7968 (mtp) cc_final: 0.7757 (mtm) REVERT: I 73 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8185 (tttt) REVERT: I 92 LEU cc_start: 0.8228 (mt) cc_final: 0.8010 (mm) REVERT: J 167 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6422 (mttm) REVERT: K 36 GLU cc_start: 0.8252 (tt0) cc_final: 0.8024 (tt0) REVERT: K 47 TYR cc_start: 0.8860 (m-80) cc_final: 0.8418 (m-80) REVERT: K 51 GLU cc_start: 0.7970 (tp30) cc_final: 0.7747 (tp30) REVERT: K 61 ASN cc_start: 0.8477 (m110) cc_final: 0.8175 (m110) REVERT: K 135 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7654 (mt-10) REVERT: K 151 ASP cc_start: 0.7922 (m-30) cc_final: 0.7556 (m-30) REVERT: L 93 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7925 (ttt180) REVERT: L 96 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7670 (mt-10) REVERT: L 184 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6717 (mmt) REVERT: M 48 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7776 (mp0) REVERT: N 20 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7420 (mp0) REVERT: N 51 ARG cc_start: 0.8458 (tpp-160) cc_final: 0.8145 (tpp-160) REVERT: N 70 ASP cc_start: 0.8555 (p0) cc_final: 0.8237 (p0) REVERT: O 116 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8484 (ttmt) REVERT: P 20 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7507 (mp0) REVERT: P 37 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8044 (tm-30) REVERT: Q 62 ASP cc_start: 0.8457 (m-30) cc_final: 0.8231 (m-30) REVERT: R 93 ARG cc_start: 0.8379 (ttt-90) cc_final: 0.8052 (ttt180) REVERT: S 73 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7947 (tttp) REVERT: S 92 LEU cc_start: 0.7960 (mt) cc_final: 0.7747 (mm) REVERT: S 96 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7607 (mt-10) REVERT: T 93 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8090 (ttt180) REVERT: U 20 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7633 (mt-10) REVERT: V 37 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7737 (tm-30) REVERT: W 48 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7831 (mp0) REVERT: W 51 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.8084 (ttm110) REVERT: X 20 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7782 (mt-10) REVERT: X 48 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7723 (mp0) REVERT: X 97 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7459 (mm-30) outliers start: 55 outliers final: 31 residues processed: 552 average time/residue: 0.7592 time to fit residues: 472.7794 Evaluate side-chains 502 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 469 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 116 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 237 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 203 optimal weight: 0.4980 chunk 83 optimal weight: 0.3980 chunk 47 optimal weight: 0.0000 chunk 16 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105911 restraints weight = 28494.392| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.27 r_work: 0.3040 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26376 Z= 0.079 Angle : 0.389 8.214 35520 Z= 0.208 Chirality : 0.037 0.115 4236 Planarity : 0.002 0.030 4560 Dihedral : 3.278 10.819 3720 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.01 % Allowed : 21.47 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3384 helix: 0.23 (0.11), residues: 2004 sheet: 2.02 (0.24), residues: 420 loop : -1.09 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 158 TYR 0.011 0.001 TYR O 61 PHE 0.004 0.000 PHE A 154 TRP 0.011 0.002 TRP A 86 HIS 0.001 0.000 HIS P 63 Details of bonding type rmsd covalent geometry : bond 0.00176 (26376) covalent geometry : angle 0.38931 (35520) hydrogen bonds : bond 0.02974 ( 1368) hydrogen bonds : angle 3.63446 ( 4032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 516 time to evaluate : 0.789 Fit side-chains REVERT: A 92 LEU cc_start: 0.8046 (mp) cc_final: 0.7824 (mm) REVERT: C 36 GLU cc_start: 0.8262 (tt0) cc_final: 0.7999 (tt0) REVERT: C 51 GLU cc_start: 0.7728 (tp30) cc_final: 0.7311 (tp30) REVERT: C 89 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7780 (ttmp) REVERT: C 184 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6807 (mmm) REVERT: D 65 LYS cc_start: 0.7563 (mtpt) cc_final: 0.6941 (mtpt) REVERT: E 20 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7480 (mp0) REVERT: E 37 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8165 (tm-30) REVERT: E 97 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7456 (mm-30) REVERT: F 37 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7930 (tm-30) REVERT: F 51 ARG cc_start: 0.8504 (tpp-160) cc_final: 0.8271 (tpp-160) REVERT: G 20 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7931 (mp0) REVERT: G 48 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7681 (mp0) REVERT: G 51 ARG cc_start: 0.8651 (ttm110) cc_final: 0.8426 (ttm170) REVERT: H 20 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7471 (mp0) REVERT: H 51 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8249 (ttm110) REVERT: I 73 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8129 (tttt) REVERT: I 92 LEU cc_start: 0.8215 (mt) cc_final: 0.7989 (mm) REVERT: J 51 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7329 (tp30) REVERT: J 77 GLU cc_start: 0.8037 (tt0) cc_final: 0.7634 (pm20) REVERT: K 36 GLU cc_start: 0.8235 (tt0) cc_final: 0.7989 (tt0) REVERT: K 47 TYR cc_start: 0.8847 (m-80) cc_final: 0.8395 (m-80) REVERT: K 51 GLU cc_start: 0.7983 (tp30) cc_final: 0.7744 (tp30) REVERT: K 61 ASN cc_start: 0.8529 (m110) cc_final: 0.8215 (m110) REVERT: K 93 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8246 (ttt180) REVERT: K 151 ASP cc_start: 0.7853 (m-30) cc_final: 0.7462 (m-30) REVERT: L 51 GLU cc_start: 0.7883 (tp30) cc_final: 0.7645 (mt-10) REVERT: L 93 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8005 (ttt180) REVERT: L 184 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6719 (mmt) REVERT: M 37 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7692 (tm-30) REVERT: M 48 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7707 (mp0) REVERT: N 20 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7478 (mp0) REVERT: N 70 ASP cc_start: 0.8549 (p0) cc_final: 0.8298 (p0) REVERT: O 116 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8516 (ttmt) REVERT: P 20 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7569 (mp0) REVERT: P 37 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8034 (tm-30) REVERT: Q 62 ASP cc_start: 0.8503 (m-30) cc_final: 0.8279 (m-30) REVERT: R 93 ARG cc_start: 0.8411 (ttt-90) cc_final: 0.8194 (ttt180) REVERT: R 184 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6463 (mmm) REVERT: S 96 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7577 (mt-10) REVERT: S 150 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8059 (m) REVERT: S 162 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7307 (mp) REVERT: T 93 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8168 (ttt180) REVERT: U 20 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7670 (mt-10) REVERT: V 20 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8035 (mt-10) REVERT: V 37 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7810 (tm-30) REVERT: V 51 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8360 (ttm110) REVERT: W 48 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7820 (mp0) REVERT: W 51 ARG cc_start: 0.8528 (tpp-160) cc_final: 0.7924 (ttm110) REVERT: X 20 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7726 (mt-10) REVERT: X 48 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7654 (mp0) REVERT: X 97 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7521 (mm-30) outliers start: 54 outliers final: 26 residues processed: 542 average time/residue: 0.8096 time to fit residues: 492.8724 Evaluate side-chains 498 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 467 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 116 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 33 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105913 restraints weight = 28004.554| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.13 r_work: 0.3064 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26376 Z= 0.092 Angle : 0.393 7.290 35520 Z= 0.209 Chirality : 0.037 0.114 4236 Planarity : 0.002 0.029 4560 Dihedral : 3.229 10.762 3720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.05 % Allowed : 21.76 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3384 helix: 0.81 (0.11), residues: 2004 sheet: 2.28 (0.23), residues: 420 loop : -0.89 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 51 TYR 0.010 0.001 TYR O 61 PHE 0.004 0.000 PHE L 154 TRP 0.010 0.002 TRP C 86 HIS 0.001 0.000 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00212 (26376) covalent geometry : angle 0.39313 (35520) hydrogen bonds : bond 0.03192 ( 1368) hydrogen bonds : angle 3.57131 ( 4032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 474 time to evaluate : 0.786 Fit side-chains REVERT: C 36 GLU cc_start: 0.8190 (tt0) cc_final: 0.7929 (tt0) REVERT: C 51 GLU cc_start: 0.7683 (tp30) cc_final: 0.7254 (tp30) REVERT: C 89 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7538 (ttmp) REVERT: C 184 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6412 (mmm) REVERT: D 65 LYS cc_start: 0.7494 (mtpt) cc_final: 0.6878 (mtpt) REVERT: E 20 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7403 (mp0) REVERT: E 37 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8178 (tm-30) REVERT: E 97 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7499 (mm-30) REVERT: F 48 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7772 (mp0) REVERT: F 51 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.8234 (tpp-160) REVERT: G 20 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7794 (mp0) REVERT: G 48 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7689 (mp0) REVERT: H 20 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7420 (mp0) REVERT: H 51 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8117 (tpp-160) REVERT: I 73 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8109 (tttt) REVERT: I 77 GLU cc_start: 0.7625 (tt0) cc_final: 0.7323 (pm20) REVERT: I 92 LEU cc_start: 0.8124 (mt) cc_final: 0.7918 (mm) REVERT: J 51 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7265 (tp30) REVERT: J 77 GLU cc_start: 0.8016 (tt0) cc_final: 0.7709 (pm20) REVERT: K 36 GLU cc_start: 0.8206 (tt0) cc_final: 0.7957 (tt0) REVERT: K 47 TYR cc_start: 0.8833 (m-80) cc_final: 0.8363 (m-80) REVERT: K 51 GLU cc_start: 0.7863 (tp30) cc_final: 0.7591 (tp30) REVERT: K 151 ASP cc_start: 0.7798 (m-30) cc_final: 0.7415 (m-30) REVERT: L 51 GLU cc_start: 0.7872 (tp30) cc_final: 0.7651 (tp30) REVERT: L 93 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7894 (ttt180) REVERT: L 184 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6574 (mmt) REVERT: M 20 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7573 (mp0) REVERT: M 48 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7764 (mp0) REVERT: M 110 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: N 20 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7596 (mp0) REVERT: O 20 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7853 (mp0) REVERT: O 116 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8517 (ttmt) REVERT: P 20 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7577 (mp0) REVERT: P 37 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8102 (tm-30) REVERT: Q 62 ASP cc_start: 0.8456 (m-30) cc_final: 0.8235 (m-30) REVERT: R 51 GLU cc_start: 0.7855 (tp30) cc_final: 0.7556 (tp30) REVERT: R 93 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.8122 (ttt180) REVERT: R 184 MET cc_start: 0.7111 (mmm) cc_final: 0.6440 (mmm) REVERT: S 162 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7393 (mp) REVERT: T 93 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7985 (ttt180) REVERT: U 20 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7628 (mp0) REVERT: V 20 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7932 (mt-10) REVERT: W 48 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7752 (mp0) REVERT: X 20 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7666 (mt-10) REVERT: X 97 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7532 (mm-30) outliers start: 55 outliers final: 36 residues processed: 499 average time/residue: 0.7934 time to fit residues: 444.8787 Evaluate side-chains 520 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 480 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 296 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 292 optimal weight: 0.0770 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106201 restraints weight = 28127.147| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.13 r_work: 0.3068 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26376 Z= 0.092 Angle : 0.393 6.833 35520 Z= 0.208 Chirality : 0.038 0.115 4236 Planarity : 0.002 0.030 4560 Dihedral : 3.195 10.776 3720 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.90 % Allowed : 21.95 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3384 helix: 1.29 (0.11), residues: 2004 sheet: 2.44 (0.23), residues: 420 loop : -0.73 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 51 TYR 0.010 0.001 TYR O 61 PHE 0.005 0.000 PHE C 154 TRP 0.010 0.002 TRP C 86 HIS 0.001 0.000 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00213 (26376) covalent geometry : angle 0.39268 (35520) hydrogen bonds : bond 0.03128 ( 1368) hydrogen bonds : angle 3.49379 ( 4032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 488 time to evaluate : 0.996 Fit side-chains REVERT: C 36 GLU cc_start: 0.8164 (tt0) cc_final: 0.7941 (tt0) REVERT: C 51 GLU cc_start: 0.7675 (tp30) cc_final: 0.7255 (tp30) REVERT: C 89 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7474 (ttmp) REVERT: C 184 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6440 (mmm) REVERT: D 65 LYS cc_start: 0.7490 (mtpt) cc_final: 0.6871 (mtpt) REVERT: E 20 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7392 (mp0) REVERT: E 70 ASP cc_start: 0.8395 (p0) cc_final: 0.8126 (p0) REVERT: G 20 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7274 (mp0) REVERT: G 48 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7762 (mp0) REVERT: H 51 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.8289 (ttm170) REVERT: I 77 GLU cc_start: 0.7623 (tt0) cc_final: 0.7359 (pm20) REVERT: I 92 LEU cc_start: 0.8054 (mt) cc_final: 0.7846 (mm) REVERT: J 51 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7272 (tp30) REVERT: J 77 GLU cc_start: 0.8016 (tt0) cc_final: 0.7713 (pm20) REVERT: K 36 GLU cc_start: 0.8211 (tt0) cc_final: 0.7821 (tt0) REVERT: K 47 TYR cc_start: 0.8820 (m-80) cc_final: 0.8410 (m-80) REVERT: K 51 GLU cc_start: 0.7807 (tp30) cc_final: 0.7605 (tp30) REVERT: K 151 ASP cc_start: 0.7781 (m-30) cc_final: 0.7375 (m-30) REVERT: L 51 GLU cc_start: 0.7885 (tp30) cc_final: 0.7623 (tp30) REVERT: L 93 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7897 (ttt180) REVERT: L 184 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6589 (mmt) REVERT: M 20 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7571 (mp0) REVERT: M 48 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7662 (mp0) REVERT: M 110 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: N 20 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7502 (mp0) REVERT: O 20 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7813 (mp0) REVERT: O 116 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8521 (ttmt) REVERT: P 20 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7336 (mp0) REVERT: P 37 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8104 (tm-30) REVERT: P 116 LYS cc_start: 0.9024 (tttm) cc_final: 0.8780 (tttt) REVERT: Q 62 ASP cc_start: 0.8452 (m-30) cc_final: 0.8233 (m-30) REVERT: R 184 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6340 (mmm) REVERT: S 150 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8014 (m) REVERT: T 93 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7945 (ttt180) REVERT: U 20 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7501 (mp0) REVERT: U 48 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7745 (mp0) REVERT: V 20 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7948 (mp0) REVERT: V 37 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7769 (tm-30) REVERT: V 48 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7841 (mp0) REVERT: W 48 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7848 (mp0) REVERT: W 51 ARG cc_start: 0.8550 (tpp-160) cc_final: 0.8022 (ttm110) REVERT: X 48 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7655 (mp0) REVERT: X 97 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7594 (mm-30) outliers start: 51 outliers final: 31 residues processed: 510 average time/residue: 0.8230 time to fit residues: 470.4905 Evaluate side-chains 492 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 456 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 60 optimal weight: 0.6980 chunk 265 optimal weight: 0.6980 chunk 307 optimal weight: 0.0980 chunk 114 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107772 restraints weight = 27979.108| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.04 r_work: 0.3094 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26376 Z= 0.084 Angle : 0.389 6.386 35520 Z= 0.206 Chirality : 0.037 0.114 4236 Planarity : 0.002 0.030 4560 Dihedral : 3.129 10.468 3720 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.56 % Allowed : 23.40 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.14), residues: 3384 helix: 1.71 (0.11), residues: 2004 sheet: 2.53 (0.23), residues: 420 loop : -0.62 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 51 TYR 0.010 0.001 TYR O 61 PHE 0.004 0.000 PHE A 154 TRP 0.011 0.002 TRP S 86 HIS 0.001 0.000 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00191 (26376) covalent geometry : angle 0.38887 (35520) hydrogen bonds : bond 0.02919 ( 1368) hydrogen bonds : angle 3.40816 ( 4032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 462 time to evaluate : 1.014 Fit side-chains REVERT: C 36 GLU cc_start: 0.8158 (tt0) cc_final: 0.7891 (tt0) REVERT: C 51 GLU cc_start: 0.7620 (tp30) cc_final: 0.7197 (tp30) REVERT: C 89 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7485 (ttmp) REVERT: C 184 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6457 (mmm) REVERT: D 65 LYS cc_start: 0.7436 (mtpt) cc_final: 0.6828 (mtpt) REVERT: E 20 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7327 (mp0) REVERT: E 70 ASP cc_start: 0.8394 (p0) cc_final: 0.8129 (p0) REVERT: G 20 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7631 (mp0) REVERT: G 48 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7718 (mp0) REVERT: H 51 ARG cc_start: 0.8538 (tpp-160) cc_final: 0.8280 (ttm170) REVERT: I 77 GLU cc_start: 0.7589 (tt0) cc_final: 0.7365 (pm20) REVERT: I 92 LEU cc_start: 0.7988 (mt) cc_final: 0.7785 (mm) REVERT: J 51 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7224 (tp30) REVERT: J 77 GLU cc_start: 0.7994 (tt0) cc_final: 0.7718 (pm20) REVERT: J 92 LEU cc_start: 0.7896 (mm) cc_final: 0.7643 (mp) REVERT: K 36 GLU cc_start: 0.8180 (tt0) cc_final: 0.7800 (tt0) REVERT: K 47 TYR cc_start: 0.8824 (m-80) cc_final: 0.8404 (m-80) REVERT: K 151 ASP cc_start: 0.7724 (m-30) cc_final: 0.7338 (m-30) REVERT: L 51 GLU cc_start: 0.7866 (tp30) cc_final: 0.7580 (tp30) REVERT: L 93 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7975 (ttt180) REVERT: L 184 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6601 (mmt) REVERT: M 48 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7676 (mp0) REVERT: M 110 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: N 20 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7535 (mp0) REVERT: O 116 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8529 (ttmt) REVERT: P 20 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7280 (mp0) REVERT: P 37 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8145 (tm-30) REVERT: P 51 ARG cc_start: 0.8676 (tpp-160) cc_final: 0.8388 (ttm110) REVERT: P 116 LYS cc_start: 0.9031 (tttm) cc_final: 0.8765 (tttt) REVERT: Q 62 ASP cc_start: 0.8435 (m-30) cc_final: 0.8212 (m-30) REVERT: R 51 GLU cc_start: 0.7841 (tp30) cc_final: 0.7540 (tp30) REVERT: S 150 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.7938 (m) REVERT: T 93 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7982 (ttt180) REVERT: T 150 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.7935 (m) REVERT: V 48 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7771 (mp0) REVERT: W 48 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7795 (mp0) REVERT: W 51 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8005 (ttm110) REVERT: X 37 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7774 (tm-30) REVERT: X 48 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7633 (mp0) REVERT: X 97 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7581 (mm-30) outliers start: 42 outliers final: 30 residues processed: 484 average time/residue: 0.7805 time to fit residues: 424.8659 Evaluate side-chains 487 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 452 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 322 optimal weight: 0.0020 chunk 199 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 196 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107156 restraints weight = 28201.552| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.04 r_work: 0.3083 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26376 Z= 0.091 Angle : 0.395 6.569 35520 Z= 0.209 Chirality : 0.038 0.114 4236 Planarity : 0.002 0.030 4560 Dihedral : 3.135 10.394 3720 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.64 % Allowed : 23.85 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.14), residues: 3384 helix: 1.90 (0.11), residues: 2004 sheet: 2.61 (0.23), residues: 420 loop : -0.54 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 51 TYR 0.010 0.001 TYR O 61 PHE 0.004 0.000 PHE C 154 TRP 0.010 0.002 TRP S 86 HIS 0.001 0.000 HIS P 63 Details of bonding type rmsd covalent geometry : bond 0.00213 (26376) covalent geometry : angle 0.39538 (35520) hydrogen bonds : bond 0.03071 ( 1368) hydrogen bonds : angle 3.42127 ( 4032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 453 time to evaluate : 0.987 Fit side-chains REVERT: C 36 GLU cc_start: 0.8171 (tt0) cc_final: 0.7894 (tt0) REVERT: C 51 GLU cc_start: 0.7610 (tp30) cc_final: 0.7247 (tp30) REVERT: C 89 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7466 (ttmp) REVERT: C 184 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6455 (mmm) REVERT: D 65 LYS cc_start: 0.7545 (mtpt) cc_final: 0.6953 (mtpt) REVERT: E 20 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7387 (mp0) REVERT: E 70 ASP cc_start: 0.8386 (p0) cc_final: 0.8164 (p0) REVERT: F 7 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: G 48 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7744 (mp0) REVERT: H 51 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.8178 (tpp-160) REVERT: I 77 GLU cc_start: 0.7666 (tt0) cc_final: 0.7269 (pm20) REVERT: I 92 LEU cc_start: 0.7977 (mt) cc_final: 0.7769 (mm) REVERT: J 51 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7304 (tp30) REVERT: J 92 LEU cc_start: 0.7905 (mm) cc_final: 0.7660 (mp) REVERT: K 36 GLU cc_start: 0.8207 (tt0) cc_final: 0.7904 (tt0) REVERT: K 47 TYR cc_start: 0.8838 (m-80) cc_final: 0.8401 (m-80) REVERT: K 151 ASP cc_start: 0.7739 (m-30) cc_final: 0.7358 (m-30) REVERT: L 51 GLU cc_start: 0.7894 (tp30) cc_final: 0.7598 (tp30) REVERT: L 93 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7941 (ttt180) REVERT: L 151 ASP cc_start: 0.7822 (m-30) cc_final: 0.7327 (m-30) REVERT: L 184 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6501 (mmt) REVERT: M 48 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7731 (mp0) REVERT: M 110 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: N 20 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7404 (mp0) REVERT: O 116 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8524 (ttmt) REVERT: P 37 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8156 (tm-30) REVERT: P 51 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8347 (ttm110) REVERT: P 116 LYS cc_start: 0.9048 (tttm) cc_final: 0.8766 (tttt) REVERT: Q 62 ASP cc_start: 0.8444 (m-30) cc_final: 0.8225 (m-30) REVERT: R 51 GLU cc_start: 0.7843 (tp30) cc_final: 0.7534 (tp30) REVERT: R 184 MET cc_start: 0.6952 (mmm) cc_final: 0.6333 (mmm) REVERT: S 150 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.7991 (m) REVERT: T 93 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7878 (ttt180) REVERT: T 150 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7902 (m) REVERT: U 51 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8252 (ttm110) REVERT: V 48 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7814 (mp0) REVERT: W 48 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7823 (mp0) REVERT: X 37 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7794 (tm-30) REVERT: X 48 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7659 (mp0) REVERT: X 97 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7624 (mm-30) outliers start: 44 outliers final: 34 residues processed: 474 average time/residue: 0.7833 time to fit residues: 418.7297 Evaluate side-chains 489 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 449 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 98 GLU Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 12 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 240 optimal weight: 0.0000 chunk 0 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 7 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106298 restraints weight = 28121.550| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.15 r_work: 0.3052 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26376 Z= 0.094 Angle : 0.400 6.875 35520 Z= 0.211 Chirality : 0.038 0.114 4236 Planarity : 0.002 0.030 4560 Dihedral : 3.135 10.560 3720 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.71 % Allowed : 24.00 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3384 helix: 2.02 (0.11), residues: 2004 sheet: 2.63 (0.23), residues: 420 loop : -0.50 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 51 TYR 0.010 0.001 TYR O 61 PHE 0.006 0.000 PHE I 154 TRP 0.010 0.002 TRP S 86 HIS 0.001 0.000 HIS P 63 Details of bonding type rmsd covalent geometry : bond 0.00219 (26376) covalent geometry : angle 0.39994 (35520) hydrogen bonds : bond 0.03098 ( 1368) hydrogen bonds : angle 3.41454 ( 4032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 449 time to evaluate : 1.068 Fit side-chains REVERT: C 36 GLU cc_start: 0.8173 (tt0) cc_final: 0.7943 (tt0) REVERT: C 51 GLU cc_start: 0.7607 (tp30) cc_final: 0.7241 (tp30) REVERT: C 89 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7457 (ttmp) REVERT: C 184 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6446 (mmm) REVERT: D 65 LYS cc_start: 0.7526 (mtpt) cc_final: 0.6938 (mtpt) REVERT: E 20 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7313 (mp0) REVERT: E 23 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7183 (mm-30) REVERT: E 37 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8313 (tm-30) REVERT: E 70 ASP cc_start: 0.8403 (p0) cc_final: 0.8177 (p0) REVERT: F 7 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: G 48 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7778 (mp0) REVERT: H 51 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8191 (tpp-160) REVERT: I 77 GLU cc_start: 0.7723 (tt0) cc_final: 0.7295 (pm20) REVERT: I 92 LEU cc_start: 0.7943 (mt) cc_final: 0.7732 (mm) REVERT: J 51 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7241 (tp30) REVERT: J 92 LEU cc_start: 0.7860 (mm) cc_final: 0.7615 (mp) REVERT: K 36 GLU cc_start: 0.8211 (tt0) cc_final: 0.7824 (tt0) REVERT: K 47 TYR cc_start: 0.8828 (m-80) cc_final: 0.8385 (m-80) REVERT: K 61 ASN cc_start: 0.8441 (m110) cc_final: 0.8132 (m110) REVERT: K 151 ASP cc_start: 0.7712 (m-30) cc_final: 0.7331 (m-30) REVERT: L 51 GLU cc_start: 0.7917 (tp30) cc_final: 0.7615 (tp30) REVERT: L 93 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7846 (ttt180) REVERT: L 151 ASP cc_start: 0.7899 (m-30) cc_final: 0.7403 (m-30) REVERT: L 184 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6563 (mmt) REVERT: M 48 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7718 (mp0) REVERT: M 51 ARG cc_start: 0.8417 (tpp-160) cc_final: 0.8095 (ttm110) REVERT: M 110 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: N 20 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7324 (mp0) REVERT: O 51 ARG cc_start: 0.8567 (tpp-160) cc_final: 0.8295 (ttm110) REVERT: O 116 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8521 (ttmt) REVERT: P 37 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8163 (tm-30) REVERT: P 51 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8387 (ttm110) REVERT: P 116 LYS cc_start: 0.9064 (tttm) cc_final: 0.8771 (tttt) REVERT: Q 62 ASP cc_start: 0.8450 (m-30) cc_final: 0.8232 (m-30) REVERT: R 51 GLU cc_start: 0.7811 (tp30) cc_final: 0.7501 (tp30) REVERT: R 184 MET cc_start: 0.6952 (mmm) cc_final: 0.6333 (mmm) REVERT: S 150 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.7981 (m) REVERT: T 93 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7902 (ttt180) REVERT: T 150 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7878 (m) REVERT: V 48 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7813 (mp0) REVERT: W 48 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7752 (mp0) REVERT: W 51 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8153 (ttm110) REVERT: X 37 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7786 (tm-30) REVERT: X 48 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7637 (mp0) REVERT: X 97 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7608 (mm-30) outliers start: 46 outliers final: 33 residues processed: 470 average time/residue: 0.7773 time to fit residues: 411.7794 Evaluate side-chains 492 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 453 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 83 SER Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 127 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 96 optimal weight: 0.2980 chunk 323 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105511 restraints weight = 28264.973| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26376 Z= 0.116 Angle : 0.421 7.123 35520 Z= 0.221 Chirality : 0.039 0.114 4236 Planarity : 0.002 0.038 4560 Dihedral : 3.233 10.857 3720 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.41 % Allowed : 24.48 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.14), residues: 3384 helix: 1.91 (0.11), residues: 2004 sheet: 2.59 (0.23), residues: 420 loop : -0.51 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 51 TYR 0.011 0.001 TYR L 94 PHE 0.005 0.001 PHE A 154 TRP 0.009 0.002 TRP S 86 HIS 0.002 0.001 HIS P 63 Details of bonding type rmsd covalent geometry : bond 0.00280 (26376) covalent geometry : angle 0.42133 (35520) hydrogen bonds : bond 0.03534 ( 1368) hydrogen bonds : angle 3.53905 ( 4032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 461 time to evaluate : 0.987 Fit side-chains REVERT: C 36 GLU cc_start: 0.8193 (tt0) cc_final: 0.7941 (tt0) REVERT: C 51 GLU cc_start: 0.7645 (tp30) cc_final: 0.7210 (tp30) REVERT: C 89 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7505 (ttmp) REVERT: C 184 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6407 (mmm) REVERT: D 65 LYS cc_start: 0.7567 (mtpt) cc_final: 0.6977 (mtpt) REVERT: E 20 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7406 (mp0) REVERT: F 7 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: F 51 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.8324 (ttm110) REVERT: G 48 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7750 (mp0) REVERT: H 51 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8265 (tpp-160) REVERT: I 77 GLU cc_start: 0.7700 (tt0) cc_final: 0.7319 (pm20) REVERT: I 92 LEU cc_start: 0.7985 (mt) cc_final: 0.7764 (mm) REVERT: J 51 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7338 (tp30) REVERT: J 77 GLU cc_start: 0.8010 (tt0) cc_final: 0.7702 (pm20) REVERT: J 92 LEU cc_start: 0.7890 (mm) cc_final: 0.7649 (mp) REVERT: K 36 GLU cc_start: 0.8239 (tt0) cc_final: 0.7916 (tt0) REVERT: K 47 TYR cc_start: 0.8861 (m-80) cc_final: 0.8417 (m-80) REVERT: K 77 GLU cc_start: 0.7877 (tt0) cc_final: 0.7338 (pm20) REVERT: K 151 ASP cc_start: 0.7708 (m-30) cc_final: 0.7322 (m-30) REVERT: L 51 GLU cc_start: 0.7949 (tp30) cc_final: 0.7573 (tp30) REVERT: L 93 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7839 (ttt180) REVERT: L 151 ASP cc_start: 0.7920 (m-30) cc_final: 0.7462 (m-30) REVERT: L 184 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6473 (mmt) REVERT: M 20 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7278 (mp0) REVERT: M 48 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7720 (mp0) REVERT: M 110 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: N 20 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7368 (mp0) REVERT: O 116 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8543 (ttmt) REVERT: P 20 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7177 (mp0) REVERT: P 37 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8150 (tm-30) REVERT: P 51 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8335 (ttm110) REVERT: P 116 LYS cc_start: 0.9055 (tttm) cc_final: 0.8766 (tttt) REVERT: Q 62 ASP cc_start: 0.8472 (m-30) cc_final: 0.8271 (m-30) REVERT: Q 77 GLU cc_start: 0.7682 (tt0) cc_final: 0.7470 (pm20) REVERT: R 184 MET cc_start: 0.6950 (mmm) cc_final: 0.6335 (mmm) REVERT: S 150 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.7990 (m) REVERT: T 93 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7895 (ttt180) REVERT: T 150 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7964 (m) REVERT: U 37 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7994 (tm-30) REVERT: U 48 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7803 (mp0) REVERT: U 51 ARG cc_start: 0.8555 (tpp-160) cc_final: 0.8171 (ttm110) REVERT: V 48 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7820 (mp0) REVERT: W 48 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7727 (mp0) REVERT: W 51 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8100 (ttm110) REVERT: X 37 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7751 (tm-30) REVERT: X 48 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7631 (mp0) REVERT: X 97 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7553 (mm-30) outliers start: 38 outliers final: 31 residues processed: 478 average time/residue: 0.8072 time to fit residues: 433.9501 Evaluate side-chains 490 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 453 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 83 SER Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 315 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101750 restraints weight = 28547.335| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.28 r_work: 0.2949 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26376 Z= 0.150 Angle : 0.449 7.045 35520 Z= 0.234 Chirality : 0.040 0.116 4236 Planarity : 0.003 0.039 4560 Dihedral : 3.384 11.739 3720 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.56 % Allowed : 24.33 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.14), residues: 3384 helix: 1.67 (0.11), residues: 2004 sheet: 2.53 (0.23), residues: 420 loop : -0.55 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 51 TYR 0.014 0.002 TYR S 94 PHE 0.004 0.001 PHE S 136 TRP 0.008 0.002 TRP T 86 HIS 0.003 0.001 HIS P 63 Details of bonding type rmsd covalent geometry : bond 0.00369 (26376) covalent geometry : angle 0.44878 (35520) hydrogen bonds : bond 0.04025 ( 1368) hydrogen bonds : angle 3.67457 ( 4032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10469.17 seconds wall clock time: 178 minutes 7.08 seconds (10687.08 seconds total)