Starting phenix.real_space_refine on Fri Feb 6 16:21:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yi9_72983/02_2026/9yi9_72983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yi9_72983/02_2026/9yi9_72983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yi9_72983/02_2026/9yi9_72983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yi9_72983/02_2026/9yi9_72983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yi9_72983/02_2026/9yi9_72983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yi9_72983/02_2026/9yi9_72983.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 126 5.16 5 C 16816 2.51 5 N 4428 2.21 5 O 4660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26030 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1452 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "P" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 162} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, S, R Time building chain proxies: 3.06, per 1000 atoms: 0.12 Number of scatterers: 26030 At special positions: 0 Unit cell: (105.648, 185.736, 189.996, 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 126 16.00 O 4660 8.00 N 4428 7.00 C 16816 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 72 sheets defined 36.8% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 198 " --> pdb=" O CYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 198 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE C 108 " --> pdb=" O PRO C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 178 through 199 removed outlier: 3.529A pdb=" N GLY C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 198 " --> pdb=" O CYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE D 108 " --> pdb=" O PRO D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU D 198 " --> pdb=" O CYS D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'E' and resid 92 through 100 Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE E 108 " --> pdb=" O PRO E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 131 Processing helix chain 'E' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU E 198 " --> pdb=" O CYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'F' and resid 92 through 100 Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE F 108 " --> pdb=" O PRO F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 131 Processing helix chain 'F' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS F 187 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU F 198 " --> pdb=" O CYS F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'G' and resid 92 through 100 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE G 108 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 131 Processing helix chain 'G' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU G 198 " --> pdb=" O CYS G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 206 through 217 Processing helix chain 'H' and resid 92 through 100 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE H 108 " --> pdb=" O PRO H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 131 Processing helix chain 'H' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS H 187 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP H 197 " --> pdb=" O ARG H 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU H 198 " --> pdb=" O CYS H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 206 through 217 Processing helix chain 'I' and resid 92 through 100 Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE I 108 " --> pdb=" O PRO I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 131 Processing helix chain 'I' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY I 185 " --> pdb=" O THR I 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS I 187 " --> pdb=" O THR I 183 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP I 197 " --> pdb=" O ARG I 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU I 198 " --> pdb=" O CYS I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 206 through 217 Processing helix chain 'J' and resid 92 through 100 Processing helix chain 'J' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE J 108 " --> pdb=" O PRO J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 131 Processing helix chain 'J' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY J 185 " --> pdb=" O THR J 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS J 187 " --> pdb=" O THR J 183 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP J 197 " --> pdb=" O ARG J 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU J 198 " --> pdb=" O CYS J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'K' and resid 92 through 100 Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE K 108 " --> pdb=" O PRO K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 131 Processing helix chain 'K' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K 187 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP K 197 " --> pdb=" O ARG K 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU K 198 " --> pdb=" O CYS K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE L 108 " --> pdb=" O PRO L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 131 Processing helix chain 'L' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY L 185 " --> pdb=" O THR L 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 187 " --> pdb=" O THR L 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU L 198 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'M' and resid 92 through 100 Processing helix chain 'M' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 131 Processing helix chain 'M' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY M 185 " --> pdb=" O THR M 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS M 187 " --> pdb=" O THR M 183 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP M 197 " --> pdb=" O ARG M 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU M 198 " --> pdb=" O CYS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 206 through 217 Processing helix chain 'N' and resid 92 through 100 Processing helix chain 'N' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE N 108 " --> pdb=" O PRO N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 131 Processing helix chain 'N' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY N 185 " --> pdb=" O THR N 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS N 187 " --> pdb=" O THR N 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP N 197 " --> pdb=" O ARG N 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU N 198 " --> pdb=" O CYS N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 206 through 217 Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE O 108 " --> pdb=" O PRO O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 131 Processing helix chain 'O' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY O 185 " --> pdb=" O THR O 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS O 187 " --> pdb=" O THR O 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP O 197 " --> pdb=" O ARG O 193 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU O 198 " --> pdb=" O CYS O 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 205 Processing helix chain 'O' and resid 206 through 217 Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE P 108 " --> pdb=" O PRO P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 131 Processing helix chain 'P' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY P 185 " --> pdb=" O THR P 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP P 197 " --> pdb=" O ARG P 193 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU P 198 " --> pdb=" O CYS P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 205 Processing helix chain 'P' and resid 206 through 217 Processing helix chain 'R' and resid 92 through 100 Processing helix chain 'R' and resid 104 through 108 removed outlier: 3.530A pdb=" N ILE R 108 " --> pdb=" O PRO R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 131 Processing helix chain 'R' and resid 178 through 199 removed outlier: 3.528A pdb=" N GLY R 185 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP R 197 " --> pdb=" O ARG R 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU R 198 " --> pdb=" O CYS R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 205 Processing helix chain 'R' and resid 206 through 217 Processing helix chain 'S' and resid 92 through 100 Processing helix chain 'S' and resid 104 through 108 removed outlier: 3.531A pdb=" N ILE S 108 " --> pdb=" O PRO S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 131 Processing helix chain 'S' and resid 178 through 199 removed outlier: 3.529A pdb=" N GLY S 185 " --> pdb=" O THR S 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 187 " --> pdb=" O THR S 183 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP S 197 " --> pdb=" O ARG S 193 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU S 198 " --> pdb=" O CYS S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 205 Processing helix chain 'S' and resid 206 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG A 153 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 165 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 159 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 140 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG B 153 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 165 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 159 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 225 Processing sheet with id=AA9, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG C 153 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 165 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS C 159 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C 163 " --> pdb=" O CYS C 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 218 through 225 Processing sheet with id=AB4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'D' and resid 136 through 140 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG D 153 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 165 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS D 159 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU D 163 " --> pdb=" O CYS D 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 218 through 225 Processing sheet with id=AB8, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB9, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG E 153 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER E 165 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS E 159 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU E 163 " --> pdb=" O CYS E 159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 218 through 225 Processing sheet with id=AC3, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AC4, first strand: chain 'F' and resid 136 through 140 Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG F 153 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER F 165 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS F 159 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU F 163 " --> pdb=" O CYS F 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 218 through 225 Processing sheet with id=AC7, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AC8, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG G 153 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER G 165 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS G 159 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU G 163 " --> pdb=" O CYS G 159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 218 through 225 Processing sheet with id=AD2, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 140 Processing sheet with id=AD4, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG H 153 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER H 165 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS H 159 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU H 163 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 218 through 225 Processing sheet with id=AD6, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AD7, first strand: chain 'I' and resid 136 through 140 Processing sheet with id=AD8, first strand: chain 'I' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG I 153 " --> pdb=" O GLY I 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER I 165 " --> pdb=" O LEU I 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS I 159 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU I 163 " --> pdb=" O CYS I 159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 218 through 225 Processing sheet with id=AE1, first strand: chain 'J' and resid 109 through 110 Processing sheet with id=AE2, first strand: chain 'J' and resid 136 through 140 Processing sheet with id=AE3, first strand: chain 'J' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG J 153 " --> pdb=" O GLY J 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER J 165 " --> pdb=" O LEU J 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS J 159 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU J 163 " --> pdb=" O CYS J 159 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 218 through 225 Processing sheet with id=AE5, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AE6, first strand: chain 'K' and resid 136 through 140 Processing sheet with id=AE7, first strand: chain 'K' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG K 153 " --> pdb=" O GLY K 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 165 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS K 159 " --> pdb=" O LEU K 163 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU K 163 " --> pdb=" O CYS K 159 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 218 through 225 Processing sheet with id=AE9, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AF1, first strand: chain 'L' and resid 136 through 140 Processing sheet with id=AF2, first strand: chain 'L' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG L 153 " --> pdb=" O GLY L 169 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER L 165 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS L 159 " --> pdb=" O LEU L 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU L 163 " --> pdb=" O CYS L 159 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 218 through 225 Processing sheet with id=AF4, first strand: chain 'M' and resid 109 through 110 Processing sheet with id=AF5, first strand: chain 'M' and resid 136 through 140 Processing sheet with id=AF6, first strand: chain 'M' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG M 153 " --> pdb=" O GLY M 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER M 165 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS M 159 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU M 163 " --> pdb=" O CYS M 159 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 218 through 225 Processing sheet with id=AF8, first strand: chain 'N' and resid 109 through 110 Processing sheet with id=AF9, first strand: chain 'N' and resid 136 through 140 Processing sheet with id=AG1, first strand: chain 'N' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG N 153 " --> pdb=" O GLY N 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER N 165 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS N 159 " --> pdb=" O LEU N 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU N 163 " --> pdb=" O CYS N 159 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 218 through 225 Processing sheet with id=AG3, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AG4, first strand: chain 'O' and resid 136 through 140 Processing sheet with id=AG5, first strand: chain 'O' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG O 153 " --> pdb=" O GLY O 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER O 165 " --> pdb=" O LEU O 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS O 159 " --> pdb=" O LEU O 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU O 163 " --> pdb=" O CYS O 159 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 218 through 225 Processing sheet with id=AG7, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AG8, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG9, first strand: chain 'P' and resid 136 through 140 removed outlier: 3.705A pdb=" N ARG P 153 " --> pdb=" O GLY P 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER P 165 " --> pdb=" O LEU P 157 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS P 159 " --> pdb=" O LEU P 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU P 163 " --> pdb=" O CYS P 159 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 218 through 225 Processing sheet with id=AH2, first strand: chain 'R' and resid 109 through 110 Processing sheet with id=AH3, first strand: chain 'R' and resid 136 through 140 Processing sheet with id=AH4, first strand: chain 'R' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG R 153 " --> pdb=" O GLY R 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER R 165 " --> pdb=" O LEU R 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS R 159 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU R 163 " --> pdb=" O CYS R 159 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 218 through 225 Processing sheet with id=AH6, first strand: chain 'S' and resid 109 through 110 Processing sheet with id=AH7, first strand: chain 'S' and resid 136 through 140 Processing sheet with id=AH8, first strand: chain 'S' and resid 136 through 140 removed outlier: 3.704A pdb=" N ARG S 153 " --> pdb=" O GLY S 169 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER S 165 " --> pdb=" O LEU S 157 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS S 159 " --> pdb=" O LEU S 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU S 163 " --> pdb=" O CYS S 159 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'S' and resid 218 through 225 1170 hydrogen bonds defined for protein. 3186 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: 5.24 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8124 1.34 - 1.46: 6061 1.46 - 1.58: 12313 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 26660 Sorted by residual: bond pdb=" CD LYS R 211 " pdb=" CE LYS R 211 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CD LYS M 211 " pdb=" CE LYS M 211 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CD LYS S 211 " pdb=" CE LYS S 211 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CD LYS O 211 " pdb=" CE LYS O 211 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CD LYS A 211 " pdb=" CE LYS A 211 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.17e+00 ... (remaining 26655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 32969 1.11 - 2.23: 2282 2.23 - 3.34: 431 3.34 - 4.46: 162 4.46 - 5.57: 106 Bond angle restraints: 35950 Sorted by residual: angle pdb=" C VAL G 215 " pdb=" N ASP G 216 " pdb=" CA ASP G 216 " ideal model delta sigma weight residual 122.26 118.08 4.18 1.73e+00 3.34e-01 5.84e+00 angle pdb=" C VAL H 215 " pdb=" N ASP H 216 " pdb=" CA ASP H 216 " ideal model delta sigma weight residual 122.26 118.08 4.18 1.73e+00 3.34e-01 5.84e+00 angle pdb=" C VAL P 215 " pdb=" N ASP P 216 " pdb=" CA ASP P 216 " ideal model delta sigma weight residual 122.26 118.10 4.16 1.73e+00 3.34e-01 5.80e+00 angle pdb=" C VAL M 215 " pdb=" N ASP M 216 " pdb=" CA ASP M 216 " ideal model delta sigma weight residual 122.26 118.10 4.16 1.73e+00 3.34e-01 5.79e+00 angle pdb=" C VAL C 215 " pdb=" N ASP C 216 " pdb=" CA ASP C 216 " ideal model delta sigma weight residual 122.26 118.10 4.16 1.73e+00 3.34e-01 5.77e+00 ... (remaining 35945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.23: 13695 12.23 - 24.46: 1623 24.46 - 36.69: 586 36.69 - 48.92: 70 48.92 - 61.15: 54 Dihedral angle restraints: 16028 sinusoidal: 6814 harmonic: 9214 Sorted by residual: dihedral pdb=" CA GLU F 92 " pdb=" C GLU F 92 " pdb=" N ALA F 93 " pdb=" CA ALA F 93 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA GLU B 92 " pdb=" C GLU B 92 " pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA GLU I 92 " pdb=" C GLU I 92 " pdb=" N ALA I 93 " pdb=" CA ALA I 93 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 16025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2273 0.035 - 0.070: 1002 0.070 - 0.105: 385 0.105 - 0.140: 156 0.140 - 0.175: 18 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CG LEU C 150 " pdb=" CB LEU C 150 " pdb=" CD1 LEU C 150 " pdb=" CD2 LEU C 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CG LEU N 150 " pdb=" CB LEU N 150 " pdb=" CD1 LEU N 150 " pdb=" CD2 LEU N 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CG LEU A 150 " pdb=" CB LEU A 150 " pdb=" CD1 LEU A 150 " pdb=" CD2 LEU A 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 3831 not shown) Planarity restraints: 4502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 190 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ALA L 190 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA L 190 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU L 191 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 190 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ALA K 190 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA K 190 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU K 191 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 190 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C ALA I 190 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA I 190 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU I 191 " -0.011 2.00e-02 2.50e+03 ... (remaining 4499 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 18011 3.09 - 3.55: 26699 3.55 - 4.00: 41147 4.00 - 4.45: 49126 4.45 - 4.90: 73202 Nonbonded interactions: 208185 Sorted by model distance: nonbonded pdb=" N TYR L 117 " pdb=" O TYR L 117 " model vdw 2.644 2.496 nonbonded pdb=" N TYR D 117 " pdb=" O TYR D 117 " model vdw 2.644 2.496 nonbonded pdb=" N TYR H 117 " pdb=" O TYR H 117 " model vdw 2.644 2.496 nonbonded pdb=" N TYR M 117 " pdb=" O TYR M 117 " model vdw 2.644 2.496 nonbonded pdb=" N TYR P 117 " pdb=" O TYR P 117 " model vdw 2.644 2.496 ... (remaining 208180 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.590 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.003 0.045 26660 Z= 0.168 Angle : 0.703 5.570 35950 Z= 0.367 Chirality : 0.048 0.175 3834 Planarity : 0.006 0.039 4502 Dihedral : 11.929 61.146 10148 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.43 (0.15), residues: 3156 helix: -0.82 (0.15), residues: 936 sheet: 1.09 (0.21), residues: 612 loop : 0.87 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG I 141 TYR 0.028 0.002 TYR O 117 PHE 0.004 0.001 PHE F 213 TRP 0.015 0.002 TRP M 235 HIS 0.005 0.002 HIS S 225 Details of bonding type rmsd covalent geometry : bond 0.00350 (26660) covalent geometry : angle 0.70277 (35950) hydrogen bonds : bond 0.17747 ( 1098) hydrogen bonds : angle 8.33524 ( 3186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 775 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8674 (tppp) cc_final: 0.8464 (tppp) REVERT: A 110 ILE cc_start: 0.8448 (tt) cc_final: 0.8112 (tp) REVERT: A 153 ARG cc_start: 0.8358 (ttt180) cc_final: 0.7987 (ttt180) REVERT: A 194 CYS cc_start: 0.6694 (m) cc_final: 0.6445 (m) REVERT: B 84 TYR cc_start: 0.8188 (t80) cc_final: 0.7803 (t80) REVERT: B 89 LYS cc_start: 0.8596 (ptmt) cc_final: 0.8297 (ptmm) REVERT: B 97 LYS cc_start: 0.8147 (tttm) cc_final: 0.7886 (tttm) REVERT: B 98 ASP cc_start: 0.6968 (m-30) cc_final: 0.6544 (m-30) REVERT: B 101 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6646 (tm-30) REVERT: B 106 LYS cc_start: 0.8497 (tppp) cc_final: 0.7919 (tppp) REVERT: B 108 ILE cc_start: 0.7799 (mt) cc_final: 0.7546 (mt) REVERT: B 109 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6386 (mm-30) REVERT: B 128 ASN cc_start: 0.8652 (m-40) cc_final: 0.8347 (m110) REVERT: B 129 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7945 (mtpp) REVERT: B 149 LYS cc_start: 0.8346 (ptpp) cc_final: 0.8005 (ptpp) REVERT: B 176 GLU cc_start: 0.7762 (tp30) cc_final: 0.7461 (tp30) REVERT: B 203 GLU cc_start: 0.7873 (mp0) cc_final: 0.7563 (mp0) REVERT: B 243 GLU cc_start: 0.7244 (mp0) cc_final: 0.6970 (mp0) REVERT: C 89 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7935 (ptmm) REVERT: C 92 GLU cc_start: 0.7327 (pp20) cc_final: 0.7014 (pp20) REVERT: C 96 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7836 (mm-40) REVERT: C 106 LYS cc_start: 0.8371 (tppp) cc_final: 0.7828 (tppp) REVERT: C 107 ASP cc_start: 0.7301 (m-30) cc_final: 0.6955 (m-30) REVERT: C 149 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7851 (ptpp) REVERT: C 217 HIS cc_start: 0.7837 (m170) cc_final: 0.7466 (m90) REVERT: D 89 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7983 (ptmm) REVERT: D 92 GLU cc_start: 0.7543 (pp20) cc_final: 0.7174 (pp20) REVERT: D 94 LYS cc_start: 0.7664 (pttp) cc_final: 0.7415 (pttp) REVERT: D 96 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7453 (mt0) REVERT: D 106 LYS cc_start: 0.8015 (tppp) cc_final: 0.7480 (tppp) REVERT: D 149 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7887 (ptpp) REVERT: D 203 GLU cc_start: 0.7885 (mp0) cc_final: 0.7295 (mp0) REVERT: D 212 LYS cc_start: 0.7712 (tttm) cc_final: 0.7378 (tttm) REVERT: E 78 ASP cc_start: 0.8256 (t0) cc_final: 0.7976 (t70) REVERT: E 106 LYS cc_start: 0.8457 (tppp) cc_final: 0.7912 (tppp) REVERT: E 117 TYR cc_start: 0.8272 (p90) cc_final: 0.7690 (p90) REVERT: E 149 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7748 (ptpp) REVERT: E 162 GLN cc_start: 0.8440 (tt0) cc_final: 0.8187 (tt0) REVERT: E 217 HIS cc_start: 0.7096 (m170) cc_final: 0.6817 (m170) REVERT: E 221 LYS cc_start: 0.7222 (ttmm) cc_final: 0.6891 (ttmm) REVERT: F 106 LYS cc_start: 0.8301 (tppp) cc_final: 0.7879 (tppp) REVERT: F 128 ASN cc_start: 0.8548 (m-40) cc_final: 0.8297 (m110) REVERT: F 149 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7723 (ptpp) REVERT: F 211 LYS cc_start: 0.7303 (pptt) cc_final: 0.6856 (pptt) REVERT: F 221 LYS cc_start: 0.7533 (ttmm) cc_final: 0.7253 (ttmm) REVERT: G 97 LYS cc_start: 0.7776 (tttm) cc_final: 0.7498 (tttm) REVERT: G 149 LYS cc_start: 0.7908 (ptpp) cc_final: 0.7656 (ptpp) REVERT: G 203 GLU cc_start: 0.7500 (mp0) cc_final: 0.7110 (mp0) REVERT: G 221 LYS cc_start: 0.7394 (ttmm) cc_final: 0.7137 (ttmm) REVERT: G 238 LYS cc_start: 0.7658 (mttt) cc_final: 0.7207 (mttp) REVERT: H 78 ASP cc_start: 0.8213 (t0) cc_final: 0.7900 (t70) REVERT: H 94 LYS cc_start: 0.7674 (pttp) cc_final: 0.6815 (pttp) REVERT: H 96 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7563 (mp10) REVERT: H 97 LYS cc_start: 0.8020 (tttm) cc_final: 0.7812 (tttm) REVERT: H 98 ASP cc_start: 0.7167 (m-30) cc_final: 0.6766 (m-30) REVERT: H 106 LYS cc_start: 0.7976 (tppp) cc_final: 0.7636 (tppp) REVERT: H 129 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8073 (ttmm) REVERT: H 143 GLN cc_start: 0.8127 (mt0) cc_final: 0.7857 (mt0) REVERT: H 162 GLN cc_start: 0.8477 (tt0) cc_final: 0.8256 (tt0) REVERT: H 203 GLU cc_start: 0.7245 (mp0) cc_final: 0.6970 (mp0) REVERT: H 235 TRP cc_start: 0.7083 (m100) cc_final: 0.5343 (m100) REVERT: I 82 SER cc_start: 0.8431 (t) cc_final: 0.8188 (p) REVERT: I 86 LEU cc_start: 0.8248 (tp) cc_final: 0.7943 (tm) REVERT: I 97 LYS cc_start: 0.8213 (tttm) cc_final: 0.7826 (tttm) REVERT: I 106 LYS cc_start: 0.8464 (tppp) cc_final: 0.7739 (tppp) REVERT: I 143 GLN cc_start: 0.8128 (mt0) cc_final: 0.7796 (mt0) REVERT: I 162 GLN cc_start: 0.8500 (tt0) cc_final: 0.8179 (tt0) REVERT: I 172 ASP cc_start: 0.7765 (m-30) cc_final: 0.7533 (m-30) REVERT: I 176 GLU cc_start: 0.7824 (tp30) cc_final: 0.7322 (tp30) REVERT: I 194 CYS cc_start: 0.7357 (m) cc_final: 0.7064 (m) REVERT: I 203 GLU cc_start: 0.7457 (mp0) cc_final: 0.7231 (mp0) REVERT: I 206 ASP cc_start: 0.7600 (t0) cc_final: 0.7175 (t0) REVERT: I 209 PHE cc_start: 0.7610 (t80) cc_final: 0.7276 (t80) REVERT: I 211 LYS cc_start: 0.7568 (pptt) cc_final: 0.6783 (pptt) REVERT: I 221 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7463 (ttmm) REVERT: I 238 LYS cc_start: 0.8302 (mttt) cc_final: 0.7984 (mtpp) REVERT: I 243 GLU cc_start: 0.7216 (mp0) cc_final: 0.6857 (mp0) REVERT: J 78 ASP cc_start: 0.7887 (t0) cc_final: 0.7593 (t70) REVERT: J 109 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6928 (mm-30) REVERT: J 128 ASN cc_start: 0.8703 (m-40) cc_final: 0.8493 (m-40) REVERT: J 145 ILE cc_start: 0.8208 (mm) cc_final: 0.8006 (mp) REVERT: J 146 VAL cc_start: 0.8007 (t) cc_final: 0.7705 (p) REVERT: J 149 LYS cc_start: 0.8256 (ptpp) cc_final: 0.7958 (ptpp) REVERT: J 184 GLU cc_start: 0.7989 (pp20) cc_final: 0.7457 (pp20) REVERT: J 203 GLU cc_start: 0.7619 (mp0) cc_final: 0.7310 (mp0) REVERT: J 206 ASP cc_start: 0.7687 (t0) cc_final: 0.7134 (t0) REVERT: J 236 LEU cc_start: 0.7885 (pt) cc_final: 0.7541 (tt) REVERT: J 246 TYR cc_start: 0.7357 (m-80) cc_final: 0.7019 (m-80) REVERT: K 94 LYS cc_start: 0.7705 (pttp) cc_final: 0.7206 (pttp) REVERT: K 97 LYS cc_start: 0.8001 (tttm) cc_final: 0.7701 (tttm) REVERT: K 115 LEU cc_start: 0.7396 (mt) cc_final: 0.7130 (pp) REVERT: K 149 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7885 (mtmm) REVERT: K 162 GLN cc_start: 0.8428 (tt0) cc_final: 0.8226 (tt0) REVERT: K 171 GLN cc_start: 0.8027 (tp40) cc_final: 0.7804 (mm-40) REVERT: K 238 LYS cc_start: 0.8706 (mttt) cc_final: 0.8135 (mttm) REVERT: L 88 MET cc_start: 0.7972 (ttp) cc_final: 0.7553 (ptp) REVERT: L 89 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7915 (ptmt) REVERT: L 96 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8025 (mp10) REVERT: L 106 LYS cc_start: 0.8434 (tppp) cc_final: 0.7783 (tppp) REVERT: L 107 ASP cc_start: 0.7694 (m-30) cc_final: 0.7464 (m-30) REVERT: L 111 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7853 (mtmt) REVERT: L 173 TYR cc_start: 0.8030 (p90) cc_final: 0.7825 (p90) REVERT: L 212 LYS cc_start: 0.8488 (tttm) cc_final: 0.8210 (tttm) REVERT: M 84 TYR cc_start: 0.8201 (t80) cc_final: 0.7735 (t80) REVERT: M 203 GLU cc_start: 0.8022 (mp0) cc_final: 0.7652 (mp0) REVERT: M 204 LEU cc_start: 0.9100 (mt) cc_final: 0.8720 (mm) REVERT: M 212 LYS cc_start: 0.8556 (tttm) cc_final: 0.8333 (tttm) REVERT: M 217 HIS cc_start: 0.7544 (m170) cc_final: 0.7293 (m170) REVERT: N 88 MET cc_start: 0.7906 (ttp) cc_final: 0.7667 (ttp) REVERT: N 101 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7216 (tm-30) REVERT: N 211 LYS cc_start: 0.8229 (pptt) cc_final: 0.8024 (pptt) REVERT: O 176 GLU cc_start: 0.6824 (tp30) cc_final: 0.6382 (tp30) REVERT: S 103 LEU cc_start: 0.8718 (mt) cc_final: 0.8252 (mm) REVERT: S 110 ILE cc_start: 0.8679 (tt) cc_final: 0.8456 (pp) REVERT: S 196 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7816 (ttmt) REVERT: S 214 LYS cc_start: 0.8228 (tttp) cc_final: 0.7967 (tttp) outliers start: 0 outliers final: 2 residues processed: 775 average time/residue: 0.6764 time to fit residues: 600.8412 Evaluate side-chains 680 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 678 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN G 189 ASN I 189 ASN S 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127369 restraints weight = 40319.180| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.35 r_work: 0.3458 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26660 Z= 0.144 Angle : 0.604 11.057 35950 Z= 0.306 Chirality : 0.044 0.146 3834 Planarity : 0.006 0.056 4502 Dihedral : 4.094 27.679 3519 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.10 % Allowed : 12.86 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3156 helix: 0.26 (0.16), residues: 972 sheet: 1.02 (0.22), residues: 612 loop : 0.91 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 230 TYR 0.014 0.001 TYR L 84 PHE 0.024 0.001 PHE H 213 TRP 0.028 0.001 TRP M 235 HIS 0.004 0.001 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00315 (26660) covalent geometry : angle 0.60413 (35950) hydrogen bonds : bond 0.04812 ( 1098) hydrogen bonds : angle 5.53560 ( 3186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 676 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8786 (tt) cc_final: 0.8449 (tp) REVERT: A 164 ILE cc_start: 0.8510 (mp) cc_final: 0.8258 (mt) REVERT: A 187 LYS cc_start: 0.7923 (tttt) cc_final: 0.7703 (tttt) REVERT: A 194 CYS cc_start: 0.7655 (m) cc_final: 0.7359 (m) REVERT: A 214 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9034 (tptm) REVERT: B 89 LYS cc_start: 0.8801 (ptmt) cc_final: 0.8534 (ptmm) REVERT: B 97 LYS cc_start: 0.8475 (tttm) cc_final: 0.8233 (tttm) REVERT: B 98 ASP cc_start: 0.7667 (m-30) cc_final: 0.7167 (m-30) REVERT: B 101 GLU cc_start: 0.7646 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 109 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 128 ASN cc_start: 0.8849 (m-40) cc_final: 0.8561 (m110) REVERT: B 129 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8260 (mtpp) REVERT: B 149 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8238 (ptpp) REVERT: B 168 ARG cc_start: 0.8818 (ttm-80) cc_final: 0.8583 (ttm110) REVERT: B 176 GLU cc_start: 0.7885 (tp30) cc_final: 0.7670 (tp30) REVERT: C 84 TYR cc_start: 0.8555 (t80) cc_final: 0.8194 (t80) REVERT: C 89 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8312 (ptmm) REVERT: C 106 LYS cc_start: 0.8619 (tppp) cc_final: 0.8176 (tppp) REVERT: C 107 ASP cc_start: 0.7854 (m-30) cc_final: 0.7614 (m-30) REVERT: C 217 HIS cc_start: 0.8071 (m170) cc_final: 0.7715 (m90) REVERT: C 235 TRP cc_start: 0.8382 (m100) cc_final: 0.8065 (m100) REVERT: D 89 LYS cc_start: 0.8586 (ptmt) cc_final: 0.8339 (ptmm) REVERT: D 106 LYS cc_start: 0.8104 (tppp) cc_final: 0.7683 (tppp) REVERT: D 149 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8287 (ptpp) REVERT: D 203 GLU cc_start: 0.8178 (mp0) cc_final: 0.7786 (mp0) REVERT: D 212 LYS cc_start: 0.8191 (tttm) cc_final: 0.7937 (tttm) REVERT: E 106 LYS cc_start: 0.8603 (tppp) cc_final: 0.8125 (tppp) REVERT: E 162 GLN cc_start: 0.8614 (tt0) cc_final: 0.8394 (tt0) REVERT: E 184 GLU cc_start: 0.7822 (pp20) cc_final: 0.7588 (pp20) REVERT: E 203 GLU cc_start: 0.8181 (mp0) cc_final: 0.7931 (mp0) REVERT: E 221 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7512 (ttmm) REVERT: F 106 LYS cc_start: 0.8430 (tppp) cc_final: 0.8044 (tppp) REVERT: F 128 ASN cc_start: 0.8753 (m-40) cc_final: 0.8476 (m110) REVERT: F 211 LYS cc_start: 0.8208 (pptt) cc_final: 0.7717 (pptt) REVERT: F 212 LYS cc_start: 0.8035 (tttm) cc_final: 0.7696 (tttm) REVERT: F 221 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7473 (ttmm) REVERT: G 97 LYS cc_start: 0.8045 (tttm) cc_final: 0.7732 (tttm) REVERT: G 107 ASP cc_start: 0.7704 (m-30) cc_final: 0.7269 (m-30) REVERT: G 109 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7740 (mm-30) REVERT: G 149 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8257 (ptpp) REVERT: G 203 GLU cc_start: 0.7988 (mp0) cc_final: 0.7701 (mp0) REVERT: G 214 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8428 (ttpt) REVERT: G 221 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7449 (ttmm) REVERT: G 238 LYS cc_start: 0.8205 (mttt) cc_final: 0.7845 (mttp) REVERT: H 78 ASP cc_start: 0.8412 (t0) cc_final: 0.8149 (t0) REVERT: H 94 LYS cc_start: 0.8086 (pttp) cc_final: 0.7229 (pttp) REVERT: H 97 LYS cc_start: 0.8248 (tttm) cc_final: 0.8010 (tttm) REVERT: H 98 ASP cc_start: 0.7764 (m-30) cc_final: 0.7409 (m-30) REVERT: H 109 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7594 (mm-30) REVERT: H 129 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8288 (ttmm) REVERT: H 162 GLN cc_start: 0.8565 (tt0) cc_final: 0.8345 (tt0) REVERT: H 170 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7168 (mt-10) REVERT: H 203 GLU cc_start: 0.7873 (mp0) cc_final: 0.7652 (mp0) REVERT: H 235 TRP cc_start: 0.8414 (m100) cc_final: 0.7739 (m100) REVERT: I 97 LYS cc_start: 0.8486 (tttm) cc_final: 0.8215 (tttm) REVERT: I 106 LYS cc_start: 0.8789 (tppp) cc_final: 0.8279 (tppp) REVERT: I 109 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7863 (mm-30) REVERT: I 143 GLN cc_start: 0.8250 (mt0) cc_final: 0.7962 (mt0) REVERT: I 145 ILE cc_start: 0.8609 (mm) cc_final: 0.8403 (mt) REVERT: I 162 GLN cc_start: 0.8593 (tt0) cc_final: 0.8324 (tt0) REVERT: I 172 ASP cc_start: 0.8122 (m-30) cc_final: 0.7921 (m-30) REVERT: I 176 GLU cc_start: 0.8168 (tp30) cc_final: 0.7831 (tp30) REVERT: I 211 LYS cc_start: 0.8330 (pptt) cc_final: 0.7825 (pptt) REVERT: I 221 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7872 (ttmm) REVERT: I 243 GLU cc_start: 0.7377 (mp0) cc_final: 0.7040 (mp0) REVERT: J 103 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8346 (mp) REVERT: J 149 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8346 (ptpp) REVERT: J 203 GLU cc_start: 0.8397 (mp0) cc_final: 0.8169 (mp0) REVERT: J 217 HIS cc_start: 0.7644 (m170) cc_final: 0.7418 (m-70) REVERT: J 232 LYS cc_start: 0.7500 (tmtm) cc_final: 0.7195 (tmtm) REVERT: J 243 GLU cc_start: 0.7335 (mp0) cc_final: 0.6767 (mp0) REVERT: J 246 TYR cc_start: 0.7509 (m-80) cc_final: 0.7187 (m-80) REVERT: K 82 SER cc_start: 0.8444 (t) cc_final: 0.8235 (p) REVERT: K 94 LYS cc_start: 0.8027 (pttp) cc_final: 0.7540 (pttp) REVERT: K 97 LYS cc_start: 0.8304 (tttm) cc_final: 0.8021 (tttm) REVERT: K 149 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8397 (mtmm) REVERT: K 162 GLN cc_start: 0.8570 (tt0) cc_final: 0.8368 (tt0) REVERT: K 238 LYS cc_start: 0.8510 (mttt) cc_final: 0.8225 (mmtm) REVERT: L 106 LYS cc_start: 0.8507 (tppp) cc_final: 0.7998 (tppp) REVERT: L 107 ASP cc_start: 0.7944 (m-30) cc_final: 0.7741 (m-30) REVERT: L 212 LYS cc_start: 0.8744 (tttm) cc_final: 0.8531 (tttm) REVERT: L 235 TRP cc_start: 0.8469 (m100) cc_final: 0.7971 (m100) REVERT: M 127 LEU cc_start: 0.8597 (mm) cc_final: 0.8349 (mt) REVERT: M 203 GLU cc_start: 0.8138 (mp0) cc_final: 0.7743 (mp0) REVERT: M 212 LYS cc_start: 0.8573 (tttm) cc_final: 0.8373 (tttm) REVERT: M 235 TRP cc_start: 0.7699 (m100) cc_final: 0.7374 (m100) REVERT: N 101 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7272 (tm-30) REVERT: N 122 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8135 (mmmm) REVERT: N 175 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7342 (p0) REVERT: N 176 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7213 (tm-30) REVERT: N 211 LYS cc_start: 0.8572 (pptt) cc_final: 0.8282 (pptt) REVERT: O 117 TYR cc_start: 0.7058 (p90) cc_final: 0.6229 (p90) REVERT: O 175 ASN cc_start: 0.7327 (p0) cc_final: 0.6899 (p0) REVERT: O 176 GLU cc_start: 0.7020 (tp30) cc_final: 0.6807 (tp30) REVERT: O 192 MET cc_start: 0.7210 (tmm) cc_final: 0.6900 (tmm) REVERT: O 211 LYS cc_start: 0.8799 (pptt) cc_final: 0.8505 (pptt) REVERT: R 94 LYS cc_start: 0.8486 (tppt) cc_final: 0.8186 (tppt) REVERT: R 118 LEU cc_start: 0.7001 (tp) cc_final: 0.6651 (tp) REVERT: S 92 GLU cc_start: 0.7392 (pp20) cc_final: 0.6985 (pp20) REVERT: S 103 LEU cc_start: 0.8650 (mt) cc_final: 0.8425 (mm) REVERT: S 109 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7633 (mm-30) REVERT: S 129 LYS cc_start: 0.8246 (ttmm) cc_final: 0.8020 (ttmm) REVERT: S 159 CYS cc_start: 0.8250 (m) cc_final: 0.8050 (p) REVERT: S 196 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8079 (ttmt) REVERT: S 205 TRP cc_start: 0.7823 (m100) cc_final: 0.7461 (m100) REVERT: S 214 LYS cc_start: 0.8723 (tttp) cc_final: 0.8384 (tttp) outliers start: 59 outliers final: 21 residues processed: 690 average time/residue: 0.7159 time to fit residues: 561.0648 Evaluate side-chains 676 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 651 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain K residue 242 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain S residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 143 optimal weight: 0.0000 chunk 275 optimal weight: 9.9990 chunk 266 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN E 217 HIS G 189 ASN S 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125786 restraints weight = 39934.058| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.33 r_work: 0.3434 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26660 Z= 0.153 Angle : 0.578 8.504 35950 Z= 0.293 Chirality : 0.044 0.150 3834 Planarity : 0.006 0.057 4502 Dihedral : 4.043 21.896 3514 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.27 % Allowed : 15.99 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.96 (0.15), residues: 3156 helix: 0.36 (0.17), residues: 972 sheet: 0.98 (0.22), residues: 612 loop : 0.89 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 230 TYR 0.016 0.001 TYR E 117 PHE 0.018 0.001 PHE B 213 TRP 0.019 0.001 TRP N 205 HIS 0.002 0.001 HIS M 160 Details of bonding type rmsd covalent geometry : bond 0.00345 (26660) covalent geometry : angle 0.57772 (35950) hydrogen bonds : bond 0.04696 ( 1098) hydrogen bonds : angle 5.21335 ( 3186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 627 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8802 (tt) cc_final: 0.8525 (tp) REVERT: A 164 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8242 (mt) REVERT: A 187 LYS cc_start: 0.8059 (tttt) cc_final: 0.7819 (ttmt) REVERT: A 194 CYS cc_start: 0.7767 (m) cc_final: 0.7491 (m) REVERT: A 214 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9067 (tptm) REVERT: B 89 LYS cc_start: 0.8864 (ptmt) cc_final: 0.8645 (ptmm) REVERT: B 97 LYS cc_start: 0.8382 (tttm) cc_final: 0.8135 (tttm) REVERT: B 98 ASP cc_start: 0.7721 (m-30) cc_final: 0.7288 (m-30) REVERT: B 106 LYS cc_start: 0.8712 (tppp) cc_final: 0.8121 (tppp) REVERT: B 129 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8275 (mtpp) REVERT: B 149 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8222 (ptpp) REVERT: B 192 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8016 (ppp) REVERT: C 84 TYR cc_start: 0.8569 (t80) cc_final: 0.7995 (t80) REVERT: C 106 LYS cc_start: 0.8654 (tppp) cc_final: 0.8161 (tppp) REVERT: C 107 ASP cc_start: 0.7883 (m-30) cc_final: 0.7643 (m-30) REVERT: C 217 HIS cc_start: 0.8149 (m170) cc_final: 0.7703 (m90) REVERT: C 235 TRP cc_start: 0.8434 (m100) cc_final: 0.8159 (m100) REVERT: D 84 TYR cc_start: 0.8649 (t80) cc_final: 0.8110 (t80) REVERT: D 89 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8352 (ptmm) REVERT: D 106 LYS cc_start: 0.8218 (tppp) cc_final: 0.7704 (tppp) REVERT: D 149 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8224 (ptpp) REVERT: D 212 LYS cc_start: 0.8140 (tttm) cc_final: 0.7892 (tttm) REVERT: E 92 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7247 (pp20) REVERT: E 106 LYS cc_start: 0.8631 (tppp) cc_final: 0.8090 (tppp) REVERT: E 162 GLN cc_start: 0.8579 (tt0) cc_final: 0.8373 (tt0) REVERT: E 203 GLU cc_start: 0.8194 (mp0) cc_final: 0.7953 (mp0) REVERT: E 214 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8314 (mttt) REVERT: E 221 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7432 (ttmm) REVERT: F 99 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7698 (mp) REVERT: F 106 LYS cc_start: 0.8463 (tppp) cc_final: 0.8066 (tppp) REVERT: F 128 ASN cc_start: 0.8795 (m-40) cc_final: 0.8529 (m110) REVERT: F 192 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7644 (ppp) REVERT: F 212 LYS cc_start: 0.8003 (tttm) cc_final: 0.7754 (tttm) REVERT: G 107 ASP cc_start: 0.7754 (m-30) cc_final: 0.7513 (m-30) REVERT: G 109 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7754 (mm-30) REVERT: G 149 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8213 (ptpp) REVERT: G 203 GLU cc_start: 0.8067 (mp0) cc_final: 0.7777 (mp0) REVERT: G 211 LYS cc_start: 0.8336 (pptt) cc_final: 0.8033 (pttt) REVERT: G 238 LYS cc_start: 0.8212 (mttt) cc_final: 0.7907 (mttp) REVERT: H 94 LYS cc_start: 0.8005 (pttp) cc_final: 0.7166 (pttp) REVERT: H 97 LYS cc_start: 0.8144 (tttm) cc_final: 0.7886 (tttm) REVERT: H 98 ASP cc_start: 0.7735 (m-30) cc_final: 0.7392 (m-30) REVERT: H 109 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7626 (mm-30) REVERT: H 129 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8269 (ttmm) REVERT: H 162 GLN cc_start: 0.8561 (tt0) cc_final: 0.8342 (tt0) REVERT: H 235 TRP cc_start: 0.8541 (m100) cc_final: 0.8177 (m100) REVERT: I 84 TYR cc_start: 0.8910 (t80) cc_final: 0.8625 (t80) REVERT: I 97 LYS cc_start: 0.8424 (tttm) cc_final: 0.8181 (tttm) REVERT: I 99 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7390 (mp) REVERT: I 106 LYS cc_start: 0.8775 (tppp) cc_final: 0.8262 (tppp) REVERT: I 109 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7872 (mm-30) REVERT: I 162 GLN cc_start: 0.8560 (tt0) cc_final: 0.8333 (tt0) REVERT: I 176 GLU cc_start: 0.8138 (tp30) cc_final: 0.7803 (tp30) REVERT: I 211 LYS cc_start: 0.8374 (pptt) cc_final: 0.8051 (pptt) REVERT: I 243 GLU cc_start: 0.7337 (mp0) cc_final: 0.7016 (mp0) REVERT: J 103 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8429 (mp) REVERT: J 109 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7815 (mm-30) REVERT: J 149 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8342 (ptpp) REVERT: J 203 GLU cc_start: 0.8432 (mp0) cc_final: 0.8117 (mp0) REVERT: J 211 LYS cc_start: 0.8618 (pptt) cc_final: 0.8381 (pptt) REVERT: J 214 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (mttt) REVERT: J 232 LYS cc_start: 0.7810 (tmtm) cc_final: 0.7438 (tmtm) REVERT: J 242 VAL cc_start: 0.8307 (m) cc_final: 0.7904 (p) REVERT: J 243 GLU cc_start: 0.7505 (mp0) cc_final: 0.7184 (mp0) REVERT: J 246 TYR cc_start: 0.7604 (m-80) cc_final: 0.7200 (m-80) REVERT: K 94 LYS cc_start: 0.7897 (pttp) cc_final: 0.7335 (pttp) REVERT: K 97 LYS cc_start: 0.8187 (tttm) cc_final: 0.7914 (tttm) REVERT: K 111 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8355 (mmtp) REVERT: K 149 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8391 (mtmm) REVERT: K 162 GLN cc_start: 0.8546 (tt0) cc_final: 0.8316 (tt0) REVERT: K 238 LYS cc_start: 0.8539 (mttt) cc_final: 0.8270 (mmtm) REVERT: K 241 GLN cc_start: 0.7166 (mm-40) cc_final: 0.6962 (mm-40) REVERT: K 242 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (t) REVERT: L 88 MET cc_start: 0.8206 (ttp) cc_final: 0.7849 (ptp) REVERT: L 92 GLU cc_start: 0.6809 (pp20) cc_final: 0.6588 (pp20) REVERT: L 106 LYS cc_start: 0.8512 (tppp) cc_final: 0.7990 (tppp) REVERT: L 107 ASP cc_start: 0.7985 (m-30) cc_final: 0.7751 (m-30) REVERT: L 235 TRP cc_start: 0.8481 (m100) cc_final: 0.7994 (m100) REVERT: L 238 LYS cc_start: 0.8422 (mptt) cc_final: 0.8143 (mptt) REVERT: M 106 LYS cc_start: 0.8675 (mmpt) cc_final: 0.8469 (mmpt) REVERT: M 127 LEU cc_start: 0.8589 (mm) cc_final: 0.8356 (mt) REVERT: M 162 GLN cc_start: 0.8613 (tt0) cc_final: 0.8392 (tt0) REVERT: M 203 GLU cc_start: 0.8242 (mp0) cc_final: 0.7833 (mp0) REVERT: N 99 LEU cc_start: 0.8044 (mm) cc_final: 0.7837 (mm) REVERT: N 101 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7210 (tm-30) REVERT: N 124 ARG cc_start: 0.8615 (mtt90) cc_final: 0.8316 (mtt90) REVERT: N 166 VAL cc_start: 0.8831 (m) cc_final: 0.8580 (t) REVERT: N 175 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7453 (p0) REVERT: N 176 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7344 (tm-30) REVERT: N 187 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7789 (tppp) REVERT: N 211 LYS cc_start: 0.8649 (pptt) cc_final: 0.8347 (pptt) REVERT: O 117 TYR cc_start: 0.7032 (p90) cc_final: 0.6246 (p90) REVERT: O 176 GLU cc_start: 0.7160 (tp30) cc_final: 0.6880 (tp30) REVERT: O 192 MET cc_start: 0.7268 (tmm) cc_final: 0.6837 (tmm) REVERT: O 211 LYS cc_start: 0.8842 (pptt) cc_final: 0.8549 (pptt) REVERT: R 94 LYS cc_start: 0.8469 (tppt) cc_final: 0.8171 (tppt) REVERT: S 92 GLU cc_start: 0.7488 (pp20) cc_final: 0.6960 (pp20) REVERT: S 94 LYS cc_start: 0.8381 (pttp) cc_final: 0.8001 (pttp) REVERT: S 103 LEU cc_start: 0.8678 (mt) cc_final: 0.8430 (mm) REVERT: S 127 LEU cc_start: 0.8276 (mm) cc_final: 0.8024 (mt) REVERT: S 159 CYS cc_start: 0.8249 (m) cc_final: 0.7942 (t) REVERT: S 196 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8117 (ttmt) REVERT: S 214 LYS cc_start: 0.8772 (tttp) cc_final: 0.8420 (tttp) outliers start: 64 outliers final: 26 residues processed: 646 average time/residue: 0.7239 time to fit residues: 531.1660 Evaluate side-chains 646 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 607 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 242 VAL Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain N residue 187 LYS Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain R residue 150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 22 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 160 optimal weight: 0.0030 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 217 HIS L 217 HIS M 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.164949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127182 restraints weight = 39726.042| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.30 r_work: 0.3456 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26660 Z= 0.133 Angle : 0.558 9.962 35950 Z= 0.283 Chirality : 0.043 0.170 3834 Planarity : 0.006 0.054 4502 Dihedral : 3.992 21.311 3514 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.16 % Allowed : 17.24 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 1.05 (0.16), residues: 3156 helix: 0.55 (0.17), residues: 954 sheet: 0.96 (0.22), residues: 612 loop : 0.90 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 230 TYR 0.017 0.001 TYR A 84 PHE 0.015 0.001 PHE B 213 TRP 0.023 0.001 TRP N 205 HIS 0.003 0.001 HIS J 217 Details of bonding type rmsd covalent geometry : bond 0.00298 (26660) covalent geometry : angle 0.55783 (35950) hydrogen bonds : bond 0.04240 ( 1098) hydrogen bonds : angle 5.00533 ( 3186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 613 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8832 (tt) cc_final: 0.8582 (tp) REVERT: A 164 ILE cc_start: 0.8565 (mp) cc_final: 0.8308 (mt) REVERT: A 187 LYS cc_start: 0.8077 (tttt) cc_final: 0.7761 (tttt) REVERT: A 194 CYS cc_start: 0.7789 (m) cc_final: 0.7488 (m) REVERT: A 214 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9061 (tptm) REVERT: B 89 LYS cc_start: 0.8885 (ptmt) cc_final: 0.8657 (ptmm) REVERT: B 97 LYS cc_start: 0.8345 (tttm) cc_final: 0.8115 (tttm) REVERT: B 98 ASP cc_start: 0.7760 (m-30) cc_final: 0.7320 (m-30) REVERT: B 108 ILE cc_start: 0.8539 (mt) cc_final: 0.8339 (mm) REVERT: B 129 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8246 (mtpp) REVERT: B 149 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8294 (ptpp) REVERT: B 187 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7716 (ttmm) REVERT: B 192 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8031 (ppp) REVERT: B 214 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8694 (mttp) REVERT: C 84 TYR cc_start: 0.8567 (t80) cc_final: 0.8119 (t80) REVERT: C 106 LYS cc_start: 0.8640 (tppp) cc_final: 0.8121 (tppp) REVERT: C 221 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8096 (ttmm) REVERT: C 235 TRP cc_start: 0.8464 (m100) cc_final: 0.8196 (m100) REVERT: D 84 TYR cc_start: 0.8649 (t80) cc_final: 0.8118 (t80) REVERT: D 89 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8409 (ptmm) REVERT: D 106 LYS cc_start: 0.8267 (tppp) cc_final: 0.7738 (tppp) REVERT: D 149 LYS cc_start: 0.8423 (ptpp) cc_final: 0.8203 (ptpp) REVERT: D 192 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7970 (ptm) REVERT: D 211 LYS cc_start: 0.8317 (pptt) cc_final: 0.8095 (pptt) REVERT: D 212 LYS cc_start: 0.8116 (tttm) cc_final: 0.7880 (tttm) REVERT: E 92 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: E 106 LYS cc_start: 0.8618 (tppp) cc_final: 0.8071 (tppp) REVERT: E 162 GLN cc_start: 0.8530 (tt0) cc_final: 0.8309 (tt0) REVERT: E 203 GLU cc_start: 0.8156 (mp0) cc_final: 0.7914 (mp0) REVERT: E 214 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (mttt) REVERT: F 99 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7802 (mp) REVERT: F 106 LYS cc_start: 0.8490 (tppp) cc_final: 0.8050 (tppp) REVERT: F 117 TYR cc_start: 0.8755 (p90) cc_final: 0.8456 (p90) REVERT: F 192 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7680 (ppp) REVERT: F 211 LYS cc_start: 0.8231 (pptt) cc_final: 0.7733 (pptt) REVERT: F 212 LYS cc_start: 0.7949 (tttm) cc_final: 0.7629 (tttm) REVERT: G 107 ASP cc_start: 0.7768 (m-30) cc_final: 0.7496 (m-30) REVERT: G 109 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7822 (mm-30) REVERT: G 125 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8508 (mtm180) REVERT: G 149 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8229 (ptpp) REVERT: G 211 LYS cc_start: 0.8298 (pptt) cc_final: 0.7993 (pttt) REVERT: G 238 LYS cc_start: 0.8179 (mttt) cc_final: 0.7872 (mttp) REVERT: H 97 LYS cc_start: 0.8169 (tttm) cc_final: 0.7945 (tttm) REVERT: H 98 ASP cc_start: 0.7772 (m-30) cc_final: 0.7435 (m-30) REVERT: H 107 ASP cc_start: 0.7819 (m-30) cc_final: 0.7606 (m-30) REVERT: H 109 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7618 (mm-30) REVERT: H 129 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8236 (ttmm) REVERT: H 192 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8151 (ppp) REVERT: H 235 TRP cc_start: 0.8579 (m100) cc_final: 0.8173 (m100) REVERT: I 84 TYR cc_start: 0.8922 (t80) cc_final: 0.8707 (t80) REVERT: I 97 LYS cc_start: 0.8383 (tttm) cc_final: 0.8146 (tttm) REVERT: I 98 ASP cc_start: 0.7800 (m-30) cc_final: 0.7366 (m-30) REVERT: I 99 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7458 (mp) REVERT: I 106 LYS cc_start: 0.8718 (tppp) cc_final: 0.8201 (tppp) REVERT: I 109 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7881 (mm-30) REVERT: I 162 GLN cc_start: 0.8510 (tt0) cc_final: 0.8282 (tt0) REVERT: I 211 LYS cc_start: 0.8370 (pptt) cc_final: 0.8079 (pptt) REVERT: I 221 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8082 (ttmm) REVERT: I 243 GLU cc_start: 0.7310 (mp0) cc_final: 0.7015 (mp0) REVERT: J 109 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7786 (mm-30) REVERT: J 149 LYS cc_start: 0.8577 (ptpp) cc_final: 0.8351 (ptpp) REVERT: J 192 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8423 (ttp) REVERT: J 203 GLU cc_start: 0.8385 (mp0) cc_final: 0.8055 (mp0) REVERT: J 211 LYS cc_start: 0.8599 (pptt) cc_final: 0.8361 (pptt) REVERT: J 214 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7893 (mttt) REVERT: J 232 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7497 (tmtm) REVERT: J 242 VAL cc_start: 0.8340 (m) cc_final: 0.8122 (p) REVERT: J 243 GLU cc_start: 0.7589 (mp0) cc_final: 0.7374 (mp0) REVERT: J 246 TYR cc_start: 0.7574 (m-80) cc_final: 0.7180 (m-80) REVERT: K 94 LYS cc_start: 0.7882 (pttp) cc_final: 0.7361 (pttp) REVERT: K 97 LYS cc_start: 0.8153 (tttm) cc_final: 0.7893 (tttm) REVERT: K 111 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8347 (mmtp) REVERT: K 149 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8365 (mtmm) REVERT: K 162 GLN cc_start: 0.8471 (tt0) cc_final: 0.8245 (tt0) REVERT: K 212 LYS cc_start: 0.8734 (tttm) cc_final: 0.8458 (tptm) REVERT: K 238 LYS cc_start: 0.8578 (mttt) cc_final: 0.8308 (mmtm) REVERT: K 241 GLN cc_start: 0.7252 (mm-40) cc_final: 0.7026 (mm-40) REVERT: K 242 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8607 (t) REVERT: L 88 MET cc_start: 0.8269 (ttp) cc_final: 0.7892 (ptp) REVERT: L 106 LYS cc_start: 0.8503 (tppp) cc_final: 0.7975 (tppp) REVERT: L 235 TRP cc_start: 0.8488 (m100) cc_final: 0.7986 (m100) REVERT: M 106 LYS cc_start: 0.8705 (mmpt) cc_final: 0.8443 (mmpt) REVERT: M 117 TYR cc_start: 0.8334 (p90) cc_final: 0.7827 (p90) REVERT: M 127 LEU cc_start: 0.8579 (mm) cc_final: 0.8339 (mt) REVERT: M 162 GLN cc_start: 0.8587 (tt0) cc_final: 0.8362 (tt0) REVERT: M 203 GLU cc_start: 0.8280 (mp0) cc_final: 0.7876 (mp0) REVERT: N 96 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8137 (mm110) REVERT: N 99 LEU cc_start: 0.8054 (mm) cc_final: 0.7827 (mm) REVERT: N 101 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7221 (tm-30) REVERT: N 119 PRO cc_start: 0.7371 (Cg_exo) cc_final: 0.7102 (Cg_endo) REVERT: N 124 ARG cc_start: 0.8660 (mtt90) cc_final: 0.8235 (mtt90) REVERT: N 166 VAL cc_start: 0.8834 (m) cc_final: 0.8601 (t) REVERT: N 175 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7398 (p0) REVERT: N 176 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7274 (tm-30) REVERT: N 187 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7816 (tppp) REVERT: N 211 LYS cc_start: 0.8684 (pptt) cc_final: 0.8454 (pptt) REVERT: N 212 LYS cc_start: 0.8562 (tttm) cc_final: 0.8120 (tttm) REVERT: O 117 TYR cc_start: 0.6949 (p90) cc_final: 0.6302 (p90) REVERT: O 176 GLU cc_start: 0.7308 (tp30) cc_final: 0.7031 (tp30) REVERT: O 192 MET cc_start: 0.7264 (tmm) cc_final: 0.6767 (tmm) REVERT: O 211 LYS cc_start: 0.8846 (pptt) cc_final: 0.8540 (pptt) REVERT: R 94 LYS cc_start: 0.8467 (tppt) cc_final: 0.8186 (tppt) REVERT: R 149 LYS cc_start: 0.8351 (ptpp) cc_final: 0.8101 (ptpp) REVERT: S 92 GLU cc_start: 0.7475 (pp20) cc_final: 0.6935 (pp20) REVERT: S 94 LYS cc_start: 0.8322 (pttp) cc_final: 0.7968 (pttp) REVERT: S 103 LEU cc_start: 0.8686 (mt) cc_final: 0.8436 (mm) REVERT: S 127 LEU cc_start: 0.8263 (mm) cc_final: 0.7990 (mt) REVERT: S 159 CYS cc_start: 0.8400 (m) cc_final: 0.8016 (t) REVERT: S 196 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8112 (ttmt) REVERT: S 214 LYS cc_start: 0.8747 (tttp) cc_final: 0.8396 (tttp) outliers start: 89 outliers final: 31 residues processed: 648 average time/residue: 0.6992 time to fit residues: 515.5673 Evaluate side-chains 647 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 600 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 232 LYS Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 242 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain N residue 89 LYS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain N residue 187 LYS Chi-restraints excluded: chain R residue 150 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 75 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 252 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 267 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126048 restraints weight = 39777.680| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.30 r_work: 0.3430 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26660 Z= 0.166 Angle : 0.580 9.109 35950 Z= 0.297 Chirality : 0.044 0.150 3834 Planarity : 0.006 0.056 4502 Dihedral : 4.077 20.760 3514 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.30 % Allowed : 17.80 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.98 (0.16), residues: 3156 helix: 0.58 (0.17), residues: 954 sheet: 0.85 (0.22), residues: 612 loop : 0.82 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 230 TYR 0.018 0.001 TYR A 84 PHE 0.015 0.001 PHE I 222 TRP 0.031 0.001 TRP M 235 HIS 0.003 0.001 HIS K 225 Details of bonding type rmsd covalent geometry : bond 0.00380 (26660) covalent geometry : angle 0.58013 (35950) hydrogen bonds : bond 0.04652 ( 1098) hydrogen bonds : angle 4.94301 ( 3186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 613 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8821 (tt) cc_final: 0.8589 (tp) REVERT: A 149 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8264 (ptpp) REVERT: A 164 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8355 (mt) REVERT: A 194 CYS cc_start: 0.7773 (m) cc_final: 0.7483 (m) REVERT: A 214 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9007 (tttt) REVERT: B 89 LYS cc_start: 0.8930 (ptmt) cc_final: 0.8707 (ptmm) REVERT: B 97 LYS cc_start: 0.8261 (tttm) cc_final: 0.8040 (tttm) REVERT: B 98 ASP cc_start: 0.7694 (m-30) cc_final: 0.7223 (m-30) REVERT: B 108 ILE cc_start: 0.8573 (mt) cc_final: 0.8366 (mm) REVERT: B 149 LYS cc_start: 0.8507 (ptpp) cc_final: 0.8019 (ptpp) REVERT: B 172 ASP cc_start: 0.8113 (m-30) cc_final: 0.7854 (m-30) REVERT: B 192 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8110 (ppp) REVERT: B 214 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8603 (mttp) REVERT: C 106 LYS cc_start: 0.8607 (tppp) cc_final: 0.8052 (tppp) REVERT: C 191 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8088 (tp) REVERT: C 235 TRP cc_start: 0.8517 (m100) cc_final: 0.8273 (m100) REVERT: D 89 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8472 (ptmm) REVERT: D 106 LYS cc_start: 0.8285 (tppp) cc_final: 0.7710 (tppp) REVERT: D 149 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8179 (ptpp) REVERT: D 211 LYS cc_start: 0.8367 (pptt) cc_final: 0.8134 (pptt) REVERT: D 212 LYS cc_start: 0.8116 (tttm) cc_final: 0.7873 (tttm) REVERT: E 92 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: E 106 LYS cc_start: 0.8565 (tppp) cc_final: 0.8060 (tppp) REVERT: E 149 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8279 (ptpp) REVERT: E 162 GLN cc_start: 0.8583 (tt0) cc_final: 0.8369 (tt0) REVERT: E 203 GLU cc_start: 0.8176 (mp0) cc_final: 0.7944 (mp0) REVERT: E 214 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8387 (mttt) REVERT: F 106 LYS cc_start: 0.8527 (tppp) cc_final: 0.8060 (tppp) REVERT: F 192 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7713 (ppp) REVERT: F 211 LYS cc_start: 0.8260 (pptt) cc_final: 0.7783 (pptt) REVERT: F 212 LYS cc_start: 0.7986 (tttm) cc_final: 0.7675 (tttm) REVERT: G 106 LYS cc_start: 0.8570 (tppp) cc_final: 0.8028 (tppp) REVERT: G 107 ASP cc_start: 0.7770 (m-30) cc_final: 0.7461 (m-30) REVERT: G 109 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7899 (mm-30) REVERT: G 125 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8514 (mtm180) REVERT: G 176 GLU cc_start: 0.7686 (tp30) cc_final: 0.7451 (tp30) REVERT: G 211 LYS cc_start: 0.8325 (pptt) cc_final: 0.8023 (pttt) REVERT: G 238 LYS cc_start: 0.8182 (mttt) cc_final: 0.7866 (mttp) REVERT: H 94 LYS cc_start: 0.7932 (pttp) cc_final: 0.7549 (pttp) REVERT: H 97 LYS cc_start: 0.8148 (tttm) cc_final: 0.7904 (tttm) REVERT: H 129 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8259 (ttmm) REVERT: H 192 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (ppp) REVERT: H 235 TRP cc_start: 0.8608 (m100) cc_final: 0.8197 (m100) REVERT: I 97 LYS cc_start: 0.8343 (tttm) cc_final: 0.8128 (tttm) REVERT: I 98 ASP cc_start: 0.7815 (m-30) cc_final: 0.7398 (m-30) REVERT: I 106 LYS cc_start: 0.8746 (tppp) cc_final: 0.8511 (tppp) REVERT: I 109 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7876 (mm-30) REVERT: I 162 GLN cc_start: 0.8561 (tt0) cc_final: 0.8347 (tt0) REVERT: I 211 LYS cc_start: 0.8387 (pptt) cc_final: 0.8110 (pptt) REVERT: I 221 LYS cc_start: 0.8324 (ttmm) cc_final: 0.8114 (ttmm) REVERT: I 243 GLU cc_start: 0.7312 (mp0) cc_final: 0.7066 (mp0) REVERT: J 103 LEU cc_start: 0.8716 (mt) cc_final: 0.8450 (mp) REVERT: J 109 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7909 (mm-30) REVERT: J 149 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8338 (ptpp) REVERT: J 203 GLU cc_start: 0.8398 (mp0) cc_final: 0.8022 (mp0) REVERT: J 211 LYS cc_start: 0.8587 (pptt) cc_final: 0.8332 (pptt) REVERT: J 214 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7918 (mttt) REVERT: J 232 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7509 (tmtm) REVERT: J 246 TYR cc_start: 0.7456 (m-80) cc_final: 0.7154 (m-80) REVERT: K 94 LYS cc_start: 0.7882 (pttp) cc_final: 0.7535 (pttp) REVERT: K 97 LYS cc_start: 0.8160 (tttm) cc_final: 0.7902 (tttm) REVERT: K 149 LYS cc_start: 0.8651 (ptpp) cc_final: 0.8390 (mtmm) REVERT: K 162 GLN cc_start: 0.8485 (tt0) cc_final: 0.8235 (tt0) REVERT: K 212 LYS cc_start: 0.8719 (tttm) cc_final: 0.8457 (tptm) REVERT: K 238 LYS cc_start: 0.8595 (mttt) cc_final: 0.8321 (mmtm) REVERT: K 241 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7129 (mm-40) REVERT: L 88 MET cc_start: 0.8240 (ttp) cc_final: 0.7902 (ptp) REVERT: L 106 LYS cc_start: 0.8482 (tppp) cc_final: 0.7953 (tppp) REVERT: L 147 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8281 (t) REVERT: L 238 LYS cc_start: 0.8520 (mptt) cc_final: 0.8300 (mptt) REVERT: M 106 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8481 (mmpt) REVERT: M 117 TYR cc_start: 0.8355 (p90) cc_final: 0.7912 (p90) REVERT: M 127 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8364 (mt) REVERT: M 162 GLN cc_start: 0.8651 (tt0) cc_final: 0.8379 (tt0) REVERT: M 203 GLU cc_start: 0.8297 (mp0) cc_final: 0.7877 (mp0) REVERT: N 86 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8109 (tp) REVERT: N 96 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8105 (mm110) REVERT: N 99 LEU cc_start: 0.8183 (mm) cc_final: 0.7919 (mm) REVERT: N 119 PRO cc_start: 0.7697 (Cg_exo) cc_final: 0.7444 (Cg_endo) REVERT: N 124 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8333 (mtt90) REVERT: N 149 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8030 (ptpp) REVERT: N 166 VAL cc_start: 0.8830 (m) cc_final: 0.8612 (t) REVERT: N 175 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7492 (p0) REVERT: N 176 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7381 (tm-30) REVERT: N 187 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7816 (tppp) REVERT: N 211 LYS cc_start: 0.8706 (pptt) cc_final: 0.8480 (pptt) REVERT: N 212 LYS cc_start: 0.8617 (tttm) cc_final: 0.8206 (tttm) REVERT: O 117 TYR cc_start: 0.6980 (p90) cc_final: 0.6403 (p90) REVERT: O 127 LEU cc_start: 0.7097 (mt) cc_final: 0.6884 (mt) REVERT: O 176 GLU cc_start: 0.7347 (tp30) cc_final: 0.7064 (tp30) REVERT: O 192 MET cc_start: 0.7366 (tmm) cc_final: 0.6835 (tmm) REVERT: O 211 LYS cc_start: 0.8846 (pptt) cc_final: 0.8536 (pptt) REVERT: R 94 LYS cc_start: 0.8518 (tppt) cc_final: 0.8263 (tppt) REVERT: R 127 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7582 (mt) REVERT: S 92 GLU cc_start: 0.7446 (pp20) cc_final: 0.6923 (pp20) REVERT: S 94 LYS cc_start: 0.8363 (pttp) cc_final: 0.8079 (pttp) REVERT: S 103 LEU cc_start: 0.8785 (mt) cc_final: 0.8529 (mm) REVERT: S 127 LEU cc_start: 0.8308 (mm) cc_final: 0.8051 (mt) REVERT: S 129 LYS cc_start: 0.8356 (ttmm) cc_final: 0.8096 (ttmm) REVERT: S 196 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8149 (ttmt) REVERT: S 214 LYS cc_start: 0.8717 (tttp) cc_final: 0.8374 (tttp) outliers start: 93 outliers final: 44 residues processed: 647 average time/residue: 0.6826 time to fit residues: 501.2526 Evaluate side-chains 663 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 601 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 232 LYS Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain M residue 168 ARG Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 89 LYS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain N residue 186 CYS Chi-restraints excluded: chain N residue 187 LYS Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain S residue 186 CYS Chi-restraints excluded: chain S residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 116 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124404 restraints weight = 39512.246| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.29 r_work: 0.3414 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26660 Z= 0.223 Angle : 0.623 9.993 35950 Z= 0.321 Chirality : 0.046 0.162 3834 Planarity : 0.006 0.054 4502 Dihedral : 4.261 20.323 3514 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.34 % Allowed : 18.98 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.71 (0.15), residues: 3156 helix: 0.51 (0.17), residues: 922 sheet: 0.72 (0.22), residues: 612 loop : 0.52 (0.17), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 230 TYR 0.024 0.001 TYR N 84 PHE 0.021 0.002 PHE F 209 TRP 0.029 0.002 TRP N 205 HIS 0.004 0.001 HIS K 225 Details of bonding type rmsd covalent geometry : bond 0.00519 (26660) covalent geometry : angle 0.62314 (35950) hydrogen bonds : bond 0.05243 ( 1098) hydrogen bonds : angle 4.99282 ( 3186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 624 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8862 (tt) cc_final: 0.8642 (tp) REVERT: A 149 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8241 (ptpp) REVERT: A 164 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 187 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7544 (ttpp) REVERT: A 214 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9106 (tptm) REVERT: A 217 HIS cc_start: 0.8852 (m-70) cc_final: 0.8479 (m-70) REVERT: B 89 LYS cc_start: 0.8982 (ptmt) cc_final: 0.8747 (ptmm) REVERT: B 106 LYS cc_start: 0.8770 (tppp) cc_final: 0.8204 (tppp) REVERT: B 149 LYS cc_start: 0.8419 (ptpp) cc_final: 0.7921 (ptpp) REVERT: B 172 ASP cc_start: 0.8055 (m-30) cc_final: 0.7791 (m-30) REVERT: B 214 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8606 (mttp) REVERT: C 106 LYS cc_start: 0.8585 (tppp) cc_final: 0.7991 (tppp) REVERT: C 191 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8098 (tp) REVERT: C 203 GLU cc_start: 0.8192 (mp0) cc_final: 0.7825 (mp0) REVERT: D 89 LYS cc_start: 0.8647 (ptmt) cc_final: 0.8426 (ptmm) REVERT: D 106 LYS cc_start: 0.8284 (tppp) cc_final: 0.7691 (tppp) REVERT: D 168 ARG cc_start: 0.8879 (ttm-80) cc_final: 0.8437 (ttm-80) REVERT: D 211 LYS cc_start: 0.8346 (pptt) cc_final: 0.8096 (pptt) REVERT: D 212 LYS cc_start: 0.8109 (tttm) cc_final: 0.7844 (tttm) REVERT: D 233 LYS cc_start: 0.7621 (ttmm) cc_final: 0.7303 (ttmm) REVERT: E 92 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: E 106 LYS cc_start: 0.8577 (tppp) cc_final: 0.8075 (tppp) REVERT: E 149 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8287 (ptpp) REVERT: E 162 GLN cc_start: 0.8641 (tt0) cc_final: 0.8405 (tt0) REVERT: E 214 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8340 (mttt) REVERT: F 106 LYS cc_start: 0.8526 (tppp) cc_final: 0.8035 (tppp) REVERT: F 192 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7776 (ppp) REVERT: F 211 LYS cc_start: 0.8247 (pptt) cc_final: 0.7793 (pptt) REVERT: F 212 LYS cc_start: 0.8014 (tttm) cc_final: 0.7698 (tttm) REVERT: G 106 LYS cc_start: 0.8566 (tppp) cc_final: 0.8023 (tppp) REVERT: G 107 ASP cc_start: 0.7798 (m-30) cc_final: 0.7475 (m-30) REVERT: G 109 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7918 (mm-30) REVERT: G 125 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8527 (mtm180) REVERT: G 211 LYS cc_start: 0.8326 (pptt) cc_final: 0.8043 (pttt) REVERT: G 221 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7297 (mtmm) REVERT: G 238 LYS cc_start: 0.8220 (mttt) cc_final: 0.7915 (mttp) REVERT: H 94 LYS cc_start: 0.7872 (pttp) cc_final: 0.7501 (pttp) REVERT: H 97 LYS cc_start: 0.8096 (tttm) cc_final: 0.7876 (tttm) REVERT: H 129 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8285 (ttmm) REVERT: H 192 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8310 (ppp) REVERT: H 211 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8249 (mtpp) REVERT: H 235 TRP cc_start: 0.8580 (m100) cc_final: 0.8235 (m100) REVERT: I 98 ASP cc_start: 0.7850 (m-30) cc_final: 0.7425 (m-30) REVERT: I 106 LYS cc_start: 0.8699 (tppp) cc_final: 0.8340 (tppp) REVERT: I 109 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7981 (mm-30) REVERT: I 162 GLN cc_start: 0.8607 (tt0) cc_final: 0.8337 (tt0) REVERT: I 168 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8467 (ttm110) REVERT: I 211 LYS cc_start: 0.8440 (pptt) cc_final: 0.8151 (pptt) REVERT: I 238 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8589 (mmmm) REVERT: J 78 ASP cc_start: 0.8017 (t0) cc_final: 0.7776 (t70) REVERT: J 103 LEU cc_start: 0.8745 (mt) cc_final: 0.8486 (mp) REVERT: J 109 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7958 (mm-30) REVERT: J 203 GLU cc_start: 0.8359 (mp0) cc_final: 0.7940 (mp0) REVERT: J 211 LYS cc_start: 0.8625 (pptt) cc_final: 0.8372 (pptt) REVERT: J 214 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7901 (mttt) REVERT: J 236 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8375 (tt) REVERT: K 94 LYS cc_start: 0.7874 (pttp) cc_final: 0.7493 (pttp) REVERT: K 97 LYS cc_start: 0.8182 (tttm) cc_final: 0.7944 (tttm) REVERT: K 106 LYS cc_start: 0.8440 (tppp) cc_final: 0.7971 (tppp) REVERT: K 149 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8342 (mtmm) REVERT: K 203 GLU cc_start: 0.8427 (mp0) cc_final: 0.8110 (mp0) REVERT: K 238 LYS cc_start: 0.8621 (mttt) cc_final: 0.8312 (mmtm) REVERT: K 241 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7218 (mm-40) REVERT: L 88 MET cc_start: 0.8237 (ttp) cc_final: 0.7915 (ptp) REVERT: L 106 LYS cc_start: 0.8515 (tppp) cc_final: 0.7977 (tppp) REVERT: L 147 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8338 (t) REVERT: M 106 LYS cc_start: 0.8716 (mmpt) cc_final: 0.8448 (mmpt) REVERT: M 109 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7435 (mm-30) REVERT: M 117 TYR cc_start: 0.8373 (p90) cc_final: 0.7968 (p90) REVERT: M 127 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8458 (mt) REVERT: M 203 GLU cc_start: 0.8316 (mp0) cc_final: 0.7890 (mp0) REVERT: N 86 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8158 (tp) REVERT: N 94 LYS cc_start: 0.8565 (pttp) cc_final: 0.8270 (pttp) REVERT: N 99 LEU cc_start: 0.8438 (mm) cc_final: 0.8135 (mm) REVERT: N 119 PRO cc_start: 0.8022 (Cg_exo) cc_final: 0.7440 (Cg_endo) REVERT: N 122 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8098 (mttm) REVERT: N 124 ARG cc_start: 0.8707 (mtt90) cc_final: 0.8398 (mtt90) REVERT: N 149 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7955 (ptpp) REVERT: N 175 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7639 (p0) REVERT: N 176 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7535 (tm-30) REVERT: N 211 LYS cc_start: 0.8715 (pptt) cc_final: 0.8501 (pptt) REVERT: N 212 LYS cc_start: 0.8717 (tttm) cc_final: 0.8326 (tttm) REVERT: O 117 TYR cc_start: 0.6979 (p90) cc_final: 0.6473 (p90) REVERT: O 192 MET cc_start: 0.7336 (tmm) cc_final: 0.6905 (tpp) REVERT: O 211 LYS cc_start: 0.8864 (pptt) cc_final: 0.8519 (pptt) REVERT: R 94 LYS cc_start: 0.8559 (tppt) cc_final: 0.8355 (tppt) REVERT: R 127 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7632 (mt) REVERT: S 88 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7378 (mtp) REVERT: S 92 GLU cc_start: 0.7430 (pp20) cc_final: 0.6915 (pp20) REVERT: S 94 LYS cc_start: 0.8447 (pttp) cc_final: 0.8151 (pttp) REVERT: S 103 LEU cc_start: 0.8903 (mt) cc_final: 0.8635 (mm) REVERT: S 127 LEU cc_start: 0.8321 (mm) cc_final: 0.8089 (mt) REVERT: S 129 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8098 (ttmm) REVERT: S 196 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8098 (ttmt) REVERT: S 214 LYS cc_start: 0.8765 (tttp) cc_final: 0.8432 (tttp) REVERT: S 232 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8105 (mptt) outliers start: 94 outliers final: 47 residues processed: 661 average time/residue: 0.7346 time to fit residues: 551.7721 Evaluate side-chains 681 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 615 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 168 ARG Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 240 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 145 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain N residue 186 CYS Chi-restraints excluded: chain O residue 94 LYS Chi-restraints excluded: chain O residue 97 LYS Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 186 CYS Chi-restraints excluded: chain S residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 196 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 272 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN N 96 GLN ** P 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.163005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126073 restraints weight = 39312.012| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.28 r_work: 0.3451 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26660 Z= 0.137 Angle : 0.584 9.768 35950 Z= 0.298 Chirality : 0.044 0.171 3834 Planarity : 0.006 0.055 4502 Dihedral : 4.090 21.175 3514 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.91 % Allowed : 20.58 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.90 (0.16), residues: 3156 helix: 0.63 (0.17), residues: 954 sheet: 0.74 (0.22), residues: 612 loop : 0.71 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 230 TYR 0.019 0.001 TYR M 173 PHE 0.013 0.001 PHE B 222 TRP 0.045 0.001 TRP N 205 HIS 0.002 0.001 HIS M 225 Details of bonding type rmsd covalent geometry : bond 0.00311 (26660) covalent geometry : angle 0.58396 (35950) hydrogen bonds : bond 0.04165 ( 1098) hydrogen bonds : angle 4.79192 ( 3186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 593 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8857 (tt) cc_final: 0.8626 (tp) REVERT: A 149 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8241 (ptpp) REVERT: A 164 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8314 (mt) REVERT: A 187 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7721 (ttmt) REVERT: A 194 CYS cc_start: 0.7890 (m) cc_final: 0.7595 (m) REVERT: A 214 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8872 (tptt) REVERT: B 89 LYS cc_start: 0.8984 (ptmt) cc_final: 0.8710 (ptmm) REVERT: B 106 LYS cc_start: 0.8744 (tppp) cc_final: 0.8152 (tppp) REVERT: B 115 LEU cc_start: 0.8222 (pp) cc_final: 0.8000 (pt) REVERT: B 149 LYS cc_start: 0.8409 (ptpp) cc_final: 0.7878 (ptpp) REVERT: B 172 ASP cc_start: 0.8088 (m-30) cc_final: 0.7823 (m-30) REVERT: C 106 LYS cc_start: 0.8588 (tppp) cc_final: 0.8013 (tppp) REVERT: C 217 HIS cc_start: 0.8222 (m170) cc_final: 0.7871 (m170) REVERT: D 89 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8414 (ptmm) REVERT: D 106 LYS cc_start: 0.8258 (tppp) cc_final: 0.7668 (tppp) REVERT: D 168 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8526 (ttm-80) REVERT: D 192 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (ptm) REVERT: D 211 LYS cc_start: 0.8347 (pptt) cc_final: 0.8089 (pptt) REVERT: D 212 LYS cc_start: 0.8089 (tttm) cc_final: 0.7834 (tttm) REVERT: D 233 LYS cc_start: 0.7638 (ttmm) cc_final: 0.7354 (ttmm) REVERT: E 92 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: E 106 LYS cc_start: 0.8556 (tppp) cc_final: 0.8034 (tppp) REVERT: E 149 LYS cc_start: 0.8580 (ptpp) cc_final: 0.8297 (ptpp) REVERT: E 162 GLN cc_start: 0.8606 (tt0) cc_final: 0.8383 (tt0) REVERT: E 214 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8313 (mttt) REVERT: F 106 LYS cc_start: 0.8540 (tppp) cc_final: 0.8324 (tppp) REVERT: F 192 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7709 (ppp) REVERT: F 212 LYS cc_start: 0.7957 (tttm) cc_final: 0.7713 (tttm) REVERT: F 236 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7862 (pp) REVERT: F 242 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7677 (p) REVERT: G 106 LYS cc_start: 0.8554 (tppp) cc_final: 0.8001 (tppp) REVERT: G 107 ASP cc_start: 0.7840 (m-30) cc_final: 0.7510 (m-30) REVERT: G 109 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7904 (mm-30) REVERT: G 125 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8505 (mtm180) REVERT: G 211 LYS cc_start: 0.8302 (pptt) cc_final: 0.8017 (pttt) REVERT: G 238 LYS cc_start: 0.8256 (mttt) cc_final: 0.7951 (mttp) REVERT: H 94 LYS cc_start: 0.7839 (pttp) cc_final: 0.7456 (pttp) REVERT: H 97 LYS cc_start: 0.7991 (tttm) cc_final: 0.7789 (tttm) REVERT: H 129 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8250 (ttmm) REVERT: H 192 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (ppp) REVERT: H 211 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (mtpp) REVERT: H 221 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7824 (ttmm) REVERT: H 235 TRP cc_start: 0.8577 (m100) cc_final: 0.8245 (m100) REVERT: I 84 TYR cc_start: 0.8876 (t80) cc_final: 0.8656 (t80) REVERT: I 98 ASP cc_start: 0.7757 (m-30) cc_final: 0.7355 (m-30) REVERT: I 106 LYS cc_start: 0.8687 (tppp) cc_final: 0.8318 (tppp) REVERT: I 109 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7862 (mm-30) REVERT: I 162 GLN cc_start: 0.8541 (tt0) cc_final: 0.8306 (tt0) REVERT: I 238 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8616 (mmmm) REVERT: J 103 LEU cc_start: 0.8729 (mt) cc_final: 0.8445 (mp) REVERT: J 109 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7949 (mm-30) REVERT: J 203 GLU cc_start: 0.8378 (mp0) cc_final: 0.7984 (mp0) REVERT: J 211 LYS cc_start: 0.8604 (pptt) cc_final: 0.8344 (pptt) REVERT: J 214 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7829 (mttt) REVERT: K 94 LYS cc_start: 0.7909 (pttp) cc_final: 0.7548 (pttp) REVERT: K 97 LYS cc_start: 0.8178 (tttm) cc_final: 0.7928 (tttm) REVERT: K 149 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8342 (mtmm) REVERT: K 203 GLU cc_start: 0.8402 (mp0) cc_final: 0.8087 (mp0) REVERT: K 238 LYS cc_start: 0.8575 (mttt) cc_final: 0.8357 (mppt) REVERT: K 241 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7254 (mm-40) REVERT: L 88 MET cc_start: 0.8252 (ttp) cc_final: 0.7889 (ptp) REVERT: L 106 LYS cc_start: 0.8489 (tppp) cc_final: 0.7933 (tppp) REVERT: L 147 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8296 (t) REVERT: L 238 LYS cc_start: 0.8663 (mptt) cc_final: 0.8279 (mmtm) REVERT: M 106 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8446 (mmpt) REVERT: M 127 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8407 (mt) REVERT: M 146 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8575 (t) REVERT: M 203 GLU cc_start: 0.8275 (mp0) cc_final: 0.7869 (mp0) REVERT: N 94 LYS cc_start: 0.8581 (pttp) cc_final: 0.8271 (pttp) REVERT: N 99 LEU cc_start: 0.8225 (mm) cc_final: 0.7960 (mm) REVERT: N 119 PRO cc_start: 0.7811 (Cg_exo) cc_final: 0.7540 (Cg_endo) REVERT: N 124 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8383 (mtt90) REVERT: N 149 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7985 (ptpp) REVERT: N 175 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7564 (p0) REVERT: N 176 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7529 (tm-30) REVERT: N 211 LYS cc_start: 0.8720 (pptt) cc_final: 0.8500 (pptt) REVERT: N 212 LYS cc_start: 0.8710 (tttm) cc_final: 0.8332 (tttm) REVERT: O 111 LYS cc_start: 0.7319 (tptp) cc_final: 0.6853 (tptp) REVERT: O 176 GLU cc_start: 0.7318 (tp30) cc_final: 0.7098 (tp30) REVERT: O 192 MET cc_start: 0.7290 (tmm) cc_final: 0.6837 (tpp) REVERT: O 211 LYS cc_start: 0.8869 (pptt) cc_final: 0.8511 (pptt) REVERT: R 99 LEU cc_start: 0.7932 (tm) cc_final: 0.7615 (pp) REVERT: R 127 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7631 (mt) REVERT: S 88 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7371 (mtp) REVERT: S 92 GLU cc_start: 0.7311 (pp20) cc_final: 0.6811 (pp20) REVERT: S 94 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8148 (pttp) REVERT: S 103 LEU cc_start: 0.8910 (mt) cc_final: 0.8650 (mm) REVERT: S 127 LEU cc_start: 0.8272 (mm) cc_final: 0.8015 (mt) REVERT: S 196 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8100 (ttmt) REVERT: S 232 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8068 (mmtt) outliers start: 82 outliers final: 43 residues processed: 625 average time/residue: 0.7527 time to fit residues: 532.1883 Evaluate side-chains 650 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 588 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 240 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 211 LYS Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain M residue 168 ARG Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain N residue 186 CYS Chi-restraints excluded: chain O residue 97 LYS Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 186 CYS Chi-restraints excluded: chain S residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 319 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 212 optimal weight: 0.0060 chunk 171 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 320 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.162331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125455 restraints weight = 39455.920| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.28 r_work: 0.3445 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26660 Z= 0.160 Angle : 0.618 10.613 35950 Z= 0.313 Chirality : 0.045 0.193 3834 Planarity : 0.006 0.055 4502 Dihedral : 4.121 20.947 3514 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.81 % Allowed : 21.18 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.83 (0.16), residues: 3156 helix: 0.68 (0.17), residues: 956 sheet: 0.10 (0.21), residues: 708 loop : 0.95 (0.18), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 230 TYR 0.019 0.001 TYR N 84 PHE 0.020 0.001 PHE I 222 TRP 0.045 0.002 TRP O 79 HIS 0.007 0.001 HIS K 225 Details of bonding type rmsd covalent geometry : bond 0.00369 (26660) covalent geometry : angle 0.61832 (35950) hydrogen bonds : bond 0.04511 ( 1098) hydrogen bonds : angle 4.81544 ( 3186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 595 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8859 (tt) cc_final: 0.8610 (tp) REVERT: A 149 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8229 (ptpp) REVERT: A 164 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 187 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7579 (ttpp) REVERT: A 194 CYS cc_start: 0.7893 (m) cc_final: 0.7609 (m) REVERT: A 214 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.9010 (tttm) REVERT: B 89 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8698 (ptmm) REVERT: B 106 LYS cc_start: 0.8775 (tppp) cc_final: 0.8174 (tppp) REVERT: B 108 ILE cc_start: 0.8492 (mm) cc_final: 0.8257 (mt) REVERT: B 115 LEU cc_start: 0.8223 (pp) cc_final: 0.7962 (pt) REVERT: B 149 LYS cc_start: 0.8388 (ptpp) cc_final: 0.7839 (ptpp) REVERT: B 172 ASP cc_start: 0.8072 (m-30) cc_final: 0.7810 (m-30) REVERT: C 106 LYS cc_start: 0.8584 (tppp) cc_final: 0.8008 (tppp) REVERT: C 203 GLU cc_start: 0.8195 (mp0) cc_final: 0.7825 (mp0) REVERT: C 217 HIS cc_start: 0.8235 (m170) cc_final: 0.7896 (m170) REVERT: C 220 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7769 (tm-30) REVERT: D 89 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8413 (ptmm) REVERT: D 106 LYS cc_start: 0.8242 (tppp) cc_final: 0.7653 (tppp) REVERT: D 168 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8564 (ttm-80) REVERT: D 211 LYS cc_start: 0.8338 (pptt) cc_final: 0.8084 (pptt) REVERT: D 212 LYS cc_start: 0.8086 (tttm) cc_final: 0.7830 (tttm) REVERT: D 233 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7387 (ttmm) REVERT: D 242 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7823 (p) REVERT: E 92 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6838 (pp20) REVERT: E 106 LYS cc_start: 0.8546 (tppp) cc_final: 0.8020 (tppp) REVERT: E 149 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8304 (ptpp) REVERT: E 162 GLN cc_start: 0.8657 (tt0) cc_final: 0.8430 (tt0) REVERT: E 214 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (mttt) REVERT: F 106 LYS cc_start: 0.8560 (tppp) cc_final: 0.8059 (tppp) REVERT: F 192 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7726 (ppp) REVERT: F 212 LYS cc_start: 0.7981 (tttm) cc_final: 0.7730 (tttm) REVERT: F 236 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7877 (pp) REVERT: F 242 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7696 (p) REVERT: G 106 LYS cc_start: 0.8558 (tppp) cc_final: 0.8012 (tppp) REVERT: G 109 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7873 (mm-30) REVERT: G 125 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8529 (mtm180) REVERT: G 211 LYS cc_start: 0.8308 (pptt) cc_final: 0.8031 (pttt) REVERT: G 220 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: G 238 LYS cc_start: 0.8223 (mttt) cc_final: 0.7911 (mttp) REVERT: H 94 LYS cc_start: 0.7842 (pttp) cc_final: 0.7467 (pttp) REVERT: H 97 LYS cc_start: 0.8032 (tttm) cc_final: 0.7832 (tttm) REVERT: H 129 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8245 (ttmm) REVERT: H 192 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8274 (ppp) REVERT: I 98 ASP cc_start: 0.7802 (m-30) cc_final: 0.7411 (m-30) REVERT: I 106 LYS cc_start: 0.8703 (tppp) cc_final: 0.8331 (tppp) REVERT: I 109 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7839 (mm-30) REVERT: I 162 GLN cc_start: 0.8581 (tt0) cc_final: 0.8336 (tt0) REVERT: I 168 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8494 (ttm110) REVERT: I 238 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8614 (mmmm) REVERT: J 103 LEU cc_start: 0.8733 (mt) cc_final: 0.8487 (mp) REVERT: J 109 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7952 (mm-30) REVERT: J 203 GLU cc_start: 0.8383 (mp0) cc_final: 0.7985 (mp0) REVERT: J 211 LYS cc_start: 0.8596 (pptt) cc_final: 0.8343 (pptt) REVERT: J 212 LYS cc_start: 0.8650 (tttm) cc_final: 0.8432 (tptm) REVERT: J 214 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7847 (mttt) REVERT: K 94 LYS cc_start: 0.7911 (pttp) cc_final: 0.7549 (pttp) REVERT: K 97 LYS cc_start: 0.8190 (tttm) cc_final: 0.7926 (tttm) REVERT: K 149 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8332 (mtmm) REVERT: K 238 LYS cc_start: 0.8571 (mttt) cc_final: 0.8363 (mppt) REVERT: K 241 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7290 (mm-40) REVERT: L 88 MET cc_start: 0.8266 (ttp) cc_final: 0.7892 (ptp) REVERT: L 106 LYS cc_start: 0.8492 (tppp) cc_final: 0.7935 (tppp) REVERT: L 147 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8339 (t) REVERT: L 238 LYS cc_start: 0.8704 (mptt) cc_final: 0.8340 (mmtm) REVERT: M 92 GLU cc_start: 0.6636 (pp20) cc_final: 0.6370 (pp20) REVERT: M 106 LYS cc_start: 0.8683 (mmpt) cc_final: 0.8427 (mmpt) REVERT: M 108 ILE cc_start: 0.8851 (mt) cc_final: 0.8196 (pp) REVERT: M 109 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7423 (mm-30) REVERT: M 127 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8391 (mt) REVERT: M 203 GLU cc_start: 0.8275 (mp0) cc_final: 0.7878 (mp0) REVERT: N 94 LYS cc_start: 0.8575 (pttp) cc_final: 0.8269 (pttp) REVERT: N 99 LEU cc_start: 0.8260 (mm) cc_final: 0.7976 (mm) REVERT: N 119 PRO cc_start: 0.7865 (Cg_exo) cc_final: 0.7612 (Cg_endo) REVERT: N 124 ARG cc_start: 0.8689 (mtt90) cc_final: 0.8368 (mtt90) REVERT: N 149 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8022 (ptpp) REVERT: N 175 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7589 (p0) REVERT: N 176 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7539 (tm-30) REVERT: N 187 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7764 (ttpp) REVERT: N 211 LYS cc_start: 0.8713 (pptt) cc_final: 0.8488 (pptt) REVERT: N 212 LYS cc_start: 0.8714 (tttm) cc_final: 0.8350 (tttm) REVERT: O 176 GLU cc_start: 0.7227 (tp30) cc_final: 0.7026 (tp30) REVERT: O 198 LEU cc_start: 0.8324 (mt) cc_final: 0.7995 (tt) REVERT: O 211 LYS cc_start: 0.8879 (pptt) cc_final: 0.8514 (pptt) REVERT: R 127 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7637 (mt) REVERT: S 88 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7393 (mtp) REVERT: S 92 GLU cc_start: 0.7328 (pp20) cc_final: 0.6852 (pp20) REVERT: S 94 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8169 (pttp) REVERT: S 103 LEU cc_start: 0.8933 (mt) cc_final: 0.8666 (mm) REVERT: S 127 LEU cc_start: 0.8286 (mm) cc_final: 0.8031 (mt) REVERT: S 196 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8114 (ttmt) REVERT: S 232 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8022 (mmtt) outliers start: 79 outliers final: 46 residues processed: 627 average time/residue: 0.7753 time to fit residues: 550.3509 Evaluate side-chains 657 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 592 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 168 ARG Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 240 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 211 LYS Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain M residue 168 ARG Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain N residue 186 CYS Chi-restraints excluded: chain N residue 187 LYS Chi-restraints excluded: chain O residue 94 LYS Chi-restraints excluded: chain O residue 97 LYS Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 186 CYS Chi-restraints excluded: chain S residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 249 optimal weight: 9.9990 chunk 191 optimal weight: 0.0870 chunk 317 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 209 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124594 restraints weight = 39573.661| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.30 r_work: 0.3442 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26660 Z= 0.196 Angle : 0.643 11.730 35950 Z= 0.326 Chirality : 0.046 0.196 3834 Planarity : 0.006 0.060 4502 Dihedral : 4.203 21.604 3514 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.16 % Allowed : 21.07 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.79 (0.16), residues: 3156 helix: 0.75 (0.17), residues: 940 sheet: 0.62 (0.22), residues: 612 loop : 0.53 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 230 TYR 0.020 0.001 TYR N 84 PHE 0.023 0.001 PHE I 222 TRP 0.040 0.002 TRP M 235 HIS 0.008 0.001 HIS K 225 Details of bonding type rmsd covalent geometry : bond 0.00456 (26660) covalent geometry : angle 0.64271 (35950) hydrogen bonds : bond 0.04898 ( 1098) hydrogen bonds : angle 4.87994 ( 3186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 601 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8861 (tt) cc_final: 0.8621 (tp) REVERT: A 149 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8207 (ptpp) REVERT: A 164 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 187 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7739 (ttmt) REVERT: A 217 HIS cc_start: 0.8894 (m-70) cc_final: 0.8598 (m-70) REVERT: B 89 LYS cc_start: 0.8985 (ptmt) cc_final: 0.8704 (ptmm) REVERT: B 106 LYS cc_start: 0.8797 (tppp) cc_final: 0.8202 (tppp) REVERT: B 108 ILE cc_start: 0.8479 (mm) cc_final: 0.8195 (mp) REVERT: B 149 LYS cc_start: 0.8380 (ptpp) cc_final: 0.7830 (ptpp) REVERT: B 172 ASP cc_start: 0.8068 (m-30) cc_final: 0.7807 (m-30) REVERT: C 106 LYS cc_start: 0.8558 (tppp) cc_final: 0.7975 (tppp) REVERT: C 109 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7617 (mm-30) REVERT: C 191 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8091 (tp) REVERT: C 203 GLU cc_start: 0.8207 (mp0) cc_final: 0.7842 (mp0) REVERT: C 217 HIS cc_start: 0.8246 (m170) cc_final: 0.7908 (m170) REVERT: C 220 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 89 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8416 (ptmm) REVERT: D 106 LYS cc_start: 0.8246 (tppp) cc_final: 0.7646 (tppp) REVERT: D 211 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8109 (pptt) REVERT: D 212 LYS cc_start: 0.8099 (tttm) cc_final: 0.7832 (tttm) REVERT: D 233 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7410 (ttmm) REVERT: D 242 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7836 (p) REVERT: E 92 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6851 (pp20) REVERT: E 106 LYS cc_start: 0.8559 (tppp) cc_final: 0.8027 (tppp) REVERT: E 149 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8305 (ptpp) REVERT: E 162 GLN cc_start: 0.8639 (tt0) cc_final: 0.8402 (tt0) REVERT: E 214 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8320 (mttt) REVERT: F 106 LYS cc_start: 0.8561 (tppp) cc_final: 0.8041 (tppp) REVERT: F 192 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7769 (ppp) REVERT: F 212 LYS cc_start: 0.7982 (tttm) cc_final: 0.7741 (tttm) REVERT: F 236 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7907 (pp) REVERT: F 242 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7706 (p) REVERT: G 106 LYS cc_start: 0.8560 (tppp) cc_final: 0.8033 (tppp) REVERT: G 109 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7967 (mm-30) REVERT: G 125 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8537 (mtm180) REVERT: G 211 LYS cc_start: 0.8322 (pptt) cc_final: 0.8052 (pttt) REVERT: G 220 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: G 238 LYS cc_start: 0.8250 (mttt) cc_final: 0.7925 (mttp) REVERT: H 97 LYS cc_start: 0.8038 (tttm) cc_final: 0.7838 (tttm) REVERT: H 129 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8265 (ttmm) REVERT: H 192 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8304 (ppp) REVERT: H 236 LEU cc_start: 0.8358 (pp) cc_final: 0.8080 (tt) REVERT: I 84 TYR cc_start: 0.8894 (t80) cc_final: 0.8573 (t80) REVERT: I 106 LYS cc_start: 0.8721 (tppp) cc_final: 0.8351 (tppp) REVERT: I 109 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7877 (mm-30) REVERT: I 162 GLN cc_start: 0.8623 (tt0) cc_final: 0.8315 (tt0) REVERT: I 168 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8505 (ttm110) REVERT: J 109 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7996 (mm-30) REVERT: J 203 GLU cc_start: 0.8385 (mp0) cc_final: 0.7975 (mp0) REVERT: J 211 LYS cc_start: 0.8605 (pptt) cc_final: 0.8355 (pptt) REVERT: J 212 LYS cc_start: 0.8680 (tttm) cc_final: 0.8459 (tptm) REVERT: J 214 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7865 (mttt) REVERT: K 94 LYS cc_start: 0.7914 (pttp) cc_final: 0.7508 (pttp) REVERT: K 97 LYS cc_start: 0.8205 (tttm) cc_final: 0.7946 (tttm) REVERT: K 149 LYS cc_start: 0.8604 (ptpp) cc_final: 0.8321 (mtmm) REVERT: K 193 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7925 (mtt180) REVERT: K 238 LYS cc_start: 0.8548 (mttt) cc_final: 0.8256 (mmtm) REVERT: K 241 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7337 (mm-40) REVERT: L 88 MET cc_start: 0.8242 (ttp) cc_final: 0.7903 (ptp) REVERT: L 106 LYS cc_start: 0.8434 (tppp) cc_final: 0.7889 (tppp) REVERT: L 147 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8326 (t) REVERT: L 238 LYS cc_start: 0.8751 (mptt) cc_final: 0.8375 (mmtm) REVERT: M 92 GLU cc_start: 0.6657 (pp20) cc_final: 0.6395 (pp20) REVERT: M 106 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8425 (mmpt) REVERT: M 108 ILE cc_start: 0.8856 (mt) cc_final: 0.8227 (pp) REVERT: M 109 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7466 (mm-30) REVERT: M 127 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8407 (mt) REVERT: M 146 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8643 (t) REVERT: M 203 GLU cc_start: 0.8270 (mp0) cc_final: 0.7869 (mp0) REVERT: N 86 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8094 (tp) REVERT: N 94 LYS cc_start: 0.8651 (pttp) cc_final: 0.8343 (pttp) REVERT: N 119 PRO cc_start: 0.8005 (Cg_exo) cc_final: 0.7682 (Cg_endo) REVERT: N 124 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8391 (mtt90) REVERT: N 149 LYS cc_start: 0.8485 (ptpp) cc_final: 0.8081 (ptpp) REVERT: N 176 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7544 (tm-30) REVERT: N 187 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7788 (ttpp) REVERT: N 211 LYS cc_start: 0.8730 (pptt) cc_final: 0.8500 (pptt) REVERT: N 212 LYS cc_start: 0.8736 (tttm) cc_final: 0.8393 (tttm) REVERT: O 211 LYS cc_start: 0.8875 (pptt) cc_final: 0.8493 (pptt) REVERT: R 127 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7669 (mt) REVERT: R 212 LYS cc_start: 0.8998 (tmmt) cc_final: 0.8585 (pptt) REVERT: S 88 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7415 (mtp) REVERT: S 92 GLU cc_start: 0.7316 (pp20) cc_final: 0.6852 (pp20) REVERT: S 94 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8188 (pttp) REVERT: S 103 LEU cc_start: 0.8965 (mt) cc_final: 0.8671 (mm) REVERT: S 127 LEU cc_start: 0.8286 (mm) cc_final: 0.8023 (mt) REVERT: S 129 LYS cc_start: 0.8358 (ttmm) cc_final: 0.8105 (ttmm) REVERT: S 196 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8141 (ttmt) REVERT: S 232 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8001 (mmtt) outliers start: 89 outliers final: 56 residues processed: 640 average time/residue: 0.7664 time to fit residues: 555.9500 Evaluate side-chains 676 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 598 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 168 ARG Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain J residue 240 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 193 ARG Chi-restraints excluded: chain K residue 211 LYS Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 97 LYS Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain M residue 168 ARG Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 186 CYS Chi-restraints excluded: chain N residue 187 LYS Chi-restraints excluded: chain N residue 214 LYS Chi-restraints excluded: chain O residue 94 LYS Chi-restraints excluded: chain O residue 97 LYS Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 186 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 253 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 GLN J 217 HIS N 96 GLN ** P 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.162655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125767 restraints weight = 39410.473| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.30 r_work: 0.3455 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26660 Z= 0.139 Angle : 0.623 12.722 35950 Z= 0.314 Chirality : 0.044 0.207 3834 Planarity : 0.006 0.059 4502 Dihedral : 4.113 21.714 3514 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.49 % Allowed : 22.25 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 3156 helix: 0.69 (0.17), residues: 956 sheet: 0.62 (0.22), residues: 612 loop : 0.64 (0.17), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 230 TYR 0.019 0.001 TYR H 84 PHE 0.023 0.001 PHE I 222 TRP 0.045 0.001 TRP M 235 HIS 0.007 0.001 HIS K 225 Details of bonding type rmsd covalent geometry : bond 0.00318 (26660) covalent geometry : angle 0.62269 (35950) hydrogen bonds : bond 0.04147 ( 1098) hydrogen bonds : angle 4.74095 ( 3186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 582 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8860 (tt) cc_final: 0.8646 (tp) REVERT: A 122 LYS cc_start: 0.8661 (mptp) cc_final: 0.8451 (mmtm) REVERT: A 149 LYS cc_start: 0.8556 (ptpp) cc_final: 0.8251 (ptpp) REVERT: A 164 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 187 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7587 (ttpp) REVERT: A 194 CYS cc_start: 0.7921 (m) cc_final: 0.7626 (m) REVERT: B 89 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8698 (ptmm) REVERT: B 106 LYS cc_start: 0.8745 (tppp) cc_final: 0.8133 (tppp) REVERT: B 108 ILE cc_start: 0.8457 (mm) cc_final: 0.8175 (mp) REVERT: B 115 LEU cc_start: 0.8185 (pp) cc_final: 0.7903 (pt) REVERT: B 129 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8149 (mtpp) REVERT: B 149 LYS cc_start: 0.8410 (ptpp) cc_final: 0.7855 (ptpp) REVERT: B 172 ASP cc_start: 0.8061 (m-30) cc_final: 0.7797 (m-30) REVERT: C 106 LYS cc_start: 0.8572 (tppp) cc_final: 0.7997 (tppp) REVERT: C 217 HIS cc_start: 0.8215 (m170) cc_final: 0.7885 (m170) REVERT: D 89 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8424 (ptmm) REVERT: D 106 LYS cc_start: 0.8232 (tppp) cc_final: 0.7640 (tppp) REVERT: D 168 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8569 (ttm-80) REVERT: D 192 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8007 (ptm) REVERT: D 211 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8092 (pptt) REVERT: D 212 LYS cc_start: 0.8060 (tttm) cc_final: 0.7790 (tttm) REVERT: D 233 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7410 (ttmm) REVERT: D 242 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7846 (p) REVERT: E 92 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: E 106 LYS cc_start: 0.8551 (tppp) cc_final: 0.8016 (tppp) REVERT: E 149 LYS cc_start: 0.8579 (ptpp) cc_final: 0.8299 (ptpp) REVERT: E 162 GLN cc_start: 0.8638 (tt0) cc_final: 0.8397 (tt0) REVERT: E 214 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8297 (mttt) REVERT: E 233 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7966 (ttmm) REVERT: F 106 LYS cc_start: 0.8549 (tppp) cc_final: 0.8041 (tppp) REVERT: F 192 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7708 (ppp) REVERT: F 212 LYS cc_start: 0.7956 (tttm) cc_final: 0.7720 (tttm) REVERT: F 236 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7875 (pp) REVERT: F 242 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7685 (p) REVERT: G 106 LYS cc_start: 0.8581 (tppp) cc_final: 0.8034 (tppp) REVERT: G 107 ASP cc_start: 0.7821 (m-30) cc_final: 0.7480 (m-30) REVERT: G 109 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7926 (mm-30) REVERT: G 125 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8516 (mtm180) REVERT: G 211 LYS cc_start: 0.8338 (pptt) cc_final: 0.8073 (pttt) REVERT: G 238 LYS cc_start: 0.8258 (mttt) cc_final: 0.7940 (mttp) REVERT: H 94 LYS cc_start: 0.7890 (pttp) cc_final: 0.7447 (pttp) REVERT: H 97 LYS cc_start: 0.7977 (tttm) cc_final: 0.7777 (tttm) REVERT: H 129 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8239 (ttmm) REVERT: H 192 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8250 (ppp) REVERT: H 236 LEU cc_start: 0.8317 (pp) cc_final: 0.8057 (tt) REVERT: I 106 LYS cc_start: 0.8709 (tppp) cc_final: 0.8323 (tppp) REVERT: I 109 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7891 (mm-30) REVERT: I 162 GLN cc_start: 0.8583 (tt0) cc_final: 0.8322 (tt0) REVERT: I 238 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8590 (mmmm) REVERT: J 103 LEU cc_start: 0.8727 (mt) cc_final: 0.8469 (mp) REVERT: J 109 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7964 (mm-30) REVERT: J 203 GLU cc_start: 0.8377 (mp0) cc_final: 0.7975 (mp0) REVERT: J 211 LYS cc_start: 0.8562 (pptt) cc_final: 0.8306 (pptt) REVERT: J 212 LYS cc_start: 0.8683 (tttm) cc_final: 0.8426 (tptm) REVERT: K 94 LYS cc_start: 0.7838 (pttp) cc_final: 0.7484 (pttp) REVERT: K 97 LYS cc_start: 0.8171 (tttm) cc_final: 0.7917 (tttm) REVERT: K 149 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8331 (mtmm) REVERT: K 238 LYS cc_start: 0.8475 (mttt) cc_final: 0.8215 (mmtm) REVERT: L 88 MET cc_start: 0.8245 (ttp) cc_final: 0.7871 (ptp) REVERT: L 106 LYS cc_start: 0.8415 (tppp) cc_final: 0.7865 (tppp) REVERT: L 147 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8341 (t) REVERT: L 238 LYS cc_start: 0.8707 (mptt) cc_final: 0.8341 (mmtm) REVERT: M 106 LYS cc_start: 0.8646 (mmpt) cc_final: 0.8407 (mmpt) REVERT: M 108 ILE cc_start: 0.8862 (mt) cc_final: 0.8259 (pp) REVERT: M 127 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8389 (mt) REVERT: M 146 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8610 (t) REVERT: M 203 GLU cc_start: 0.8272 (mp0) cc_final: 0.7888 (mp0) REVERT: N 94 LYS cc_start: 0.8674 (pttp) cc_final: 0.8370 (pttp) REVERT: N 119 PRO cc_start: 0.7759 (Cg_exo) cc_final: 0.7532 (Cg_endo) REVERT: N 124 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8386 (mtt90) REVERT: N 149 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8147 (ptpp) REVERT: N 187 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7751 (ttpp) REVERT: N 211 LYS cc_start: 0.8723 (pptt) cc_final: 0.8496 (pptt) REVERT: N 212 LYS cc_start: 0.8725 (tttm) cc_final: 0.8401 (tttm) REVERT: O 175 ASN cc_start: 0.7579 (p0) cc_final: 0.6975 (p0) REVERT: O 211 LYS cc_start: 0.8870 (pptt) cc_final: 0.8482 (pptt) REVERT: R 127 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7731 (mt) REVERT: S 88 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7413 (mtp) REVERT: S 92 GLU cc_start: 0.7229 (pp20) cc_final: 0.6798 (pp20) REVERT: S 94 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8199 (pttp) REVERT: S 99 LEU cc_start: 0.8989 (tp) cc_final: 0.8684 (tt) REVERT: S 103 LEU cc_start: 0.8977 (mt) cc_final: 0.8701 (mm) REVERT: S 196 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8083 (ttmt) REVERT: S 232 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8007 (mmtt) outliers start: 70 outliers final: 45 residues processed: 612 average time/residue: 0.7586 time to fit residues: 524.9887 Evaluate side-chains 644 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 582 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 240 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 211 LYS Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 163 LEU Chi-restraints excluded: chain M residue 168 ARG Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain N residue 186 CYS Chi-restraints excluded: chain N residue 187 LYS Chi-restraints excluded: chain N residue 214 LYS Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain S residue 186 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 245 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 283 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 chunk 181 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.161809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124906 restraints weight = 39386.599| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.30 r_work: 0.3443 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26660 Z= 0.168 Angle : 0.640 12.366 35950 Z= 0.323 Chirality : 0.045 0.231 3834 Planarity : 0.006 0.058 4502 Dihedral : 4.155 21.680 3514 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.56 % Allowed : 22.32 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.11 % 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: 0.82 (0.16), residues: 3156 helix: 0.78 (0.17), residues: 940 sheet: 0.60 (0.22), residues: 612 loop : 0.55 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 230 TYR 0.018 0.001 TYR N 84 PHE 0.019 0.001 PHE I 222 TRP 0.044 0.002 TRP M 235 HIS 0.007 0.001 HIS K 225 Details of bonding type rmsd covalent geometry : bond 0.00389 (26660) covalent geometry : angle 0.64007 (35950) hydrogen bonds : bond 0.04572 ( 1098) hydrogen bonds : angle 4.79088 ( 3186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13253.50 seconds wall clock time: 225 minutes 56.48 seconds (13556.48 seconds total)