Starting phenix.real_space_refine on Fri Feb 6 20:39:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yia_72984/02_2026/9yia_72984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yia_72984/02_2026/9yia_72984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yia_72984/02_2026/9yia_72984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yia_72984/02_2026/9yia_72984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yia_72984/02_2026/9yia_72984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yia_72984/02_2026/9yia_72984.map" } resolution = 2.69 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 133 5.16 5 C 17822 2.51 5 N 4693 2.21 5 O 4940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s 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: 27588 Number of models: 1 Model: "" Number of chains: 1 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: {'PTRANS': 10, 'TRANS': 169} Chain breaks: 1 Restraints were copied for chains: S, R, Q, P, O, N, M, L, K, J, I, H, G, F, E, D, C, B Time building chain proxies: 2.51, per 1000 atoms: 0.09 Number of scatterers: 27588 At special positions: 0 Unit cell: (190.848, 190.848, 63.048, 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 133 16.00 O 4940 8.00 N 4693 7.00 C 17822 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: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6232 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 76 sheets defined 36.1% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.655A pdb=" N ILE A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'S' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE S 100 " --> pdb=" O GLN S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR S 123 " --> pdb=" O PRO S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 177 No H-bonds generated for 'chain 'S' and resid 175 through 177' Processing helix chain 'S' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU S 184 " --> pdb=" O PRO S 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY S 185 " --> pdb=" O THR S 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS S 187 " --> pdb=" O THR S 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS S 196 " --> pdb=" O MET S 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP S 197 " --> pdb=" O ARG S 193 " (cutoff:3.500A) removed outlier: 3.946A 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 helix chain 'R' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE R 100 " --> pdb=" O GLN R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR R 123 " --> pdb=" O PRO R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'R' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU R 184 " --> pdb=" O PRO R 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY R 185 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS R 196 " --> pdb=" O MET R 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP R 197 " --> pdb=" O ARG R 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'Q' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE Q 100 " --> pdb=" O GLN Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR Q 123 " --> pdb=" O PRO Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 177 No H-bonds generated for 'chain 'Q' and resid 175 through 177' Processing helix chain 'Q' and resid 178 through 199 removed outlier: 4.362A pdb=" N GLU Q 184 " --> pdb=" O PRO Q 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY Q 185 " --> pdb=" O THR Q 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS Q 187 " --> pdb=" O THR Q 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS Q 196 " --> pdb=" O MET Q 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP Q 197 " --> pdb=" O ARG Q 193 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU Q 198 " --> pdb=" O CYS Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 201 through 205 Processing helix chain 'Q' and resid 206 through 217 Processing helix chain 'P' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE P 100 " --> pdb=" O GLN P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR P 123 " --> pdb=" O PRO P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 177 No H-bonds generated for 'chain 'P' and resid 175 through 177' Processing helix chain 'P' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU P 184 " --> pdb=" O PRO P 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY P 185 " --> pdb=" O THR P 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS P 196 " --> pdb=" O MET P 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP P 197 " --> pdb=" O ARG P 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'O' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE O 100 " --> pdb=" O GLN O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR O 123 " --> pdb=" O PRO O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 177 No H-bonds generated for 'chain 'O' and resid 175 through 177' Processing helix chain 'O' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU O 184 " --> pdb=" O PRO O 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY O 185 " --> pdb=" O THR O 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS O 187 " --> pdb=" O THR O 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS O 196 " --> pdb=" O MET O 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP O 197 " --> pdb=" O ARG O 193 " (cutoff:3.500A) removed outlier: 3.946A 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 'N' and resid 92 through 100 removed outlier: 3.655A pdb=" N ILE N 100 " --> pdb=" O GLN N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR N 123 " --> pdb=" O PRO N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 177 No H-bonds generated for 'chain 'N' and resid 175 through 177' Processing helix chain 'N' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU N 184 " --> pdb=" O PRO N 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY N 185 " --> pdb=" O THR N 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS N 187 " --> pdb=" O THR N 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS N 196 " --> pdb=" O MET N 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP N 197 " --> pdb=" O ARG N 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'M' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR M 123 " --> pdb=" O PRO M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 177 No H-bonds generated for 'chain 'M' and resid 175 through 177' Processing helix chain 'M' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU M 184 " --> pdb=" O PRO M 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY M 185 " --> pdb=" O THR M 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS M 187 " --> pdb=" O THR M 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS M 196 " --> pdb=" O MET M 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP M 197 " --> pdb=" O ARG M 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'L' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE L 100 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR L 123 " --> pdb=" O PRO L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 177 No H-bonds generated for 'chain 'L' and resid 175 through 177' Processing helix chain 'L' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU L 184 " --> pdb=" O PRO L 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY L 185 " --> pdb=" O THR L 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS L 187 " --> pdb=" O THR L 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS L 196 " --> pdb=" O MET L 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'K' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE K 100 " --> pdb=" O GLN K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR K 123 " --> pdb=" O PRO K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 177 No H-bonds generated for 'chain 'K' and resid 175 through 177' Processing helix chain 'K' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU K 184 " --> pdb=" O PRO K 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS K 187 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS K 196 " --> pdb=" O MET K 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP K 197 " --> pdb=" O ARG K 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'J' and resid 92 through 100 removed outlier: 3.655A pdb=" N ILE J 100 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR J 123 " --> pdb=" O PRO J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU J 184 " --> pdb=" O PRO J 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY J 185 " --> pdb=" O THR J 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS J 187 " --> pdb=" O THR J 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS J 196 " --> pdb=" O MET J 192 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP J 197 " --> pdb=" O ARG J 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'I' and resid 92 through 100 removed outlier: 3.655A pdb=" N ILE I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR I 123 " --> pdb=" O PRO I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 178 through 199 removed outlier: 4.364A pdb=" N GLU I 184 " --> pdb=" O PRO I 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY I 185 " --> pdb=" O THR I 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS I 187 " --> pdb=" O THR I 183 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS I 196 " --> pdb=" O MET I 192 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP I 197 " --> pdb=" O ARG I 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'H' and resid 92 through 100 removed outlier: 3.655A pdb=" N ILE H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR H 123 " --> pdb=" O PRO H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS H 187 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS H 196 " --> pdb=" O MET H 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP H 197 " --> pdb=" O ARG H 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'G' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU G 184 " --> pdb=" O PRO G 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS G 196 " --> pdb=" O MET G 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 3.946A 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 'F' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 178 through 199 removed outlier: 4.364A pdb=" N GLU F 184 " --> pdb=" O PRO F 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS F 187 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS F 196 " --> pdb=" O MET F 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'E' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR E 123 " --> pdb=" O PRO E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'D' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 178 through 199 removed outlier: 4.362A pdb=" N GLU D 184 " --> pdb=" O PRO D 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS D 196 " --> pdb=" O MET D 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'C' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.520A pdb=" N TYR C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU C 184 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 3.945A 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 'B' and resid 92 through 100 removed outlier: 3.656A pdb=" N ILE B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.519A pdb=" N TYR B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 199 removed outlier: 4.363A pdb=" N GLU B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 3.945A 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 sheet with id=AA1, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.917A pdb=" N SER A 165 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS A 159 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 225 Processing sheet with id=AA5, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'S' and resid 53 through 55 removed outlier: 3.917A pdb=" N SER S 165 " --> pdb=" O LEU S 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS S 159 " --> pdb=" O LEU S 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU S 163 " --> pdb=" O CYS S 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 109 through 110 Processing sheet with id=AA8, first strand: chain 'S' and resid 218 through 225 Processing sheet with id=AA9, first strand: chain 'R' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'R' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER R 165 " --> pdb=" O LEU R 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS R 159 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU R 163 " --> pdb=" O CYS R 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 109 through 110 Processing sheet with id=AB3, first strand: chain 'R' and resid 218 through 225 Processing sheet with id=AB4, first strand: chain 'Q' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'Q' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER Q 165 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N CYS Q 159 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU Q 163 " --> pdb=" O CYS Q 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 109 through 110 Processing sheet with id=AB7, first strand: chain 'Q' and resid 218 through 225 Processing sheet with id=AB8, first strand: chain 'P' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'P' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER P 165 " --> pdb=" O LEU P 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS P 159 " --> pdb=" O LEU P 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU P 163 " --> pdb=" O CYS P 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AC2, first strand: chain 'P' and resid 218 through 225 Processing sheet with id=AC3, first strand: chain 'O' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'O' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER O 165 " --> pdb=" O LEU O 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS O 159 " --> pdb=" O LEU O 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU O 163 " --> pdb=" O CYS O 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AC6, first strand: chain 'O' and resid 218 through 225 Processing sheet with id=AC7, first strand: chain 'N' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 55 removed outlier: 3.917A pdb=" N SER N 165 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS N 159 " --> pdb=" O LEU N 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU N 163 " --> pdb=" O CYS N 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 109 through 110 Processing sheet with id=AD1, first strand: chain 'N' and resid 218 through 225 Processing sheet with id=AD2, first strand: chain 'M' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'M' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER M 165 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS M 159 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU M 163 " --> pdb=" O CYS M 159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 109 through 110 Processing sheet with id=AD5, first strand: chain 'M' and resid 218 through 225 Processing sheet with id=AD6, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'L' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER L 165 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS L 159 " --> pdb=" O LEU L 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU L 163 " --> pdb=" O CYS L 159 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AD9, first strand: chain 'L' and resid 218 through 225 Processing sheet with id=AE1, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AE2, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER K 165 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS K 159 " --> pdb=" O LEU K 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU K 163 " --> pdb=" O CYS K 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AE4, first strand: chain 'K' and resid 218 through 225 Processing sheet with id=AE5, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AE6, first strand: chain 'J' and resid 53 through 55 removed outlier: 3.917A pdb=" N SER J 165 " --> pdb=" O LEU J 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS J 159 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU J 163 " --> pdb=" O CYS J 159 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 109 through 110 Processing sheet with id=AE8, first strand: chain 'J' and resid 218 through 225 Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER I 165 " --> pdb=" O LEU I 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS I 159 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU I 163 " --> pdb=" O CYS I 159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AF3, first strand: chain 'I' and resid 218 through 225 Processing sheet with id=AF4, first strand: chain 'H' and resid 53 through 55 Processing sheet with id=AF5, first strand: chain 'H' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER H 165 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS H 159 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU H 163 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AF7, first strand: chain 'H' and resid 218 through 225 Processing sheet with id=AF8, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AF9, first strand: chain 'G' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER G 165 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS G 159 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G 163 " --> pdb=" O CYS G 159 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AG2, first strand: chain 'G' and resid 218 through 225 Processing sheet with id=AG3, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AG4, first strand: chain 'F' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER F 165 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS F 159 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU F 163 " --> pdb=" O CYS F 159 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AG6, first strand: chain 'F' and resid 218 through 225 Processing sheet with id=AG7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AG8, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER E 165 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS E 159 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU E 163 " --> pdb=" O CYS E 159 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AH1, first strand: chain 'E' and resid 218 through 225 Processing sheet with id=AH2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AH3, first strand: chain 'D' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER D 165 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS D 159 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU D 163 " --> pdb=" O CYS D 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AH5, first strand: chain 'D' and resid 218 through 225 Processing sheet with id=AH6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AH7, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER C 165 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS C 159 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 163 " --> pdb=" O CYS C 159 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AH9, first strand: chain 'C' and resid 218 through 225 Processing sheet with id=AI1, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AI2, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.918A pdb=" N SER B 165 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS B 159 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AI4, first strand: chain 'B' and resid 218 through 225 1292 hydrogen bonds defined for protein. 3420 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: 5.27 Time building geometry restraints manager: 2.89 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: 8626 1.34 - 1.46: 6311 1.46 - 1.58: 13145 1.58 - 1.69: 0 1.69 - 1.81: 171 Bond restraints: 28253 Sorted by residual: bond pdb=" CG1 ILE F 179 " pdb=" CD1 ILE F 179 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.69e-01 bond pdb=" CG1 ILE H 179 " pdb=" CD1 ILE H 179 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.48e-01 bond pdb=" CG1 ILE O 179 " pdb=" CD1 ILE O 179 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.25e-01 bond pdb=" CG1 ILE R 179 " pdb=" CD1 ILE R 179 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.24e-01 bond pdb=" CG1 ILE A 179 " pdb=" CD1 ILE A 179 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.22e-01 ... (remaining 28248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 34802 0.99 - 1.97: 2497 1.97 - 2.96: 491 2.96 - 3.95: 229 3.95 - 4.94: 76 Bond angle restraints: 38095 Sorted by residual: angle pdb=" C VAL O 215 " pdb=" N ASP O 216 " pdb=" CA ASP O 216 " ideal model delta sigma weight residual 122.24 118.39 3.85 1.57e+00 4.06e-01 6.02e+00 angle pdb=" C VAL A 215 " pdb=" N ASP A 216 " pdb=" CA ASP A 216 " ideal model delta sigma weight residual 122.24 118.40 3.84 1.57e+00 4.06e-01 5.99e+00 angle pdb=" C VAL B 215 " pdb=" N ASP B 216 " pdb=" CA ASP B 216 " ideal model delta sigma weight residual 122.24 118.41 3.83 1.57e+00 4.06e-01 5.95e+00 angle pdb=" C VAL E 215 " pdb=" N ASP E 216 " pdb=" CA ASP E 216 " ideal model delta sigma weight residual 122.24 118.42 3.82 1.57e+00 4.06e-01 5.92e+00 angle pdb=" C VAL C 215 " pdb=" N ASP C 216 " pdb=" CA ASP C 216 " ideal model delta sigma weight residual 122.24 118.42 3.82 1.57e+00 4.06e-01 5.91e+00 ... (remaining 38090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 14976 15.07 - 30.14: 1611 30.14 - 45.21: 323 45.21 - 60.28: 38 60.28 - 75.35: 38 Dihedral angle restraints: 16986 sinusoidal: 7220 harmonic: 9766 Sorted by residual: dihedral pdb=" CA TYR R 244 " pdb=" C TYR R 244 " pdb=" N PRO R 245 " pdb=" CA PRO R 245 " ideal model delta harmonic sigma weight residual 180.00 117.66 62.34 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA TYR H 244 " pdb=" C TYR H 244 " pdb=" N PRO H 245 " pdb=" CA PRO H 245 " ideal model delta harmonic sigma weight residual 180.00 117.67 62.33 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA TYR D 244 " pdb=" C TYR D 244 " pdb=" N PRO D 245 " pdb=" CA PRO D 245 " ideal model delta harmonic sigma weight residual 180.00 117.67 62.33 0 5.00e+00 4.00e-02 1.55e+02 ... (remaining 16983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2057 0.026 - 0.052: 1016 0.052 - 0.078: 580 0.078 - 0.104: 310 0.104 - 0.130: 103 Chirality restraints: 4066 Sorted by residual: chirality pdb=" CA ILE Q 158 " pdb=" N ILE Q 158 " pdb=" C ILE Q 158 " pdb=" CB ILE Q 158 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE S 158 " pdb=" N ILE S 158 " pdb=" C ILE S 158 " pdb=" CB ILE S 158 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE E 158 " pdb=" N ILE E 158 " pdb=" C ILE E 158 " pdb=" CB ILE E 158 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 4063 not shown) Planarity restraints: 4769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 104 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO L 105 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 105 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 105 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 104 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO E 105 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 105 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 105 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP N 104 " 0.043 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO N 105 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO N 105 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO N 105 " 0.037 5.00e-02 4.00e+02 ... (remaining 4766 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 18052 3.06 - 3.52: 28179 3.52 - 3.98: 45305 3.98 - 4.44: 52868 4.44 - 4.90: 82080 Nonbonded interactions: 226484 Sorted by model distance: nonbonded pdb=" N PRO B 245 " pdb=" N TYR B 246 " model vdw 2.604 2.560 nonbonded pdb=" N PRO O 245 " pdb=" N TYR O 246 " model vdw 2.604 2.560 nonbonded pdb=" N PRO P 245 " pdb=" N TYR P 246 " model vdw 2.604 2.560 nonbonded pdb=" N PRO M 245 " pdb=" N TYR M 246 " model vdw 2.604 2.560 nonbonded pdb=" N PRO L 245 " pdb=" N TYR L 246 " model vdw 2.604 2.560 ... (remaining 226479 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 'S' selection = chain 'R' selection = chain 'Q' selection = chain 'P' selection = chain 'O' selection = chain 'N' selection = chain 'M' selection = chain 'L' selection = chain 'K' selection = chain 'J' selection = chain 'I' selection = chain 'H' selection = chain 'G' selection = chain 'F' selection = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.020 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 0.038 28253 Z= 0.138 Angle : 0.655 4.937 38095 Z= 0.346 Chirality : 0.045 0.130 4066 Planarity : 0.007 0.066 4769 Dihedral : 13.035 75.347 10754 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.04 (0.15), residues: 3344 helix: -0.65 (0.17), residues: 912 sheet: 0.99 (0.21), residues: 608 loop : 0.19 (0.16), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 237 TYR 0.021 0.002 TYR L 244 PHE 0.011 0.001 PHE B 222 TRP 0.020 0.002 TRP B 205 HIS 0.004 0.001 HIS O 225 Details of bonding type rmsd covalent geometry : bond 0.00296 (28253) covalent geometry : angle 0.65498 (38095) hydrogen bonds : bond 0.15209 ( 1178) hydrogen bonds : angle 8.61027 ( 3420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8286 (mtpp) REVERT: A 198 LEU cc_start: 0.7797 (mp) cc_final: 0.7592 (mt) REVERT: A 214 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7989 (mtmm) REVERT: S 97 LYS cc_start: 0.7864 (mptt) cc_final: 0.7373 (mptt) REVERT: S 214 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7752 (mttm) REVERT: R 84 TYR cc_start: 0.8329 (t80) cc_final: 0.8018 (t80) REVERT: Q 203 GLU cc_start: 0.7963 (mp0) cc_final: 0.7725 (mp0) REVERT: Q 214 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8127 (mtmm) REVERT: P 97 LYS cc_start: 0.8068 (mptt) cc_final: 0.7832 (mptt) REVERT: P 170 GLU cc_start: 0.6833 (pp20) cc_final: 0.6559 (pp20) REVERT: P 198 LEU cc_start: 0.7738 (mp) cc_final: 0.7496 (mt) REVERT: P 214 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8095 (mtmm) REVERT: P 221 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7831 (mtpp) REVERT: O 84 TYR cc_start: 0.8222 (t80) cc_final: 0.7883 (t80) REVERT: O 97 LYS cc_start: 0.7934 (mptt) cc_final: 0.7702 (mptt) REVERT: O 149 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8051 (mtpm) REVERT: N 97 LYS cc_start: 0.7954 (mptt) cc_final: 0.7478 (mptt) REVERT: N 111 LYS cc_start: 0.8129 (mptt) cc_final: 0.7736 (mptt) REVERT: M 97 LYS cc_start: 0.7970 (mptt) cc_final: 0.7525 (mptt) REVERT: M 203 GLU cc_start: 0.8110 (mp0) cc_final: 0.7766 (mp0) REVERT: M 214 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7855 (mtmm) REVERT: L 84 TYR cc_start: 0.8116 (t80) cc_final: 0.7796 (t80) REVERT: L 97 LYS cc_start: 0.8003 (mptt) cc_final: 0.7744 (mptt) REVERT: L 111 LYS cc_start: 0.8221 (mptt) cc_final: 0.7875 (mptt) REVERT: L 153 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8191 (ttt180) REVERT: L 198 LEU cc_start: 0.7834 (mp) cc_final: 0.7588 (mt) REVERT: L 214 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7936 (mtmm) REVERT: K 84 TYR cc_start: 0.8155 (t80) cc_final: 0.7918 (t80) REVERT: K 203 GLU cc_start: 0.8123 (mp0) cc_final: 0.7838 (mp0) REVERT: J 84 TYR cc_start: 0.8228 (t80) cc_final: 0.7988 (t80) REVERT: J 97 LYS cc_start: 0.8050 (mptt) cc_final: 0.7843 (mptt) REVERT: J 198 LEU cc_start: 0.7910 (mp) cc_final: 0.7677 (mt) REVERT: J 214 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7955 (mtmm) REVERT: I 111 LYS cc_start: 0.8433 (mptt) cc_final: 0.7868 (mptt) REVERT: I 214 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7756 (mtmm) REVERT: H 152 THR cc_start: 0.8331 (p) cc_final: 0.8072 (t) REVERT: H 203 GLU cc_start: 0.8003 (mp0) cc_final: 0.7780 (mp0) REVERT: H 214 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7977 (mtpm) REVERT: H 221 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8183 (mtpp) REVERT: G 97 LYS cc_start: 0.7903 (mptt) cc_final: 0.7647 (mptt) REVERT: G 214 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7889 (mtmm) REVERT: F 170 GLU cc_start: 0.7105 (pp20) cc_final: 0.6894 (pp20) REVERT: F 203 GLU cc_start: 0.7788 (mp0) cc_final: 0.7581 (mp0) REVERT: F 221 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7855 (mtpp) REVERT: E 97 LYS cc_start: 0.7884 (mptt) cc_final: 0.7674 (mptt) REVERT: E 214 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7889 (mtmm) REVERT: D 97 LYS cc_start: 0.7904 (mptt) cc_final: 0.7386 (mptt) REVERT: D 128 ASN cc_start: 0.8808 (m-40) cc_final: 0.8602 (m110) REVERT: C 97 LYS cc_start: 0.7870 (mptt) cc_final: 0.7628 (mptt) REVERT: C 214 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7864 (mttm) REVERT: C 238 LYS cc_start: 0.8186 (mttt) cc_final: 0.7937 (mttt) REVERT: B 84 TYR cc_start: 0.8065 (t80) cc_final: 0.7767 (t80) REVERT: B 97 LYS cc_start: 0.7702 (mptt) cc_final: 0.7266 (mptt) REVERT: B 152 THR cc_start: 0.8244 (p) cc_final: 0.7988 (t) REVERT: B 214 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7861 (mttm) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.7008 time to fit residues: 531.6718 Evaluate side-chains 631 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.160471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132539 restraints weight = 36551.877| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.18 r_work: 0.3531 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28253 Z= 0.124 Angle : 0.609 7.760 38095 Z= 0.311 Chirality : 0.045 0.172 4066 Planarity : 0.006 0.053 4769 Dihedral : 6.262 52.897 3724 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.54 % Allowed : 11.43 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3344 helix: 0.36 (0.19), residues: 950 sheet: 1.20 (0.21), residues: 608 loop : 0.48 (0.16), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 240 TYR 0.021 0.002 TYR H 244 PHE 0.011 0.001 PHE P 222 TRP 0.009 0.001 TRP J 205 HIS 0.003 0.001 HIS H 225 Details of bonding type rmsd covalent geometry : bond 0.00286 (28253) covalent geometry : angle 0.60890 (38095) hydrogen bonds : bond 0.03699 ( 1178) hydrogen bonds : angle 6.03502 ( 3420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 602 time to evaluate : 1.007 Fit side-chains REVERT: A 86 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 97 LYS cc_start: 0.8098 (mptt) cc_final: 0.7876 (mptt) REVERT: A 149 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8315 (mtpp) REVERT: A 214 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7940 (mtmm) REVERT: S 97 LYS cc_start: 0.8144 (mptt) cc_final: 0.7814 (tptt) REVERT: S 189 ASN cc_start: 0.8252 (t0) cc_final: 0.8014 (t160) REVERT: R 84 TYR cc_start: 0.8506 (t80) cc_final: 0.8113 (t80) REVERT: Q 214 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8067 (mtmm) REVERT: P 97 LYS cc_start: 0.8287 (mptt) cc_final: 0.8022 (mptt) REVERT: P 203 GLU cc_start: 0.8150 (mp0) cc_final: 0.7886 (mp0) REVERT: P 214 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8133 (mtmm) REVERT: P 221 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7671 (mtpp) REVERT: O 97 LYS cc_start: 0.8180 (mptt) cc_final: 0.7882 (mptt) REVERT: O 149 LYS cc_start: 0.8492 (ptpp) cc_final: 0.8139 (mtpp) REVERT: O 193 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7823 (mtt180) REVERT: O 214 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7952 (mttm) REVERT: N 86 LEU cc_start: 0.8603 (tp) cc_final: 0.8369 (tm) REVERT: N 97 LYS cc_start: 0.8269 (mptt) cc_final: 0.7866 (mptt) REVERT: N 111 LYS cc_start: 0.8162 (mptt) cc_final: 0.7669 (mptt) REVERT: M 97 LYS cc_start: 0.8237 (mptt) cc_final: 0.8032 (tptt) REVERT: M 203 GLU cc_start: 0.8164 (mp0) cc_final: 0.7834 (mp0) REVERT: M 214 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7878 (mtmm) REVERT: L 84 TYR cc_start: 0.8399 (t80) cc_final: 0.7856 (t80) REVERT: L 97 LYS cc_start: 0.8241 (mptt) cc_final: 0.8040 (mptt) REVERT: L 111 LYS cc_start: 0.8220 (mptt) cc_final: 0.7715 (mptt) REVERT: L 153 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8600 (ttt180) REVERT: L 214 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7775 (mtmm) REVERT: K 84 TYR cc_start: 0.8478 (t80) cc_final: 0.8260 (t80) REVERT: K 89 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8315 (ptpp) REVERT: K 97 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7976 (tttt) REVERT: K 203 GLU cc_start: 0.8372 (mp0) cc_final: 0.8039 (mp0) REVERT: J 97 LYS cc_start: 0.8254 (mptt) cc_final: 0.8011 (mptt) REVERT: J 149 LYS cc_start: 0.8346 (ptpp) cc_final: 0.8103 (mtpm) REVERT: J 198 LEU cc_start: 0.7978 (mp) cc_final: 0.7682 (mt) REVERT: J 214 LYS cc_start: 0.8368 (mtpt) cc_final: 0.7980 (mtmm) REVERT: I 97 LYS cc_start: 0.8245 (mptt) cc_final: 0.8020 (tptt) REVERT: I 111 LYS cc_start: 0.8471 (mptt) cc_final: 0.7785 (mptt) REVERT: I 166 VAL cc_start: 0.8596 (m) cc_final: 0.8395 (t) REVERT: I 214 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7774 (mtmm) REVERT: H 88 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7829 (ttm) REVERT: H 203 GLU cc_start: 0.8093 (mp0) cc_final: 0.7758 (mp0) REVERT: H 221 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8122 (mtpp) REVERT: G 97 LYS cc_start: 0.8084 (mptt) cc_final: 0.7735 (mptt) REVERT: G 214 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7754 (mtmm) REVERT: F 88 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7764 (ttm) REVERT: F 221 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7699 (mtpp) REVERT: E 111 LYS cc_start: 0.8463 (mptt) cc_final: 0.7876 (mptt) REVERT: E 170 GLU cc_start: 0.7657 (pp20) cc_final: 0.7374 (pp20) REVERT: E 214 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7994 (mtmm) REVERT: D 128 ASN cc_start: 0.8829 (m-40) cc_final: 0.8575 (m110) REVERT: C 97 LYS cc_start: 0.8172 (mptt) cc_final: 0.7871 (mptt) REVERT: C 214 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7936 (mtmm) REVERT: C 238 LYS cc_start: 0.8240 (mttt) cc_final: 0.7944 (mttt) REVERT: B 84 TYR cc_start: 0.8472 (t80) cc_final: 0.7925 (t80) REVERT: B 97 LYS cc_start: 0.8096 (mptt) cc_final: 0.7763 (tptt) REVERT: B 214 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7824 (mtpm) outliers start: 46 outliers final: 14 residues processed: 607 average time/residue: 0.6897 time to fit residues: 475.0539 Evaluate side-chains 603 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 585 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain P residue 129 LYS Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 162 GLN Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 209 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 228 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN N 189 ASN K 171 GLN I 189 ASN G 189 ASN C 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123234 restraints weight = 37041.438| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.05 r_work: 0.3474 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28253 Z= 0.197 Angle : 0.631 7.806 38095 Z= 0.319 Chirality : 0.047 0.164 4066 Planarity : 0.006 0.053 4769 Dihedral : 5.994 48.237 3724 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.28 % Allowed : 14.11 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.86 (0.15), residues: 3344 helix: 0.34 (0.18), residues: 950 sheet: 2.64 (0.25), residues: 418 loop : 0.32 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 240 TYR 0.017 0.002 TYR E 244 PHE 0.007 0.001 PHE N 209 TRP 0.014 0.001 TRP F 205 HIS 0.004 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00465 (28253) covalent geometry : angle 0.63131 (38095) hydrogen bonds : bond 0.04308 ( 1178) hydrogen bonds : angle 5.88450 ( 3420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 575 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.8419 (pt) cc_final: 0.8071 (mt) REVERT: A 170 GLU cc_start: 0.7933 (pp20) cc_final: 0.7725 (pp20) REVERT: A 214 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8209 (mtmm) REVERT: S 97 LYS cc_start: 0.8228 (mptt) cc_final: 0.8011 (tptt) REVERT: R 84 TYR cc_start: 0.8510 (t80) cc_final: 0.8143 (t80) REVERT: R 97 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8141 (tttt) REVERT: R 162 GLN cc_start: 0.8564 (tt0) cc_final: 0.8359 (tt0) REVERT: R 196 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8427 (mtmm) REVERT: Q 171 GLN cc_start: 0.8851 (tp40) cc_final: 0.8371 (tp-100) REVERT: Q 214 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8244 (mtmm) REVERT: P 97 LYS cc_start: 0.8334 (mptt) cc_final: 0.8122 (mptt) REVERT: P 151 VAL cc_start: 0.8771 (p) cc_final: 0.8570 (t) REVERT: P 170 GLU cc_start: 0.7853 (pp20) cc_final: 0.7598 (pp20) REVERT: P 203 GLU cc_start: 0.8222 (mp0) cc_final: 0.7841 (mp0) REVERT: P 214 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8232 (mtmm) REVERT: P 221 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7728 (mtpp) REVERT: O 97 LYS cc_start: 0.8225 (mptt) cc_final: 0.7949 (mptt) REVERT: N 97 LYS cc_start: 0.8362 (mptt) cc_final: 0.8158 (tptt) REVERT: N 98 ASP cc_start: 0.7792 (p0) cc_final: 0.7472 (p0) REVERT: N 206 ASP cc_start: 0.7928 (t0) cc_final: 0.7646 (t0) REVERT: M 203 GLU cc_start: 0.8183 (mp0) cc_final: 0.7761 (mp0) REVERT: M 214 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8066 (mttp) REVERT: L 84 TYR cc_start: 0.8441 (t80) cc_final: 0.8120 (t80) REVERT: L 97 LYS cc_start: 0.8263 (mptt) cc_final: 0.8049 (tptt) REVERT: L 214 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8036 (mtmm) REVERT: K 89 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8476 (ptpp) REVERT: K 97 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8075 (tttt) REVERT: K 203 GLU cc_start: 0.8386 (mp0) cc_final: 0.8045 (mp0) REVERT: J 97 LYS cc_start: 0.8266 (mptt) cc_final: 0.8047 (mptt) REVERT: J 106 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7436 (mmtm) REVERT: J 170 GLU cc_start: 0.7950 (pp20) cc_final: 0.7595 (pp20) REVERT: J 206 ASP cc_start: 0.7863 (t0) cc_final: 0.7617 (t0) REVERT: J 211 LYS cc_start: 0.7544 (tmtt) cc_final: 0.7333 (tttt) REVERT: J 214 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8162 (mtmm) REVERT: I 97 LYS cc_start: 0.8320 (mptt) cc_final: 0.8114 (tptt) REVERT: H 78 ASP cc_start: 0.7957 (t0) cc_final: 0.7685 (t70) REVERT: H 88 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7966 (ttm) REVERT: H 170 GLU cc_start: 0.7775 (pp20) cc_final: 0.7561 (pp20) REVERT: H 197 ASP cc_start: 0.7428 (t0) cc_final: 0.7223 (t0) REVERT: H 203 GLU cc_start: 0.8212 (mp0) cc_final: 0.7815 (mp0) REVERT: H 214 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8270 (mtpp) REVERT: H 221 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8118 (mtpp) REVERT: G 84 TYR cc_start: 0.8363 (t80) cc_final: 0.8161 (t80) REVERT: G 97 LYS cc_start: 0.8126 (mptt) cc_final: 0.7896 (tptt) REVERT: G 206 ASP cc_start: 0.7785 (t0) cc_final: 0.7448 (t0) REVERT: G 214 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8105 (mtmm) REVERT: F 88 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7853 (ttm) REVERT: F 89 LYS cc_start: 0.8631 (ptpp) cc_final: 0.8426 (ptpp) REVERT: F 170 GLU cc_start: 0.7998 (pp20) cc_final: 0.7621 (pp20) REVERT: F 171 GLN cc_start: 0.8872 (tp40) cc_final: 0.8667 (tp-100) REVERT: F 221 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7771 (mtpp) REVERT: E 97 LYS cc_start: 0.8347 (tptt) cc_final: 0.8141 (tttt) REVERT: E 110 ILE cc_start: 0.8571 (pt) cc_final: 0.8314 (pp) REVERT: E 149 LYS cc_start: 0.8532 (ptpp) cc_final: 0.8315 (ptpp) REVERT: E 170 GLU cc_start: 0.8016 (pp20) cc_final: 0.7644 (pp20) REVERT: E 214 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8168 (mtmm) REVERT: D 86 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8214 (tp) REVERT: D 128 ASN cc_start: 0.8779 (m-40) cc_final: 0.8500 (m110) REVERT: D 214 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8214 (mtmm) REVERT: C 50 LYS cc_start: 0.5629 (tmmt) cc_final: 0.4964 (ttmp) REVERT: C 97 LYS cc_start: 0.8278 (mptt) cc_final: 0.8056 (tptt) REVERT: C 170 GLU cc_start: 0.7874 (pp20) cc_final: 0.7499 (pp20) REVERT: C 214 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8085 (mtmm) REVERT: C 238 LYS cc_start: 0.8215 (mttt) cc_final: 0.7941 (mttt) REVERT: B 84 TYR cc_start: 0.8414 (t80) cc_final: 0.8192 (t80) REVERT: B 145 ILE cc_start: 0.8807 (mp) cc_final: 0.8584 (mp) REVERT: B 214 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8048 (mtpp) outliers start: 68 outliers final: 28 residues processed: 596 average time/residue: 0.7698 time to fit residues: 518.2134 Evaluate side-chains 591 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 558 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 162 GLN Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 152 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 306 optimal weight: 0.0670 chunk 200 optimal weight: 0.5980 chunk 300 optimal weight: 0.7980 chunk 251 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 171 GLN H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.152745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127131 restraints weight = 36946.848| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.97 r_work: 0.3485 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 28253 Z= 0.122 Angle : 0.570 9.023 38095 Z= 0.288 Chirality : 0.044 0.167 4066 Planarity : 0.005 0.054 4769 Dihedral : 5.642 44.267 3724 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.94 % Allowed : 16.36 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.99 (0.15), residues: 3344 helix: 0.46 (0.18), residues: 950 sheet: 2.62 (0.25), residues: 418 loop : 0.44 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 240 TYR 0.011 0.001 TYR C 244 PHE 0.006 0.001 PHE O 213 TRP 0.007 0.001 TRP K 235 HIS 0.003 0.001 HIS N 217 Details of bonding type rmsd covalent geometry : bond 0.00282 (28253) covalent geometry : angle 0.57011 (38095) hydrogen bonds : bond 0.03208 ( 1178) hydrogen bonds : angle 5.55490 ( 3420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 565 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8512 (tptt) cc_final: 0.8194 (tttt) REVERT: A 170 GLU cc_start: 0.7914 (pp20) cc_final: 0.7620 (pp20) REVERT: A 214 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8249 (mtmm) REVERT: S 97 LYS cc_start: 0.8219 (mptt) cc_final: 0.8017 (tptt) REVERT: S 151 VAL cc_start: 0.8797 (p) cc_final: 0.8575 (t) REVERT: R 84 TYR cc_start: 0.8494 (t80) cc_final: 0.8022 (t80) REVERT: R 97 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8094 (tttt) REVERT: R 196 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8395 (mtmm) REVERT: R 214 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8311 (mtpp) REVERT: Q 89 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8374 (ptpp) REVERT: Q 214 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8303 (mtmm) REVERT: P 203 GLU cc_start: 0.8212 (mp0) cc_final: 0.7822 (mp0) REVERT: P 214 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8113 (mtmm) REVERT: O 97 LYS cc_start: 0.8251 (mptt) cc_final: 0.8015 (tptt) REVERT: O 193 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7907 (mtt180) REVERT: N 97 LYS cc_start: 0.8368 (mptt) cc_final: 0.8133 (tptt) REVERT: N 98 ASP cc_start: 0.7774 (p0) cc_final: 0.7453 (p0) REVERT: N 206 ASP cc_start: 0.7916 (t0) cc_final: 0.7663 (t0) REVERT: M 82 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8434 (t) REVERT: M 97 LYS cc_start: 0.8519 (tptt) cc_final: 0.8251 (tttt) REVERT: M 203 GLU cc_start: 0.8151 (mp0) cc_final: 0.7752 (mp0) REVERT: M 214 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8059 (mttp) REVERT: L 84 TYR cc_start: 0.8430 (t80) cc_final: 0.8086 (t80) REVERT: L 97 LYS cc_start: 0.8267 (mptt) cc_final: 0.8050 (tptt) REVERT: L 170 GLU cc_start: 0.7865 (pp20) cc_final: 0.7556 (pp20) REVERT: L 214 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8082 (mtmm) REVERT: K 89 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8414 (ptpp) REVERT: K 203 GLU cc_start: 0.8381 (mp0) cc_final: 0.8026 (mp0) REVERT: J 97 LYS cc_start: 0.8238 (mptt) cc_final: 0.8024 (mptt) REVERT: J 106 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7545 (mmtm) REVERT: J 170 GLU cc_start: 0.7945 (pp20) cc_final: 0.7587 (pp20) REVERT: J 206 ASP cc_start: 0.7853 (t0) cc_final: 0.7619 (t0) REVERT: J 211 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7406 (tttt) REVERT: J 214 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8196 (mtmm) REVERT: I 214 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8238 (mtmm) REVERT: H 78 ASP cc_start: 0.7898 (t0) cc_final: 0.7652 (t70) REVERT: H 88 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7989 (ttm) REVERT: H 197 ASP cc_start: 0.7440 (t0) cc_final: 0.7232 (t0) REVERT: H 203 GLU cc_start: 0.8201 (mp0) cc_final: 0.7802 (mp0) REVERT: H 221 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8135 (mtpp) REVERT: G 84 TYR cc_start: 0.8355 (t80) cc_final: 0.8093 (t80) REVERT: G 97 LYS cc_start: 0.8128 (mptt) cc_final: 0.7904 (tptt) REVERT: G 214 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8076 (mtmm) REVERT: F 170 GLU cc_start: 0.7972 (pp20) cc_final: 0.7615 (pp20) REVERT: F 171 GLN cc_start: 0.8841 (tp40) cc_final: 0.8640 (tp-100) REVERT: F 211 LYS cc_start: 0.7785 (tmtt) cc_final: 0.7542 (tttt) REVERT: F 221 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7745 (mtpp) REVERT: E 97 LYS cc_start: 0.8356 (tptt) cc_final: 0.8132 (tttt) REVERT: E 110 ILE cc_start: 0.8564 (pt) cc_final: 0.8236 (mt) REVERT: E 149 LYS cc_start: 0.8447 (ptpp) cc_final: 0.8216 (ptpp) REVERT: E 170 GLU cc_start: 0.7994 (pp20) cc_final: 0.7640 (pp20) REVERT: E 214 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8102 (mtmm) REVERT: D 86 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8266 (tp) REVERT: D 128 ASN cc_start: 0.8768 (m-40) cc_final: 0.8469 (m110) REVERT: D 196 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8338 (mtmm) REVERT: D 214 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8215 (mtmm) REVERT: C 97 LYS cc_start: 0.8268 (mptt) cc_final: 0.8049 (tptt) REVERT: C 170 GLU cc_start: 0.7823 (pp20) cc_final: 0.7412 (pp20) REVERT: C 238 LYS cc_start: 0.8212 (mttt) cc_final: 0.7934 (mttt) REVERT: B 84 TYR cc_start: 0.8482 (t80) cc_final: 0.8163 (t80) REVERT: B 97 LYS cc_start: 0.8267 (tptt) cc_final: 0.8002 (tttt) REVERT: B 145 ILE cc_start: 0.8758 (mp) cc_final: 0.8532 (mp) REVERT: B 214 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8133 (mtpp) outliers start: 58 outliers final: 22 residues processed: 584 average time/residue: 0.8457 time to fit residues: 555.4038 Evaluate side-chains 583 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 557 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 30 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 296 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 171 GLN L 162 GLN L 189 ASN H 171 GLN H 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127325 restraints weight = 36590.009| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.04 r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28253 Z= 0.134 Angle : 0.572 7.852 38095 Z= 0.288 Chirality : 0.044 0.171 4066 Planarity : 0.005 0.050 4769 Dihedral : 5.411 40.596 3724 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.35 % Allowed : 16.56 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 1.03 (0.15), residues: 3344 helix: 0.46 (0.18), residues: 950 sheet: 2.18 (0.26), residues: 437 loop : 0.58 (0.15), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 240 TYR 0.010 0.001 TYR K 173 PHE 0.007 0.001 PHE L 91 TRP 0.007 0.001 TRP K 235 HIS 0.003 0.001 HIS N 217 Details of bonding type rmsd covalent geometry : bond 0.00315 (28253) covalent geometry : angle 0.57240 (38095) hydrogen bonds : bond 0.03392 ( 1178) hydrogen bonds : angle 5.49967 ( 3420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 571 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8493 (tptt) cc_final: 0.8166 (tttt) REVERT: A 170 GLU cc_start: 0.7928 (pp20) cc_final: 0.7616 (pp20) REVERT: A 214 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8232 (mtmm) REVERT: S 97 LYS cc_start: 0.8241 (mptt) cc_final: 0.8036 (tptt) REVERT: R 84 TYR cc_start: 0.8518 (t80) cc_final: 0.8052 (t80) REVERT: R 97 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8097 (tttt) REVERT: Q 89 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8369 (ptpp) REVERT: Q 214 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8375 (mtmm) REVERT: P 88 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7925 (ttm) REVERT: P 151 VAL cc_start: 0.8760 (p) cc_final: 0.8505 (t) REVERT: P 203 GLU cc_start: 0.8240 (mp0) cc_final: 0.7786 (mp0) REVERT: P 214 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8120 (mtmm) REVERT: P 221 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7894 (mtpp) REVERT: O 97 LYS cc_start: 0.8267 (mptt) cc_final: 0.8013 (tptt) REVERT: N 97 LYS cc_start: 0.8381 (mptt) cc_final: 0.8149 (tptt) REVERT: N 98 ASP cc_start: 0.7772 (p0) cc_final: 0.7451 (p0) REVERT: N 206 ASP cc_start: 0.7945 (t0) cc_final: 0.7694 (t0) REVERT: M 97 LYS cc_start: 0.8481 (tptt) cc_final: 0.8201 (tttt) REVERT: M 106 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7584 (mmtm) REVERT: M 151 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8257 (t) REVERT: M 203 GLU cc_start: 0.8135 (mp0) cc_final: 0.7734 (mp0) REVERT: M 211 LYS cc_start: 0.7464 (tmtt) cc_final: 0.7216 (tttt) REVERT: M 214 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8127 (mtmm) REVERT: L 84 TYR cc_start: 0.8425 (t80) cc_final: 0.8114 (t80) REVERT: L 97 LYS cc_start: 0.8283 (mptt) cc_final: 0.8047 (tptt) REVERT: L 106 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7467 (mmtm) REVERT: L 170 GLU cc_start: 0.7954 (pp20) cc_final: 0.7548 (pp20) REVERT: L 214 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8135 (mtmm) REVERT: K 97 LYS cc_start: 0.8468 (tttt) cc_final: 0.8147 (ttmm) REVERT: K 170 GLU cc_start: 0.8099 (pp20) cc_final: 0.7791 (pp20) REVERT: K 203 GLU cc_start: 0.8371 (mp0) cc_final: 0.8012 (mp0) REVERT: K 206 ASP cc_start: 0.7925 (t0) cc_final: 0.7561 (t0) REVERT: J 106 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7679 (mmtm) REVERT: J 170 GLU cc_start: 0.8055 (pp20) cc_final: 0.7669 (pp20) REVERT: J 206 ASP cc_start: 0.7858 (t0) cc_final: 0.7624 (t0) REVERT: J 211 LYS cc_start: 0.7812 (tmtt) cc_final: 0.7567 (tttt) REVERT: J 214 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8271 (mtmm) REVERT: I 97 LYS cc_start: 0.8435 (tptt) cc_final: 0.8164 (tttt) REVERT: I 109 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7308 (mm-30) REVERT: I 111 LYS cc_start: 0.8431 (mptt) cc_final: 0.7799 (mptt) REVERT: I 170 GLU cc_start: 0.7982 (pp20) cc_final: 0.7576 (pp20) REVERT: I 203 GLU cc_start: 0.8150 (mp0) cc_final: 0.7786 (mp0) REVERT: I 214 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8255 (mtmm) REVERT: H 78 ASP cc_start: 0.7928 (t0) cc_final: 0.7678 (t70) REVERT: H 88 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7993 (ttm) REVERT: H 197 ASP cc_start: 0.7501 (t0) cc_final: 0.7286 (t0) REVERT: H 203 GLU cc_start: 0.8224 (mp0) cc_final: 0.7812 (mp0) REVERT: H 211 LYS cc_start: 0.7478 (tmtt) cc_final: 0.7231 (tttt) REVERT: H 221 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8179 (mtpp) REVERT: G 84 TYR cc_start: 0.8381 (t80) cc_final: 0.8122 (t80) REVERT: G 97 LYS cc_start: 0.8160 (mptt) cc_final: 0.7941 (tptt) REVERT: G 214 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8083 (mtmm) REVERT: F 88 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: F 170 GLU cc_start: 0.8040 (pp20) cc_final: 0.7681 (pp20) REVERT: F 211 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7667 (tttt) REVERT: F 221 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7778 (mtpp) REVERT: E 97 LYS cc_start: 0.8385 (tptt) cc_final: 0.8125 (tttt) REVERT: E 110 ILE cc_start: 0.8571 (pt) cc_final: 0.8279 (mt) REVERT: E 149 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8265 (ptpp) REVERT: E 170 GLU cc_start: 0.8056 (pp20) cc_final: 0.7726 (pp20) REVERT: E 214 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8123 (mtmm) REVERT: D 86 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8229 (tp) REVERT: D 128 ASN cc_start: 0.8764 (m-40) cc_final: 0.8454 (m110) REVERT: D 196 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8334 (mtmm) REVERT: D 214 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8197 (mtmm) REVERT: C 97 LYS cc_start: 0.8281 (mptt) cc_final: 0.8066 (tptt) REVERT: C 170 GLU cc_start: 0.7848 (pp20) cc_final: 0.7457 (pp20) REVERT: C 238 LYS cc_start: 0.8231 (mttt) cc_final: 0.7930 (mttt) REVERT: B 84 TYR cc_start: 0.8480 (t80) cc_final: 0.8149 (t80) REVERT: B 97 LYS cc_start: 0.8240 (tptt) cc_final: 0.7947 (tttt) REVERT: B 109 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 145 ILE cc_start: 0.8779 (mp) cc_final: 0.8565 (mp) outliers start: 70 outliers final: 43 residues processed: 591 average time/residue: 0.8370 time to fit residues: 556.4661 Evaluate side-chains 614 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 565 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 92 GLU Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 88 MET Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 220 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 322 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN H 171 GLN H 189 ASN F 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.126227 restraints weight = 36860.427| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.94 r_work: 0.3470 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28253 Z= 0.154 Angle : 0.585 8.799 38095 Z= 0.294 Chirality : 0.045 0.180 4066 Planarity : 0.005 0.051 4769 Dihedral : 5.328 38.230 3724 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.08 % Allowed : 17.63 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 1.00 (0.15), residues: 3344 helix: 0.39 (0.17), residues: 950 sheet: 2.22 (0.26), residues: 437 loop : 0.58 (0.15), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 240 TYR 0.010 0.001 TYR K 173 PHE 0.006 0.001 PHE K 213 TRP 0.006 0.001 TRP C 235 HIS 0.007 0.001 HIS K 217 Details of bonding type rmsd covalent geometry : bond 0.00367 (28253) covalent geometry : angle 0.58504 (38095) hydrogen bonds : bond 0.03400 ( 1178) hydrogen bonds : angle 5.48033 ( 3420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 573 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8462 (tptt) cc_final: 0.8152 (tttt) REVERT: A 170 GLU cc_start: 0.7921 (pp20) cc_final: 0.7597 (pp20) REVERT: A 214 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8328 (mtmm) REVERT: R 84 TYR cc_start: 0.8512 (t80) cc_final: 0.8029 (t80) REVERT: R 97 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8155 (tttt) REVERT: R 106 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7608 (mmtm) REVERT: Q 214 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8456 (mtmm) REVERT: P 88 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7899 (ttm) REVERT: P 151 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8509 (t) REVERT: P 184 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7425 (tm-30) REVERT: P 203 GLU cc_start: 0.8249 (mp0) cc_final: 0.7787 (mp0) REVERT: P 214 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8194 (mtmm) REVERT: O 97 LYS cc_start: 0.8242 (mptt) cc_final: 0.8011 (tptt) REVERT: O 151 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8400 (t) REVERT: N 97 LYS cc_start: 0.8355 (mptt) cc_final: 0.8132 (tptt) REVERT: N 98 ASP cc_start: 0.7811 (p0) cc_final: 0.7481 (p0) REVERT: M 89 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8298 (ptpp) REVERT: M 97 LYS cc_start: 0.8498 (tptt) cc_final: 0.8216 (tttt) REVERT: M 106 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7695 (mmtm) REVERT: M 203 GLU cc_start: 0.8163 (mp0) cc_final: 0.7763 (mp0) REVERT: M 211 LYS cc_start: 0.7552 (tmtt) cc_final: 0.7307 (tttt) REVERT: M 214 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8209 (mtmm) REVERT: L 84 TYR cc_start: 0.8449 (t80) cc_final: 0.8180 (t80) REVERT: L 97 LYS cc_start: 0.8268 (mptt) cc_final: 0.8048 (tptt) REVERT: L 170 GLU cc_start: 0.7993 (pp20) cc_final: 0.7560 (pp20) REVERT: L 214 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8266 (mtmm) REVERT: K 97 LYS cc_start: 0.8491 (tttt) cc_final: 0.8179 (ttmm) REVERT: K 106 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7801 (mmtm) REVERT: K 170 GLU cc_start: 0.8121 (pp20) cc_final: 0.7801 (pp20) REVERT: K 203 GLU cc_start: 0.8347 (mp0) cc_final: 0.7996 (mp0) REVERT: K 206 ASP cc_start: 0.7881 (t0) cc_final: 0.7574 (t0) REVERT: K 214 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8289 (mttm) REVERT: J 97 LYS cc_start: 0.8421 (tptt) cc_final: 0.8112 (tttt) REVERT: J 106 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7787 (mmtm) REVERT: J 170 GLU cc_start: 0.8028 (pp20) cc_final: 0.7618 (pp20) REVERT: J 206 ASP cc_start: 0.7861 (t0) cc_final: 0.7640 (t0) REVERT: J 211 LYS cc_start: 0.7944 (tmtt) cc_final: 0.7679 (tttt) REVERT: J 214 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8340 (mtmm) REVERT: I 97 LYS cc_start: 0.8387 (tptt) cc_final: 0.8135 (tttt) REVERT: I 107 ASP cc_start: 0.7713 (p0) cc_final: 0.7484 (p0) REVERT: I 109 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7323 (mm-30) REVERT: I 111 LYS cc_start: 0.8436 (mptt) cc_final: 0.8187 (mttt) REVERT: I 170 GLU cc_start: 0.7981 (pp20) cc_final: 0.7566 (pp20) REVERT: I 203 GLU cc_start: 0.8244 (mp0) cc_final: 0.7863 (mp0) REVERT: H 78 ASP cc_start: 0.7877 (t0) cc_final: 0.7621 (t70) REVERT: H 88 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8003 (ttm) REVERT: H 197 ASP cc_start: 0.7523 (t0) cc_final: 0.7300 (t0) REVERT: H 203 GLU cc_start: 0.8224 (mp0) cc_final: 0.7792 (mp0) REVERT: H 211 LYS cc_start: 0.7602 (tmtt) cc_final: 0.7354 (tttt) REVERT: H 221 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8158 (mtpp) REVERT: G 84 TYR cc_start: 0.8379 (t80) cc_final: 0.8155 (t80) REVERT: G 97 LYS cc_start: 0.8161 (mptt) cc_final: 0.7951 (tptt) REVERT: G 98 ASP cc_start: 0.7561 (p0) cc_final: 0.7122 (p0) REVERT: G 206 ASP cc_start: 0.7810 (t0) cc_final: 0.7464 (t0) REVERT: G 214 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8154 (mtmm) REVERT: F 170 GLU cc_start: 0.8043 (pp20) cc_final: 0.7670 (pp20) REVERT: F 171 GLN cc_start: 0.8861 (tp40) cc_final: 0.8624 (tp-100) REVERT: F 211 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7762 (tttt) REVERT: F 214 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8393 (mtpt) REVERT: F 221 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7810 (mtpp) REVERT: E 97 LYS cc_start: 0.8377 (tptt) cc_final: 0.8140 (tttt) REVERT: E 110 ILE cc_start: 0.8600 (pt) cc_final: 0.8334 (mt) REVERT: E 170 GLU cc_start: 0.8010 (pp20) cc_final: 0.7690 (pp20) REVERT: E 214 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8181 (mtmm) REVERT: D 86 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8244 (tp) REVERT: D 128 ASN cc_start: 0.8765 (m-40) cc_final: 0.8460 (m110) REVERT: D 196 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8345 (mtmm) REVERT: D 214 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8254 (mtmm) REVERT: C 97 LYS cc_start: 0.8306 (mptt) cc_final: 0.8105 (tptt) REVERT: C 170 GLU cc_start: 0.7902 (pp20) cc_final: 0.7498 (pp20) REVERT: C 238 LYS cc_start: 0.8217 (mttt) cc_final: 0.7927 (mttt) REVERT: B 97 LYS cc_start: 0.8281 (tptt) cc_final: 0.7993 (tttt) REVERT: B 109 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 145 ILE cc_start: 0.8788 (mp) cc_final: 0.8577 (mp) REVERT: B 214 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8378 (mttp) outliers start: 62 outliers final: 38 residues processed: 587 average time/residue: 0.8521 time to fit residues: 560.7398 Evaluate side-chains 615 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 571 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 321 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN H 171 GLN C 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125240 restraints weight = 36595.764| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.95 r_work: 0.3443 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 28253 Z= 0.241 Angle : 0.640 9.312 38095 Z= 0.320 Chirality : 0.048 0.187 4066 Planarity : 0.006 0.056 4769 Dihedral : 5.372 36.984 3724 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.48 % Allowed : 17.83 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.85 (0.15), residues: 3344 helix: 0.16 (0.17), residues: 950 sheet: 2.13 (0.26), residues: 437 loop : 0.54 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 240 TYR 0.015 0.001 TYR K 173 PHE 0.006 0.001 PHE E 91 TRP 0.011 0.002 TRP F 205 HIS 0.006 0.001 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00578 (28253) covalent geometry : angle 0.64002 (38095) hydrogen bonds : bond 0.04107 ( 1178) hydrogen bonds : angle 5.61808 ( 3420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 555 time to evaluate : 1.046 Fit side-chains REVERT: A 92 GLU cc_start: 0.7186 (pp20) cc_final: 0.6959 (pp20) REVERT: A 97 LYS cc_start: 0.8439 (tptt) cc_final: 0.8139 (tttt) REVERT: A 111 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8313 (tppp) REVERT: A 170 GLU cc_start: 0.7964 (pp20) cc_final: 0.7588 (pp20) REVERT: A 214 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8366 (mtmm) REVERT: S 97 LYS cc_start: 0.8401 (tptt) cc_final: 0.8186 (tttt) REVERT: R 84 TYR cc_start: 0.8524 (t80) cc_final: 0.8163 (t80) REVERT: R 106 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7861 (mmtm) REVERT: Q 214 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8485 (mtmm) REVERT: P 106 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8053 (mmtm) REVERT: P 151 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8567 (t) REVERT: P 184 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7458 (tm-30) REVERT: P 203 GLU cc_start: 0.8246 (mp0) cc_final: 0.7757 (mp0) REVERT: P 211 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7749 (tttt) REVERT: P 214 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8366 (mtmm) REVERT: O 97 LYS cc_start: 0.8242 (mptt) cc_final: 0.8020 (tptt) REVERT: N 97 LYS cc_start: 0.8403 (mptt) cc_final: 0.8177 (tptt) REVERT: N 98 ASP cc_start: 0.7802 (p0) cc_final: 0.7501 (p0) REVERT: M 82 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8426 (t) REVERT: M 89 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8410 (ptpp) REVERT: M 97 LYS cc_start: 0.8484 (tptt) cc_final: 0.8215 (tttt) REVERT: M 151 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (t) REVERT: M 203 GLU cc_start: 0.8159 (mp0) cc_final: 0.7757 (mp0) REVERT: M 211 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7423 (tttt) REVERT: M 214 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8247 (mtpp) REVERT: L 84 TYR cc_start: 0.8435 (t80) cc_final: 0.8196 (t80) REVERT: L 97 LYS cc_start: 0.8291 (mptt) cc_final: 0.8068 (tptt) REVERT: L 170 GLU cc_start: 0.8000 (pp20) cc_final: 0.7541 (pp20) REVERT: L 193 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: L 214 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8145 (mtmm) REVERT: K 97 LYS cc_start: 0.8504 (tttt) cc_final: 0.8182 (ttmm) REVERT: K 151 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8388 (t) REVERT: K 170 GLU cc_start: 0.8188 (pp20) cc_final: 0.7834 (pp20) REVERT: K 203 GLU cc_start: 0.8440 (mp0) cc_final: 0.8063 (mp0) REVERT: K 206 ASP cc_start: 0.7912 (t0) cc_final: 0.7594 (t0) REVERT: J 97 LYS cc_start: 0.8443 (tptt) cc_final: 0.8124 (tttt) REVERT: J 106 LYS cc_start: 0.8460 (mmtm) cc_final: 0.7982 (mmtm) REVERT: J 151 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (t) REVERT: J 170 GLU cc_start: 0.8105 (pp20) cc_final: 0.7698 (pp20) REVERT: J 211 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7749 (tttt) REVERT: J 214 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8418 (mtmm) REVERT: I 97 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8172 (tttt) REVERT: I 106 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7909 (mmtm) REVERT: I 107 ASP cc_start: 0.7822 (p0) cc_final: 0.7611 (p0) REVERT: I 109 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7365 (mm-30) REVERT: I 170 GLU cc_start: 0.8001 (pp20) cc_final: 0.7594 (pp20) REVERT: I 203 GLU cc_start: 0.8253 (mp0) cc_final: 0.7822 (mp0) REVERT: H 88 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7975 (ttm) REVERT: H 98 ASP cc_start: 0.7635 (p0) cc_final: 0.7374 (p0) REVERT: H 106 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7589 (mmtm) REVERT: H 197 ASP cc_start: 0.7513 (t0) cc_final: 0.7300 (t0) REVERT: H 211 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7447 (tttt) REVERT: H 214 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8356 (mtpp) REVERT: H 221 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8172 (mtpp) REVERT: G 50 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.6021 (tmmt) REVERT: G 97 LYS cc_start: 0.8181 (mptt) cc_final: 0.7970 (tptt) REVERT: G 98 ASP cc_start: 0.7509 (p0) cc_final: 0.7092 (p0) REVERT: G 170 GLU cc_start: 0.8028 (pp20) cc_final: 0.7621 (pp20) REVERT: G 206 ASP cc_start: 0.7835 (t0) cc_final: 0.7500 (t0) REVERT: G 214 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8160 (mtmm) REVERT: F 151 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8507 (t) REVERT: F 170 GLU cc_start: 0.8083 (pp20) cc_final: 0.7703 (pp20) REVERT: F 171 GLN cc_start: 0.8868 (tp40) cc_final: 0.8624 (tp-100) REVERT: F 211 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7900 (tttt) REVERT: F 214 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8448 (mtpt) REVERT: E 97 LYS cc_start: 0.8381 (tptt) cc_final: 0.8143 (tttt) REVERT: E 110 ILE cc_start: 0.8647 (pt) cc_final: 0.8416 (mt) REVERT: E 111 LYS cc_start: 0.8493 (mptt) cc_final: 0.8163 (mttt) REVERT: E 170 GLU cc_start: 0.8041 (pp20) cc_final: 0.7730 (pp20) REVERT: D 86 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8251 (tp) REVERT: D 92 GLU cc_start: 0.7244 (pp20) cc_final: 0.7022 (pp20) REVERT: D 106 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7977 (mmmm) REVERT: D 128 ASN cc_start: 0.8792 (m-40) cc_final: 0.8502 (m110) REVERT: D 214 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8376 (mtmm) REVERT: C 106 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7816 (mmtm) REVERT: C 170 GLU cc_start: 0.7955 (pp20) cc_final: 0.7514 (pp20) REVERT: C 238 LYS cc_start: 0.8241 (mttt) cc_final: 0.7950 (mttt) REVERT: B 89 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8146 (ptpp) REVERT: B 97 LYS cc_start: 0.8307 (tptt) cc_final: 0.8027 (tttt) REVERT: B 145 ILE cc_start: 0.8840 (mp) cc_final: 0.8628 (mp) REVERT: B 196 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8390 (mtmm) REVERT: B 198 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7889 (mt) outliers start: 74 outliers final: 43 residues processed: 581 average time/residue: 0.8609 time to fit residues: 560.0654 Evaluate side-chains 606 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 550 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain S residue 88 MET Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 193 ARG Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 17 optimal weight: 0.0000 chunk 247 optimal weight: 0.9990 chunk 307 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128668 restraints weight = 36260.047| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.02 r_work: 0.3475 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28253 Z= 0.114 Angle : 0.575 8.972 38095 Z= 0.288 Chirality : 0.044 0.177 4066 Planarity : 0.005 0.055 4769 Dihedral : 5.230 36.383 3724 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.18 % Allowed : 18.61 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.97 (0.15), residues: 3344 helix: 0.30 (0.17), residues: 950 sheet: 2.10 (0.26), residues: 437 loop : 0.62 (0.15), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 240 TYR 0.007 0.001 TYR K 173 PHE 0.007 0.001 PHE A 213 TRP 0.006 0.001 TRP K 235 HIS 0.003 0.001 HIS K 217 Details of bonding type rmsd covalent geometry : bond 0.00268 (28253) covalent geometry : angle 0.57518 (38095) hydrogen bonds : bond 0.03052 ( 1178) hydrogen bonds : angle 5.37791 ( 3420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 564 time to evaluate : 1.086 Fit side-chains REVERT: A 97 LYS cc_start: 0.8455 (tptt) cc_final: 0.8153 (tttt) REVERT: A 170 GLU cc_start: 0.7978 (pp20) cc_final: 0.7615 (pp20) REVERT: A 214 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8399 (mtmm) REVERT: R 84 TYR cc_start: 0.8500 (t80) cc_final: 0.8017 (t80) REVERT: R 97 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (tttt) REVERT: R 106 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7835 (mmtm) REVERT: Q 214 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8430 (mtmm) REVERT: P 106 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8045 (mmtm) REVERT: P 151 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8472 (t) REVERT: P 184 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7427 (tm-30) REVERT: P 203 GLU cc_start: 0.8246 (mp0) cc_final: 0.7751 (mp0) REVERT: P 211 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7711 (tttt) REVERT: P 214 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8304 (mtmm) REVERT: O 97 LYS cc_start: 0.8230 (mptt) cc_final: 0.8013 (tptt) REVERT: N 97 LYS cc_start: 0.8368 (mptt) cc_final: 0.8136 (tptt) REVERT: N 98 ASP cc_start: 0.7809 (p0) cc_final: 0.7501 (p0) REVERT: M 82 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8429 (t) REVERT: M 89 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8310 (ptpp) REVERT: M 97 LYS cc_start: 0.8444 (tptt) cc_final: 0.8169 (tttt) REVERT: M 203 GLU cc_start: 0.8149 (mp0) cc_final: 0.7727 (mp0) REVERT: M 211 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7396 (tttt) REVERT: M 214 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8155 (mtmm) REVERT: L 84 TYR cc_start: 0.8442 (t80) cc_final: 0.8131 (t80) REVERT: L 97 LYS cc_start: 0.8247 (mptt) cc_final: 0.8033 (tptt) REVERT: L 170 GLU cc_start: 0.7977 (pp20) cc_final: 0.7509 (pp20) REVERT: L 193 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8274 (mtt-85) REVERT: L 214 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8059 (mtmm) REVERT: K 97 LYS cc_start: 0.8504 (tttt) cc_final: 0.8173 (ttmm) REVERT: K 151 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8371 (t) REVERT: K 203 GLU cc_start: 0.8396 (mp0) cc_final: 0.7995 (mp0) REVERT: K 206 ASP cc_start: 0.7794 (t0) cc_final: 0.7449 (t0) REVERT: J 97 LYS cc_start: 0.8406 (tptt) cc_final: 0.8075 (tttt) REVERT: J 106 LYS cc_start: 0.8488 (mmtm) cc_final: 0.7981 (mmtm) REVERT: J 151 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8475 (t) REVERT: J 170 GLU cc_start: 0.8034 (pp20) cc_final: 0.7635 (pp20) REVERT: J 206 ASP cc_start: 0.7859 (t0) cc_final: 0.7629 (t0) REVERT: J 211 LYS cc_start: 0.7992 (tmtt) cc_final: 0.7703 (tttt) REVERT: J 214 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8383 (mtmm) REVERT: I 97 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8088 (tttt) REVERT: I 106 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7840 (mmtm) REVERT: H 78 ASP cc_start: 0.7857 (t0) cc_final: 0.7609 (t70) REVERT: H 106 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7565 (mmtm) REVERT: H 197 ASP cc_start: 0.7521 (t0) cc_final: 0.7290 (t0) REVERT: H 211 LYS cc_start: 0.7625 (tmtt) cc_final: 0.7349 (tttt) REVERT: H 221 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8126 (mtpp) REVERT: G 50 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6178 (tmmt) REVERT: G 88 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7790 (ptp) REVERT: G 97 LYS cc_start: 0.8188 (mptt) cc_final: 0.7977 (tptt) REVERT: G 98 ASP cc_start: 0.7487 (p0) cc_final: 0.7089 (p0) REVERT: G 214 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8108 (mtmm) REVERT: F 151 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8499 (t) REVERT: F 170 GLU cc_start: 0.8057 (pp20) cc_final: 0.7673 (pp20) REVERT: F 211 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7852 (tttt) REVERT: F 214 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8415 (mtpt) REVERT: F 221 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7796 (mtpp) REVERT: E 97 LYS cc_start: 0.8361 (tptt) cc_final: 0.8123 (tttt) REVERT: E 110 ILE cc_start: 0.8591 (pt) cc_final: 0.8346 (mt) REVERT: E 111 LYS cc_start: 0.8491 (mptt) cc_final: 0.8146 (mttt) REVERT: E 170 GLU cc_start: 0.8015 (pp20) cc_final: 0.7721 (pp20) REVERT: D 86 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8262 (tp) REVERT: D 92 GLU cc_start: 0.7201 (pp20) cc_final: 0.6962 (pp20) REVERT: D 106 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7949 (mmmm) REVERT: D 214 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8265 (mtmm) REVERT: C 97 LYS cc_start: 0.8421 (tptt) cc_final: 0.8119 (tttt) REVERT: C 170 GLU cc_start: 0.7963 (pp20) cc_final: 0.7525 (pp20) REVERT: C 238 LYS cc_start: 0.8242 (mttt) cc_final: 0.7942 (mttt) REVERT: B 89 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8128 (ptpp) REVERT: B 97 LYS cc_start: 0.8252 (tptt) cc_final: 0.7981 (tttt) REVERT: B 109 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: B 145 ILE cc_start: 0.8792 (mp) cc_final: 0.8564 (mp) REVERT: B 170 GLU cc_start: 0.7989 (pp20) cc_final: 0.7781 (pp20) REVERT: B 196 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8436 (mtmm) REVERT: B 211 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7581 (tmtt) outliers start: 65 outliers final: 38 residues processed: 583 average time/residue: 0.8490 time to fit residues: 555.0880 Evaluate side-chains 611 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 561 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 193 ARG Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain G residue 50 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 148 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 119 optimal weight: 0.0770 chunk 186 optimal weight: 0.9990 chunk 340 optimal weight: 0.0570 chunk 133 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 256 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN H 171 GLN F 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129654 restraints weight = 36123.317| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.06 r_work: 0.3473 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28253 Z= 0.114 Angle : 0.576 9.161 38095 Z= 0.286 Chirality : 0.044 0.177 4066 Planarity : 0.005 0.054 4769 Dihedral : 5.093 35.581 3724 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.78 % Allowed : 19.14 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 1.01 (0.15), residues: 3344 helix: 0.36 (0.17), residues: 950 sheet: 2.10 (0.26), residues: 437 loop : 0.63 (0.15), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 240 TYR 0.007 0.001 TYR R 173 PHE 0.006 0.001 PHE E 91 TRP 0.006 0.001 TRP C 235 HIS 0.005 0.001 HIS H 225 Details of bonding type rmsd covalent geometry : bond 0.00267 (28253) covalent geometry : angle 0.57600 (38095) hydrogen bonds : bond 0.02964 ( 1178) hydrogen bonds : angle 5.27765 ( 3420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 558 time to evaluate : 0.945 Fit side-chains REVERT: A 97 LYS cc_start: 0.8476 (tptt) cc_final: 0.8156 (tttt) REVERT: A 170 GLU cc_start: 0.7972 (pp20) cc_final: 0.7623 (pp20) REVERT: A 214 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8336 (mtmm) REVERT: R 84 TYR cc_start: 0.8500 (t80) cc_final: 0.7970 (t80) REVERT: R 106 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7771 (mmtm) REVERT: Q 214 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8420 (mtmm) REVERT: P 106 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8068 (mmtm) REVERT: P 151 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8457 (t) REVERT: P 170 GLU cc_start: 0.7968 (pp20) cc_final: 0.7664 (pp20) REVERT: P 184 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7446 (tm-30) REVERT: P 203 GLU cc_start: 0.8245 (mp0) cc_final: 0.7850 (mp0) REVERT: P 211 LYS cc_start: 0.7996 (tmtt) cc_final: 0.7744 (tttt) REVERT: P 214 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8219 (mttm) REVERT: O 97 LYS cc_start: 0.8227 (mptt) cc_final: 0.8010 (tptt) REVERT: N 97 LYS cc_start: 0.8351 (mptt) cc_final: 0.8117 (tptt) REVERT: N 98 ASP cc_start: 0.7797 (p0) cc_final: 0.7504 (p0) REVERT: N 196 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8445 (mtmm) REVERT: M 82 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8424 (t) REVERT: M 89 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8316 (ptpp) REVERT: M 97 LYS cc_start: 0.8459 (tptt) cc_final: 0.8177 (tttt) REVERT: M 203 GLU cc_start: 0.8159 (mp0) cc_final: 0.7732 (mp0) REVERT: M 211 LYS cc_start: 0.7628 (tmtt) cc_final: 0.7371 (tttt) REVERT: M 214 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8150 (mtmm) REVERT: L 84 TYR cc_start: 0.8471 (t80) cc_final: 0.8171 (t80) REVERT: L 97 LYS cc_start: 0.8243 (mptt) cc_final: 0.8031 (tptt) REVERT: L 170 GLU cc_start: 0.7981 (pp20) cc_final: 0.7500 (pp20) REVERT: L 193 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8295 (mtt-85) REVERT: L 214 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8068 (mtmm) REVERT: K 97 LYS cc_start: 0.8506 (tttt) cc_final: 0.8166 (ttmm) REVERT: K 151 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8367 (t) REVERT: K 203 GLU cc_start: 0.8389 (mp0) cc_final: 0.7991 (mp0) REVERT: K 206 ASP cc_start: 0.7812 (t0) cc_final: 0.7433 (t0) REVERT: J 97 LYS cc_start: 0.8414 (tptt) cc_final: 0.8099 (tttt) REVERT: J 106 LYS cc_start: 0.8467 (mmtm) cc_final: 0.7930 (mmtm) REVERT: J 151 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8485 (t) REVERT: J 206 ASP cc_start: 0.7851 (t0) cc_final: 0.7633 (t0) REVERT: J 211 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7699 (tttt) REVERT: J 214 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8363 (mtmm) REVERT: I 97 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8062 (ttmm) REVERT: I 106 LYS cc_start: 0.8182 (mmtm) cc_final: 0.7839 (mmtm) REVERT: H 78 ASP cc_start: 0.7883 (t0) cc_final: 0.7642 (t70) REVERT: H 197 ASP cc_start: 0.7552 (t0) cc_final: 0.7325 (t0) REVERT: H 211 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7351 (tttt) REVERT: H 221 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8148 (mtpp) REVERT: G 88 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7841 (ptp) REVERT: G 97 LYS cc_start: 0.8225 (mptt) cc_final: 0.8003 (tptt) REVERT: G 98 ASP cc_start: 0.7478 (p0) cc_final: 0.7071 (p0) REVERT: G 206 ASP cc_start: 0.7785 (t0) cc_final: 0.7422 (t0) REVERT: G 214 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8066 (mtmm) REVERT: F 170 GLU cc_start: 0.8058 (pp20) cc_final: 0.7676 (pp20) REVERT: F 171 GLN cc_start: 0.8851 (tp40) cc_final: 0.8621 (tp-100) REVERT: F 211 LYS cc_start: 0.8133 (tmtt) cc_final: 0.7846 (tttt) REVERT: F 214 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8386 (mtpt) REVERT: F 221 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7811 (mtpp) REVERT: E 97 LYS cc_start: 0.8331 (tptt) cc_final: 0.8098 (tttt) REVERT: E 110 ILE cc_start: 0.8560 (pt) cc_final: 0.8332 (mt) REVERT: E 111 LYS cc_start: 0.8410 (mptt) cc_final: 0.8072 (mttt) REVERT: E 170 GLU cc_start: 0.8022 (pp20) cc_final: 0.7728 (pp20) REVERT: D 92 GLU cc_start: 0.7193 (pp20) cc_final: 0.6953 (pp20) REVERT: D 106 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7995 (mmmm) REVERT: D 196 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8320 (mtmm) REVERT: D 214 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8319 (mtmm) REVERT: C 97 LYS cc_start: 0.8396 (tptt) cc_final: 0.8094 (tttt) REVERT: C 211 LYS cc_start: 0.7868 (tmtt) cc_final: 0.7619 (tttt) REVERT: C 238 LYS cc_start: 0.8245 (mttt) cc_final: 0.7933 (mttt) REVERT: B 89 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8109 (ptpp) REVERT: B 97 LYS cc_start: 0.8221 (tptt) cc_final: 0.7952 (tttt) REVERT: B 145 ILE cc_start: 0.8784 (mp) cc_final: 0.8559 (mp) REVERT: B 170 GLU cc_start: 0.8005 (pp20) cc_final: 0.7750 (pp20) REVERT: B 196 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8410 (mtmm) REVERT: B 211 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7604 (tmtt) outliers start: 53 outliers final: 36 residues processed: 577 average time/residue: 0.8546 time to fit residues: 552.7364 Evaluate side-chains 597 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 554 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 193 ARG Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 296 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 280 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 328 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.154036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128533 restraints weight = 36248.856| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.98 r_work: 0.3456 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28253 Z= 0.149 Angle : 0.600 9.089 38095 Z= 0.298 Chirality : 0.045 0.189 4066 Planarity : 0.005 0.053 4769 Dihedral : 5.102 36.488 3724 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.54 % Allowed : 19.51 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 3344 helix: 0.32 (0.17), residues: 950 sheet: 1.25 (0.22), residues: 627 loop : 0.74 (0.16), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 240 TYR 0.019 0.001 TYR H 246 PHE 0.006 0.001 PHE B 213 TRP 0.007 0.001 TRP C 235 HIS 0.003 0.001 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00359 (28253) covalent geometry : angle 0.59998 (38095) hydrogen bonds : bond 0.03289 ( 1178) hydrogen bonds : angle 5.35584 ( 3420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6688 Ramachandran restraints generated. 3344 Oldfield, 0 Emsley, 3344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 558 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8471 (tptt) cc_final: 0.8167 (tttt) REVERT: A 170 GLU cc_start: 0.8002 (pp20) cc_final: 0.7647 (pp20) REVERT: A 214 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8326 (mtmm) REVERT: R 84 TYR cc_start: 0.8499 (t80) cc_final: 0.8039 (t80) REVERT: R 97 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8144 (tttt) REVERT: R 106 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7872 (mmtm) REVERT: Q 101 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: P 106 LYS cc_start: 0.8373 (mmtm) cc_final: 0.8117 (mmtm) REVERT: P 151 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8499 (t) REVERT: P 170 GLU cc_start: 0.7965 (pp20) cc_final: 0.7667 (pp20) REVERT: P 184 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7467 (tm-30) REVERT: P 203 GLU cc_start: 0.8302 (mp0) cc_final: 0.7910 (mp0) REVERT: P 211 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7782 (tttt) REVERT: P 214 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8241 (mttm) REVERT: O 97 LYS cc_start: 0.8246 (mptt) cc_final: 0.8033 (tptt) REVERT: N 97 LYS cc_start: 0.8365 (mptt) cc_final: 0.8137 (tptt) REVERT: M 82 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8421 (t) REVERT: M 89 LYS cc_start: 0.8597 (ptpp) cc_final: 0.8344 (ptpp) REVERT: M 97 LYS cc_start: 0.8446 (tptt) cc_final: 0.8178 (tttt) REVERT: M 203 GLU cc_start: 0.8167 (mp0) cc_final: 0.7741 (mp0) REVERT: M 211 LYS cc_start: 0.7640 (tmtt) cc_final: 0.7372 (tttt) REVERT: M 214 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8163 (mtmm) REVERT: L 84 TYR cc_start: 0.8461 (t80) cc_final: 0.8150 (t80) REVERT: L 97 LYS cc_start: 0.8246 (mptt) cc_final: 0.8040 (tptt) REVERT: L 170 GLU cc_start: 0.7983 (pp20) cc_final: 0.7507 (pp20) REVERT: L 193 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8297 (mtt-85) REVERT: K 97 LYS cc_start: 0.8520 (tttt) cc_final: 0.8173 (ttmm) REVERT: K 151 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8384 (t) REVERT: K 203 GLU cc_start: 0.8397 (mp0) cc_final: 0.7993 (mp0) REVERT: K 206 ASP cc_start: 0.7811 (t0) cc_final: 0.7419 (t0) REVERT: J 97 LYS cc_start: 0.8425 (tptt) cc_final: 0.8113 (tttt) REVERT: J 106 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8003 (mmtm) REVERT: J 151 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8499 (t) REVERT: J 170 GLU cc_start: 0.8048 (pp20) cc_final: 0.7655 (pp20) REVERT: J 206 ASP cc_start: 0.7859 (t0) cc_final: 0.7653 (t0) REVERT: J 211 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7724 (tttt) REVERT: J 214 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8376 (mtmm) REVERT: I 97 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8084 (ttmm) REVERT: I 106 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7919 (mmtm) REVERT: H 78 ASP cc_start: 0.7889 (t0) cc_final: 0.7659 (t70) REVERT: H 106 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7682 (mmtm) REVERT: H 197 ASP cc_start: 0.7536 (t0) cc_final: 0.7317 (t0) REVERT: H 211 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7362 (tttt) REVERT: H 221 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8127 (mtpp) REVERT: G 88 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7819 (ptp) REVERT: G 97 LYS cc_start: 0.8227 (mptt) cc_final: 0.8001 (tptt) REVERT: G 98 ASP cc_start: 0.7462 (p0) cc_final: 0.7062 (p0) REVERT: G 206 ASP cc_start: 0.7818 (t0) cc_final: 0.7444 (t0) REVERT: G 214 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8074 (mtmm) REVERT: F 170 GLU cc_start: 0.8044 (pp20) cc_final: 0.7662 (pp20) REVERT: F 171 GLN cc_start: 0.8848 (tp40) cc_final: 0.8641 (tp-100) REVERT: F 211 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7844 (tttt) REVERT: F 214 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8421 (mtpt) REVERT: F 221 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7823 (mtpp) REVERT: E 97 LYS cc_start: 0.8311 (tptt) cc_final: 0.8098 (tttt) REVERT: E 110 ILE cc_start: 0.8590 (pt) cc_final: 0.8359 (mt) REVERT: E 111 LYS cc_start: 0.8463 (mptt) cc_final: 0.8143 (mttt) REVERT: E 170 GLU cc_start: 0.8030 (pp20) cc_final: 0.7741 (pp20) REVERT: D 92 GLU cc_start: 0.7214 (pp20) cc_final: 0.6980 (pp20) REVERT: D 106 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8020 (mmtm) REVERT: D 214 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8359 (mtmm) REVERT: C 97 LYS cc_start: 0.8404 (tptt) cc_final: 0.8108 (tttt) REVERT: C 106 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7799 (mmtm) REVERT: C 211 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7650 (tttt) REVERT: C 238 LYS cc_start: 0.8228 (mttt) cc_final: 0.7911 (mttt) REVERT: B 89 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8215 (ptpp) REVERT: B 97 LYS cc_start: 0.8229 (tptt) cc_final: 0.7963 (tttt) REVERT: B 145 ILE cc_start: 0.8811 (mp) cc_final: 0.8587 (mp) REVERT: B 196 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8426 (mtmm) REVERT: B 211 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7611 (tmtt) outliers start: 46 outliers final: 33 residues processed: 575 average time/residue: 0.8750 time to fit residues: 563.2122 Evaluate side-chains 598 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 556 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 193 ARG Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 162 GLN Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 135 optimal weight: 0.1980 chunk 137 optimal weight: 0.0980 chunk 21 optimal weight: 0.0670 chunk 147 optimal weight: 0.6980 chunk 244 optimal weight: 0.0270 chunk 323 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 282 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.155705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130048 restraints weight = 36347.883| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.01 r_work: 0.3492 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28253 Z= 0.100 Angle : 0.568 9.132 38095 Z= 0.282 Chirality : 0.043 0.176 4066 Planarity : 0.005 0.058 4769 Dihedral : 5.005 35.593 3724 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.37 % Allowed : 19.95 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 1.08 (0.15), residues: 3344 helix: 0.50 (0.17), residues: 950 sheet: 2.07 (0.26), residues: 437 loop : 0.66 (0.15), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 240 TYR 0.018 0.001 TYR H 246 PHE 0.006 0.001 PHE E 91 TRP 0.006 0.001 TRP K 235 HIS 0.005 0.001 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00229 (28253) covalent geometry : angle 0.56756 (38095) hydrogen bonds : bond 0.02691 ( 1178) hydrogen bonds : angle 5.18624 ( 3420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12245.53 seconds wall clock time: 209 minutes 2.33 seconds (12542.33 seconds total)