Starting phenix.real_space_refine on Fri Sep 19 12:17:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvf_47202/09_2025/9dvf_47202.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvf_47202/09_2025/9dvf_47202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dvf_47202/09_2025/9dvf_47202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvf_47202/09_2025/9dvf_47202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dvf_47202/09_2025/9dvf_47202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvf_47202/09_2025/9dvf_47202.map" } resolution = 3.38 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= 0.000 sd= 0.088 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 192 5.16 5 C 16296 2.51 5 N 4572 2.21 5 O 4908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25968 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2164 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.01, per 1000 atoms: 0.12 Number of scatterers: 25968 At special positions: 0 Unit cell: (130.9, 122.1, 112.2, 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 192 16.00 O 4908 8.00 N 4572 7.00 C 16296 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 56.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.784A pdb=" N PHE A 128 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.509A pdb=" N MET A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU A 296 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN A 297 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE B 128 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 164 through 181 removed outlier: 3.505A pdb=" N ALA B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.865A pdb=" N MET B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.509A pdb=" N MET B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.279A pdb=" N PHE B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU B 296 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN B 297 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 55 through 63 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE C 128 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU C 296 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN C 297 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 55 through 63 Processing helix chain 'D' and resid 70 through 81 Processing helix chain 'D' and resid 95 through 104 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE D 128 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.646A pdb=" N GLU D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU D 296 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN D 297 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 55 through 63 Processing helix chain 'E' and resid 70 through 81 Processing helix chain 'E' and resid 95 through 104 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE E 128 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 210 Processing helix chain 'E' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE E 246 " --> pdb=" O GLY E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN E 263 " --> pdb=" O VAL E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 291 through 299 removed outlier: 6.057A pdb=" N LEU E 296 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN E 297 " --> pdb=" O GLU E 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 34 through 45 Processing helix chain 'F' and resid 55 through 63 Processing helix chain 'F' and resid 70 through 81 Processing helix chain 'F' and resid 95 through 104 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE F 128 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 164 through 181 removed outlier: 3.505A pdb=" N ALA F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.867A pdb=" N MET F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 210 Processing helix chain 'F' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE F 246 " --> pdb=" O GLY F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN F 263 " --> pdb=" O VAL F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU F 273 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS F 276 " --> pdb=" O ALA F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU F 296 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN F 297 " --> pdb=" O GLU F 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 34 through 45 Processing helix chain 'G' and resid 55 through 63 Processing helix chain 'G' and resid 70 through 81 Processing helix chain 'G' and resid 95 through 104 Processing helix chain 'G' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE G 128 " --> pdb=" O LYS G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 164 through 181 removed outlier: 3.505A pdb=" N ALA G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 210 Processing helix chain 'G' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE G 246 " --> pdb=" O GLY G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 263 " --> pdb=" O VAL G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU G 273 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS G 276 " --> pdb=" O ALA G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU G 296 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN G 297 " --> pdb=" O GLU G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 34 through 45 Processing helix chain 'H' and resid 55 through 63 Processing helix chain 'H' and resid 70 through 81 Processing helix chain 'H' and resid 95 through 104 Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.784A pdb=" N PHE H 128 " --> pdb=" O LYS H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 210 Processing helix chain 'H' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 247 removed outlier: 4.279A pdb=" N PHE H 246 " --> pdb=" O GLY H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 264 removed outlier: 3.572A pdb=" N LYS H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN H 263 " --> pdb=" O VAL H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 276 removed outlier: 3.646A pdb=" N GLU H 273 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS H 276 " --> pdb=" O ALA H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 290 Processing helix chain 'H' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU H 296 " --> pdb=" O GLN H 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN H 297 " --> pdb=" O GLU H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 18 Processing helix chain 'I' and resid 34 through 45 Processing helix chain 'I' and resid 55 through 63 Processing helix chain 'I' and resid 70 through 81 Processing helix chain 'I' and resid 95 through 104 Processing helix chain 'I' and resid 124 through 128 removed outlier: 3.784A pdb=" N PHE I 128 " --> pdb=" O LYS I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 210 Processing helix chain 'I' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 264 removed outlier: 3.572A pdb=" N LYS I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN I 263 " --> pdb=" O VAL I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 276 removed outlier: 3.646A pdb=" N GLU I 273 " --> pdb=" O VAL I 269 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS I 276 " --> pdb=" O ALA I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 290 Processing helix chain 'I' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU I 296 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN I 297 " --> pdb=" O GLU I 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 34 through 45 Processing helix chain 'J' and resid 55 through 63 Processing helix chain 'J' and resid 70 through 81 Processing helix chain 'J' and resid 95 through 104 Processing helix chain 'J' and resid 124 through 128 removed outlier: 3.784A pdb=" N PHE J 128 " --> pdb=" O LYS J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA J 180 " --> pdb=" O GLY J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 196 removed outlier: 3.865A pdb=" N MET J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 210 Processing helix chain 'J' and resid 224 through 234 removed outlier: 3.509A pdb=" N MET J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 247 removed outlier: 4.279A pdb=" N PHE J 246 " --> pdb=" O GLY J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN J 263 " --> pdb=" O VAL J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 276 removed outlier: 3.645A pdb=" N GLU J 273 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS J 276 " --> pdb=" O ALA J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU J 296 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN J 297 " --> pdb=" O GLU J 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 18 Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 55 through 63 Processing helix chain 'K' and resid 70 through 81 Processing helix chain 'K' and resid 95 through 104 Processing helix chain 'K' and resid 124 through 128 removed outlier: 3.785A pdb=" N PHE K 128 " --> pdb=" O LYS K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 149 Processing helix chain 'K' and resid 164 through 181 removed outlier: 3.506A pdb=" N ALA K 180 " --> pdb=" O GLY K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 196 removed outlier: 3.866A pdb=" N MET K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 210 Processing helix chain 'K' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 247 removed outlier: 4.279A pdb=" N PHE K 246 " --> pdb=" O GLY K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 264 removed outlier: 3.571A pdb=" N LYS K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN K 263 " --> pdb=" O VAL K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 276 removed outlier: 3.644A pdb=" N GLU K 273 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS K 276 " --> pdb=" O ALA K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 290 Processing helix chain 'K' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU K 296 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN K 297 " --> pdb=" O GLU K 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 18 Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 55 through 63 Processing helix chain 'L' and resid 70 through 81 Processing helix chain 'L' and resid 95 through 104 Processing helix chain 'L' and resid 124 through 128 removed outlier: 3.784A pdb=" N PHE L 128 " --> pdb=" O LYS L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 Processing helix chain 'L' and resid 164 through 181 removed outlier: 3.505A pdb=" N ALA L 180 " --> pdb=" O GLY L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 196 removed outlier: 3.867A pdb=" N MET L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 210 Processing helix chain 'L' and resid 224 through 234 removed outlier: 3.510A pdb=" N MET L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 247 removed outlier: 4.280A pdb=" N PHE L 246 " --> pdb=" O GLY L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 264 removed outlier: 3.572A pdb=" N LYS L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 276 removed outlier: 3.644A pdb=" N GLU L 273 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS L 276 " --> pdb=" O ALA L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 290 Processing helix chain 'L' and resid 291 through 299 removed outlier: 6.058A pdb=" N LEU L 296 " --> pdb=" O GLN L 293 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN L 297 " --> pdb=" O GLU L 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE A 153 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG A 154 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS A 134 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 135 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 85 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP A 109 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 87 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 49 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS A 88 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA A 51 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 48 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY A 27 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 241 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE A 29 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 216 through 217 removed outlier: 6.669A pdb=" N ILE B 153 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ARG B 154 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS B 134 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY B 135 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 85 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP B 109 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 87 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 49 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS B 88 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ALA B 51 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 48 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY B 27 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 241 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE B 29 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE C 153 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG C 154 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS C 134 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY C 135 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 85 " --> pdb=" O MET C 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP C 109 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 87 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 49 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS C 88 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA C 51 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 48 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY C 27 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 241 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE C 29 " --> pdb=" O VAL C 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE D 153 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG D 154 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS D 134 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY D 135 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL D 85 " --> pdb=" O MET D 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP D 109 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA D 87 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 49 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS D 88 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA D 51 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA D 48 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY D 27 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL D 241 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE D 29 " --> pdb=" O VAL D 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE E 153 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ARG E 154 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS E 134 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY E 135 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL E 85 " --> pdb=" O MET E 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP E 109 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA E 87 " --> pdb=" O ASP E 109 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 49 " --> pdb=" O MET E 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS E 88 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ALA E 51 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA E 48 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY E 27 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL E 241 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE E 29 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 216 through 217 removed outlier: 6.669A pdb=" N ILE F 153 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ARG F 154 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS F 134 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY F 135 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL F 85 " --> pdb=" O MET F 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP F 109 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA F 87 " --> pdb=" O ASP F 109 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 49 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS F 88 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA F 51 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA F 48 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY F 27 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL F 241 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE F 29 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE G 153 " --> pdb=" O PHE G 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG G 154 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS G 134 " --> pdb=" O ARG G 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY G 135 " --> pdb=" O GLU G 110 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G 85 " --> pdb=" O MET G 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP G 109 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA G 87 " --> pdb=" O ASP G 109 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL G 49 " --> pdb=" O MET G 86 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LYS G 88 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA G 51 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA G 48 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY G 27 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL G 241 " --> pdb=" O GLY G 27 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE G 29 " --> pdb=" O VAL G 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 216 through 217 removed outlier: 6.669A pdb=" N ILE H 153 " --> pdb=" O PHE H 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG H 154 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS H 134 " --> pdb=" O ARG H 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY H 135 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL H 85 " --> pdb=" O MET H 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP H 109 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA H 87 " --> pdb=" O ASP H 109 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL H 49 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS H 88 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA H 51 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA H 48 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY H 27 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL H 241 " --> pdb=" O GLY H 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE H 29 " --> pdb=" O VAL H 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE I 153 " --> pdb=" O PHE I 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG I 154 " --> pdb=" O PHE I 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS I 134 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY I 135 " --> pdb=" O GLU I 110 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL I 85 " --> pdb=" O MET I 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP I 109 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA I 87 " --> pdb=" O ASP I 109 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL I 49 " --> pdb=" O MET I 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS I 88 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA I 51 " --> pdb=" O LYS I 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I 48 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY I 27 " --> pdb=" O VAL I 239 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL I 241 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE I 29 " --> pdb=" O VAL I 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 216 through 217 removed outlier: 6.670A pdb=" N ILE J 153 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG J 154 " --> pdb=" O PHE J 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS J 134 " --> pdb=" O ARG J 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY J 135 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL J 85 " --> pdb=" O MET J 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP J 109 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA J 87 " --> pdb=" O ASP J 109 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL J 49 " --> pdb=" O MET J 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS J 88 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA J 51 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA J 48 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY J 27 " --> pdb=" O VAL J 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL J 241 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE J 29 " --> pdb=" O VAL J 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 216 through 217 removed outlier: 6.669A pdb=" N ILE K 153 " --> pdb=" O PHE K 217 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ARG K 154 " --> pdb=" O PHE K 132 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS K 134 " --> pdb=" O ARG K 154 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY K 135 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL K 85 " --> pdb=" O MET K 107 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP K 109 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA K 87 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL K 49 " --> pdb=" O MET K 86 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LYS K 88 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ALA K 51 " --> pdb=" O LYS K 88 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA K 48 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY K 27 " --> pdb=" O VAL K 239 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL K 241 " --> pdb=" O GLY K 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE K 29 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 216 through 217 removed outlier: 6.669A pdb=" N ILE L 153 " --> pdb=" O PHE L 217 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG L 154 " --> pdb=" O PHE L 132 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS L 134 " --> pdb=" O ARG L 154 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY L 135 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL L 85 " --> pdb=" O MET L 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP L 109 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA L 87 " --> pdb=" O ASP L 109 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL L 49 " --> pdb=" O MET L 86 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS L 88 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ALA L 51 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA L 48 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY L 27 " --> pdb=" O VAL L 239 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL L 241 " --> pdb=" O GLY L 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE L 29 " --> pdb=" O VAL L 241 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3240 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: 5.03 Time building geometry restraints manager: 2.87 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: 8988 1.34 - 1.46: 3100 1.46 - 1.57: 13844 1.57 - 1.69: 0 1.69 - 1.81: 372 Bond restraints: 26304 Sorted by residual: bond pdb=" N ARG K 18 " pdb=" CA ARG K 18 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.65e+00 bond pdb=" N ARG G 18 " pdb=" CA ARG G 18 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.64e+00 bond pdb=" N ARG L 18 " pdb=" CA ARG L 18 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.58e+00 bond pdb=" N ARG I 18 " pdb=" CA ARG I 18 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.51e+00 bond pdb=" N ARG F 18 " pdb=" CA ARG F 18 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.49e+00 ... (remaining 26299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 34787 1.89 - 3.78: 649 3.78 - 5.67: 48 5.67 - 7.56: 12 7.56 - 9.45: 12 Bond angle restraints: 35508 Sorted by residual: angle pdb=" N PHE J 20 " pdb=" CA PHE J 20 " pdb=" C PHE J 20 " ideal model delta sigma weight residual 113.41 103.96 9.45 1.22e+00 6.72e-01 6.00e+01 angle pdb=" N PHE A 20 " pdb=" CA PHE A 20 " pdb=" C PHE A 20 " ideal model delta sigma weight residual 113.41 103.97 9.44 1.22e+00 6.72e-01 5.98e+01 angle pdb=" N PHE E 20 " pdb=" CA PHE E 20 " pdb=" C PHE E 20 " ideal model delta sigma weight residual 113.41 103.98 9.43 1.22e+00 6.72e-01 5.97e+01 angle pdb=" N PHE H 20 " pdb=" CA PHE H 20 " pdb=" C PHE H 20 " ideal model delta sigma weight residual 113.41 103.98 9.43 1.22e+00 6.72e-01 5.97e+01 angle pdb=" N PHE C 20 " pdb=" CA PHE C 20 " pdb=" C PHE C 20 " ideal model delta sigma weight residual 113.41 103.98 9.43 1.22e+00 6.72e-01 5.97e+01 ... (remaining 35503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14724 17.97 - 35.94: 1092 35.94 - 53.90: 336 53.90 - 71.87: 84 71.87 - 89.84: 12 Dihedral angle restraints: 16248 sinusoidal: 6432 harmonic: 9816 Sorted by residual: dihedral pdb=" CB ARG F 194 " pdb=" CG ARG F 194 " pdb=" CD ARG F 194 " pdb=" NE ARG F 194 " ideal model delta sinusoidal sigma weight residual 60.00 118.96 -58.96 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB ARG B 194 " pdb=" CG ARG B 194 " pdb=" CD ARG B 194 " pdb=" NE ARG B 194 " ideal model delta sinusoidal sigma weight residual 60.00 118.95 -58.95 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB ARG K 194 " pdb=" CG ARG K 194 " pdb=" CD ARG K 194 " pdb=" NE ARG K 194 " ideal model delta sinusoidal sigma weight residual 60.00 118.94 -58.94 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 16245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2575 0.034 - 0.068: 1045 0.068 - 0.101: 300 0.101 - 0.135: 184 0.135 - 0.169: 12 Chirality restraints: 4116 Sorted by residual: chirality pdb=" CA LYS L 17 " pdb=" N LYS L 17 " pdb=" C LYS L 17 " pdb=" CB LYS L 17 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA LYS F 17 " pdb=" N LYS F 17 " pdb=" C LYS F 17 " pdb=" CB LYS F 17 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA LYS H 17 " pdb=" N LYS H 17 " pdb=" C LYS H 17 " pdb=" CB LYS H 17 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 4113 not shown) Planarity restraints: 4704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 18 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.86e+00 pdb=" NE ARG F 18 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 18 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 18 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 18 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 18 " 0.282 9.50e-02 1.11e+02 1.27e-01 9.83e+00 pdb=" NE ARG A 18 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 18 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 18 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 18 " -0.282 9.50e-02 1.11e+02 1.26e-01 9.82e+00 pdb=" NE ARG D 18 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 18 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 18 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 18 " -0.010 2.00e-02 2.50e+03 ... (remaining 4701 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 8444 2.85 - 3.36: 24066 3.36 - 3.87: 39355 3.87 - 4.39: 49729 4.39 - 4.90: 82473 Nonbonded interactions: 204067 Sorted by model distance: nonbonded pdb=" OG SER L 286 " pdb=" OD1 ASP L 288 " model vdw 2.333 3.040 nonbonded pdb=" OG SER G 286 " pdb=" OD1 ASP G 288 " model vdw 2.333 3.040 nonbonded pdb=" OG SER K 286 " pdb=" OD1 ASP K 288 " model vdw 2.333 3.040 nonbonded pdb=" OG SER E 286 " pdb=" OD1 ASP E 288 " model vdw 2.333 3.040 nonbonded pdb=" OG SER F 286 " pdb=" OD1 ASP F 288 " model vdw 2.333 3.040 ... (remaining 204062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.380 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.004 0.039 26304 Z= 0.213 Angle : 0.637 9.446 35508 Z= 0.397 Chirality : 0.044 0.169 4116 Planarity : 0.008 0.127 4704 Dihedral : 15.041 89.841 9936 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.46 % Allowed : 10.05 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3468 helix: -1.50 (0.12), residues: 1740 sheet: -1.35 (0.23), residues: 468 loop : 0.90 (0.20), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 233 TYR 0.010 0.002 TYR L 265 PHE 0.013 0.002 PHE F 128 TRP 0.003 0.001 TRP H 301 HIS 0.002 0.001 HIS G 11 Details of bonding type rmsd covalent geometry : bond 0.00411 (26304) covalent geometry : angle 0.63673 (35508) hydrogen bonds : bond 0.33115 ( 1164) hydrogen bonds : angle 9.13381 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 502 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.5086 (tpp) cc_final: 0.4863 (tpp) REVERT: A 75 GLN cc_start: 0.8170 (tp40) cc_final: 0.7551 (mt0) REVERT: A 107 MET cc_start: 0.8592 (ttm) cc_final: 0.8272 (ttm) REVERT: A 231 MET cc_start: 0.8303 (mmm) cc_final: 0.8092 (mmm) REVERT: B 23 MET cc_start: 0.5049 (tpp) cc_final: 0.4757 (tpp) REVERT: B 36 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6365 (mp0) REVERT: B 50 MET cc_start: 0.8486 (ttm) cc_final: 0.8266 (ttm) REVERT: B 270 LYS cc_start: 0.7399 (tptt) cc_final: 0.7196 (tppt) REVERT: C 36 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6439 (pm20) REVERT: C 75 GLN cc_start: 0.8219 (tp40) cc_final: 0.7385 (mt0) REVERT: C 107 MET cc_start: 0.8650 (ttm) cc_final: 0.8332 (ttm) REVERT: C 282 MET cc_start: 0.8353 (ptm) cc_final: 0.8076 (ptm) REVERT: D 23 MET cc_start: 0.5107 (tpp) cc_final: 0.4843 (tpp) REVERT: D 36 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6528 (pm20) REVERT: D 73 ILE cc_start: 0.7319 (mt) cc_final: 0.7052 (tp) REVERT: D 107 MET cc_start: 0.8627 (ttm) cc_final: 0.8326 (ttm) REVERT: D 231 MET cc_start: 0.8280 (mmm) cc_final: 0.8022 (mmm) REVERT: E 23 MET cc_start: 0.5200 (tpp) cc_final: 0.4842 (tpp) REVERT: E 36 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6491 (mp0) REVERT: E 50 MET cc_start: 0.8457 (ttm) cc_final: 0.8227 (ttm) REVERT: E 75 GLN cc_start: 0.8222 (tp40) cc_final: 0.7513 (mt0) REVERT: E 270 LYS cc_start: 0.7367 (tptt) cc_final: 0.7157 (mmtm) REVERT: F 36 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6739 (pm20) REVERT: F 75 GLN cc_start: 0.8209 (tp40) cc_final: 0.7380 (mt0) REVERT: F 107 MET cc_start: 0.8643 (ttm) cc_final: 0.8318 (ttm) REVERT: F 231 MET cc_start: 0.8338 (mmm) cc_final: 0.7125 (mmt) REVERT: F 282 MET cc_start: 0.8339 (ptm) cc_final: 0.8067 (ptm) REVERT: G 23 MET cc_start: 0.5027 (tpp) cc_final: 0.4748 (tpp) REVERT: G 75 GLN cc_start: 0.8170 (tp40) cc_final: 0.7573 (mt0) REVERT: G 107 MET cc_start: 0.8599 (ttm) cc_final: 0.8262 (ttm) REVERT: G 231 MET cc_start: 0.8304 (mmm) cc_final: 0.8043 (mmm) REVERT: G 253 LYS cc_start: 0.8230 (mttt) cc_final: 0.7631 (mtpp) REVERT: H 23 MET cc_start: 0.5154 (tpp) cc_final: 0.4803 (tpp) REVERT: H 36 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6431 (mp0) REVERT: H 50 MET cc_start: 0.8471 (ttm) cc_final: 0.8261 (ttm) REVERT: I 36 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6400 (pm20) REVERT: I 75 GLN cc_start: 0.8217 (tp40) cc_final: 0.7384 (mt0) REVERT: I 107 MET cc_start: 0.8651 (ttm) cc_final: 0.8344 (ttm) REVERT: I 282 MET cc_start: 0.8371 (ptm) cc_final: 0.8108 (ptm) REVERT: J 23 MET cc_start: 0.5104 (tpp) cc_final: 0.4825 (tpp) REVERT: J 36 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6527 (pm20) REVERT: J 73 ILE cc_start: 0.7296 (mt) cc_final: 0.7070 (tp) REVERT: J 107 MET cc_start: 0.8623 (ttm) cc_final: 0.8324 (ttm) REVERT: J 231 MET cc_start: 0.8289 (mmm) cc_final: 0.8019 (mmm) REVERT: K 23 MET cc_start: 0.5179 (tpp) cc_final: 0.4787 (tpp) REVERT: K 36 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6274 (mp0) REVERT: K 75 GLN cc_start: 0.8214 (tp40) cc_final: 0.7514 (mt0) REVERT: L 36 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6471 (pm20) REVERT: L 75 GLN cc_start: 0.8216 (tp40) cc_final: 0.7388 (mt0) REVERT: L 107 MET cc_start: 0.8670 (ttm) cc_final: 0.8334 (ttm) REVERT: L 282 MET cc_start: 0.8341 (ptm) cc_final: 0.8072 (ptm) outliers start: 12 outliers final: 4 residues processed: 514 average time/residue: 0.1868 time to fit residues: 150.8392 Evaluate side-chains 470 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 466 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain L residue 110 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.185536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.154051 restraints weight = 24221.357| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.79 r_work: 0.3500 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 26304 Z= 0.177 Angle : 0.544 6.110 35508 Z= 0.288 Chirality : 0.045 0.135 4116 Planarity : 0.005 0.033 4704 Dihedral : 4.994 58.905 3708 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 1.22 % Allowed : 9.89 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3468 helix: -0.31 (0.12), residues: 1776 sheet: -1.07 (0.23), residues: 468 loop : 0.59 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.005 0.001 TYR G 121 PHE 0.014 0.002 PHE K 128 TRP 0.010 0.003 TRP I 301 HIS 0.002 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00442 (26304) covalent geometry : angle 0.54356 (35508) hydrogen bonds : bond 0.05472 ( 1164) hydrogen bonds : angle 5.04495 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 436 time to evaluate : 0.954 Fit side-chains REVERT: A 23 MET cc_start: 0.5014 (tpp) cc_final: 0.4642 (tpp) REVERT: A 36 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6677 (pm20) REVERT: A 107 MET cc_start: 0.8810 (ttm) cc_final: 0.8509 (ttm) REVERT: A 110 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: A 195 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7123 (tt0) REVERT: B 36 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6494 (pm20) REVERT: B 191 MET cc_start: 0.7774 (ttt) cc_final: 0.7490 (ttm) REVERT: C 36 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6515 (pm20) REVERT: C 107 MET cc_start: 0.8811 (ttm) cc_final: 0.8433 (ttm) REVERT: C 195 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7267 (tt0) REVERT: C 282 MET cc_start: 0.8275 (ptm) cc_final: 0.8052 (ptp) REVERT: D 23 MET cc_start: 0.5045 (tpp) cc_final: 0.4580 (tpp) REVERT: D 36 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6603 (pm20) REVERT: D 107 MET cc_start: 0.8791 (ttm) cc_final: 0.8496 (ttm) REVERT: D 110 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8480 (tp30) REVERT: D 195 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7143 (tt0) REVERT: E 36 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6503 (pm20) REVERT: E 191 MET cc_start: 0.7966 (ttt) cc_final: 0.7680 (ttm) REVERT: F 36 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6782 (pm20) REVERT: F 107 MET cc_start: 0.8826 (ttm) cc_final: 0.8449 (ttm) REVERT: F 110 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: F 195 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7255 (tt0) REVERT: F 282 MET cc_start: 0.8309 (ptm) cc_final: 0.8085 (ptp) REVERT: G 23 MET cc_start: 0.5057 (tpp) cc_final: 0.4624 (tpp) REVERT: G 36 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6676 (pm20) REVERT: G 107 MET cc_start: 0.8813 (ttm) cc_final: 0.8516 (ttm) REVERT: G 110 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8505 (tp30) REVERT: G 195 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7160 (tt0) REVERT: G 253 LYS cc_start: 0.8045 (mttt) cc_final: 0.7718 (mttm) REVERT: H 36 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6497 (pm20) REVERT: H 191 MET cc_start: 0.7875 (ttt) cc_final: 0.7608 (ttm) REVERT: I 36 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6509 (pm20) REVERT: I 107 MET cc_start: 0.8807 (ttm) cc_final: 0.8438 (ttm) REVERT: J 23 MET cc_start: 0.5035 (tpp) cc_final: 0.4588 (tpp) REVERT: J 36 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6587 (pm20) REVERT: J 107 MET cc_start: 0.8799 (ttm) cc_final: 0.8506 (ttm) REVERT: J 110 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8497 (tp30) REVERT: J 195 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7140 (tt0) REVERT: K 36 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6500 (pm20) REVERT: K 191 MET cc_start: 0.7950 (ttt) cc_final: 0.7652 (ttm) REVERT: L 36 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6756 (pm20) REVERT: L 107 MET cc_start: 0.8823 (ttm) cc_final: 0.8458 (ttm) REVERT: L 110 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: L 282 MET cc_start: 0.8320 (ptm) cc_final: 0.8111 (ptp) outliers start: 32 outliers final: 24 residues processed: 464 average time/residue: 0.1861 time to fit residues: 135.6651 Evaluate side-chains 454 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 424 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 111 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 165 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 27 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 213 optimal weight: 0.0970 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 333 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.178994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150999 restraints weight = 24881.144| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.57 r_work: 0.3686 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 26304 Z= 0.185 Angle : 0.536 5.433 35508 Z= 0.282 Chirality : 0.045 0.137 4116 Planarity : 0.005 0.037 4704 Dihedral : 4.591 54.504 3702 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.37 % Allowed : 10.81 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3468 helix: -0.06 (0.12), residues: 1836 sheet: -0.98 (0.24), residues: 468 loop : -0.07 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 154 TYR 0.006 0.001 TYR A 121 PHE 0.016 0.002 PHE G 128 TRP 0.009 0.002 TRP H 301 HIS 0.002 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00468 (26304) covalent geometry : angle 0.53555 (35508) hydrogen bonds : bond 0.05428 ( 1164) hydrogen bonds : angle 4.66443 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 446 time to evaluate : 1.036 Fit side-chains REVERT: A 23 MET cc_start: 0.5039 (tpp) cc_final: 0.4619 (tpp) REVERT: A 36 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6902 (pm20) REVERT: A 107 MET cc_start: 0.8762 (ttm) cc_final: 0.8475 (ttm) REVERT: B 23 MET cc_start: 0.5319 (tpp) cc_final: 0.5016 (tpp) REVERT: B 36 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6743 (pm20) REVERT: C 36 GLU cc_start: 0.7727 (mm-30) cc_final: 0.6901 (pm20) REVERT: C 107 MET cc_start: 0.8841 (ttm) cc_final: 0.8412 (ttm) REVERT: D 23 MET cc_start: 0.5067 (tpp) cc_final: 0.4654 (tpp) REVERT: D 36 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6870 (pm20) REVERT: D 43 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 107 MET cc_start: 0.8727 (ttm) cc_final: 0.8444 (ttm) REVERT: D 110 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8388 (tp30) REVERT: D 253 LYS cc_start: 0.8343 (mttt) cc_final: 0.8018 (mttm) REVERT: E 23 MET cc_start: 0.5280 (tpp) cc_final: 0.4969 (tpp) REVERT: E 36 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6643 (pm20) REVERT: F 36 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6918 (pm20) REVERT: F 107 MET cc_start: 0.8833 (ttm) cc_final: 0.8426 (ttm) REVERT: G 23 MET cc_start: 0.5042 (tpp) cc_final: 0.4642 (tpp) REVERT: G 36 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6850 (pm20) REVERT: G 43 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7390 (mm-30) REVERT: G 107 MET cc_start: 0.8771 (ttm) cc_final: 0.8479 (ttm) REVERT: H 23 MET cc_start: 0.5252 (tpp) cc_final: 0.4935 (tpp) REVERT: H 36 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6679 (pm20) REVERT: I 36 GLU cc_start: 0.7735 (mm-30) cc_final: 0.6926 (pm20) REVERT: I 107 MET cc_start: 0.8827 (ttm) cc_final: 0.8412 (ttm) REVERT: I 270 LYS cc_start: 0.7404 (tptt) cc_final: 0.7113 (mmtm) REVERT: J 23 MET cc_start: 0.5064 (tpp) cc_final: 0.4659 (tpp) REVERT: J 36 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6858 (pm20) REVERT: J 43 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7390 (mm-30) REVERT: J 107 MET cc_start: 0.8738 (ttm) cc_final: 0.8450 (ttm) REVERT: J 110 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8401 (tp30) REVERT: J 253 LYS cc_start: 0.8341 (mttt) cc_final: 0.8017 (mttm) REVERT: K 23 MET cc_start: 0.5251 (tpp) cc_final: 0.4925 (tpp) REVERT: K 36 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6645 (pm20) REVERT: L 36 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6937 (pm20) REVERT: L 107 MET cc_start: 0.8837 (ttm) cc_final: 0.8449 (ttm) REVERT: L 270 LYS cc_start: 0.7439 (tptt) cc_final: 0.7135 (mmtm) outliers start: 36 outliers final: 23 residues processed: 482 average time/residue: 0.1873 time to fit residues: 141.9582 Evaluate side-chains 443 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 418 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 35 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 240 optimal weight: 0.0470 chunk 319 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.1280 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.184546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162866 restraints weight = 23722.462| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.04 r_work: 0.3511 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26304 Z= 0.121 Angle : 0.460 5.248 35508 Z= 0.242 Chirality : 0.043 0.131 4116 Planarity : 0.004 0.035 4704 Dihedral : 3.962 13.441 3696 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.99 % Allowed : 11.80 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 3468 helix: 0.41 (0.12), residues: 1836 sheet: -0.84 (0.25), residues: 480 loop : 0.08 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 154 TYR 0.005 0.001 TYR D 121 PHE 0.009 0.002 PHE A 240 TRP 0.010 0.002 TRP I 301 HIS 0.001 0.000 HIS L 11 Details of bonding type rmsd covalent geometry : bond 0.00296 (26304) covalent geometry : angle 0.45984 (35508) hydrogen bonds : bond 0.04095 ( 1164) hydrogen bonds : angle 4.21730 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 404 time to evaluate : 0.933 Fit side-chains REVERT: A 23 MET cc_start: 0.5150 (tpp) cc_final: 0.4756 (tpp) REVERT: A 36 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6851 (pm20) REVERT: A 107 MET cc_start: 0.8666 (ttm) cc_final: 0.8386 (ttm) REVERT: A 247 LYS cc_start: 0.8267 (mmmm) cc_final: 0.8026 (mtpt) REVERT: B 36 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6803 (pm20) REVERT: C 36 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6950 (pm20) REVERT: C 107 MET cc_start: 0.8581 (ttm) cc_final: 0.8292 (ttm) REVERT: D 23 MET cc_start: 0.5186 (tpp) cc_final: 0.4776 (tpp) REVERT: D 36 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6837 (pm20) REVERT: D 107 MET cc_start: 0.8625 (ttm) cc_final: 0.8355 (ttm) REVERT: D 247 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8067 (mtpt) REVERT: D 253 LYS cc_start: 0.8321 (mttt) cc_final: 0.8018 (mttm) REVERT: E 23 MET cc_start: 0.5428 (tpp) cc_final: 0.5153 (tpp) REVERT: E 36 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6803 (pm20) REVERT: F 36 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6931 (pm20) REVERT: F 107 MET cc_start: 0.8607 (ttm) cc_final: 0.8298 (ttm) REVERT: G 23 MET cc_start: 0.5149 (tpp) cc_final: 0.4772 (tpp) REVERT: G 36 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6823 (pm20) REVERT: G 107 MET cc_start: 0.8658 (ttm) cc_final: 0.8378 (ttm) REVERT: G 110 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8320 (tp30) REVERT: G 253 LYS cc_start: 0.8383 (mttt) cc_final: 0.8055 (mttm) REVERT: H 23 MET cc_start: 0.5389 (tpp) cc_final: 0.5107 (tpp) REVERT: H 36 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6815 (pm20) REVERT: I 36 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6939 (pm20) REVERT: I 107 MET cc_start: 0.8594 (ttm) cc_final: 0.8305 (ttm) REVERT: J 23 MET cc_start: 0.5169 (tpp) cc_final: 0.4754 (tpp) REVERT: J 36 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6824 (pm20) REVERT: J 107 MET cc_start: 0.8652 (ttm) cc_final: 0.8380 (ttm) REVERT: J 253 LYS cc_start: 0.8330 (mttt) cc_final: 0.8028 (mttm) REVERT: K 23 MET cc_start: 0.5419 (tpp) cc_final: 0.5139 (tpp) REVERT: K 36 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6764 (pm20) REVERT: L 36 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6923 (pm20) REVERT: L 107 MET cc_start: 0.8615 (ttm) cc_final: 0.8301 (ttm) outliers start: 26 outliers final: 18 residues processed: 426 average time/residue: 0.1857 time to fit residues: 123.7193 Evaluate side-chains 414 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 395 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 241 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 182 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 341 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.189251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.158332 restraints weight = 23918.470| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.72 r_work: 0.3536 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26304 Z= 0.119 Angle : 0.452 7.327 35508 Z= 0.236 Chirality : 0.043 0.132 4116 Planarity : 0.004 0.034 4704 Dihedral : 3.837 15.225 3696 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.10 % Allowed : 12.21 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3468 helix: 0.71 (0.12), residues: 1824 sheet: -0.70 (0.25), residues: 480 loop : 0.11 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.006 0.001 TYR A 121 PHE 0.008 0.002 PHE A 240 TRP 0.009 0.002 TRP A 301 HIS 0.001 0.000 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00292 (26304) covalent geometry : angle 0.45247 (35508) hydrogen bonds : bond 0.03952 ( 1164) hydrogen bonds : angle 4.04494 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 413 time to evaluate : 0.985 Fit side-chains REVERT: A 23 MET cc_start: 0.4875 (tpp) cc_final: 0.4483 (tpp) REVERT: A 36 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6704 (pm20) REVERT: A 107 MET cc_start: 0.8816 (ttm) cc_final: 0.8522 (ttm) REVERT: A 247 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7790 (mtpt) REVERT: A 253 LYS cc_start: 0.8087 (mttt) cc_final: 0.7755 (mttm) REVERT: B 36 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6556 (pm20) REVERT: C 36 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6704 (pm20) REVERT: C 107 MET cc_start: 0.8764 (ttm) cc_final: 0.8431 (ttm) REVERT: D 23 MET cc_start: 0.4974 (tpp) cc_final: 0.4566 (tpp) REVERT: D 36 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6686 (pm20) REVERT: D 107 MET cc_start: 0.8797 (ttm) cc_final: 0.8514 (ttm) REVERT: D 110 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: D 247 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7786 (mtpt) REVERT: D 253 LYS cc_start: 0.8095 (mttt) cc_final: 0.7731 (mttp) REVERT: E 36 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6560 (pm20) REVERT: F 36 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6725 (pm20) REVERT: F 107 MET cc_start: 0.8788 (ttm) cc_final: 0.8432 (ttm) REVERT: G 23 MET cc_start: 0.4844 (tpp) cc_final: 0.4488 (tpp) REVERT: G 36 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6691 (pm20) REVERT: G 107 MET cc_start: 0.8814 (ttm) cc_final: 0.8522 (ttm) REVERT: G 110 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8545 (tp30) REVERT: G 253 LYS cc_start: 0.8095 (mttt) cc_final: 0.7773 (mttm) REVERT: H 36 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6550 (pm20) REVERT: I 36 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6751 (pm20) REVERT: I 107 MET cc_start: 0.8779 (ttm) cc_final: 0.8436 (ttm) REVERT: J 23 MET cc_start: 0.4877 (tpp) cc_final: 0.4481 (tpp) REVERT: J 36 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6697 (pm20) REVERT: J 107 MET cc_start: 0.8798 (ttm) cc_final: 0.8518 (ttm) REVERT: J 110 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8526 (tp30) REVERT: J 253 LYS cc_start: 0.8080 (mttt) cc_final: 0.7723 (mttp) REVERT: K 36 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6551 (pm20) REVERT: L 36 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6705 (pm20) REVERT: L 107 MET cc_start: 0.8791 (ttm) cc_final: 0.8432 (ttm) outliers start: 29 outliers final: 23 residues processed: 439 average time/residue: 0.1776 time to fit residues: 121.7921 Evaluate side-chains 433 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 407 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 165 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 3 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 338 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 231 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.200834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.174329 restraints weight = 25258.900| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.59 r_work: 0.3723 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 26304 Z= 0.150 Angle : 0.491 8.265 35508 Z= 0.256 Chirality : 0.044 0.133 4116 Planarity : 0.005 0.036 4704 Dihedral : 3.954 15.846 3696 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.56 % Allowed : 12.75 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.15), residues: 3468 helix: 0.72 (0.12), residues: 1800 sheet: -0.71 (0.25), residues: 480 loop : 0.02 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 154 TYR 0.006 0.001 TYR I 121 PHE 0.010 0.002 PHE H 128 TRP 0.008 0.002 TRP I 301 HIS 0.002 0.001 HIS L 11 Details of bonding type rmsd covalent geometry : bond 0.00376 (26304) covalent geometry : angle 0.49071 (35508) hydrogen bonds : bond 0.04461 ( 1164) hydrogen bonds : angle 4.17683 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 419 time to evaluate : 0.981 Fit side-chains REVERT: A 23 MET cc_start: 0.4977 (tpp) cc_final: 0.4627 (tpp) REVERT: A 36 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6844 (pm20) REVERT: A 107 MET cc_start: 0.8797 (ttm) cc_final: 0.8509 (ttm) REVERT: B 36 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6775 (pm20) REVERT: B 254 MET cc_start: 0.8263 (tpt) cc_final: 0.8015 (tpt) REVERT: C 36 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6850 (pm20) REVERT: C 107 MET cc_start: 0.8790 (ttm) cc_final: 0.8432 (ttm) REVERT: D 23 MET cc_start: 0.5081 (tpp) cc_final: 0.4740 (tpp) REVERT: D 36 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6863 (pm20) REVERT: D 107 MET cc_start: 0.8756 (ttm) cc_final: 0.8482 (ttm) REVERT: D 110 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: E 36 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6769 (pm20) REVERT: E 254 MET cc_start: 0.8229 (tpt) cc_final: 0.8002 (tpt) REVERT: F 36 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6850 (pm20) REVERT: F 50 MET cc_start: 0.8130 (ttm) cc_final: 0.7804 (ttm) REVERT: F 107 MET cc_start: 0.8789 (ttm) cc_final: 0.8401 (ttm) REVERT: F 209 MET cc_start: 0.8205 (mtp) cc_final: 0.7955 (mtp) REVERT: G 23 MET cc_start: 0.5026 (tpp) cc_final: 0.4707 (tpp) REVERT: G 36 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6878 (pm20) REVERT: G 107 MET cc_start: 0.8776 (ttm) cc_final: 0.8499 (ttm) REVERT: G 110 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: G 253 LYS cc_start: 0.8389 (mttt) cc_final: 0.8079 (mttm) REVERT: H 36 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6777 (pm20) REVERT: H 254 MET cc_start: 0.8229 (tpt) cc_final: 0.8000 (tpt) REVERT: I 36 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6887 (pm20) REVERT: I 107 MET cc_start: 0.8773 (ttm) cc_final: 0.8415 (ttm) REVERT: I 270 LYS cc_start: 0.7624 (tptt) cc_final: 0.7344 (tppt) REVERT: J 23 MET cc_start: 0.4992 (tpp) cc_final: 0.4647 (tpp) REVERT: J 36 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6871 (pm20) REVERT: J 107 MET cc_start: 0.8759 (ttm) cc_final: 0.8485 (ttm) REVERT: J 110 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: K 36 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6684 (pm20) REVERT: L 36 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6863 (pm20) REVERT: L 107 MET cc_start: 0.8793 (ttm) cc_final: 0.8424 (ttm) REVERT: L 209 MET cc_start: 0.8192 (mtp) cc_final: 0.7944 (mtp) REVERT: L 270 LYS cc_start: 0.7641 (tptt) cc_final: 0.7353 (tppt) outliers start: 41 outliers final: 34 residues processed: 453 average time/residue: 0.1857 time to fit residues: 131.4622 Evaluate side-chains 450 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 413 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 270 LYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 165 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 141 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 334 optimal weight: 0.9980 chunk 61 optimal weight: 0.0000 chunk 55 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 250 optimal weight: 0.4980 chunk 217 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN I 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.190606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160007 restraints weight = 23771.844| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.73 r_work: 0.3575 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26304 Z= 0.091 Angle : 0.432 8.879 35508 Z= 0.224 Chirality : 0.042 0.129 4116 Planarity : 0.004 0.033 4704 Dihedral : 3.679 16.048 3696 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.18 % Allowed : 13.93 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 3468 helix: 1.03 (0.12), residues: 1824 sheet: -0.41 (0.25), residues: 480 loop : 0.13 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 154 TYR 0.006 0.001 TYR L 121 PHE 0.007 0.001 PHE A 240 TRP 0.009 0.002 TRP D 301 HIS 0.001 0.000 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00216 (26304) covalent geometry : angle 0.43211 (35508) hydrogen bonds : bond 0.03228 ( 1164) hydrogen bonds : angle 3.79155 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 413 time to evaluate : 0.977 Fit side-chains REVERT: A 23 MET cc_start: 0.4767 (tpp) cc_final: 0.4432 (tpp) REVERT: A 36 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6700 (pm20) REVERT: A 107 MET cc_start: 0.8825 (ttm) cc_final: 0.8563 (ttm) REVERT: A 253 LYS cc_start: 0.7975 (mttt) cc_final: 0.7637 (mttm) REVERT: B 36 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6677 (pm20) REVERT: C 36 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6712 (pm20) REVERT: C 107 MET cc_start: 0.8750 (ttm) cc_final: 0.8436 (ttm) REVERT: D 23 MET cc_start: 0.4894 (tpp) cc_final: 0.4544 (tpp) REVERT: D 36 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6691 (pm20) REVERT: D 107 MET cc_start: 0.8813 (ttm) cc_final: 0.8554 (ttm) REVERT: D 171 MET cc_start: 0.8043 (tpp) cc_final: 0.7800 (ttt) REVERT: D 253 LYS cc_start: 0.8137 (mttt) cc_final: 0.7857 (mttm) REVERT: E 36 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6640 (pm20) REVERT: F 36 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6806 (pm20) REVERT: F 50 MET cc_start: 0.8297 (ttm) cc_final: 0.7978 (ttm) REVERT: F 107 MET cc_start: 0.8782 (ttm) cc_final: 0.8451 (ttm) REVERT: F 209 MET cc_start: 0.8182 (mtp) cc_final: 0.7944 (mtp) REVERT: G 23 MET cc_start: 0.4818 (tpp) cc_final: 0.4483 (tpp) REVERT: G 36 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6623 (pm20) REVERT: G 107 MET cc_start: 0.8810 (ttm) cc_final: 0.8546 (ttm) REVERT: G 171 MET cc_start: 0.8058 (tpp) cc_final: 0.7821 (ttt) REVERT: H 36 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6688 (pm20) REVERT: I 36 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6731 (pm20) REVERT: I 107 MET cc_start: 0.8765 (ttm) cc_final: 0.8451 (ttm) REVERT: J 23 MET cc_start: 0.4898 (tpp) cc_final: 0.4535 (tpp) REVERT: J 36 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6694 (pm20) REVERT: J 107 MET cc_start: 0.8816 (ttm) cc_final: 0.8565 (ttm) REVERT: J 171 MET cc_start: 0.8048 (tpp) cc_final: 0.7803 (ttt) REVERT: J 253 LYS cc_start: 0.8105 (mttt) cc_final: 0.7823 (mttm) REVERT: K 36 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6683 (pm20) REVERT: L 36 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6795 (pm20) REVERT: L 107 MET cc_start: 0.8777 (ttm) cc_final: 0.8446 (ttm) outliers start: 31 outliers final: 29 residues processed: 441 average time/residue: 0.1628 time to fit residues: 112.5744 Evaluate side-chains 428 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 399 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 270 LYS Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 254 optimal weight: 0.8980 chunk 213 optimal weight: 0.0370 chunk 270 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 334 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 306 optimal weight: 0.5980 chunk 312 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 GLN F 210 GLN K 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.190604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159565 restraints weight = 23803.975| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.75 r_work: 0.3594 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26304 Z= 0.095 Angle : 0.431 9.068 35508 Z= 0.224 Chirality : 0.042 0.136 4116 Planarity : 0.004 0.032 4704 Dihedral : 3.625 16.520 3696 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.14 % Allowed : 13.74 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.15), residues: 3468 helix: 1.10 (0.12), residues: 1836 sheet: -0.32 (0.25), residues: 480 loop : 0.18 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 154 TYR 0.003 0.001 TYR F 121 PHE 0.008 0.001 PHE G 240 TRP 0.009 0.002 TRP A 301 HIS 0.001 0.000 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00227 (26304) covalent geometry : angle 0.43113 (35508) hydrogen bonds : bond 0.03344 ( 1164) hydrogen bonds : angle 3.72186 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 409 time to evaluate : 1.014 Fit side-chains REVERT: A 23 MET cc_start: 0.4848 (tpp) cc_final: 0.4505 (tpp) REVERT: A 36 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6711 (pm20) REVERT: A 107 MET cc_start: 0.8816 (ttm) cc_final: 0.8570 (ttm) REVERT: B 36 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6697 (pm20) REVERT: C 36 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6824 (pm20) REVERT: C 107 MET cc_start: 0.8749 (ttm) cc_final: 0.8434 (ttm) REVERT: D 23 MET cc_start: 0.4934 (tpp) cc_final: 0.4611 (tpp) REVERT: D 36 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6720 (pm20) REVERT: D 107 MET cc_start: 0.8814 (ttm) cc_final: 0.8561 (ttm) REVERT: D 253 LYS cc_start: 0.8131 (mttt) cc_final: 0.7751 (mttm) REVERT: E 36 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6687 (pm20) REVERT: F 36 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6829 (pm20) REVERT: F 107 MET cc_start: 0.8780 (ttm) cc_final: 0.8455 (ttm) REVERT: F 209 MET cc_start: 0.8178 (mtp) cc_final: 0.7927 (mtp) REVERT: G 23 MET cc_start: 0.4755 (tpp) cc_final: 0.4427 (tpp) REVERT: G 36 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6638 (pm20) REVERT: G 107 MET cc_start: 0.8836 (ttm) cc_final: 0.8576 (ttm) REVERT: G 253 LYS cc_start: 0.8124 (mttt) cc_final: 0.7833 (mttm) REVERT: H 36 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6687 (pm20) REVERT: I 36 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6758 (pm20) REVERT: I 50 MET cc_start: 0.8288 (ttm) cc_final: 0.7974 (ttm) REVERT: I 107 MET cc_start: 0.8759 (ttm) cc_final: 0.8448 (ttm) REVERT: J 23 MET cc_start: 0.4872 (tpp) cc_final: 0.4558 (tpp) REVERT: J 36 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6741 (pm20) REVERT: J 107 MET cc_start: 0.8800 (ttm) cc_final: 0.8566 (ttm) REVERT: J 253 LYS cc_start: 0.8114 (mttt) cc_final: 0.7734 (mttm) REVERT: K 36 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6683 (pm20) REVERT: L 36 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6825 (pm20) REVERT: L 50 MET cc_start: 0.8291 (ttm) cc_final: 0.7972 (ttm) REVERT: L 107 MET cc_start: 0.8769 (ttm) cc_final: 0.8448 (ttm) REVERT: L 209 MET cc_start: 0.8191 (mtp) cc_final: 0.7942 (mtp) outliers start: 30 outliers final: 29 residues processed: 434 average time/residue: 0.1878 time to fit residues: 127.4356 Evaluate side-chains 431 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 402 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 270 LYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 165 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.199642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.172463 restraints weight = 25249.926| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.63 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26304 Z= 0.173 Angle : 0.521 9.701 35508 Z= 0.270 Chirality : 0.044 0.149 4116 Planarity : 0.005 0.034 4704 Dihedral : 3.946 18.452 3696 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.26 % Allowed : 13.66 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3468 helix: 0.78 (0.12), residues: 1812 sheet: -0.54 (0.25), residues: 480 loop : -0.00 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 22 TYR 0.007 0.001 TYR F 121 PHE 0.012 0.002 PHE K 240 TRP 0.007 0.002 TRP A 301 HIS 0.002 0.001 HIS L 11 Details of bonding type rmsd covalent geometry : bond 0.00438 (26304) covalent geometry : angle 0.52082 (35508) hydrogen bonds : bond 0.04676 ( 1164) hydrogen bonds : angle 4.14143 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 410 time to evaluate : 1.018 Fit side-chains REVERT: A 23 MET cc_start: 0.5335 (tpp) cc_final: 0.5056 (tpp) REVERT: A 107 MET cc_start: 0.8283 (ttm) cc_final: 0.8076 (ttm) REVERT: C 50 MET cc_start: 0.7973 (ttm) cc_final: 0.7655 (ttm) REVERT: C 107 MET cc_start: 0.8280 (ttm) cc_final: 0.8000 (ttm) REVERT: D 23 MET cc_start: 0.5337 (tpp) cc_final: 0.5049 (tpp) REVERT: D 107 MET cc_start: 0.8270 (ttm) cc_final: 0.8070 (ttm) REVERT: D 253 LYS cc_start: 0.8551 (mttt) cc_final: 0.8235 (mttm) REVERT: F 50 MET cc_start: 0.7923 (ttm) cc_final: 0.7621 (ttm) REVERT: F 107 MET cc_start: 0.8286 (ttm) cc_final: 0.8017 (ttm) REVERT: F 209 MET cc_start: 0.7734 (mtp) cc_final: 0.7468 (mtp) REVERT: G 23 MET cc_start: 0.5314 (tpp) cc_final: 0.5049 (tpp) REVERT: G 107 MET cc_start: 0.8275 (ttm) cc_final: 0.8073 (ttm) REVERT: G 253 LYS cc_start: 0.8556 (mttt) cc_final: 0.8225 (mttm) REVERT: I 50 MET cc_start: 0.7979 (ttm) cc_final: 0.7661 (ttm) REVERT: I 107 MET cc_start: 0.8272 (ttm) cc_final: 0.7994 (ttm) REVERT: J 23 MET cc_start: 0.5331 (tpp) cc_final: 0.5058 (tpp) REVERT: J 107 MET cc_start: 0.8281 (ttm) cc_final: 0.8080 (ttm) REVERT: J 253 LYS cc_start: 0.8561 (mttt) cc_final: 0.8235 (mttm) REVERT: L 50 MET cc_start: 0.7980 (ttm) cc_final: 0.7668 (ttm) REVERT: L 107 MET cc_start: 0.8293 (ttm) cc_final: 0.8024 (ttm) REVERT: L 209 MET cc_start: 0.7739 (mtp) cc_final: 0.7477 (mtp) outliers start: 33 outliers final: 33 residues processed: 438 average time/residue: 0.1850 time to fit residues: 126.1698 Evaluate side-chains 440 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 407 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 165 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 165 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 chunk 321 optimal weight: 0.7980 chunk 225 optimal weight: 0.6980 chunk 99 optimal weight: 0.0970 chunk 80 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.204511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.178408 restraints weight = 25129.324| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.59 r_work: 0.3807 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26304 Z= 0.094 Angle : 0.451 10.464 35508 Z= 0.232 Chirality : 0.042 0.138 4116 Planarity : 0.004 0.033 4704 Dihedral : 3.681 19.347 3696 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.10 % Allowed : 14.16 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3468 helix: 1.18 (0.12), residues: 1800 sheet: -0.37 (0.26), residues: 480 loop : 0.22 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 154 TYR 0.004 0.001 TYR F 121 PHE 0.007 0.001 PHE G 240 TRP 0.009 0.002 TRP D 301 HIS 0.001 0.000 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00226 (26304) covalent geometry : angle 0.45051 (35508) hydrogen bonds : bond 0.03267 ( 1164) hydrogen bonds : angle 3.74940 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 392 time to evaluate : 0.776 Fit side-chains REVERT: A 23 MET cc_start: 0.4980 (tpp) cc_final: 0.4670 (tpp) REVERT: A 107 MET cc_start: 0.8735 (ttm) cc_final: 0.8494 (ttm) REVERT: A 231 MET cc_start: 0.8503 (tpp) cc_final: 0.8297 (mmt) REVERT: C 50 MET cc_start: 0.8047 (ttm) cc_final: 0.7709 (ttm) REVERT: C 107 MET cc_start: 0.8654 (ttm) cc_final: 0.8349 (ttm) REVERT: C 289 MET cc_start: 0.5594 (tmm) cc_final: 0.4815 (mtp) REVERT: D 23 MET cc_start: 0.4967 (tpp) cc_final: 0.4652 (tpp) REVERT: D 107 MET cc_start: 0.8705 (ttm) cc_final: 0.8478 (ttm) REVERT: D 253 LYS cc_start: 0.8307 (mttt) cc_final: 0.8038 (mttm) REVERT: F 23 MET cc_start: 0.5122 (tpp) cc_final: 0.4588 (tpt) REVERT: F 107 MET cc_start: 0.8685 (ttm) cc_final: 0.8378 (ttm) REVERT: F 209 MET cc_start: 0.8133 (mtp) cc_final: 0.7864 (mtp) REVERT: G 23 MET cc_start: 0.4994 (tpp) cc_final: 0.4683 (tpp) REVERT: G 36 GLU cc_start: 0.7150 (pm20) cc_final: 0.6754 (pm20) REVERT: G 107 MET cc_start: 0.8724 (ttm) cc_final: 0.8495 (ttm) REVERT: G 253 LYS cc_start: 0.8302 (mttt) cc_final: 0.8034 (mttm) REVERT: I 50 MET cc_start: 0.8037 (ttm) cc_final: 0.7687 (ttm) REVERT: I 107 MET cc_start: 0.8650 (ttm) cc_final: 0.8347 (ttm) REVERT: J 23 MET cc_start: 0.4953 (tpp) cc_final: 0.4627 (tpp) REVERT: J 107 MET cc_start: 0.8713 (ttm) cc_final: 0.8490 (ttm) REVERT: J 253 LYS cc_start: 0.8301 (mttt) cc_final: 0.8043 (mttm) REVERT: L 50 MET cc_start: 0.8015 (ttm) cc_final: 0.7675 (ttm) REVERT: L 107 MET cc_start: 0.8693 (ttm) cc_final: 0.8381 (ttm) REVERT: L 209 MET cc_start: 0.8130 (mtp) cc_final: 0.7860 (mtp) REVERT: L 252 GLU cc_start: 0.7657 (tp30) cc_final: 0.7075 (mt-10) outliers start: 29 outliers final: 29 residues processed: 416 average time/residue: 0.1822 time to fit residues: 117.9832 Evaluate side-chains 419 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 390 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 264 optimal weight: 0.0970 chunk 296 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 157 optimal weight: 0.1980 chunk 18 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 202 optimal weight: 0.0000 chunk 163 optimal weight: 0.5980 chunk 283 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN D 210 GLN E 210 GLN G 210 GLN H 210 GLN J 210 GLN L 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.211106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.185464 restraints weight = 24995.511| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.58 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26304 Z= 0.076 Angle : 0.426 10.721 35508 Z= 0.216 Chirality : 0.041 0.137 4116 Planarity : 0.004 0.031 4704 Dihedral : 3.370 10.418 3696 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.53 % Allowed : 14.95 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.15), residues: 3468 helix: 1.41 (0.12), residues: 1836 sheet: -0.05 (0.26), residues: 480 loop : 0.35 (0.21), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 154 TYR 0.003 0.000 TYR J 121 PHE 0.004 0.001 PHE F 240 TRP 0.009 0.002 TRP D 301 HIS 0.001 0.000 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00172 (26304) covalent geometry : angle 0.42557 (35508) hydrogen bonds : bond 0.02584 ( 1164) hydrogen bonds : angle 3.46673 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5424.21 seconds wall clock time: 93 minutes 36.48 seconds (5616.48 seconds total)