Starting phenix.real_space_refine on Sun Jun 22 10:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvf_47202/06_2025/9dvf_47202.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvf_47202/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvf_47202/06_2025/9dvf_47202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvf_47202/06_2025/9dvf_47202.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvf_47202/06_2025/9dvf_47202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvf_47202/06_2025/9dvf_47202.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 7.03, per 1000 atoms: 0.27 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: 5.80 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 2.96 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: 9.14 Time building geometry restraints manager: 6.92 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain '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: 1.460 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: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 48.110 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (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 TRP 0.003 0.001 TRP H 301 HIS 0.002 0.001 HIS G 11 PHE 0.013 0.002 PHE F 128 TYR 0.010 0.002 TYR L 265 ARG 0.002 0.000 ARG H 233 Details of bonding type rmsd hydrogen bonds : bond 0.33115 ( 1164) hydrogen bonds : angle 9.13381 ( 3240) covalent geometry : bond 0.00411 (26304) covalent geometry : angle 0.63673 (35508) *********************** 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 : 2.802 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: 0.3833 time to fit residues: 307.2162 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 : 2.590 ------------------------------------------------------------------------------- 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 293 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 140 optimal weight: 0.0770 chunk 272 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.185168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.154666 restraints weight = 24086.477| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.71 r_work: 0.3508 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1633 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= 0.174 Angle : 0.539 6.094 35508 Z= 0.285 Chirality : 0.045 0.134 4116 Planarity : 0.005 0.033 4704 Dihedral : 4.974 59.039 3708 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.22 % Allowed : 9.59 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3468 helix: -0.32 (0.12), residues: 1776 sheet: -1.05 (0.23), residues: 468 loop : 0.62 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 301 HIS 0.002 0.001 HIS B 11 PHE 0.014 0.002 PHE K 128 TYR 0.005 0.001 TYR A 121 ARG 0.002 0.000 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.05629 ( 1164) hydrogen bonds : angle 5.05777 ( 3240) covalent geometry : bond 0.00431 (26304) covalent geometry : angle 0.53883 (35508) *********************** 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 467 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 435 time to evaluate : 2.591 Fit side-chains REVERT: A 23 MET cc_start: 0.5016 (tpp) cc_final: 0.4650 (tpp) REVERT: A 36 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6701 (pm20) REVERT: A 107 MET cc_start: 0.8804 (ttm) cc_final: 0.8509 (ttm) REVERT: A 110 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8470 (tp30) REVERT: A 195 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7103 (tt0) REVERT: B 36 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6513 (pm20) REVERT: B 191 MET cc_start: 0.7801 (ttt) cc_final: 0.7520 (ttm) REVERT: C 36 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6545 (pm20) REVERT: C 107 MET cc_start: 0.8797 (ttm) cc_final: 0.8428 (ttm) REVERT: C 195 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7260 (tt0) REVERT: C 282 MET cc_start: 0.8285 (ptm) cc_final: 0.8067 (ptp) REVERT: D 23 MET cc_start: 0.5051 (tpp) cc_final: 0.4588 (tpp) REVERT: D 36 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6616 (pm20) REVERT: D 107 MET cc_start: 0.8800 (ttm) cc_final: 0.8509 (ttm) REVERT: D 110 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: D 195 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7133 (tt0) REVERT: E 36 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6523 (pm20) REVERT: E 191 MET cc_start: 0.7994 (ttt) cc_final: 0.7708 (ttm) REVERT: F 36 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6805 (pm20) REVERT: F 107 MET cc_start: 0.8817 (ttm) cc_final: 0.8452 (ttm) REVERT: F 110 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: F 195 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7252 (tt0) REVERT: F 282 MET cc_start: 0.8323 (ptm) cc_final: 0.8103 (ptp) REVERT: G 23 MET cc_start: 0.5061 (tpp) cc_final: 0.4632 (tpp) REVERT: G 36 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6685 (pm20) REVERT: G 107 MET cc_start: 0.8802 (ttm) cc_final: 0.8508 (ttm) REVERT: G 110 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8490 (tp30) REVERT: G 195 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7158 (tt0) REVERT: G 253 LYS cc_start: 0.8076 (mttt) cc_final: 0.7747 (mttm) REVERT: H 36 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6520 (pm20) REVERT: H 191 MET cc_start: 0.7900 (ttt) cc_final: 0.7636 (ttm) REVERT: I 36 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6532 (pm20) REVERT: I 107 MET cc_start: 0.8791 (ttm) cc_final: 0.8418 (ttm) REVERT: J 23 MET cc_start: 0.5039 (tpp) cc_final: 0.4598 (tpp) REVERT: J 36 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6604 (pm20) REVERT: J 107 MET cc_start: 0.8809 (ttm) cc_final: 0.8518 (ttm) REVERT: J 110 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: J 195 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7127 (tt0) REVERT: K 36 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6519 (pm20) REVERT: K 191 MET cc_start: 0.7977 (ttt) cc_final: 0.7680 (ttm) REVERT: K 274 ILE cc_start: 0.6888 (mm) cc_final: 0.6677 (mt) REVERT: L 36 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6776 (pm20) REVERT: L 107 MET cc_start: 0.8791 (ttm) cc_final: 0.8420 (ttm) REVERT: L 282 MET cc_start: 0.8335 (ptm) cc_final: 0.8117 (ptp) outliers start: 32 outliers final: 24 residues processed: 463 average time/residue: 0.3905 time to fit residues: 281.0810 Evaluate side-chains 451 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 422 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 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 312 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 252 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.190085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.158408 restraints weight = 23854.782| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.79 r_work: 0.3548 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 26304 Z= 0.120 Angle : 0.458 5.569 35508 Z= 0.240 Chirality : 0.042 0.131 4116 Planarity : 0.004 0.032 4704 Dihedral : 4.083 52.118 3699 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.14 % Allowed : 10.46 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3468 helix: 0.50 (0.12), residues: 1764 sheet: -0.74 (0.24), residues: 468 loop : 0.64 (0.20), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 301 HIS 0.001 0.000 HIS B 11 PHE 0.008 0.002 PHE D 240 TYR 0.006 0.001 TYR G 121 ARG 0.002 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 1164) hydrogen bonds : angle 4.35561 ( 3240) covalent geometry : bond 0.00288 (26304) covalent geometry : angle 0.45847 (35508) *********************** 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 474 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 444 time to evaluate : 2.630 Fit side-chains REVERT: A 23 MET cc_start: 0.4845 (tpp) cc_final: 0.4398 (tpp) REVERT: A 36 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6670 (pm20) REVERT: A 107 MET cc_start: 0.8774 (ttm) cc_final: 0.8512 (ttm) REVERT: B 23 MET cc_start: 0.5147 (tpp) cc_final: 0.4851 (tpp) REVERT: B 36 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6519 (pm20) REVERT: B 191 MET cc_start: 0.7855 (ttt) cc_final: 0.7601 (ttm) REVERT: C 36 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6822 (pm20) REVERT: C 107 MET cc_start: 0.8801 (ttm) cc_final: 0.8430 (ttm) REVERT: D 23 MET cc_start: 0.4855 (tpp) cc_final: 0.4379 (tpp) REVERT: D 36 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6677 (pm20) REVERT: D 43 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7207 (mm-30) REVERT: D 107 MET cc_start: 0.8771 (ttm) cc_final: 0.8503 (ttm) REVERT: D 247 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7769 (mtpt) REVERT: D 253 LYS cc_start: 0.8063 (mttt) cc_final: 0.7700 (mttm) REVERT: E 23 MET cc_start: 0.5054 (tpp) cc_final: 0.4752 (tpp) REVERT: E 36 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6437 (pm20) REVERT: E 110 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: E 191 MET cc_start: 0.7905 (ttt) cc_final: 0.7649 (ttm) REVERT: F 36 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6801 (pm20) REVERT: F 107 MET cc_start: 0.8791 (ttm) cc_final: 0.8431 (ttm) REVERT: F 282 MET cc_start: 0.8265 (ptm) cc_final: 0.8028 (ptp) REVERT: G 23 MET cc_start: 0.4848 (tpp) cc_final: 0.4399 (tpp) REVERT: G 36 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6638 (pm20) REVERT: G 43 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7333 (mm-30) REVERT: G 107 MET cc_start: 0.8802 (ttm) cc_final: 0.8527 (ttm) REVERT: H 23 MET cc_start: 0.5090 (tpp) cc_final: 0.4773 (tpp) REVERT: H 36 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6447 (pm20) REVERT: H 191 MET cc_start: 0.7861 (ttt) cc_final: 0.7616 (ttm) REVERT: I 36 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6793 (pm20) REVERT: I 107 MET cc_start: 0.8795 (ttm) cc_final: 0.8444 (ttm) REVERT: J 23 MET cc_start: 0.4805 (tpp) cc_final: 0.4346 (tpp) REVERT: J 36 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6686 (pm20) REVERT: J 43 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7199 (mm-30) REVERT: J 107 MET cc_start: 0.8774 (ttm) cc_final: 0.8502 (ttm) REVERT: J 253 LYS cc_start: 0.8049 (mttt) cc_final: 0.7699 (mttm) REVERT: K 23 MET cc_start: 0.5064 (tpp) cc_final: 0.4741 (tpp) REVERT: K 36 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6510 (pm20) REVERT: K 110 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: K 191 MET cc_start: 0.7921 (ttt) cc_final: 0.7649 (ttm) REVERT: K 274 ILE cc_start: 0.7030 (mm) cc_final: 0.6825 (mt) REVERT: L 36 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6851 (pm20) REVERT: L 107 MET cc_start: 0.8805 (ttm) cc_final: 0.8424 (ttm) REVERT: L 282 MET cc_start: 0.8284 (ptm) cc_final: 0.8054 (ptp) outliers start: 30 outliers final: 18 residues processed: 474 average time/residue: 0.3824 time to fit residues: 282.0524 Evaluate side-chains 427 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 407 time to evaluate : 2.941 ------------------------------------------------------------------------------- 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 110 GLU 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 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 110 GLU Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 220 optimal weight: 0.7980 chunk 328 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 262 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.188749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157604 restraints weight = 24043.995| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.74 r_work: 0.3626 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26304 Z= 0.127 Angle : 0.460 5.367 35508 Z= 0.241 Chirality : 0.043 0.133 4116 Planarity : 0.004 0.033 4704 Dihedral : 3.845 13.335 3696 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.14 % Allowed : 10.39 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3468 helix: 0.78 (0.12), residues: 1764 sheet: -0.74 (0.25), residues: 480 loop : 0.52 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 301 HIS 0.001 0.000 HIS L 11 PHE 0.010 0.002 PHE A 128 TYR 0.004 0.001 TYR C 121 ARG 0.002 0.000 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1164) hydrogen bonds : angle 4.16867 ( 3240) covalent geometry : bond 0.00313 (26304) covalent geometry : angle 0.46013 (35508) *********************** 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 455 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 425 time to evaluate : 3.351 Fit side-chains REVERT: A 23 MET cc_start: 0.4807 (tpp) cc_final: 0.4372 (tpp) REVERT: A 36 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6699 (pm20) REVERT: A 107 MET cc_start: 0.8813 (ttm) cc_final: 0.8537 (ttm) REVERT: A 253 LYS cc_start: 0.8288 (mttt) cc_final: 0.7920 (mttm) REVERT: B 23 MET cc_start: 0.5168 (tpp) cc_final: 0.4856 (tpp) REVERT: B 36 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6533 (pm20) REVERT: B 191 MET cc_start: 0.7897 (ttt) cc_final: 0.7619 (ttm) REVERT: C 36 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6739 (pm20) REVERT: C 107 MET cc_start: 0.8771 (ttm) cc_final: 0.8436 (ttm) REVERT: D 23 MET cc_start: 0.4832 (tpp) cc_final: 0.4401 (tpp) REVERT: D 36 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6706 (pm20) REVERT: D 43 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 107 MET cc_start: 0.8804 (ttm) cc_final: 0.8524 (ttm) REVERT: D 110 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: E 23 MET cc_start: 0.5048 (tpp) cc_final: 0.4731 (tpp) REVERT: E 36 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6544 (pm20) REVERT: E 110 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: F 36 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6772 (pm20) REVERT: F 107 MET cc_start: 0.8799 (ttm) cc_final: 0.8443 (ttm) REVERT: F 282 MET cc_start: 0.8215 (ptm) cc_final: 0.7971 (ptp) REVERT: G 23 MET cc_start: 0.4816 (tpp) cc_final: 0.4404 (tpp) REVERT: G 36 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6661 (pm20) REVERT: G 43 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7293 (mm-30) REVERT: G 107 MET cc_start: 0.8810 (ttm) cc_final: 0.8531 (ttm) REVERT: G 247 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7817 (mtpt) REVERT: G 253 LYS cc_start: 0.8257 (mttt) cc_final: 0.7901 (mttm) REVERT: H 23 MET cc_start: 0.5107 (tpp) cc_final: 0.4814 (tpp) REVERT: H 36 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6544 (pm20) REVERT: H 191 MET cc_start: 0.7913 (ttt) cc_final: 0.7635 (ttm) REVERT: I 36 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6754 (pm20) REVERT: I 107 MET cc_start: 0.8793 (ttm) cc_final: 0.8450 (ttm) REVERT: J 23 MET cc_start: 0.4797 (tpp) cc_final: 0.4365 (tpp) REVERT: J 36 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6671 (pm20) REVERT: J 43 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7347 (mm-30) REVERT: J 107 MET cc_start: 0.8805 (ttm) cc_final: 0.8521 (ttm) REVERT: J 110 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: J 253 LYS cc_start: 0.8154 (mttt) cc_final: 0.7831 (mttm) REVERT: K 23 MET cc_start: 0.5092 (tpp) cc_final: 0.4810 (tpp) REVERT: K 36 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6529 (pm20) REVERT: K 110 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: L 36 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6787 (pm20) REVERT: L 107 MET cc_start: 0.8792 (ttm) cc_final: 0.8443 (ttm) REVERT: L 282 MET cc_start: 0.8252 (ptm) cc_final: 0.8003 (ptp) outliers start: 30 outliers final: 22 residues processed: 451 average time/residue: 0.4204 time to fit residues: 294.6774 Evaluate side-chains 441 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 415 time to evaluate : 2.918 ------------------------------------------------------------------------------- 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 81 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 110 GLU 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 81 VAL Chi-restraints excluded: chain I residue 133 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 110 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 25 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 157 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.194437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.163865 restraints weight = 23584.306| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.70 r_work: 0.3623 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26304 Z= 0.080 Angle : 0.406 5.239 35508 Z= 0.211 Chirality : 0.041 0.128 4116 Planarity : 0.004 0.029 4704 Dihedral : 3.554 11.131 3696 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.72 % Allowed : 11.61 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3468 helix: 1.34 (0.13), residues: 1752 sheet: -0.47 (0.25), residues: 480 loop : 0.76 (0.21), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 301 HIS 0.001 0.000 HIS B 11 PHE 0.006 0.001 PHE G 240 TYR 0.004 0.001 TYR L 121 ARG 0.002 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 1164) hydrogen bonds : angle 3.76523 ( 3240) covalent geometry : bond 0.00181 (26304) covalent geometry : angle 0.40629 (35508) *********************** 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: 19 poor density : 423 time to evaluate : 2.792 Fit side-chains REVERT: A 23 MET cc_start: 0.4741 (tpp) cc_final: 0.4319 (tpp) REVERT: A 36 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6730 (pm20) REVERT: A 107 MET cc_start: 0.8825 (ttm) cc_final: 0.8562 (ttm) REVERT: A 253 LYS cc_start: 0.8189 (mttt) cc_final: 0.7814 (mttm) REVERT: B 36 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6666 (pm20) REVERT: B 191 MET cc_start: 0.7922 (ttt) cc_final: 0.7660 (ttm) REVERT: C 36 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6718 (pm20) REVERT: C 107 MET cc_start: 0.8724 (ttm) cc_final: 0.8422 (ttm) REVERT: C 253 LYS cc_start: 0.8286 (mttt) cc_final: 0.7866 (mttp) REVERT: D 23 MET cc_start: 0.4747 (tpp) cc_final: 0.4377 (tpp) REVERT: D 36 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6741 (pm20) REVERT: D 107 MET cc_start: 0.8826 (ttm) cc_final: 0.8564 (ttm) REVERT: D 253 LYS cc_start: 0.8151 (mttt) cc_final: 0.7834 (mttm) REVERT: E 23 MET cc_start: 0.4919 (tpp) cc_final: 0.4659 (tpp) REVERT: E 36 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6636 (pm20) REVERT: F 36 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6780 (pm20) REVERT: F 107 MET cc_start: 0.8740 (ttm) cc_final: 0.8432 (ttm) REVERT: F 282 MET cc_start: 0.8091 (ptm) cc_final: 0.7825 (ptp) REVERT: G 23 MET cc_start: 0.4746 (tpp) cc_final: 0.4468 (tpt) REVERT: G 36 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6704 (pm20) REVERT: G 43 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7278 (mm-30) REVERT: G 107 MET cc_start: 0.8820 (ttm) cc_final: 0.8551 (ttm) REVERT: G 247 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7819 (mtpt) REVERT: G 253 LYS cc_start: 0.8186 (mttt) cc_final: 0.7815 (mttm) REVERT: H 36 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6636 (pm20) REVERT: H 191 MET cc_start: 0.7944 (ttt) cc_final: 0.7684 (ttm) REVERT: I 36 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6741 (pm20) REVERT: I 107 MET cc_start: 0.8728 (ttm) cc_final: 0.8429 (ttm) REVERT: I 253 LYS cc_start: 0.8322 (mttt) cc_final: 0.7898 (mttp) REVERT: J 23 MET cc_start: 0.4796 (tpp) cc_final: 0.4421 (tpp) REVERT: J 36 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6723 (pm20) REVERT: J 107 MET cc_start: 0.8819 (ttm) cc_final: 0.8558 (ttm) REVERT: J 253 LYS cc_start: 0.8033 (mttt) cc_final: 0.7670 (mttp) REVERT: K 23 MET cc_start: 0.4899 (tpp) cc_final: 0.4639 (tpp) REVERT: K 36 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6645 (pm20) REVERT: L 36 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6773 (pm20) REVERT: L 107 MET cc_start: 0.8735 (ttm) cc_final: 0.8424 (ttm) outliers start: 19 outliers final: 13 residues processed: 438 average time/residue: 0.4510 time to fit residues: 307.6193 Evaluate side-chains 425 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 412 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 161 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 249 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.204109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178352 restraints weight = 25065.656| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.53 r_work: 0.3477 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26304 Z= 0.193 Angle : 0.525 8.149 35508 Z= 0.275 Chirality : 0.045 0.134 4116 Planarity : 0.005 0.034 4704 Dihedral : 4.002 14.387 3696 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.26 % Allowed : 12.56 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3468 helix: 0.68 (0.12), residues: 1800 sheet: -0.72 (0.25), residues: 480 loop : 0.15 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 301 HIS 0.002 0.001 HIS H 11 PHE 0.014 0.002 PHE A 128 TYR 0.004 0.001 TYR B 265 ARG 0.001 0.000 ARG J 18 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 1164) hydrogen bonds : angle 4.32791 ( 3240) covalent geometry : bond 0.00492 (26304) covalent geometry : angle 0.52503 (35508) *********************** 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: 33 poor density : 427 time to evaluate : 2.611 Fit side-chains REVERT: A 23 MET cc_start: 0.4974 (tpp) cc_final: 0.4607 (tpp) REVERT: A 36 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6735 (pm20) REVERT: A 107 MET cc_start: 0.8774 (ttm) cc_final: 0.8441 (ttm) REVERT: A 110 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: B 36 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6638 (pm20) REVERT: C 36 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6781 (pm20) REVERT: C 50 MET cc_start: 0.8314 (ttm) cc_final: 0.8016 (ttm) REVERT: C 107 MET cc_start: 0.8710 (ttm) cc_final: 0.8359 (ttm) REVERT: D 23 MET cc_start: 0.4988 (tpp) cc_final: 0.4631 (tpp) REVERT: D 36 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6749 (pm20) REVERT: D 107 MET cc_start: 0.8766 (ttm) cc_final: 0.8431 (ttm) REVERT: D 110 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8529 (tp30) REVERT: D 253 LYS cc_start: 0.8294 (mttt) cc_final: 0.7906 (mttm) REVERT: E 36 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6661 (pm20) REVERT: F 36 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6756 (pm20) REVERT: F 50 MET cc_start: 0.8322 (ttm) cc_final: 0.8015 (ttm) REVERT: F 107 MET cc_start: 0.8715 (ttm) cc_final: 0.8363 (ttm) REVERT: F 209 MET cc_start: 0.8212 (mtp) cc_final: 0.7972 (mtp) REVERT: F 247 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7735 (mtpt) REVERT: G 23 MET cc_start: 0.4972 (tpp) cc_final: 0.4601 (tpp) REVERT: G 36 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6716 (pm20) REVERT: G 43 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7376 (mm-30) REVERT: G 107 MET cc_start: 0.8771 (ttm) cc_final: 0.8433 (ttm) REVERT: H 36 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6684 (pm20) REVERT: I 36 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6786 (pm20) REVERT: I 50 MET cc_start: 0.8326 (ttm) cc_final: 0.8019 (ttm) REVERT: I 107 MET cc_start: 0.8705 (ttm) cc_final: 0.8351 (ttm) REVERT: I 270 LYS cc_start: 0.7321 (tptt) cc_final: 0.6953 (mmtm) REVERT: J 23 MET cc_start: 0.4959 (tpp) cc_final: 0.4600 (tpp) REVERT: J 36 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6759 (pm20) REVERT: J 107 MET cc_start: 0.8773 (ttm) cc_final: 0.8445 (ttm) REVERT: J 110 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8518 (tp30) REVERT: K 36 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6593 (pm20) REVERT: K 110 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: L 36 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6746 (pm20) REVERT: L 50 MET cc_start: 0.8326 (ttm) cc_final: 0.8012 (ttm) REVERT: L 107 MET cc_start: 0.8690 (ttm) cc_final: 0.8325 (ttm) REVERT: L 209 MET cc_start: 0.8225 (mtp) cc_final: 0.8004 (mtp) REVERT: L 247 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7721 (mtpt) REVERT: L 270 LYS cc_start: 0.7343 (tptt) cc_final: 0.7069 (tppt) outliers start: 33 outliers final: 21 residues processed: 450 average time/residue: 0.3839 time to fit residues: 267.6432 Evaluate side-chains 454 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 429 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 133 VAL 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 133 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 111 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 347 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 325 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.190059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159020 restraints weight = 23861.044| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.74 r_work: 0.3554 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26304 Z= 0.101 Angle : 0.450 8.784 35508 Z= 0.232 Chirality : 0.042 0.127 4116 Planarity : 0.004 0.032 4704 Dihedral : 3.743 14.073 3696 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.95 % Allowed : 13.17 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3468 helix: 1.08 (0.12), residues: 1788 sheet: -0.50 (0.25), residues: 480 loop : 0.32 (0.20), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 301 HIS 0.001 0.000 HIS F 11 PHE 0.009 0.001 PHE F 246 TYR 0.005 0.001 TYR F 121 ARG 0.002 0.000 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1164) hydrogen bonds : angle 3.88204 ( 3240) covalent geometry : bond 0.00244 (26304) covalent geometry : angle 0.45011 (35508) *********************** 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 433 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 408 time to evaluate : 2.995 Fit side-chains REVERT: A 23 MET cc_start: 0.4934 (tpp) cc_final: 0.4567 (tpp) REVERT: A 36 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6639 (pm20) REVERT: A 107 MET cc_start: 0.8683 (ttm) cc_final: 0.8415 (ttm) REVERT: A 110 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: A 253 LYS cc_start: 0.8163 (mttt) cc_final: 0.7827 (mttp) REVERT: B 36 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6673 (pm20) REVERT: C 36 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6726 (pm20) REVERT: C 50 MET cc_start: 0.8122 (ttm) cc_final: 0.7782 (ttm) REVERT: C 107 MET cc_start: 0.8637 (ttm) cc_final: 0.8314 (ttm) REVERT: D 23 MET cc_start: 0.4956 (tpp) cc_final: 0.4615 (tpp) REVERT: D 36 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6689 (pm20) REVERT: D 107 MET cc_start: 0.8704 (ttm) cc_final: 0.8433 (ttm) REVERT: D 253 LYS cc_start: 0.8140 (mttt) cc_final: 0.7870 (mttm) REVERT: E 36 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6652 (pm20) REVERT: F 36 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6737 (pm20) REVERT: F 50 MET cc_start: 0.8113 (ttm) cc_final: 0.7761 (ttm) REVERT: F 107 MET cc_start: 0.8643 (ttm) cc_final: 0.8315 (ttm) REVERT: F 209 MET cc_start: 0.8103 (mtp) cc_final: 0.7834 (mtp) REVERT: F 247 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7875 (mtpt) REVERT: G 23 MET cc_start: 0.4917 (tpp) cc_final: 0.4568 (tpp) REVERT: G 36 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6662 (pm20) REVERT: G 43 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7158 (mm-30) REVERT: G 107 MET cc_start: 0.8658 (ttm) cc_final: 0.8389 (ttm) REVERT: G 171 MET cc_start: 0.7879 (tpp) cc_final: 0.7630 (ttt) REVERT: H 36 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6654 (pm20) REVERT: I 36 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6730 (pm20) REVERT: I 50 MET cc_start: 0.8120 (ttm) cc_final: 0.7784 (ttm) REVERT: I 107 MET cc_start: 0.8643 (ttm) cc_final: 0.8313 (ttm) REVERT: J 23 MET cc_start: 0.4953 (tpp) cc_final: 0.4610 (tpp) REVERT: J 36 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6652 (pm20) REVERT: J 107 MET cc_start: 0.8696 (ttm) cc_final: 0.8429 (ttm) REVERT: K 36 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6638 (pm20) REVERT: L 36 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6712 (pm20) REVERT: L 50 MET cc_start: 0.8120 (ttm) cc_final: 0.7785 (ttm) REVERT: L 107 MET cc_start: 0.8629 (ttm) cc_final: 0.8306 (ttm) REVERT: L 209 MET cc_start: 0.8096 (mtp) cc_final: 0.7836 (mtp) REVERT: L 247 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7833 (mtpt) outliers start: 25 outliers final: 24 residues processed: 430 average time/residue: 0.3995 time to fit residues: 266.0703 Evaluate side-chains 426 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 401 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 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 270 LYS 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 133 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 222 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 346 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 226 optimal weight: 0.0470 chunk 276 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 286 optimal weight: 1.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.188836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158153 restraints weight = 23801.033| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.72 r_work: 0.3528 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26304 Z= 0.124 Angle : 0.465 7.192 35508 Z= 0.241 Chirality : 0.043 0.130 4116 Planarity : 0.004 0.033 4704 Dihedral : 3.763 15.816 3696 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.95 % Allowed : 13.28 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3468 helix: 0.98 (0.12), residues: 1812 sheet: -0.49 (0.25), residues: 480 loop : 0.23 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 301 HIS 0.001 0.000 HIS F 11 PHE 0.009 0.002 PHE E 246 TYR 0.007 0.001 TYR I 121 ARG 0.001 0.000 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 1164) hydrogen bonds : angle 3.92957 ( 3240) covalent geometry : bond 0.00309 (26304) covalent geometry : angle 0.46519 (35508) *********************** 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 442 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 417 time to evaluate : 2.826 Fit side-chains REVERT: A 23 MET cc_start: 0.4756 (tpp) cc_final: 0.4441 (tpp) REVERT: A 36 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6640 (pm20) REVERT: A 107 MET cc_start: 0.8815 (ttm) cc_final: 0.8520 (ttm) REVERT: A 110 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8544 (tp30) REVERT: A 253 LYS cc_start: 0.8215 (mttt) cc_final: 0.7936 (mttm) REVERT: B 36 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6592 (pm20) REVERT: B 270 LYS cc_start: 0.7418 (tptp) cc_final: 0.6967 (tptp) REVERT: C 36 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6703 (pm20) REVERT: C 50 MET cc_start: 0.8256 (ttm) cc_final: 0.7930 (ttm) REVERT: C 107 MET cc_start: 0.8741 (ttm) cc_final: 0.8528 (ttm) REVERT: C 133 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7766 (t) REVERT: D 23 MET cc_start: 0.4931 (tpp) cc_final: 0.4586 (tpp) REVERT: D 36 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6669 (pm20) REVERT: D 107 MET cc_start: 0.8802 (ttm) cc_final: 0.8509 (ttm) REVERT: D 253 LYS cc_start: 0.8219 (mttt) cc_final: 0.7966 (mttm) REVERT: E 36 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6586 (pm20) REVERT: F 36 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6711 (pm20) REVERT: F 50 MET cc_start: 0.8259 (ttm) cc_final: 0.7932 (ttm) REVERT: F 107 MET cc_start: 0.8753 (ttm) cc_final: 0.8410 (ttm) REVERT: F 209 MET cc_start: 0.8151 (mtp) cc_final: 0.7917 (mtp) REVERT: F 247 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7733 (mtpt) REVERT: G 23 MET cc_start: 0.4835 (tpp) cc_final: 0.4513 (tpp) REVERT: G 36 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6623 (pm20) REVERT: G 43 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7350 (mm-30) REVERT: G 107 MET cc_start: 0.8783 (ttm) cc_final: 0.8501 (ttm) REVERT: G 253 LYS cc_start: 0.8220 (mttt) cc_final: 0.7950 (mttm) REVERT: H 36 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6599 (pm20) REVERT: I 36 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6712 (pm20) REVERT: I 107 MET cc_start: 0.8757 (ttm) cc_final: 0.8540 (ttm) REVERT: I 133 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7776 (t) REVERT: I 270 LYS cc_start: 0.7316 (tptt) cc_final: 0.6979 (tppt) REVERT: J 23 MET cc_start: 0.4896 (tpp) cc_final: 0.4553 (tpp) REVERT: J 36 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6664 (pm20) REVERT: J 107 MET cc_start: 0.8794 (ttm) cc_final: 0.8514 (ttm) REVERT: J 253 LYS cc_start: 0.8218 (mttt) cc_final: 0.7944 (mttm) REVERT: K 36 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6574 (pm20) REVERT: L 36 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6703 (pm20) REVERT: L 50 MET cc_start: 0.8254 (ttm) cc_final: 0.7922 (ttm) REVERT: L 107 MET cc_start: 0.8744 (ttm) cc_final: 0.8525 (ttm) REVERT: L 133 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7795 (t) REVERT: L 209 MET cc_start: 0.8184 (mtp) cc_final: 0.7958 (mtp) REVERT: L 247 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7687 (mtpt) REVERT: L 270 LYS cc_start: 0.7317 (tptt) cc_final: 0.6971 (tppt) outliers start: 25 outliers final: 20 residues processed: 440 average time/residue: 0.3953 time to fit residues: 269.9433 Evaluate side-chains 438 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 414 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 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 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 81 VAL Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 328 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 226 optimal weight: 0.0170 chunk 266 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 128 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.3836 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.187895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.157512 restraints weight = 23912.819| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.69 r_work: 0.3516 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26304 Z= 0.140 Angle : 0.484 6.413 35508 Z= 0.252 Chirality : 0.043 0.130 4116 Planarity : 0.004 0.033 4704 Dihedral : 3.834 17.125 3696 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.99 % Allowed : 13.17 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3468 helix: 0.89 (0.12), residues: 1812 sheet: -0.51 (0.25), residues: 480 loop : 0.17 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 301 HIS 0.001 0.000 HIS B 11 PHE 0.009 0.002 PHE D 240 TYR 0.005 0.001 TYR C 121 ARG 0.001 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1164) hydrogen bonds : angle 4.00560 ( 3240) covalent geometry : bond 0.00351 (26304) covalent geometry : angle 0.48417 (35508) *********************** 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: 26 poor density : 417 time to evaluate : 2.820 Fit side-chains REVERT: A 23 MET cc_start: 0.4781 (tpp) cc_final: 0.4460 (tpp) REVERT: A 36 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6648 (pm20) REVERT: A 107 MET cc_start: 0.8828 (ttm) cc_final: 0.8526 (ttm) REVERT: A 110 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: A 253 LYS cc_start: 0.8217 (mttt) cc_final: 0.7955 (mttm) REVERT: B 36 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6596 (pm20) REVERT: B 270 LYS cc_start: 0.7384 (tptp) cc_final: 0.6948 (tptp) REVERT: C 36 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6793 (pm20) REVERT: C 50 MET cc_start: 0.8257 (ttm) cc_final: 0.7935 (ttm) REVERT: C 107 MET cc_start: 0.8750 (ttm) cc_final: 0.8397 (ttm) REVERT: D 23 MET cc_start: 0.4862 (tpp) cc_final: 0.4546 (tpp) REVERT: D 36 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6676 (pm20) REVERT: D 107 MET cc_start: 0.8815 (ttm) cc_final: 0.8515 (ttm) REVERT: D 110 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8521 (tp30) REVERT: D 253 LYS cc_start: 0.8214 (mttt) cc_final: 0.7970 (mttm) REVERT: E 36 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6603 (pm20) REVERT: F 36 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6792 (pm20) REVERT: F 50 MET cc_start: 0.8261 (ttm) cc_final: 0.7932 (ttm) REVERT: F 107 MET cc_start: 0.8759 (ttm) cc_final: 0.8401 (ttm) REVERT: F 209 MET cc_start: 0.8184 (mtp) cc_final: 0.7979 (mtp) REVERT: F 247 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7717 (mtpt) REVERT: G 23 MET cc_start: 0.4847 (tpp) cc_final: 0.4516 (tpp) REVERT: G 36 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6633 (pm20) REVERT: G 43 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7375 (mm-30) REVERT: G 107 MET cc_start: 0.8806 (ttm) cc_final: 0.8512 (ttm) REVERT: G 253 LYS cc_start: 0.8222 (mttt) cc_final: 0.7958 (mttm) REVERT: H 36 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6609 (pm20) REVERT: I 36 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6797 (pm20) REVERT: I 107 MET cc_start: 0.8751 (ttm) cc_final: 0.8403 (ttm) REVERT: I 270 LYS cc_start: 0.7357 (tptt) cc_final: 0.6994 (tppt) REVERT: J 23 MET cc_start: 0.4898 (tpp) cc_final: 0.4563 (tpp) REVERT: J 36 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6689 (pm20) REVERT: J 107 MET cc_start: 0.8805 (ttm) cc_final: 0.8517 (ttm) REVERT: J 110 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: J 253 LYS cc_start: 0.8213 (mttt) cc_final: 0.7942 (mttm) REVERT: K 36 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6529 (pm20) REVERT: L 36 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6794 (pm20) REVERT: L 50 MET cc_start: 0.8258 (ttm) cc_final: 0.7935 (ttm) REVERT: L 107 MET cc_start: 0.8756 (ttm) cc_final: 0.8532 (ttm) REVERT: L 133 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7785 (t) REVERT: L 209 MET cc_start: 0.8192 (mtp) cc_final: 0.7960 (mtp) REVERT: L 247 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7685 (mtpt) REVERT: L 270 LYS cc_start: 0.7357 (tptt) cc_final: 0.6994 (tppt) outliers start: 26 outliers final: 22 residues processed: 441 average time/residue: 0.4650 time to fit residues: 319.9741 Evaluate side-chains 442 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 416 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 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 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 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 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 329 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 323 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.189020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157828 restraints weight = 23847.318| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.76 r_work: 0.3546 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26304 Z= 0.109 Angle : 0.455 10.859 35508 Z= 0.235 Chirality : 0.042 0.128 4116 Planarity : 0.004 0.033 4704 Dihedral : 3.703 17.694 3696 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.03 % Allowed : 13.13 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3468 helix: 1.11 (0.12), residues: 1800 sheet: -0.40 (0.25), residues: 480 loop : 0.27 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 301 HIS 0.001 0.000 HIS L 11 PHE 0.008 0.001 PHE A 240 TYR 0.004 0.001 TYR F 121 ARG 0.002 0.000 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 1164) hydrogen bonds : angle 3.81473 ( 3240) covalent geometry : bond 0.00267 (26304) covalent geometry : angle 0.45539 (35508) ********************** 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 426 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 399 time to evaluate : 2.854 Fit side-chains REVERT: A 23 MET cc_start: 0.4751 (tpp) cc_final: 0.4429 (tpp) REVERT: A 36 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6628 (pm20) REVERT: A 107 MET cc_start: 0.8831 (ttm) cc_final: 0.8547 (ttm) REVERT: A 110 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8536 (tp30) REVERT: A 253 LYS cc_start: 0.8104 (mttt) cc_final: 0.7845 (mttm) REVERT: B 36 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6619 (pm20) REVERT: B 270 LYS cc_start: 0.7448 (tptp) cc_final: 0.7016 (tptp) REVERT: C 23 MET cc_start: 0.4759 (tpp) cc_final: 0.4232 (tpp) REVERT: C 36 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6815 (pm20) REVERT: C 50 MET cc_start: 0.8250 (ttm) cc_final: 0.7914 (ttm) REVERT: C 107 MET cc_start: 0.8744 (ttm) cc_final: 0.8541 (ttm) REVERT: C 133 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7743 (t) REVERT: D 23 MET cc_start: 0.4812 (tpp) cc_final: 0.4494 (tpp) REVERT: D 36 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6605 (pm20) REVERT: D 107 MET cc_start: 0.8816 (ttm) cc_final: 0.8534 (ttm) REVERT: D 110 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8492 (tp30) REVERT: D 231 MET cc_start: 0.8456 (tpp) cc_final: 0.8250 (mmt) REVERT: D 253 LYS cc_start: 0.8112 (mttt) cc_final: 0.7858 (mttm) REVERT: E 36 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6618 (pm20) REVERT: F 23 MET cc_start: 0.4979 (tpp) cc_final: 0.4580 (tpp) REVERT: F 36 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6792 (pm20) REVERT: F 50 MET cc_start: 0.8254 (ttm) cc_final: 0.7921 (ttm) REVERT: F 107 MET cc_start: 0.8761 (ttm) cc_final: 0.8427 (ttm) REVERT: F 209 MET cc_start: 0.8161 (mtp) cc_final: 0.7948 (mtp) REVERT: F 247 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7722 (mtpt) REVERT: G 23 MET cc_start: 0.4801 (tpp) cc_final: 0.4496 (tpp) REVERT: G 36 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6666 (pm20) REVERT: G 43 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7340 (mm-30) REVERT: G 107 MET cc_start: 0.8803 (ttm) cc_final: 0.8525 (ttm) REVERT: G 253 LYS cc_start: 0.8099 (mttt) cc_final: 0.7834 (mttm) REVERT: H 36 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6631 (pm20) REVERT: I 23 MET cc_start: 0.4805 (tpp) cc_final: 0.4256 (tpp) REVERT: I 36 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6816 (pm20) REVERT: I 50 MET cc_start: 0.8257 (ttm) cc_final: 0.7928 (ttm) REVERT: I 133 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7750 (t) REVERT: J 23 MET cc_start: 0.4871 (tpp) cc_final: 0.4540 (tpp) REVERT: J 36 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6609 (pm20) REVERT: J 107 MET cc_start: 0.8810 (ttm) cc_final: 0.8540 (ttm) REVERT: J 110 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: J 231 MET cc_start: 0.8457 (tpp) cc_final: 0.8232 (mmt) REVERT: J 253 LYS cc_start: 0.8099 (mttt) cc_final: 0.7837 (mttm) REVERT: K 36 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6584 (pm20) REVERT: L 36 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6790 (pm20) REVERT: L 50 MET cc_start: 0.8237 (ttm) cc_final: 0.7910 (ttm) REVERT: L 133 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7755 (t) REVERT: L 209 MET cc_start: 0.8176 (mtp) cc_final: 0.7945 (mtp) REVERT: L 247 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7703 (mtpt) REVERT: L 270 LYS cc_start: 0.7355 (tptt) cc_final: 0.6992 (tppt) outliers start: 27 outliers final: 21 residues processed: 423 average time/residue: 0.3995 time to fit residues: 261.0436 Evaluate side-chains 425 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 398 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 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 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 110 GLU 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 192 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 262 optimal weight: 0.0770 chunk 264 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 324 optimal weight: 8.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.186470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154909 restraints weight = 23956.736| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.77 r_work: 0.3528 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26304 Z= 0.169 Angle : 0.520 10.442 35508 Z= 0.269 Chirality : 0.044 0.130 4116 Planarity : 0.005 0.034 4704 Dihedral : 3.906 19.384 3696 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.10 % Allowed : 13.39 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3468 helix: 0.77 (0.12), residues: 1812 sheet: -0.52 (0.25), residues: 480 loop : 0.08 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 301 HIS 0.002 0.001 HIS F 11 PHE 0.011 0.002 PHE L 128 TYR 0.005 0.001 TYR F 121 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 1164) hydrogen bonds : angle 4.10287 ( 3240) covalent geometry : bond 0.00431 (26304) covalent geometry : angle 0.51976 (35508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12873.04 seconds wall clock time: 225 minutes 44.45 seconds (13544.45 seconds total)