Starting phenix.real_space_refine on Thu Oct 29 17:34:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9szb_55364/10_2026/9szb_55364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9szb_55364/10_2026/9szb_55364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9szb_55364/10_2026/9szb_55364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9szb_55364/10_2026/9szb_55364.map" model { file = "/net/cci-nas-00/data/ceres_data/9szb_55364/10_2026/9szb_55364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9szb_55364/10_2026/9szb_55364.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 168 5.16 5 C 21000 2.51 5 N 5472 2.21 5 O 6516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2098 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 6, 'TRANS': 261} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 665 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain breaks: 1 Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 3.36, per 1000 atoms: 0.10 Number of scatterers: 33156 At special positions: 0 Unit cell: (155.817, 155.817, 139.374, 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 168 16.00 O 6516 8.00 N 5472 7.00 C 21000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 48 sheets defined 57.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 141 through 162 Processing helix chain 'A' and resid 176 through 198 Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 64 Processing helix chain 'B' and resid 72 through 93 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 80 Processing helix chain 'C' and resid 141 through 162 Processing helix chain 'C' and resid 176 through 198 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.548A pdb=" N ALA C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER D 21 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 64 Processing helix chain 'D' and resid 72 through 93 Processing helix chain 'E' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 80 Processing helix chain 'E' and resid 141 through 162 Processing helix chain 'E' and resid 176 through 198 Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA E 226 " --> pdb=" O THR E 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 Processing helix chain 'E' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR E 270 " --> pdb=" O GLN E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL F 22 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 64 Processing helix chain 'F' and resid 72 through 93 Processing helix chain 'G' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 80 Processing helix chain 'G' and resid 141 through 162 Processing helix chain 'G' and resid 176 through 198 Processing helix chain 'G' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 236 " --> pdb=" O ALA G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 244 Processing helix chain 'G' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR G 270 " --> pdb=" O GLN G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 282 No H-bonds generated for 'chain 'G' and resid 280 through 282' Processing helix chain 'G' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET G 287 " --> pdb=" O PHE G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER H 21 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL H 22 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 64 Processing helix chain 'H' and resid 72 through 93 Processing helix chain 'I' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 80 Processing helix chain 'I' and resid 141 through 162 Processing helix chain 'I' and resid 176 through 198 Processing helix chain 'I' and resid 221 through 236 removed outlier: 3.548A pdb=" N ALA I 226 " --> pdb=" O THR I 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU I 236 " --> pdb=" O ALA I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 244 Processing helix chain 'I' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET I 256 " --> pdb=" O LYS I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 282 No H-bonds generated for 'chain 'I' and resid 280 through 282' Processing helix chain 'I' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET I 287 " --> pdb=" O PHE I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 298 Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL J 22 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN J 25 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER J 26 " --> pdb=" O VAL J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 64 Processing helix chain 'J' and resid 72 through 93 Processing helix chain 'K' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR K 49 " --> pdb=" O SER K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 80 Processing helix chain 'K' and resid 141 through 162 Processing helix chain 'K' and resid 176 through 198 Processing helix chain 'K' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU K 236 " --> pdb=" O ALA K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 Processing helix chain 'K' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET K 256 " --> pdb=" O LYS K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR K 270 " --> pdb=" O GLN K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 282 No H-bonds generated for 'chain 'K' and resid 280 through 282' Processing helix chain 'K' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET K 287 " --> pdb=" O PHE K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 298 Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER L 21 " --> pdb=" O SER L 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL L 22 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN L 25 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER L 26 " --> pdb=" O VAL L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 64 Processing helix chain 'L' and resid 72 through 93 Processing helix chain 'M' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR M 49 " --> pdb=" O SER M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 80 Processing helix chain 'M' and resid 141 through 162 Processing helix chain 'M' and resid 176 through 198 Processing helix chain 'M' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA M 226 " --> pdb=" O THR M 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 244 Processing helix chain 'M' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET M 256 " --> pdb=" O LYS M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR M 270 " --> pdb=" O GLN M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 282 No H-bonds generated for 'chain 'M' and resid 280 through 282' Processing helix chain 'M' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET M 287 " --> pdb=" O PHE M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER N 21 " --> pdb=" O SER N 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL N 22 " --> pdb=" O ILE N 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER N 26 " --> pdb=" O VAL N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 64 Processing helix chain 'N' and resid 72 through 93 Processing helix chain 'O' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR O 49 " --> pdb=" O SER O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 80 Processing helix chain 'O' and resid 141 through 162 Processing helix chain 'O' and resid 176 through 198 Processing helix chain 'O' and resid 221 through 236 removed outlier: 3.548A pdb=" N ALA O 226 " --> pdb=" O THR O 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU O 236 " --> pdb=" O ALA O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 244 Processing helix chain 'O' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET O 256 " --> pdb=" O LYS O 252 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR O 270 " --> pdb=" O GLN O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 282 No H-bonds generated for 'chain 'O' and resid 280 through 282' Processing helix chain 'O' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET O 287 " --> pdb=" O PHE O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 298 Processing helix chain 'P' and resid 3 through 13 Processing helix chain 'P' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER P 21 " --> pdb=" O SER P 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL P 22 " --> pdb=" O ILE P 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN P 25 " --> pdb=" O SER P 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER P 26 " --> pdb=" O VAL P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 64 Processing helix chain 'P' and resid 72 through 93 Processing helix chain 'Q' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR Q 49 " --> pdb=" O SER Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 80 Processing helix chain 'Q' and resid 141 through 162 Processing helix chain 'Q' and resid 176 through 198 Processing helix chain 'Q' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA Q 226 " --> pdb=" O THR Q 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU Q 236 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 244 Processing helix chain 'Q' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET Q 256 " --> pdb=" O LYS Q 252 " (cutoff:3.500A) Processing helix chain 'Q' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR Q 270 " --> pdb=" O GLN Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 282 No H-bonds generated for 'chain 'Q' and resid 280 through 282' Processing helix chain 'Q' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET Q 287 " --> pdb=" O PHE Q 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 298 Processing helix chain 'R' and resid 3 through 13 Processing helix chain 'R' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER R 21 " --> pdb=" O SER R 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL R 22 " --> pdb=" O ILE R 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER R 26 " --> pdb=" O VAL R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 64 Processing helix chain 'R' and resid 72 through 93 Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR S 49 " --> pdb=" O SER S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 80 Processing helix chain 'S' and resid 141 through 162 Processing helix chain 'S' and resid 176 through 198 Processing helix chain 'S' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA S 226 " --> pdb=" O THR S 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU S 236 " --> pdb=" O ALA S 232 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 244 Processing helix chain 'S' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET S 256 " --> pdb=" O LYS S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR S 270 " --> pdb=" O GLN S 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 280 through 282 No H-bonds generated for 'chain 'S' and resid 280 through 282' Processing helix chain 'S' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET S 287 " --> pdb=" O PHE S 283 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 298 Processing helix chain 'T' and resid 3 through 13 Processing helix chain 'T' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL T 22 " --> pdb=" O ILE T 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP T 24 " --> pdb=" O GLU T 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER T 26 " --> pdb=" O VAL T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 64 Processing helix chain 'T' and resid 72 through 93 Processing helix chain 'U' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR U 49 " --> pdb=" O SER U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 80 Processing helix chain 'U' and resid 141 through 162 Processing helix chain 'U' and resid 176 through 198 Processing helix chain 'U' and resid 221 through 236 removed outlier: 3.548A pdb=" N ALA U 226 " --> pdb=" O THR U 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU U 236 " --> pdb=" O ALA U 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 239 through 244 Processing helix chain 'U' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET U 256 " --> pdb=" O LYS U 252 " (cutoff:3.500A) Processing helix chain 'U' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR U 270 " --> pdb=" O GLN U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 280 through 282 No H-bonds generated for 'chain 'U' and resid 280 through 282' Processing helix chain 'U' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET U 287 " --> pdb=" O PHE U 283 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 298 Processing helix chain 'V' and resid 3 through 13 Processing helix chain 'V' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER V 21 " --> pdb=" O SER V 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL V 22 " --> pdb=" O ILE V 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP V 24 " --> pdb=" O GLU V 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN V 25 " --> pdb=" O SER V 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER V 26 " --> pdb=" O VAL V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 64 Processing helix chain 'V' and resid 72 through 93 Processing helix chain 'W' and resid 37 through 49 removed outlier: 3.701A pdb=" N TYR W 49 " --> pdb=" O SER W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 80 Processing helix chain 'W' and resid 141 through 162 Processing helix chain 'W' and resid 176 through 198 Processing helix chain 'W' and resid 221 through 236 removed outlier: 3.549A pdb=" N ALA W 226 " --> pdb=" O THR W 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU W 236 " --> pdb=" O ALA W 232 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 244 Processing helix chain 'W' and resid 248 through 259 removed outlier: 3.505A pdb=" N MET W 256 " --> pdb=" O LYS W 252 " (cutoff:3.500A) Processing helix chain 'W' and resid 260 through 271 removed outlier: 3.680A pdb=" N TYR W 270 " --> pdb=" O GLN W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 282 No H-bonds generated for 'chain 'W' and resid 280 through 282' Processing helix chain 'W' and resid 283 through 289 removed outlier: 3.750A pdb=" N MET W 287 " --> pdb=" O PHE W 283 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 298 Processing helix chain 'X' and resid 3 through 13 Processing helix chain 'X' and resid 15 through 33 removed outlier: 3.786A pdb=" N SER X 21 " --> pdb=" O SER X 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL X 22 " --> pdb=" O ILE X 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP X 24 " --> pdb=" O GLU X 20 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER X 26 " --> pdb=" O VAL X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 64 Processing helix chain 'X' and resid 72 through 93 Processing sheet with id=1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=2, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=3, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=4, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=6, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=7, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=8, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=9, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=10, first strand: chain 'E' and resid 92 through 96 Processing sheet with id=11, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=12, first strand: chain 'E' and resid 167 through 169 Processing sheet with id=13, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=14, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=15, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=16, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=17, first strand: chain 'I' and resid 53 through 56 Processing sheet with id=18, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=19, first strand: chain 'I' and resid 99 through 101 Processing sheet with id=20, first strand: chain 'I' and resid 167 through 169 Processing sheet with id=21, first strand: chain 'K' and resid 53 through 56 Processing sheet with id=22, first strand: chain 'K' and resid 92 through 96 Processing sheet with id=23, first strand: chain 'K' and resid 99 through 101 Processing sheet with id=24, first strand: chain 'K' and resid 167 through 169 Processing sheet with id=25, first strand: chain 'M' and resid 53 through 56 Processing sheet with id=26, first strand: chain 'M' and resid 92 through 96 Processing sheet with id=27, first strand: chain 'M' and resid 99 through 101 Processing sheet with id=28, first strand: chain 'M' and resid 167 through 169 Processing sheet with id=29, first strand: chain 'O' and resid 53 through 56 Processing sheet with id=30, first strand: chain 'O' and resid 92 through 96 Processing sheet with id=31, first strand: chain 'O' and resid 99 through 101 Processing sheet with id=32, first strand: chain 'O' and resid 167 through 169 Processing sheet with id=33, first strand: chain 'Q' and resid 53 through 56 Processing sheet with id=34, first strand: chain 'Q' and resid 92 through 96 Processing sheet with id=35, first strand: chain 'Q' and resid 99 through 101 Processing sheet with id=36, first strand: chain 'Q' and resid 167 through 169 Processing sheet with id=37, first strand: chain 'S' and resid 53 through 56 Processing sheet with id=38, first strand: chain 'S' and resid 92 through 96 Processing sheet with id=39, first strand: chain 'S' and resid 99 through 101 Processing sheet with id=40, first strand: chain 'S' and resid 167 through 169 Processing sheet with id=41, first strand: chain 'U' and resid 53 through 56 Processing sheet with id=42, first strand: chain 'U' and resid 92 through 96 Processing sheet with id=43, first strand: chain 'U' and resid 99 through 101 Processing sheet with id=44, first strand: chain 'U' and resid 167 through 169 Processing sheet with id=45, first strand: chain 'W' and resid 53 through 56 Processing sheet with id=46, first strand: chain 'W' and resid 92 through 96 Processing sheet with id=47, first strand: chain 'W' and resid 99 through 101 Processing sheet with id=48, first strand: chain 'W' and resid 167 through 169 1908 hydrogen bonds defined for protein. 5616 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: 7.72 Time building geometry restraints manager: 3.67 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: 10836 1.34 - 1.46: 5146 1.46 - 1.57: 17318 1.57 - 1.69: 0 1.69 - 1.80: 336 Bond restraints: 33636 Sorted by residual: bond pdb=" CG PRO D 45 " pdb=" CD PRO D 45 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.65e-01 bond pdb=" CG PRO J 45 " pdb=" CD PRO J 45 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.65e-01 bond pdb=" CG PRO V 45 " pdb=" CD PRO V 45 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.65e-01 bond pdb=" CG PRO P 45 " pdb=" CD PRO P 45 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.65e-01 bond pdb=" CG PRO B 45 " pdb=" CD PRO B 45 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.53e-01 ... (remaining 33631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 44604 0.92 - 1.85: 828 1.85 - 2.77: 48 2.77 - 3.70: 48 3.70 - 4.62: 36 Bond angle restraints: 45564 Sorted by residual: angle pdb=" N SER W 246 " pdb=" CA SER W 246 " pdb=" C SER W 246 " ideal model delta sigma weight residual 112.93 110.81 2.12 1.12e+00 7.97e-01 3.60e+00 angle pdb=" N SER E 246 " pdb=" CA SER E 246 " pdb=" C SER E 246 " ideal model delta sigma weight residual 112.93 110.81 2.12 1.12e+00 7.97e-01 3.60e+00 angle pdb=" N SER K 246 " pdb=" CA SER K 246 " pdb=" C SER K 246 " ideal model delta sigma weight residual 112.93 110.81 2.12 1.12e+00 7.97e-01 3.60e+00 angle pdb=" N SER Q 246 " pdb=" CA SER Q 246 " pdb=" C SER Q 246 " ideal model delta sigma weight residual 112.93 110.81 2.12 1.12e+00 7.97e-01 3.60e+00 angle pdb=" N SER M 246 " pdb=" CA SER M 246 " pdb=" C SER M 246 " ideal model delta sigma weight residual 112.93 110.82 2.11 1.12e+00 7.97e-01 3.56e+00 ... (remaining 45559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.28: 18324 12.28 - 24.56: 1704 24.56 - 36.84: 360 36.84 - 49.12: 72 49.12 - 61.40: 72 Dihedral angle restraints: 20532 sinusoidal: 8004 harmonic: 12528 Sorted by residual: dihedral pdb=" CA ARG D 81 " pdb=" CB ARG D 81 " pdb=" CG ARG D 81 " pdb=" CD ARG D 81 " ideal model delta sinusoidal sigma weight residual -180.00 -127.59 -52.41 3 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CA ARG J 81 " pdb=" CB ARG J 81 " pdb=" CG ARG J 81 " pdb=" CD ARG J 81 " ideal model delta sinusoidal sigma weight residual -180.00 -127.59 -52.41 3 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CA ARG V 81 " pdb=" CB ARG V 81 " pdb=" CG ARG V 81 " pdb=" CD ARG V 81 " ideal model delta sinusoidal sigma weight residual -180.00 -127.59 -52.41 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 20529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3534 0.025 - 0.050: 1102 0.050 - 0.075: 416 0.075 - 0.100: 244 0.100 - 0.125: 164 Chirality restraints: 5460 Sorted by residual: chirality pdb=" CA ILE W 165 " pdb=" N ILE W 165 " pdb=" C ILE W 165 " pdb=" CB ILE W 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE E 165 " pdb=" N ILE E 165 " pdb=" C ILE E 165 " pdb=" CB ILE E 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE Q 165 " pdb=" N ILE Q 165 " pdb=" C ILE Q 165 " pdb=" CB ILE Q 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 5457 not shown) Planarity restraints: 5784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE U 69 " -0.007 2.00e-02 2.50e+03 7.70e-03 1.04e+00 pdb=" CG PHE U 69 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE U 69 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE U 69 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE U 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE U 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE U 69 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 69 " 0.007 2.00e-02 2.50e+03 7.70e-03 1.04e+00 pdb=" CG PHE C 69 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 69 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 69 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 69 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 69 " -0.007 2.00e-02 2.50e+03 7.70e-03 1.04e+00 pdb=" CG PHE O 69 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE O 69 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE O 69 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE O 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE O 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE O 69 " -0.002 2.00e-02 2.50e+03 ... (remaining 5781 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 10324 2.82 - 3.34: 30608 3.34 - 3.86: 55716 3.86 - 4.38: 66008 4.38 - 4.90: 110910 Nonbonded interactions: 273566 Sorted by model distance: nonbonded pdb=" OH TYR F 43 " pdb=" OD2 ASP H 24 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR L 43 " pdb=" OD2 ASP N 24 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR R 43 " pdb=" OD2 ASP T 24 " model vdw 2.306 3.040 nonbonded pdb=" OD2 ASP B 24 " pdb=" OH TYR X 43 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR B 43 " pdb=" OD2 ASP D 24 " model vdw 2.306 3.040 ... (remaining 273561 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.180 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: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.990 Find NCS groups from input model: 0.330 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 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 : 0.001 0.021 33636 Z= 0.069 Angle : 0.337 4.619 45564 Z= 0.191 Chirality : 0.037 0.125 5460 Planarity : 0.003 0.022 5784 Dihedral : 10.834 61.399 12372 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4176 helix: 1.30 (0.11), residues: 2232 sheet: 0.66 (0.21), residues: 552 loop : -0.24 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 279 TYR 0.005 0.001 TYR O 276 PHE 0.018 0.001 PHE U 69 TRP 0.002 0.001 TRP U 301 HIS 0.010 0.004 HIS G 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00136 / 0.07 (33636) covalent geometry : angle 0.33711 / 0.19 (45564) hydrogen bonds : bond 0.19410 / 12.90 ( 1908) hydrogen bonds : angle 5.66279 / 3.96 ( 5616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1256 time to evaluate : 1.083 Fit side-chains REVERT: A 180 MET cc_start: 0.8991 (ttm) cc_final: 0.8740 (ttp) REVERT: A 193 LYS cc_start: 0.9012 (tttt) cc_final: 0.8770 (tttm) REVERT: A 209 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8173 (mp0) REVERT: A 218 THR cc_start: 0.7801 (m) cc_final: 0.7579 (p) REVERT: A 222 THR cc_start: 0.7833 (p) cc_final: 0.7532 (t) REVERT: A 224 ASP cc_start: 0.7931 (m-30) cc_final: 0.7662 (m-30) REVERT: A 279 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7987 (mtp180) REVERT: B 24 ASP cc_start: 0.8195 (m-30) cc_final: 0.7985 (m-30) REVERT: B 80 LYS cc_start: 0.8697 (tttt) cc_final: 0.8368 (tttp) REVERT: C 180 MET cc_start: 0.8954 (ttm) cc_final: 0.8655 (ttp) REVERT: C 208 ASP cc_start: 0.7692 (m-30) cc_final: 0.7392 (m-30) REVERT: C 209 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8206 (mp0) REVERT: D 24 ASP cc_start: 0.8342 (m-30) cc_final: 0.8081 (m-30) REVERT: D 80 LYS cc_start: 0.8656 (tttt) cc_final: 0.8281 (tttp) REVERT: D 82 GLN cc_start: 0.8876 (tp40) cc_final: 0.8648 (tp-100) REVERT: E 66 ASN cc_start: 0.8808 (m-40) cc_final: 0.8561 (m110) REVERT: E 126 LEU cc_start: 0.8111 (tp) cc_final: 0.7804 (OUTLIER) REVERT: E 209 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8165 (mp0) REVERT: E 224 ASP cc_start: 0.7955 (m-30) cc_final: 0.7731 (m-30) REVERT: F 10 ARG cc_start: 0.8801 (tpt90) cc_final: 0.8508 (tpt-90) REVERT: F 24 ASP cc_start: 0.8299 (m-30) cc_final: 0.8000 (m-30) REVERT: F 73 SER cc_start: 0.7412 (m) cc_final: 0.6967 (p) REVERT: F 80 LYS cc_start: 0.8712 (tttt) cc_final: 0.8455 (tttp) REVERT: G 180 MET cc_start: 0.8990 (ttm) cc_final: 0.8739 (ttp) REVERT: G 193 LYS cc_start: 0.9012 (tttt) cc_final: 0.8768 (tttm) REVERT: G 209 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8168 (mp0) REVERT: G 218 THR cc_start: 0.7801 (m) cc_final: 0.7580 (p) REVERT: G 222 THR cc_start: 0.7833 (p) cc_final: 0.7532 (t) REVERT: G 224 ASP cc_start: 0.7930 (m-30) cc_final: 0.7660 (m-30) REVERT: G 279 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7985 (mtp180) REVERT: H 24 ASP cc_start: 0.8195 (m-30) cc_final: 0.7986 (m-30) REVERT: H 80 LYS cc_start: 0.8696 (tttt) cc_final: 0.8367 (tttp) REVERT: I 180 MET cc_start: 0.8952 (ttm) cc_final: 0.8654 (ttp) REVERT: I 208 ASP cc_start: 0.7693 (m-30) cc_final: 0.7393 (m-30) REVERT: I 209 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8207 (mp0) REVERT: J 24 ASP cc_start: 0.8342 (m-30) cc_final: 0.8081 (m-30) REVERT: J 80 LYS cc_start: 0.8657 (tttt) cc_final: 0.8283 (tttp) REVERT: J 82 GLN cc_start: 0.8877 (tp40) cc_final: 0.8649 (tp-100) REVERT: K 66 ASN cc_start: 0.8807 (m-40) cc_final: 0.8561 (m110) REVERT: K 126 LEU cc_start: 0.8111 (tp) cc_final: 0.7803 (OUTLIER) REVERT: K 209 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8162 (mp0) REVERT: K 224 ASP cc_start: 0.7954 (m-30) cc_final: 0.7732 (m-30) REVERT: L 10 ARG cc_start: 0.8801 (tpt90) cc_final: 0.8509 (tpt-90) REVERT: L 24 ASP cc_start: 0.8301 (m-30) cc_final: 0.8002 (m-30) REVERT: L 73 SER cc_start: 0.7412 (m) cc_final: 0.6968 (p) REVERT: L 80 LYS cc_start: 0.8712 (tttt) cc_final: 0.8455 (tttp) REVERT: M 180 MET cc_start: 0.8990 (ttm) cc_final: 0.8738 (ttp) REVERT: M 193 LYS cc_start: 0.9013 (tttt) cc_final: 0.8770 (tttm) REVERT: M 209 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8167 (mp0) REVERT: M 218 THR cc_start: 0.7800 (m) cc_final: 0.7579 (p) REVERT: M 222 THR cc_start: 0.7831 (p) cc_final: 0.7530 (t) REVERT: M 224 ASP cc_start: 0.7931 (m-30) cc_final: 0.7662 (m-30) REVERT: M 279 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7985 (mtp180) REVERT: N 24 ASP cc_start: 0.8198 (m-30) cc_final: 0.7988 (m-30) REVERT: N 80 LYS cc_start: 0.8696 (tttt) cc_final: 0.8369 (tttp) REVERT: O 180 MET cc_start: 0.8953 (ttm) cc_final: 0.8656 (ttp) REVERT: O 208 ASP cc_start: 0.7692 (m-30) cc_final: 0.7391 (m-30) REVERT: O 209 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8207 (mp0) REVERT: P 24 ASP cc_start: 0.8343 (m-30) cc_final: 0.8081 (m-30) REVERT: P 80 LYS cc_start: 0.8657 (tttt) cc_final: 0.8283 (tttp) REVERT: P 82 GLN cc_start: 0.8875 (tp40) cc_final: 0.8647 (tp-100) REVERT: Q 66 ASN cc_start: 0.8806 (m-40) cc_final: 0.8559 (m110) REVERT: Q 126 LEU cc_start: 0.8113 (tp) cc_final: 0.7806 (OUTLIER) REVERT: Q 209 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8162 (mp0) REVERT: Q 224 ASP cc_start: 0.7954 (m-30) cc_final: 0.7732 (m-30) REVERT: R 10 ARG cc_start: 0.8801 (tpt90) cc_final: 0.8508 (tpt-90) REVERT: R 24 ASP cc_start: 0.8300 (m-30) cc_final: 0.8000 (m-30) REVERT: R 73 SER cc_start: 0.7412 (m) cc_final: 0.6969 (p) REVERT: R 80 LYS cc_start: 0.8711 (tttt) cc_final: 0.8454 (tttp) REVERT: S 180 MET cc_start: 0.8990 (ttm) cc_final: 0.8739 (ttp) REVERT: S 193 LYS cc_start: 0.9012 (tttt) cc_final: 0.8770 (tttm) REVERT: S 209 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8169 (mp0) REVERT: S 218 THR cc_start: 0.7803 (m) cc_final: 0.7580 (p) REVERT: S 222 THR cc_start: 0.7831 (p) cc_final: 0.7529 (t) REVERT: S 224 ASP cc_start: 0.7932 (m-30) cc_final: 0.7663 (m-30) REVERT: S 279 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7984 (mtp180) REVERT: T 24 ASP cc_start: 0.8195 (m-30) cc_final: 0.7985 (m-30) REVERT: T 80 LYS cc_start: 0.8696 (tttt) cc_final: 0.8368 (tttp) REVERT: U 180 MET cc_start: 0.8954 (ttm) cc_final: 0.8657 (ttp) REVERT: U 208 ASP cc_start: 0.7691 (m-30) cc_final: 0.7390 (m-30) REVERT: U 209 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8206 (mp0) REVERT: V 24 ASP cc_start: 0.8342 (m-30) cc_final: 0.8081 (m-30) REVERT: V 80 LYS cc_start: 0.8656 (tttt) cc_final: 0.8282 (tttp) REVERT: V 82 GLN cc_start: 0.8875 (tp40) cc_final: 0.8647 (tp-100) REVERT: W 66 ASN cc_start: 0.8806 (m-40) cc_final: 0.8560 (m110) REVERT: W 126 LEU cc_start: 0.8114 (tp) cc_final: 0.7805 (OUTLIER) REVERT: W 209 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8120 (mp0) REVERT: W 224 ASP cc_start: 0.7956 (m-30) cc_final: 0.7734 (m-30) REVERT: X 10 ARG cc_start: 0.8801 (tpt90) cc_final: 0.8509 (tpt-90) REVERT: X 24 ASP cc_start: 0.8299 (m-30) cc_final: 0.8000 (m-30) REVERT: X 73 SER cc_start: 0.7412 (m) cc_final: 0.6968 (p) REVERT: X 80 LYS cc_start: 0.8711 (tttt) cc_final: 0.8455 (tttp) outliers start: 0 outliers final: 4 residues processed: 1256 average time/residue: 0.7126 time to fit residues: 1047.1816 Evaluate side-chains 776 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN B 86 ASN D 86 ASN E 185 ASN E 265 GLN F 86 ASN G 185 ASN G 265 GLN H 86 ASN J 86 ASN K 185 ASN K 265 GLN L 86 ASN M 185 ASN N 86 ASN P 86 ASN Q 185 ASN Q 265 GLN R 86 ASN S 185 ASN S 265 GLN T 86 ASN V 86 ASN W 185 ASN W 265 GLN X 86 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.101898 restraints weight = 37954.348| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.44 r_work: 0.2915 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33636 Z= 0.124 Angle : 0.453 6.762 45564 Z= 0.241 Chirality : 0.040 0.119 5460 Planarity : 0.003 0.027 5784 Dihedral : 3.148 14.536 4512 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.59 % Allowed : 13.30 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 4176 helix: 2.07 (0.11), residues: 2244 sheet: 0.65 (0.19), residues: 552 loop : -0.27 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 229 TYR 0.011 0.001 TYR Q 116 PHE 0.010 0.002 PHE W 69 TRP 0.003 0.001 TRP E 301 HIS 0.001 0.000 HIS I 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33636) covalent geometry : angle 0.45339 / 0.24 (45564) hydrogen bonds : bond 0.04214 / 2.81 ( 1908) hydrogen bonds : angle 3.85343 / 2.70 ( 5616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 820 time to evaluate : 0.847 Fit side-chains REVERT: A 180 MET cc_start: 0.9032 (ttm) cc_final: 0.8772 (ttp) REVERT: A 208 ASP cc_start: 0.7808 (m-30) cc_final: 0.7585 (m-30) REVERT: A 224 ASP cc_start: 0.7893 (m-30) cc_final: 0.7602 (m-30) REVERT: A 279 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7800 (mtm-85) REVERT: B 80 LYS cc_start: 0.8684 (tttt) cc_final: 0.8462 (tttp) REVERT: C 108 MET cc_start: 0.7796 (mtm) cc_final: 0.7349 (mtp) REVERT: C 180 MET cc_start: 0.9010 (ttm) cc_final: 0.8748 (ttp) REVERT: D 24 ASP cc_start: 0.8382 (m-30) cc_final: 0.8151 (m-30) REVERT: D 78 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: D 80 LYS cc_start: 0.8658 (tttt) cc_final: 0.8438 (tttp) REVERT: E 108 MET cc_start: 0.7871 (mtm) cc_final: 0.7487 (mtp) REVERT: E 208 ASP cc_start: 0.7795 (m-30) cc_final: 0.7471 (m-30) REVERT: E 209 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8095 (mp0) REVERT: E 224 ASP cc_start: 0.7798 (m-30) cc_final: 0.7547 (m-30) REVERT: E 279 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7842 (mtt-85) REVERT: F 10 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8536 (tpt-90) REVERT: F 24 ASP cc_start: 0.8319 (m-30) cc_final: 0.8091 (m-30) REVERT: F 78 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: G 180 MET cc_start: 0.9037 (ttm) cc_final: 0.8776 (ttp) REVERT: G 208 ASP cc_start: 0.7819 (m-30) cc_final: 0.7596 (m-30) REVERT: G 224 ASP cc_start: 0.7891 (m-30) cc_final: 0.7602 (m-30) REVERT: G 279 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7799 (mtm-85) REVERT: H 80 LYS cc_start: 0.8688 (tttt) cc_final: 0.8465 (tttp) REVERT: I 108 MET cc_start: 0.7800 (mtm) cc_final: 0.7358 (mtp) REVERT: I 180 MET cc_start: 0.9001 (ttm) cc_final: 0.8748 (ttp) REVERT: J 24 ASP cc_start: 0.8391 (m-30) cc_final: 0.8159 (m-30) REVERT: J 78 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: J 80 LYS cc_start: 0.8646 (tttt) cc_final: 0.8427 (tttp) REVERT: K 108 MET cc_start: 0.7873 (mtm) cc_final: 0.7493 (mtp) REVERT: K 208 ASP cc_start: 0.7795 (m-30) cc_final: 0.7474 (m-30) REVERT: K 209 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8087 (mp0) REVERT: K 224 ASP cc_start: 0.7799 (m-30) cc_final: 0.7549 (m-30) REVERT: K 279 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7842 (mtt-85) REVERT: L 10 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8533 (tpt-90) REVERT: L 24 ASP cc_start: 0.8308 (m-30) cc_final: 0.8080 (m-30) REVERT: L 78 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: M 180 MET cc_start: 0.9037 (ttm) cc_final: 0.8774 (ttp) REVERT: M 208 ASP cc_start: 0.7826 (m-30) cc_final: 0.7599 (m-30) REVERT: M 224 ASP cc_start: 0.7886 (m-30) cc_final: 0.7596 (m-30) REVERT: M 279 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7819 (mtm-85) REVERT: N 80 LYS cc_start: 0.8673 (tttt) cc_final: 0.8456 (tttp) REVERT: O 108 MET cc_start: 0.7795 (mtm) cc_final: 0.7349 (mtp) REVERT: O 180 MET cc_start: 0.9010 (ttm) cc_final: 0.8746 (ttp) REVERT: P 24 ASP cc_start: 0.8389 (m-30) cc_final: 0.8159 (m-30) REVERT: P 78 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: P 80 LYS cc_start: 0.8653 (tttt) cc_final: 0.8436 (tttp) REVERT: Q 108 MET cc_start: 0.7872 (mtm) cc_final: 0.7494 (mtp) REVERT: Q 208 ASP cc_start: 0.7788 (m-30) cc_final: 0.7467 (m-30) REVERT: Q 209 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8075 (mp0) REVERT: Q 224 ASP cc_start: 0.7790 (m-30) cc_final: 0.7540 (m-30) REVERT: Q 279 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7848 (mtt-85) REVERT: R 10 ARG cc_start: 0.8829 (tpt90) cc_final: 0.8542 (tpt-90) REVERT: R 24 ASP cc_start: 0.8317 (m-30) cc_final: 0.8090 (m-30) REVERT: R 78 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: S 180 MET cc_start: 0.9033 (ttm) cc_final: 0.8773 (ttp) REVERT: S 208 ASP cc_start: 0.7806 (m-30) cc_final: 0.7583 (m-30) REVERT: S 224 ASP cc_start: 0.7892 (m-30) cc_final: 0.7604 (m-30) REVERT: S 279 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7799 (mtm-85) REVERT: T 80 LYS cc_start: 0.8681 (tttt) cc_final: 0.8462 (tttp) REVERT: U 108 MET cc_start: 0.7804 (mtm) cc_final: 0.7357 (mtp) REVERT: U 180 MET cc_start: 0.9007 (ttm) cc_final: 0.8744 (ttp) REVERT: V 24 ASP cc_start: 0.8387 (m-30) cc_final: 0.8155 (m-30) REVERT: V 78 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: V 80 LYS cc_start: 0.8656 (tttt) cc_final: 0.8436 (tttp) REVERT: W 108 MET cc_start: 0.7875 (mtm) cc_final: 0.7494 (mtp) REVERT: W 208 ASP cc_start: 0.7784 (m-30) cc_final: 0.7454 (m-30) REVERT: W 209 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8081 (mp0) REVERT: W 224 ASP cc_start: 0.7792 (m-30) cc_final: 0.7540 (m-30) REVERT: W 279 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7843 (mtt-85) REVERT: X 10 ARG cc_start: 0.8824 (tpt90) cc_final: 0.8538 (tpt-90) REVERT: X 24 ASP cc_start: 0.8316 (m-30) cc_final: 0.8088 (m-30) REVERT: X 78 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8163 (mt0) outliers start: 96 outliers final: 20 residues processed: 884 average time/residue: 0.7790 time to fit residues: 794.8629 Evaluate side-chains 748 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 720 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain P residue 78 GLN Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [87, 247, 325, 369, 77, 54, 187, 65, 8, 340, 373] chunk 87 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 chunk 369 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 340 optimal weight: 0.9990 chunk 373 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN A 266 GLN B 78 GLN C 205 ASN C 265 GLN D 46 ASN D 82 GLN E 185 ASN E 265 GLN F 46 ASN F 76 ASN G 185 ASN G 265 GLN G 266 GLN H 78 GLN I 205 ASN I 265 GLN J 46 ASN J 82 GLN K 185 ASN K 265 GLN L 46 ASN L 76 ASN M 185 ASN M 265 GLN M 266 GLN N 78 GLN O 205 ASN O 265 GLN P 46 ASN P 82 GLN Q 185 ASN Q 265 GLN R 46 ASN R 76 ASN S 185 ASN S 265 GLN S 266 GLN T 78 GLN U 205 ASN U 265 GLN V 46 ASN V 82 GLN W 185 ASN W 265 GLN X 46 ASN X 76 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.098955 restraints weight = 37687.875| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.41 r_work: 0.2870 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33636 Z= 0.174 Angle : 0.490 6.108 45564 Z= 0.262 Chirality : 0.042 0.129 5460 Planarity : 0.004 0.033 5784 Dihedral : 3.510 16.232 4512 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.70 % Allowed : 15.32 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.12), residues: 4176 helix: 2.00 (0.11), residues: 2244 sheet: 0.64 (0.20), residues: 552 loop : -0.26 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 229 TYR 0.009 0.001 TYR Q 116 PHE 0.012 0.002 PHE E 69 TRP 0.004 0.001 TRP M 301 HIS 0.001 0.001 HIS W 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (33636) covalent geometry : angle 0.49038 / 0.26 (45564) hydrogen bonds : bond 0.04612 / 3.08 ( 1908) hydrogen bonds : angle 3.77451 / 2.65 ( 5616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 736 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8891 (tttm) REVERT: A 180 MET cc_start: 0.9026 (ttm) cc_final: 0.8764 (ttp) REVERT: A 205 ASN cc_start: 0.8284 (t0) cc_final: 0.8052 (t0) REVERT: A 224 ASP cc_start: 0.7901 (m-30) cc_final: 0.7541 (m-30) REVERT: A 279 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7791 (mtm-85) REVERT: C 180 MET cc_start: 0.8962 (ttm) cc_final: 0.8719 (ttp) REVERT: D 78 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: D 80 LYS cc_start: 0.8736 (tttt) cc_final: 0.8495 (tttp) REVERT: E 108 MET cc_start: 0.7837 (mtm) cc_final: 0.7416 (mtp) REVERT: E 279 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7830 (mtt-85) REVERT: F 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8506 (tpt-90) REVERT: F 24 ASP cc_start: 0.8344 (m-30) cc_final: 0.8076 (m-30) REVERT: F 78 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: G 166 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8897 (tttm) REVERT: G 180 MET cc_start: 0.9028 (ttm) cc_final: 0.8766 (ttp) REVERT: G 205 ASN cc_start: 0.8296 (t0) cc_final: 0.8063 (t0) REVERT: G 224 ASP cc_start: 0.7896 (m-30) cc_final: 0.7536 (m-30) REVERT: G 279 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7789 (mtm-85) REVERT: I 180 MET cc_start: 0.8964 (ttm) cc_final: 0.8721 (ttp) REVERT: J 78 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: J 80 LYS cc_start: 0.8737 (tttt) cc_final: 0.8496 (tttp) REVERT: K 108 MET cc_start: 0.7841 (mtm) cc_final: 0.7417 (mtp) REVERT: K 279 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7831 (mtt-85) REVERT: L 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8505 (tpt-90) REVERT: L 24 ASP cc_start: 0.8343 (m-30) cc_final: 0.8073 (m-30) REVERT: L 78 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: M 166 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8898 (tttm) REVERT: M 180 MET cc_start: 0.9029 (ttm) cc_final: 0.8765 (ttp) REVERT: M 205 ASN cc_start: 0.8292 (t0) cc_final: 0.8060 (t0) REVERT: M 224 ASP cc_start: 0.7892 (m-30) cc_final: 0.7529 (m-30) REVERT: M 279 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7802 (mtm-85) REVERT: O 180 MET cc_start: 0.8962 (ttm) cc_final: 0.8720 (ttp) REVERT: P 78 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: P 80 LYS cc_start: 0.8743 (tttt) cc_final: 0.8501 (tttp) REVERT: Q 108 MET cc_start: 0.7840 (mtm) cc_final: 0.7416 (mtp) REVERT: Q 279 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7834 (mtt-85) REVERT: R 10 ARG cc_start: 0.8829 (tpt90) cc_final: 0.8509 (tpt-90) REVERT: R 24 ASP cc_start: 0.8350 (m-30) cc_final: 0.8081 (m-30) REVERT: R 78 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: S 166 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8900 (tttm) REVERT: S 180 MET cc_start: 0.9028 (ttm) cc_final: 0.8765 (ttp) REVERT: S 205 ASN cc_start: 0.8290 (t0) cc_final: 0.8058 (t0) REVERT: S 224 ASP cc_start: 0.7899 (m-30) cc_final: 0.7537 (m-30) REVERT: S 279 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7785 (mtm-85) REVERT: U 180 MET cc_start: 0.8966 (ttm) cc_final: 0.8723 (ttp) REVERT: V 78 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: V 80 LYS cc_start: 0.8738 (tttt) cc_final: 0.8498 (tttp) REVERT: W 108 MET cc_start: 0.7840 (mtm) cc_final: 0.7415 (mtp) REVERT: W 279 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7828 (mtt-85) REVERT: X 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8508 (tpt-90) REVERT: X 24 ASP cc_start: 0.8348 (m-30) cc_final: 0.8078 (m-30) REVERT: X 78 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8177 (mt0) outliers start: 100 outliers final: 44 residues processed: 808 average time/residue: 0.7612 time to fit residues: 713.6061 Evaluate side-chains 760 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 704 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 166 LYS Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 166 LYS Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain P residue 78 GLN Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain U residue 107 THR Chi-restraints excluded: chain U residue 166 LYS Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [102, 396, 126, 294, 371, 156, 322, 97, 120, 292, 23] chunk 102 optimal weight: 0.8980 chunk 396 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 322 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN B 78 GLN C 205 ASN C 265 GLN D 46 ASN D 82 GLN E 185 ASN E 205 ASN F 46 ASN G 185 ASN G 265 GLN H 78 GLN I 205 ASN I 265 GLN J 46 ASN J 82 GLN K 185 ASN K 205 ASN L 46 ASN M 185 ASN M 265 GLN N 78 GLN O 205 ASN O 265 GLN P 46 ASN P 82 GLN Q 185 ASN Q 205 ASN R 46 ASN S 185 ASN S 265 GLN T 78 GLN U 205 ASN U 265 GLN V 46 ASN V 82 GLN W 185 ASN W 205 ASN X 46 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.123254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100456 restraints weight = 37571.819| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.44 r_work: 0.2901 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33636 Z= 0.117 Angle : 0.435 5.609 45564 Z= 0.232 Chirality : 0.040 0.120 5460 Planarity : 0.003 0.036 5784 Dihedral : 3.349 15.727 4512 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.05 % Allowed : 16.72 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.13), residues: 4176 helix: 2.21 (0.11), residues: 2244 sheet: 0.61 (0.20), residues: 552 loop : -0.19 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 279 TYR 0.008 0.001 TYR K 116 PHE 0.010 0.001 PHE E 69 TRP 0.003 0.001 TRP K 301 HIS 0.001 0.000 HIS I 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (33636) covalent geometry : angle 0.43468 / 0.23 (45564) hydrogen bonds : bond 0.03749 / 2.50 ( 1908) hydrogen bonds : angle 3.58813 / 2.52 ( 5616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 728 time to evaluate : 1.117 Fit side-chains REVERT: A 180 MET cc_start: 0.9021 (ttm) cc_final: 0.8778 (ttp) REVERT: A 205 ASN cc_start: 0.8295 (t0) cc_final: 0.8061 (t0) REVERT: A 224 ASP cc_start: 0.7818 (m-30) cc_final: 0.7483 (m-30) REVERT: A 279 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7775 (mtm-85) REVERT: B 78 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8075 (mm110) REVERT: C 121 TYR cc_start: 0.7306 (m-80) cc_final: 0.7065 (m-10) REVERT: C 122 LEU cc_start: 0.8143 (mt) cc_final: 0.7864 (mt) REVERT: C 180 MET cc_start: 0.8958 (ttm) cc_final: 0.8724 (ttp) REVERT: D 78 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7981 (mm-40) REVERT: D 80 LYS cc_start: 0.8759 (tttt) cc_final: 0.8549 (tttp) REVERT: E 222 THR cc_start: 0.7766 (m) cc_final: 0.7532 (p) REVERT: E 279 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7849 (mtt-85) REVERT: F 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8502 (tpt-90) REVERT: F 24 ASP cc_start: 0.8349 (m-30) cc_final: 0.8072 (m-30) REVERT: F 40 ASP cc_start: 0.8594 (p0) cc_final: 0.8392 (p0) REVERT: F 78 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8100 (mm110) REVERT: G 180 MET cc_start: 0.9018 (ttm) cc_final: 0.8774 (ttp) REVERT: G 205 ASN cc_start: 0.8308 (t0) cc_final: 0.8075 (t0) REVERT: G 224 ASP cc_start: 0.7817 (m-30) cc_final: 0.7483 (m-30) REVERT: G 279 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7777 (mtm-85) REVERT: H 78 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8078 (mm110) REVERT: I 121 TYR cc_start: 0.7302 (m-80) cc_final: 0.7060 (m-10) REVERT: I 122 LEU cc_start: 0.8151 (mt) cc_final: 0.7871 (mt) REVERT: I 180 MET cc_start: 0.8958 (ttm) cc_final: 0.8723 (ttp) REVERT: J 78 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7979 (mm-40) REVERT: J 80 LYS cc_start: 0.8754 (tttt) cc_final: 0.8546 (tttp) REVERT: K 222 THR cc_start: 0.7772 (m) cc_final: 0.7538 (p) REVERT: K 279 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7848 (mtt-85) REVERT: L 10 ARG cc_start: 0.8833 (tpt90) cc_final: 0.8508 (tpt-90) REVERT: L 24 ASP cc_start: 0.8345 (m-30) cc_final: 0.8067 (m-30) REVERT: L 40 ASP cc_start: 0.8601 (p0) cc_final: 0.8401 (p0) REVERT: L 78 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8103 (mm110) REVERT: M 180 MET cc_start: 0.9016 (ttm) cc_final: 0.8769 (ttp) REVERT: M 205 ASN cc_start: 0.8305 (t0) cc_final: 0.8070 (t0) REVERT: M 224 ASP cc_start: 0.7808 (m-30) cc_final: 0.7473 (m-30) REVERT: M 279 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7786 (mtm-85) REVERT: N 78 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8082 (mm110) REVERT: O 121 TYR cc_start: 0.7316 (m-80) cc_final: 0.7070 (m-10) REVERT: O 122 LEU cc_start: 0.8148 (mt) cc_final: 0.7863 (mt) REVERT: O 180 MET cc_start: 0.8963 (ttm) cc_final: 0.8730 (ttp) REVERT: P 78 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: P 80 LYS cc_start: 0.8765 (tttt) cc_final: 0.8554 (tttp) REVERT: Q 222 THR cc_start: 0.7773 (m) cc_final: 0.7540 (p) REVERT: Q 279 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7851 (mtt-85) REVERT: R 10 ARG cc_start: 0.8830 (tpt90) cc_final: 0.8506 (tpt-90) REVERT: R 24 ASP cc_start: 0.8347 (m-30) cc_final: 0.8069 (m-30) REVERT: R 40 ASP cc_start: 0.8583 (p0) cc_final: 0.8381 (p0) REVERT: R 78 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8101 (mm110) REVERT: S 180 MET cc_start: 0.9024 (ttm) cc_final: 0.8780 (ttp) REVERT: S 205 ASN cc_start: 0.8301 (t0) cc_final: 0.8067 (t0) REVERT: S 224 ASP cc_start: 0.7821 (m-30) cc_final: 0.7487 (m-30) REVERT: S 279 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7776 (mtm-85) REVERT: T 78 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8077 (mm110) REVERT: U 121 TYR cc_start: 0.7302 (m-80) cc_final: 0.7060 (m-10) REVERT: U 122 LEU cc_start: 0.8146 (mt) cc_final: 0.7864 (mt) REVERT: U 180 MET cc_start: 0.8967 (ttm) cc_final: 0.8734 (ttp) REVERT: V 78 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7986 (mm-40) REVERT: V 80 LYS cc_start: 0.8767 (tttt) cc_final: 0.8558 (tttp) REVERT: W 222 THR cc_start: 0.7767 (m) cc_final: 0.7534 (p) REVERT: W 279 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7853 (mtt-85) REVERT: X 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8504 (tpt-90) REVERT: X 24 ASP cc_start: 0.8353 (m-30) cc_final: 0.8075 (m-30) REVERT: X 40 ASP cc_start: 0.8592 (p0) cc_final: 0.8392 (p0) REVERT: X 78 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8100 (mm110) outliers start: 76 outliers final: 24 residues processed: 776 average time/residue: 0.7573 time to fit residues: 683.3608 Evaluate side-chains 740 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 704 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain P residue 78 GLN Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 78 GLN Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [187, 305, 132, 295, 313, 310, 388, 146, 273, 361, 405] chunk 187 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 361 optimal weight: 0.6980 chunk 405 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN B 46 ASN C 205 ASN C 265 GLN D 46 ASN D 82 GLN E 185 ASN E 205 ASN F 46 ASN G 185 ASN G 265 GLN H 46 ASN I 205 ASN I 265 GLN J 46 ASN J 82 GLN K 185 ASN K 205 ASN L 46 ASN M 185 ASN M 265 GLN N 46 ASN O 205 ASN O 265 GLN P 46 ASN P 82 GLN Q 185 ASN Q 205 ASN R 46 ASN S 185 ASN S 265 GLN T 46 ASN U 205 ASN U 265 GLN V 46 ASN V 82 GLN W 185 ASN W 205 ASN X 46 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098349 restraints weight = 37873.214| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.42 r_work: 0.2870 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33636 Z= 0.202 Angle : 0.509 5.627 45564 Z= 0.271 Chirality : 0.044 0.134 5460 Planarity : 0.004 0.032 5784 Dihedral : 3.668 16.988 4512 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.16 % Allowed : 16.15 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.12), residues: 4176 helix: 1.96 (0.11), residues: 2244 sheet: 0.63 (0.21), residues: 552 loop : -0.24 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 279 TYR 0.010 0.002 TYR W 91 PHE 0.013 0.002 PHE Q 69 TRP 0.004 0.002 TRP A 93 HIS 0.002 0.001 HIS W 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (33636) covalent geometry : angle 0.50881 / 0.27 (45564) hydrogen bonds : bond 0.04687 / 3.13 ( 1908) hydrogen bonds : angle 3.77160 / 2.65 ( 5616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 716 time to evaluate : 1.187 Fit side-chains REVERT: A 166 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8923 (tttm) REVERT: A 180 MET cc_start: 0.9029 (ttm) cc_final: 0.8777 (ttp) REVERT: A 205 ASN cc_start: 0.8308 (t0) cc_final: 0.8062 (t0) REVERT: C 122 LEU cc_start: 0.8151 (mt) cc_final: 0.7843 (mt) REVERT: C 180 MET cc_start: 0.8952 (ttm) cc_final: 0.8735 (ttp) REVERT: D 47 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: D 80 LYS cc_start: 0.8774 (tttt) cc_final: 0.8546 (tttp) REVERT: F 10 ARG cc_start: 0.8848 (tpt90) cc_final: 0.8540 (tpt-90) REVERT: F 78 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: G 166 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8923 (tttm) REVERT: G 180 MET cc_start: 0.9024 (ttm) cc_final: 0.8771 (ttp) REVERT: G 205 ASN cc_start: 0.8317 (t0) cc_final: 0.8073 (t0) REVERT: I 122 LEU cc_start: 0.8158 (mt) cc_final: 0.7847 (mt) REVERT: I 180 MET cc_start: 0.8949 (ttm) cc_final: 0.8731 (ttp) REVERT: J 47 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: J 80 LYS cc_start: 0.8777 (tttt) cc_final: 0.8547 (tttp) REVERT: L 10 ARG cc_start: 0.8847 (tpt90) cc_final: 0.8538 (tpt-90) REVERT: L 78 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: M 166 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8919 (tttm) REVERT: M 180 MET cc_start: 0.9021 (ttm) cc_final: 0.8765 (ttp) REVERT: M 205 ASN cc_start: 0.8318 (t0) cc_final: 0.8074 (t0) REVERT: O 122 LEU cc_start: 0.8162 (mt) cc_final: 0.7855 (mt) REVERT: O 180 MET cc_start: 0.8955 (ttm) cc_final: 0.8736 (ttp) REVERT: P 47 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: P 80 LYS cc_start: 0.8781 (tttt) cc_final: 0.8552 (tttp) REVERT: R 10 ARG cc_start: 0.8848 (tpt90) cc_final: 0.8539 (tpt-90) REVERT: R 78 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: S 166 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8923 (tttm) REVERT: S 180 MET cc_start: 0.9028 (ttm) cc_final: 0.8777 (ttp) REVERT: S 205 ASN cc_start: 0.8311 (t0) cc_final: 0.8067 (t0) REVERT: U 122 LEU cc_start: 0.8156 (mt) cc_final: 0.7848 (mt) REVERT: U 180 MET cc_start: 0.8961 (ttm) cc_final: 0.8743 (ttp) REVERT: V 47 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: V 80 LYS cc_start: 0.8776 (tttt) cc_final: 0.8551 (tttp) REVERT: X 10 ARG cc_start: 0.8852 (tpt90) cc_final: 0.8544 (tpt-90) REVERT: X 78 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8206 (mt0) outliers start: 117 outliers final: 48 residues processed: 792 average time/residue: 0.7527 time to fit residues: 699.5676 Evaluate side-chains 748 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 688 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain U residue 107 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [109, 251, 156, 16, 215, 269, 241, 86, 232, 62, 6] chunk 109 optimal weight: 0.7980 chunk 251 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN C 205 ASN C 265 GLN D 46 ASN D 82 GLN E 185 ASN E 205 ASN F 46 ASN F 76 ASN G 185 ASN G 265 GLN I 205 ASN I 265 GLN J 46 ASN J 82 GLN K 185 ASN K 205 ASN L 46 ASN L 76 ASN M 185 ASN M 265 GLN N 76 ASN O 205 ASN O 265 GLN P 46 ASN P 78 GLN P 82 GLN Q 185 ASN Q 205 ASN R 46 ASN R 76 ASN S 185 ASN S 265 GLN U 205 ASN U 265 GLN V 46 ASN V 82 GLN W 185 ASN W 205 ASN X 46 ASN X 76 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.099816 restraints weight = 37577.591| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.41 r_work: 0.2896 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33636 Z= 0.139 Angle : 0.457 5.305 45564 Z= 0.244 Chirality : 0.041 0.137 5460 Planarity : 0.003 0.032 5784 Dihedral : 3.531 16.708 4512 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.05 % Allowed : 16.37 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.13), residues: 4176 helix: 2.13 (0.11), residues: 2244 sheet: 0.63 (0.21), residues: 552 loop : -0.17 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 229 TYR 0.012 0.001 TYR W 91 PHE 0.012 0.002 PHE K 69 TRP 0.003 0.001 TRP W 301 HIS 0.002 0.001 HIS C 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (33636) covalent geometry : angle 0.45716 / 0.24 (45564) hydrogen bonds : bond 0.03999 / 2.66 ( 1908) hydrogen bonds : angle 3.64137 / 2.55 ( 5616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 720 time to evaluate : 1.410 Fit side-chains REVERT: A 166 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8903 (tttm) REVERT: A 180 MET cc_start: 0.9011 (ttm) cc_final: 0.8767 (ttp) REVERT: A 205 ASN cc_start: 0.8276 (t0) cc_final: 0.8028 (t0) REVERT: B 42 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: C 121 TYR cc_start: 0.7313 (m-80) cc_final: 0.7001 (m-10) REVERT: C 122 LEU cc_start: 0.8174 (mt) cc_final: 0.7875 (mt) REVERT: C 180 MET cc_start: 0.8928 (ttm) cc_final: 0.8697 (ttp) REVERT: D 80 LYS cc_start: 0.8754 (tttt) cc_final: 0.8535 (tttp) REVERT: E 126 LEU cc_start: 0.8159 (mt) cc_final: 0.7923 (mt) REVERT: E 166 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8551 (tttm) REVERT: E 222 THR cc_start: 0.7736 (m) cc_final: 0.7508 (p) REVERT: F 10 ARG cc_start: 0.8830 (tpt90) cc_final: 0.8521 (tpt-90) REVERT: F 78 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: G 166 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8904 (tttm) REVERT: G 180 MET cc_start: 0.9016 (ttm) cc_final: 0.8770 (ttp) REVERT: G 205 ASN cc_start: 0.8288 (t0) cc_final: 0.8042 (t0) REVERT: H 42 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: I 121 TYR cc_start: 0.7310 (m-80) cc_final: 0.6998 (m-10) REVERT: I 122 LEU cc_start: 0.8174 (mt) cc_final: 0.7872 (mt) REVERT: I 180 MET cc_start: 0.8930 (ttm) cc_final: 0.8697 (ttp) REVERT: J 80 LYS cc_start: 0.8757 (tttt) cc_final: 0.8539 (tttp) REVERT: K 126 LEU cc_start: 0.8155 (mt) cc_final: 0.7916 (mt) REVERT: K 166 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8551 (tttm) REVERT: K 222 THR cc_start: 0.7738 (m) cc_final: 0.7512 (p) REVERT: L 10 ARG cc_start: 0.8828 (tpt90) cc_final: 0.8518 (tpt-90) REVERT: L 78 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: M 166 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8899 (tttm) REVERT: M 180 MET cc_start: 0.9012 (ttm) cc_final: 0.8766 (ttp) REVERT: M 205 ASN cc_start: 0.8284 (t0) cc_final: 0.8036 (t0) REVERT: N 42 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: O 121 TYR cc_start: 0.7326 (m-80) cc_final: 0.7017 (m-10) REVERT: O 122 LEU cc_start: 0.8181 (mt) cc_final: 0.7879 (mt) REVERT: O 180 MET cc_start: 0.8938 (ttm) cc_final: 0.8705 (ttp) REVERT: P 80 LYS cc_start: 0.8767 (tttt) cc_final: 0.8548 (tttp) REVERT: Q 126 LEU cc_start: 0.8162 (mt) cc_final: 0.7923 (mt) REVERT: Q 166 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8549 (tttm) REVERT: Q 222 THR cc_start: 0.7739 (m) cc_final: 0.7517 (p) REVERT: R 10 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8514 (tpt-90) REVERT: R 78 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: S 166 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8902 (tttm) REVERT: S 180 MET cc_start: 0.9018 (ttm) cc_final: 0.8775 (ttp) REVERT: S 205 ASN cc_start: 0.8277 (t0) cc_final: 0.8029 (t0) REVERT: T 42 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: U 121 TYR cc_start: 0.7310 (m-80) cc_final: 0.6999 (m-10) REVERT: U 122 LEU cc_start: 0.8171 (mt) cc_final: 0.7871 (mt) REVERT: U 180 MET cc_start: 0.8940 (ttm) cc_final: 0.8709 (ttp) REVERT: V 80 LYS cc_start: 0.8763 (tttt) cc_final: 0.8546 (tttp) REVERT: W 126 LEU cc_start: 0.8165 (mt) cc_final: 0.7928 (mt) REVERT: W 166 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8548 (tttm) REVERT: W 222 THR cc_start: 0.7730 (m) cc_final: 0.7504 (p) REVERT: X 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8519 (tpt-90) REVERT: X 78 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8170 (mt0) outliers start: 113 outliers final: 53 residues processed: 804 average time/residue: 0.7480 time to fit residues: 699.9239 Evaluate side-chains 773 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 704 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 241 LYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 241 LYS Chi-restraints excluded: chain P residue 78 GLN Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 166 LYS Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain U residue 107 THR Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain U residue 241 LYS Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 166 LYS Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [112, 233, 31, 62, 125, 37, 4, 88, 305, 290, 368] chunk 112 optimal weight: 1.9990 chunk 233 optimal weight: 0.0020 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 368 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN C 205 ASN C 265 GLN D 46 ASN D 82 GLN E 185 ASN E 205 ASN G 185 ASN G 265 GLN I 205 ASN I 265 GLN J 46 ASN J 82 GLN K 185 ASN K 205 ASN M 185 ASN M 265 GLN O 205 ASN O 265 GLN P 46 ASN P 82 GLN Q 185 ASN Q 205 ASN S 185 ASN S 265 GLN U 205 ASN U 265 GLN V 46 ASN V 82 GLN W 185 ASN W 205 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100719 restraints weight = 37729.721| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.42 r_work: 0.2911 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33636 Z= 0.120 Angle : 0.444 5.174 45564 Z= 0.237 Chirality : 0.040 0.138 5460 Planarity : 0.003 0.034 5784 Dihedral : 3.457 17.495 4512 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.45 % Allowed : 17.45 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.13), residues: 4176 helix: 2.18 (0.11), residues: 2256 sheet: 0.65 (0.21), residues: 552 loop : -0.11 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 279 TYR 0.012 0.001 TYR Q 91 PHE 0.011 0.001 PHE E 69 TRP 0.003 0.001 TRP K 301 HIS 0.001 0.001 HIS O 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (33636) covalent geometry : angle 0.44352 / 0.24 (45564) hydrogen bonds : bond 0.03713 / 2.48 ( 1908) hydrogen bonds : angle 3.57018 / 2.50 ( 5616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 717 time to evaluate : 1.165 Fit side-chains REVERT: A 166 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8896 (tttm) REVERT: A 180 MET cc_start: 0.9014 (ttm) cc_final: 0.8781 (ttp) REVERT: A 205 ASN cc_start: 0.8282 (t0) cc_final: 0.8024 (t0) REVERT: B 42 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: C 121 TYR cc_start: 0.7308 (m-80) cc_final: 0.6994 (m-10) REVERT: C 122 LEU cc_start: 0.8164 (mt) cc_final: 0.7880 (mt) REVERT: C 180 MET cc_start: 0.8931 (ttm) cc_final: 0.8707 (ttp) REVERT: C 261 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8688 (m-30) REVERT: C 279 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7680 (mtt-85) REVERT: D 78 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: D 80 LYS cc_start: 0.8719 (tttt) cc_final: 0.8518 (tttp) REVERT: E 166 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8562 (tttm) REVERT: F 10 ARG cc_start: 0.8831 (tpt90) cc_final: 0.8517 (tpt-90) REVERT: F 78 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8097 (mm110) REVERT: G 166 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8897 (tttm) REVERT: G 180 MET cc_start: 0.9011 (ttm) cc_final: 0.8781 (ttp) REVERT: G 205 ASN cc_start: 0.8285 (t0) cc_final: 0.8030 (t0) REVERT: H 42 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: I 121 TYR cc_start: 0.7315 (m-80) cc_final: 0.6999 (m-10) REVERT: I 122 LEU cc_start: 0.8164 (mt) cc_final: 0.7879 (mt) REVERT: I 180 MET cc_start: 0.8931 (ttm) cc_final: 0.8706 (ttp) REVERT: I 261 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8693 (m-30) REVERT: I 279 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7672 (mtt-85) REVERT: J 78 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: J 80 LYS cc_start: 0.8718 (tttt) cc_final: 0.8517 (tttp) REVERT: K 166 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8564 (tttm) REVERT: L 10 ARG cc_start: 0.8833 (tpt90) cc_final: 0.8518 (tpt-90) REVERT: L 78 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8100 (mm110) REVERT: M 166 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8896 (tttm) REVERT: M 180 MET cc_start: 0.9007 (ttm) cc_final: 0.8775 (ttp) REVERT: M 205 ASN cc_start: 0.8286 (t0) cc_final: 0.8028 (t0) REVERT: N 42 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: O 121 TYR cc_start: 0.7325 (m-80) cc_final: 0.7007 (m-10) REVERT: O 122 LEU cc_start: 0.8173 (mt) cc_final: 0.7889 (mt) REVERT: O 180 MET cc_start: 0.8937 (ttm) cc_final: 0.8711 (ttp) REVERT: O 261 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8686 (m-30) REVERT: O 279 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7675 (mtt-85) REVERT: P 80 LYS cc_start: 0.8740 (tttt) cc_final: 0.8492 (tttp) REVERT: Q 166 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8557 (tttm) REVERT: R 10 ARG cc_start: 0.8826 (tpt90) cc_final: 0.8514 (tpt-90) REVERT: R 78 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8095 (mm110) REVERT: S 166 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8898 (tttm) REVERT: S 180 MET cc_start: 0.9015 (ttm) cc_final: 0.8784 (ttp) REVERT: S 205 ASN cc_start: 0.8279 (t0) cc_final: 0.8020 (t0) REVERT: T 42 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: U 121 TYR cc_start: 0.7317 (m-80) cc_final: 0.7001 (m-10) REVERT: U 122 LEU cc_start: 0.8165 (mt) cc_final: 0.7882 (mt) REVERT: U 180 MET cc_start: 0.8941 (ttm) cc_final: 0.8718 (ttp) REVERT: U 261 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8689 (m-30) REVERT: U 279 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7681 (mtt-85) REVERT: V 78 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: V 80 LYS cc_start: 0.8729 (tttt) cc_final: 0.8528 (tttp) REVERT: W 166 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8564 (tttm) REVERT: X 10 ARG cc_start: 0.8831 (tpt90) cc_final: 0.8520 (tpt-90) REVERT: X 78 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8100 (mm110) outliers start: 91 outliers final: 44 residues processed: 773 average time/residue: 0.7739 time to fit residues: 693.6916 Evaluate side-chains 757 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 690 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 166 LYS Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 166 LYS Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [100, 352, 68, 239, 135, 101, 27, 397, 226, 399, 33] chunk 100 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 239 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 397 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 399 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN C 205 ASN C 265 GLN D 46 ASN D 82 GLN E 185 ASN G 185 ASN G 265 GLN I 205 ASN I 265 GLN J 46 ASN J 82 GLN K 185 ASN M 185 ASN M 265 GLN O 205 ASN O 265 GLN P 46 ASN P 78 GLN P 82 GLN Q 185 ASN S 185 ASN S 265 GLN U 205 ASN U 265 GLN V 46 ASN V 82 GLN W 185 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.124202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101666 restraints weight = 37574.550| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.42 r_work: 0.2915 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 33636 Z= 0.107 Angle : 0.434 5.062 45564 Z= 0.231 Chirality : 0.040 0.124 5460 Planarity : 0.003 0.034 5784 Dihedral : 3.381 17.117 4512 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.59 % Allowed : 18.12 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.13), residues: 4176 helix: 2.21 (0.11), residues: 2280 sheet: 0.66 (0.21), residues: 552 loop : 0.05 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 279 TYR 0.014 0.001 TYR W 91 PHE 0.010 0.001 PHE W 69 TRP 0.003 0.001 TRP K 301 HIS 0.001 0.000 HIS I 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (33636) covalent geometry : angle 0.43372 / 0.23 (45564) hydrogen bonds : bond 0.03473 / 2.31 ( 1908) hydrogen bonds : angle 3.50075 / 2.45 ( 5616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 722 time to evaluate : 1.266 Fit side-chains REVERT: A 166 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8893 (tttm) REVERT: A 180 MET cc_start: 0.9018 (ttm) cc_final: 0.8778 (ttp) REVERT: A 205 ASN cc_start: 0.8263 (t0) cc_final: 0.8002 (t0) REVERT: A 279 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7665 (mtt-85) REVERT: B 42 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: C 121 TYR cc_start: 0.7278 (m-80) cc_final: 0.6945 (m-10) REVERT: C 122 LEU cc_start: 0.8161 (mt) cc_final: 0.7880 (mt) REVERT: C 180 MET cc_start: 0.8943 (ttm) cc_final: 0.8724 (ttp) REVERT: C 261 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8666 (m-30) REVERT: C 279 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7738 (mtt-85) REVERT: D 73 SER cc_start: 0.7365 (m) cc_final: 0.6827 (p) REVERT: D 78 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: E 166 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8582 (tttm) REVERT: F 10 ARG cc_start: 0.8825 (tpt90) cc_final: 0.8511 (tpt-90) REVERT: F 78 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8096 (mm110) REVERT: G 166 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8898 (tttm) REVERT: G 180 MET cc_start: 0.9012 (ttm) cc_final: 0.8772 (ttp) REVERT: G 205 ASN cc_start: 0.8266 (t0) cc_final: 0.8010 (t0) REVERT: H 42 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: I 121 TYR cc_start: 0.7281 (m-80) cc_final: 0.6947 (m-10) REVERT: I 122 LEU cc_start: 0.8165 (mt) cc_final: 0.7884 (mt) REVERT: I 180 MET cc_start: 0.8947 (ttm) cc_final: 0.8726 (ttp) REVERT: I 261 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8664 (m-30) REVERT: I 279 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7734 (mtt-85) REVERT: J 73 SER cc_start: 0.7366 (m) cc_final: 0.6826 (p) REVERT: J 78 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: K 166 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: L 10 ARG cc_start: 0.8831 (tpt90) cc_final: 0.8515 (tpt-90) REVERT: L 24 ASP cc_start: 0.8301 (m-30) cc_final: 0.7951 (m-30) REVERT: L 78 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8095 (mm110) REVERT: M 166 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8893 (tttm) REVERT: M 180 MET cc_start: 0.9012 (ttm) cc_final: 0.8770 (ttp) REVERT: M 205 ASN cc_start: 0.8268 (t0) cc_final: 0.8010 (t0) REVERT: N 42 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: N 78 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7881 (mm110) REVERT: O 121 TYR cc_start: 0.7289 (m-80) cc_final: 0.6954 (m-10) REVERT: O 122 LEU cc_start: 0.8170 (mt) cc_final: 0.7890 (mt) REVERT: O 180 MET cc_start: 0.8955 (ttm) cc_final: 0.8735 (ttp) REVERT: O 261 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: O 279 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7739 (mtt-85) REVERT: P 80 LYS cc_start: 0.8727 (tttt) cc_final: 0.8526 (tttp) REVERT: Q 166 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: R 10 ARG cc_start: 0.8819 (tpt90) cc_final: 0.8506 (tpt-90) REVERT: R 24 ASP cc_start: 0.8300 (m-30) cc_final: 0.7953 (m-30) REVERT: R 78 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8094 (mm110) REVERT: S 166 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8894 (tttm) REVERT: S 180 MET cc_start: 0.9015 (ttm) cc_final: 0.8776 (ttp) REVERT: S 205 ASN cc_start: 0.8264 (t0) cc_final: 0.8004 (t0) REVERT: T 42 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: U 121 TYR cc_start: 0.7275 (m-80) cc_final: 0.6939 (m-10) REVERT: U 122 LEU cc_start: 0.8163 (mt) cc_final: 0.7883 (mt) REVERT: U 180 MET cc_start: 0.8957 (ttm) cc_final: 0.8739 (ttp) REVERT: U 261 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8665 (m-30) REVERT: U 279 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7735 (mtt-85) REVERT: V 73 SER cc_start: 0.7369 (m) cc_final: 0.6830 (p) REVERT: V 78 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7986 (mm-40) REVERT: W 166 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8591 (tttm) REVERT: X 10 ARG cc_start: 0.8822 (tpt90) cc_final: 0.8512 (tpt-90) REVERT: X 78 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8099 (mm110) outliers start: 96 outliers final: 41 residues processed: 786 average time/residue: 0.7275 time to fit residues: 666.6672 Evaluate side-chains 750 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 686 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain P residue 78 GLN Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 166 LYS Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 166 LYS Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [148, 349, 77, 355, 370, 308, 174, 376, 238, 107, 326] chunk 148 optimal weight: 0.7980 chunk 349 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 370 optimal weight: 0.9980 chunk 308 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 376 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 326 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN C 205 ASN C 265 GLN D 46 ASN E 185 ASN G 185 ASN G 265 GLN I 205 ASN I 265 GLN J 46 ASN K 185 ASN M 185 ASN M 265 GLN O 205 ASN O 265 GLN P 46 ASN P 78 GLN Q 185 ASN S 185 ASN S 265 GLN U 205 ASN U 265 GLN V 46 ASN W 185 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101109 restraints weight = 37658.143| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.42 r_work: 0.2904 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33636 Z= 0.119 Angle : 0.450 5.532 45564 Z= 0.238 Chirality : 0.040 0.123 5460 Planarity : 0.003 0.034 5784 Dihedral : 3.436 17.488 4512 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.05 % Allowed : 18.80 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.13), residues: 4176 helix: 2.27 (0.11), residues: 2256 sheet: 0.63 (0.21), residues: 552 loop : -0.01 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 279 TYR 0.014 0.001 TYR K 91 PHE 0.010 0.001 PHE W 69 TRP 0.003 0.001 TRP W 301 HIS 0.001 0.001 HIS S 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (33636) covalent geometry : angle 0.45036 / 0.24 (45564) hydrogen bonds : bond 0.03589 / 2.39 ( 1908) hydrogen bonds : angle 3.51374 / 2.46 ( 5616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 712 time to evaluate : 1.419 Fit side-chains REVERT: A 166 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8874 (tttm) REVERT: A 180 MET cc_start: 0.9026 (ttm) cc_final: 0.8800 (ttp) REVERT: A 205 ASN cc_start: 0.8267 (t0) cc_final: 0.8009 (t0) REVERT: A 279 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7678 (mtt-85) REVERT: B 42 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 78 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7878 (mm110) REVERT: C 122 LEU cc_start: 0.8174 (mt) cc_final: 0.7918 (mt) REVERT: C 180 MET cc_start: 0.8938 (ttm) cc_final: 0.8719 (ttp) REVERT: C 261 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8673 (m-30) REVERT: C 279 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7741 (mtt-85) REVERT: D 73 SER cc_start: 0.7408 (m) cc_final: 0.6888 (p) REVERT: D 78 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7995 (mm-40) REVERT: E 166 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8514 (tttm) REVERT: E 224 ASP cc_start: 0.7622 (m-30) cc_final: 0.7388 (m-30) REVERT: F 10 ARG cc_start: 0.8822 (tpt90) cc_final: 0.8510 (tpt-90) REVERT: F 78 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8081 (mm110) REVERT: G 166 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8874 (tttm) REVERT: G 180 MET cc_start: 0.9020 (ttm) cc_final: 0.8793 (ttp) REVERT: G 205 ASN cc_start: 0.8275 (t0) cc_final: 0.8020 (t0) REVERT: G 279 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7631 (mtt-85) REVERT: H 42 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: H 78 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7882 (mm110) REVERT: I 122 LEU cc_start: 0.8174 (mt) cc_final: 0.7918 (mt) REVERT: I 180 MET cc_start: 0.8937 (ttm) cc_final: 0.8716 (ttp) REVERT: I 261 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8676 (m-30) REVERT: I 279 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7744 (mtt-85) REVERT: J 73 SER cc_start: 0.7407 (m) cc_final: 0.6885 (p) REVERT: J 78 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7993 (mm-40) REVERT: K 166 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8521 (tttm) REVERT: K 224 ASP cc_start: 0.7616 (m-30) cc_final: 0.7381 (m-30) REVERT: L 10 ARG cc_start: 0.8824 (tpt90) cc_final: 0.8511 (tpt-90) REVERT: L 24 ASP cc_start: 0.8311 (m-30) cc_final: 0.7948 (m-30) REVERT: L 78 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8076 (mm110) REVERT: M 166 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8875 (tttm) REVERT: M 180 MET cc_start: 0.9014 (ttm) cc_final: 0.8784 (ttp) REVERT: M 205 ASN cc_start: 0.8274 (t0) cc_final: 0.8018 (t0) REVERT: M 279 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7648 (mtt-85) REVERT: N 42 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: N 78 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7890 (mm110) REVERT: O 122 LEU cc_start: 0.8183 (mt) cc_final: 0.7925 (mt) REVERT: O 180 MET cc_start: 0.8954 (ttm) cc_final: 0.8732 (ttp) REVERT: O 261 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8669 (m-30) REVERT: O 279 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7745 (mtt-85) REVERT: Q 166 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8512 (tttm) REVERT: Q 224 ASP cc_start: 0.7611 (m-30) cc_final: 0.7377 (m-30) REVERT: R 10 ARG cc_start: 0.8814 (tpt90) cc_final: 0.8502 (tpt-90) REVERT: R 24 ASP cc_start: 0.8315 (m-30) cc_final: 0.7952 (m-30) REVERT: R 78 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8078 (mm110) REVERT: S 166 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8874 (tttm) REVERT: S 180 MET cc_start: 0.9026 (ttm) cc_final: 0.8800 (ttp) REVERT: S 205 ASN cc_start: 0.8264 (t0) cc_final: 0.8007 (t0) REVERT: S 279 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7631 (mtt-85) REVERT: T 42 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: T 78 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7883 (mm110) REVERT: U 122 LEU cc_start: 0.8175 (mt) cc_final: 0.7920 (mt) REVERT: U 180 MET cc_start: 0.8952 (ttm) cc_final: 0.8733 (ttp) REVERT: U 261 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8674 (m-30) REVERT: U 279 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7741 (mtt-85) REVERT: V 73 SER cc_start: 0.7412 (m) cc_final: 0.6891 (p) REVERT: V 78 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: W 166 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8518 (tttm) REVERT: W 224 ASP cc_start: 0.7613 (m-30) cc_final: 0.7378 (m-30) REVERT: X 10 ARG cc_start: 0.8820 (tpt90) cc_final: 0.8510 (tpt-90) REVERT: X 78 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8081 (mm110) outliers start: 76 outliers final: 41 residues processed: 756 average time/residue: 0.7507 time to fit residues: 660.1889 Evaluate side-chains 759 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 695 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain P residue 78 GLN Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 166 LYS Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 166 LYS Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [179, 70, 0, 102, 284, 318, 295, 161, 264, 126, 145] chunk 179 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 284 optimal weight: 0.9980 chunk 318 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 264 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN C 205 ASN C 265 GLN D 46 ASN E 185 ASN G 185 ASN G 265 GLN I 205 ASN I 265 GLN J 46 ASN K 185 ASN M 185 ASN M 265 GLN O 205 ASN O 265 GLN P 46 ASN P 78 GLN Q 185 ASN S 185 ASN S 265 GLN U 205 ASN U 265 GLN V 46 ASN W 185 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101553 restraints weight = 37793.836| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.42 r_work: 0.2948 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33636 Z= 0.112 Angle : 0.449 5.381 45564 Z= 0.237 Chirality : 0.040 0.120 5460 Planarity : 0.003 0.034 5784 Dihedral : 3.424 17.450 4512 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.16 % Allowed : 19.01 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.13), residues: 4176 helix: 2.19 (0.11), residues: 2280 sheet: 0.64 (0.21), residues: 552 loop : 0.08 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 229 TYR 0.015 0.001 TYR K 91 PHE 0.010 0.001 PHE K 69 TRP 0.003 0.001 TRP W 301 HIS 0.001 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (33636) covalent geometry : angle 0.44932 / 0.24 (45564) hydrogen bonds : bond 0.03520 / 2.34 ( 1908) hydrogen bonds : angle 3.49057 / 2.44 ( 5616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 700 time to evaluate : 1.292 Fit side-chains REVERT: A 166 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8859 (tttm) REVERT: A 180 MET cc_start: 0.9009 (ttm) cc_final: 0.8749 (ttp) REVERT: A 205 ASN cc_start: 0.8261 (t0) cc_final: 0.7996 (t0) REVERT: A 279 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7680 (mtt-85) REVERT: B 42 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: B 78 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7870 (mm110) REVERT: C 122 LEU cc_start: 0.8172 (mt) cc_final: 0.7915 (mt) REVERT: C 180 MET cc_start: 0.8928 (ttm) cc_final: 0.8709 (ttp) REVERT: C 205 ASN cc_start: 0.8331 (t0) cc_final: 0.7987 (t0) REVERT: C 261 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: C 279 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7762 (mtt-85) REVERT: D 73 SER cc_start: 0.7410 (m) cc_final: 0.6899 (p) REVERT: D 78 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7989 (mm-40) REVERT: E 166 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8533 (tttm) REVERT: E 224 ASP cc_start: 0.7597 (m-30) cc_final: 0.7378 (m-30) REVERT: F 10 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8515 (tpt-90) REVERT: F 24 ASP cc_start: 0.8296 (m-30) cc_final: 0.7934 (m-30) REVERT: F 78 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8086 (mm110) REVERT: G 166 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8862 (tttm) REVERT: G 180 MET cc_start: 0.9007 (ttm) cc_final: 0.8747 (ttp) REVERT: G 205 ASN cc_start: 0.8263 (t0) cc_final: 0.8001 (t0) REVERT: G 279 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7643 (mtt-85) REVERT: H 42 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: H 78 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7875 (mm110) REVERT: I 122 LEU cc_start: 0.8178 (mt) cc_final: 0.7919 (mt) REVERT: I 180 MET cc_start: 0.8934 (ttm) cc_final: 0.8711 (ttp) REVERT: I 205 ASN cc_start: 0.8341 (t0) cc_final: 0.8007 (t0) REVERT: I 261 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: I 279 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7765 (mtt-85) REVERT: J 73 SER cc_start: 0.7410 (m) cc_final: 0.6900 (p) REVERT: J 78 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: K 166 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8542 (tttm) REVERT: K 224 ASP cc_start: 0.7589 (m-30) cc_final: 0.7372 (m-30) REVERT: L 10 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8517 (tpt-90) REVERT: L 24 ASP cc_start: 0.8307 (m-30) cc_final: 0.7943 (m-30) REVERT: L 78 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8085 (mm110) REVERT: M 166 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8858 (tttm) REVERT: M 180 MET cc_start: 0.9009 (ttm) cc_final: 0.8746 (ttp) REVERT: M 205 ASN cc_start: 0.8264 (t0) cc_final: 0.8002 (t0) REVERT: M 279 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7658 (mtt-85) REVERT: N 42 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: N 73 SER cc_start: 0.7443 (m) cc_final: 0.6817 (p) REVERT: N 78 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7901 (mm110) REVERT: O 122 LEU cc_start: 0.8178 (mt) cc_final: 0.7918 (mt) REVERT: O 180 MET cc_start: 0.8939 (ttm) cc_final: 0.8718 (ttp) REVERT: O 205 ASN cc_start: 0.8343 (t0) cc_final: 0.8005 (t0) REVERT: O 261 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: O 279 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7768 (mtt-85) REVERT: Q 166 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8539 (tttm) REVERT: Q 224 ASP cc_start: 0.7593 (m-30) cc_final: 0.7375 (m-30) REVERT: R 10 ARG cc_start: 0.8824 (tpt90) cc_final: 0.8514 (tpt-90) REVERT: R 24 ASP cc_start: 0.8305 (m-30) cc_final: 0.7943 (m-30) REVERT: R 78 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8080 (mm110) REVERT: S 166 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8859 (tttm) REVERT: S 180 MET cc_start: 0.9016 (ttm) cc_final: 0.8757 (ttp) REVERT: S 205 ASN cc_start: 0.8260 (t0) cc_final: 0.7996 (t0) REVERT: S 279 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7642 (mtt-85) REVERT: T 42 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: T 78 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7878 (mm110) REVERT: U 122 LEU cc_start: 0.8173 (mt) cc_final: 0.7916 (mt) REVERT: U 180 MET cc_start: 0.8943 (ttm) cc_final: 0.8724 (ttp) REVERT: U 205 ASN cc_start: 0.8343 (t0) cc_final: 0.8002 (t0) REVERT: U 261 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8656 (m-30) REVERT: U 279 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7763 (mtt-85) REVERT: V 73 SER cc_start: 0.7402 (m) cc_final: 0.6893 (p) REVERT: V 78 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: W 166 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8539 (tttm) REVERT: W 224 ASP cc_start: 0.7588 (m-30) cc_final: 0.7368 (m-30) REVERT: X 10 ARG cc_start: 0.8830 (tpt90) cc_final: 0.8522 (tpt-90) REVERT: X 24 ASP cc_start: 0.8306 (m-30) cc_final: 0.7943 (m-30) REVERT: X 78 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8085 (mm110) outliers start: 80 outliers final: 36 residues processed: 748 average time/residue: 0.7456 time to fit residues: 649.8654 Evaluate side-chains 743 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 684 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 185 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain J residue 78 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 237 SER Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 166 LYS Chi-restraints excluded: chain Q residue 237 SER Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 209 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain U residue 171 SER Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 166 LYS Chi-restraints excluded: chain W residue 237 SER Chi-restraints excluded: chain X residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: [375, 107, 230, 10, 0, 351, 44, 32, 229, 300, 336] chunk 375 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 230 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 351 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 336 optimal weight: 0.0010 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 265 GLN C 265 GLN D 46 ASN E 185 ASN G 185 ASN G 265 GLN I 265 GLN J 46 ASN K 185 ASN M 185 ASN M 265 GLN O 265 GLN P 46 ASN P 78 GLN Q 185 ASN S 185 ASN S 265 GLN U 265 GLN V 46 ASN W 185 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.100635 restraints weight = 37612.405| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.41 r_work: 0.2886 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33636 Z= 0.147 Angle : 0.482 5.157 45564 Z= 0.255 Chirality : 0.041 0.151 5460 Planarity : 0.004 0.033 5784 Dihedral : 3.559 17.900 4512 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.75 % Allowed : 19.85 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.13), residues: 4176 helix: 2.14 (0.11), residues: 2280 sheet: 0.66 (0.21), residues: 552 loop : -0.04 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 229 TYR 0.018 0.001 TYR K 91 PHE 0.012 0.002 PHE K 69 TRP 0.003 0.001 TRP S 301 HIS 0.001 0.001 HIS E 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (33636) covalent geometry : angle 0.48236 / 0.25 (45564) hydrogen bonds : bond 0.03978 / 2.65 ( 1908) hydrogen bonds : angle 3.57215 / 2.50 ( 5616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15185.69 seconds wall clock time: 258 minutes 0.70 seconds (15480.70 seconds total)