Starting phenix.real_space_refine on Sat Mar 7 04:12:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjt_4567/03_2026/6qjt_4567.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjt_4567/03_2026/6qjt_4567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qjt_4567/03_2026/6qjt_4567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjt_4567/03_2026/6qjt_4567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qjt_4567/03_2026/6qjt_4567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjt_4567/03_2026/6qjt_4567.map" } resolution = 3.74 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= 0.003 sd= 0.027 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 120 5.16 5 C 24792 2.51 5 N 6468 2.21 5 O 7080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.54, per 1000 atoms: 0.12 Number of scatterers: 38460 At special positions: 0 Unit cell: (158.153, 158.153, 132.593, 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 120 16.00 O 7080 8.00 N 6468 7.00 C 24792 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: 2.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 60 sheets defined 45.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 117 through 132 Processing helix chain 'A' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 297 through 312 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 92 through 107 Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 272 Processing helix chain 'B' and resid 297 through 312 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 80 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 238 " --> pdb=" O HIS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 272 Processing helix chain 'C' and resid 297 through 312 Processing helix chain 'C' and resid 335 through 356 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 80 Processing helix chain 'D' and resid 92 through 107 Processing helix chain 'D' and resid 117 through 132 Processing helix chain 'D' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 238 " --> pdb=" O HIS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 272 Processing helix chain 'D' and resid 297 through 312 Processing helix chain 'D' and resid 335 through 356 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 423 Processing helix chain 'D' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 80 Processing helix chain 'E' and resid 92 through 107 Processing helix chain 'E' and resid 117 through 132 Processing helix chain 'E' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG E 238 " --> pdb=" O HIS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 272 Processing helix chain 'E' and resid 297 through 312 Processing helix chain 'E' and resid 335 through 356 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 423 Processing helix chain 'E' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 80 Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 117 through 132 Processing helix chain 'F' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG F 238 " --> pdb=" O HIS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 272 Processing helix chain 'F' and resid 297 through 312 Processing helix chain 'F' and resid 335 through 356 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 423 Processing helix chain 'F' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 80 Processing helix chain 'G' and resid 92 through 107 Processing helix chain 'G' and resid 117 through 132 Processing helix chain 'G' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU G 237 " --> pdb=" O ASN G 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG G 238 " --> pdb=" O HIS G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 272 Processing helix chain 'G' and resid 297 through 312 Processing helix chain 'G' and resid 335 through 356 Processing helix chain 'G' and resid 357 through 362 Processing helix chain 'G' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU G 407 " --> pdb=" O ASP G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 423 Processing helix chain 'G' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU G 431 " --> pdb=" O ASP G 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 80 Processing helix chain 'H' and resid 92 through 107 Processing helix chain 'H' and resid 117 through 132 Processing helix chain 'H' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG H 238 " --> pdb=" O HIS H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 272 Processing helix chain 'H' and resid 297 through 312 Processing helix chain 'H' and resid 335 through 356 Processing helix chain 'H' and resid 357 through 362 Processing helix chain 'H' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA H 387 " --> pdb=" O ASP H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU H 407 " --> pdb=" O ASP H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 423 Processing helix chain 'H' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU I 57 " --> pdb=" O LYS I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 80 Processing helix chain 'I' and resid 92 through 107 Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU I 237 " --> pdb=" O ASN I 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 272 Processing helix chain 'I' and resid 297 through 312 Processing helix chain 'I' and resid 335 through 356 Processing helix chain 'I' and resid 357 through 362 Processing helix chain 'I' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA I 387 " --> pdb=" O ASP I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU I 407 " --> pdb=" O ASP I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 423 Processing helix chain 'I' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 80 Processing helix chain 'J' and resid 92 through 107 Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU J 237 " --> pdb=" O ASN J 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG J 238 " --> pdb=" O HIS J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 272 Processing helix chain 'J' and resid 297 through 312 Processing helix chain 'J' and resid 335 through 356 Processing helix chain 'J' and resid 357 through 362 Processing helix chain 'J' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA J 387 " --> pdb=" O ASP J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU J 407 " --> pdb=" O ASP J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 423 Processing helix chain 'J' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU J 431 " --> pdb=" O ASP J 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU K 57 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 80 Processing helix chain 'K' and resid 92 through 107 Processing helix chain 'K' and resid 117 through 132 Processing helix chain 'K' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU K 237 " --> pdb=" O ASN K 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG K 238 " --> pdb=" O HIS K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 272 Processing helix chain 'K' and resid 297 through 312 Processing helix chain 'K' and resid 335 through 356 Processing helix chain 'K' and resid 357 through 362 Processing helix chain 'K' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU K 407 " --> pdb=" O ASP K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 423 Processing helix chain 'K' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU K 431 " --> pdb=" O ASP K 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU L 57 " --> pdb=" O LYS L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 80 Processing helix chain 'L' and resid 92 through 107 Processing helix chain 'L' and resid 117 through 132 Processing helix chain 'L' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU L 237 " --> pdb=" O ASN L 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG L 238 " --> pdb=" O HIS L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 272 Processing helix chain 'L' and resid 297 through 312 Processing helix chain 'L' and resid 335 through 356 Processing helix chain 'L' and resid 357 through 362 Processing helix chain 'L' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA L 387 " --> pdb=" O ASP L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU L 407 " --> pdb=" O ASP L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 423 Processing helix chain 'L' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU L 431 " --> pdb=" O ASP L 427 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=2, first strand: chain 'A' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA A 135 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL A 139 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU A 163 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 174 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR A 247 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 284 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=7, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA B 135 " --> pdb=" O ILE B 156 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL B 139 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU B 163 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 174 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR B 247 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 284 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=12, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA C 135 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL C 139 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU C 163 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 174 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR C 247 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 284 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 84 through 87 Processing sheet with id=17, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA D 135 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL D 139 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU D 163 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 174 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR D 247 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 284 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 84 through 87 Processing sheet with id=22, first strand: chain 'E' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA E 135 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL E 139 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU E 163 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 174 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR E 247 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 284 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'F' and resid 84 through 87 Processing sheet with id=27, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA F 135 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL F 139 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'F' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU F 163 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA F 174 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR F 247 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'G' and resid 84 through 87 Processing sheet with id=32, first strand: chain 'G' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA G 135 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL G 139 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU G 163 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA G 174 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'G' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR G 247 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 284 " --> pdb=" O THR G 247 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'H' and resid 84 through 87 Processing sheet with id=37, first strand: chain 'H' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA H 135 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'H' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL H 139 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'H' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU H 163 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA H 174 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'H' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR H 247 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS H 284 " --> pdb=" O THR H 247 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'I' and resid 84 through 87 Processing sheet with id=42, first strand: chain 'I' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA I 135 " --> pdb=" O ILE I 156 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL I 139 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'I' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU I 163 " --> pdb=" O LYS I 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA I 174 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'I' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR I 247 " --> pdb=" O LYS I 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 284 " --> pdb=" O THR I 247 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'J' and resid 84 through 87 Processing sheet with id=47, first strand: chain 'J' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA J 135 " --> pdb=" O ILE J 156 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'J' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL J 139 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'J' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU J 163 " --> pdb=" O LYS J 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA J 174 " --> pdb=" O LEU J 165 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'J' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR J 247 " --> pdb=" O LYS J 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS J 284 " --> pdb=" O THR J 247 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'K' and resid 84 through 87 Processing sheet with id=52, first strand: chain 'K' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA K 135 " --> pdb=" O ILE K 156 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'K' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL K 139 " --> pdb=" O ASP K 151 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'K' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU K 163 " --> pdb=" O LYS K 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA K 174 " --> pdb=" O LEU K 165 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'K' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR K 247 " --> pdb=" O LYS K 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS K 284 " --> pdb=" O THR K 247 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'L' and resid 84 through 87 Processing sheet with id=57, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA L 135 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'L' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL L 139 " --> pdb=" O ASP L 151 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'L' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU L 163 " --> pdb=" O LYS L 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA L 174 " --> pdb=" O LEU L 165 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'L' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR L 247 " --> pdb=" O LYS L 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 284 " --> pdb=" O THR L 247 " (cutoff:3.500A) 1800 hydrogen bonds defined for protein. 5328 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: 6.94 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12332 1.34 - 1.45: 5463 1.45 - 1.57: 21277 1.57 - 1.69: 0 1.69 - 1.80: 240 Bond restraints: 39312 Sorted by residual: bond pdb=" N ASP L 110 " pdb=" CA ASP L 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP C 110 " pdb=" CA ASP C 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP I 110 " pdb=" CA ASP I 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP F 110 " pdb=" CA ASP F 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.16e-02 7.43e+03 4.06e+00 ... (remaining 39307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 51415 1.92 - 3.85: 1665 3.85 - 5.77: 224 5.77 - 7.70: 36 7.70 - 9.62: 60 Bond angle restraints: 53400 Sorted by residual: angle pdb=" C LEU J 356 " pdb=" N ILE J 357 " pdb=" CA ILE J 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU A 356 " pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU G 356 " pdb=" N ILE G 357 " pdb=" CA ILE G 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU D 356 " pdb=" N ILE D 357 " pdb=" CA ILE D 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU I 356 " pdb=" N ILE I 357 " pdb=" CA ILE I 357 " ideal model delta sigma weight residual 120.33 124.32 -3.99 8.00e-01 1.56e+00 2.48e+01 ... (remaining 53395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.42: 22380 14.42 - 28.84: 924 28.84 - 43.25: 216 43.25 - 57.67: 12 57.67 - 72.09: 36 Dihedral angle restraints: 23568 sinusoidal: 9384 harmonic: 14184 Sorted by residual: dihedral pdb=" CA ASP K 109 " pdb=" C ASP K 109 " pdb=" N ASP K 110 " pdb=" CA ASP K 110 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASP H 109 " pdb=" C ASP H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASP B 109 " pdb=" C ASP B 109 " pdb=" N ASP B 110 " pdb=" CA ASP B 110 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 23565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4313 0.048 - 0.095: 1215 0.095 - 0.143: 492 0.143 - 0.191: 16 0.191 - 0.239: 24 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CA ASN E 204 " pdb=" N ASN E 204 " pdb=" C ASN E 204 " pdb=" CB ASN E 204 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASN B 204 " pdb=" N ASN B 204 " pdb=" C ASN B 204 " pdb=" CB ASN B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASN K 204 " pdb=" N ASN K 204 " pdb=" C ASN K 204 " pdb=" CB ASN K 204 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 6057 not shown) Planarity restraints: 6888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 435 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO E 436 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 435 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO B 436 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 436 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 436 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 435 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO H 436 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 436 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 436 " -0.037 5.00e-02 4.00e+02 ... (remaining 6885 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 11176 2.82 - 3.34: 35442 3.34 - 3.86: 63824 3.86 - 4.38: 70092 4.38 - 4.90: 121678 Nonbonded interactions: 302212 Sorted by model distance: nonbonded pdb=" O ILE F 130 " pdb=" OG SER F 213 " model vdw 2.298 3.040 nonbonded pdb=" O ILE G 130 " pdb=" OG SER G 213 " model vdw 2.298 3.040 nonbonded pdb=" O ILE A 130 " pdb=" OG SER A 213 " model vdw 2.298 3.040 nonbonded pdb=" O ILE J 130 " pdb=" OG SER J 213 " model vdw 2.298 3.040 nonbonded pdb=" O ILE D 130 " pdb=" OG SER D 213 " model vdw 2.298 3.040 ... (remaining 302207 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.130 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.950 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.005 0.051 39312 Z= 0.247 Angle : 0.850 9.621 53400 Z= 0.470 Chirality : 0.051 0.239 6060 Planarity : 0.007 0.061 6888 Dihedral : 9.403 72.091 14448 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -3.36 (0.10), residues: 4908 helix: -2.00 (0.08), residues: 2220 sheet: -2.40 (0.16), residues: 660 loop : -2.24 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 238 TYR 0.029 0.003 TYR H 116 PHE 0.018 0.002 PHE H 76 TRP 0.007 0.001 TRP B 259 HIS 0.005 0.002 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00528 (39312) covalent geometry : angle 0.84970 (53400) hydrogen bonds : bond 0.16658 ( 1800) hydrogen bonds : angle 7.64211 ( 5328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 920 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8556 (t0) cc_final: 0.7825 (t70) REVERT: A 49 LEU cc_start: 0.9015 (tp) cc_final: 0.8373 (mp) REVERT: A 125 TYR cc_start: 0.9302 (t80) cc_final: 0.9083 (t80) REVERT: A 126 GLU cc_start: 0.8436 (pt0) cc_final: 0.8107 (pt0) REVERT: A 180 GLU cc_start: 0.7872 (mp0) cc_final: 0.7385 (mm-30) REVERT: A 237 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8081 (tt0) REVERT: A 289 ASP cc_start: 0.8091 (m-30) cc_final: 0.6937 (m-30) REVERT: A 303 TYR cc_start: 0.9118 (t80) cc_final: 0.8885 (t80) REVERT: A 314 ILE cc_start: 0.9335 (tt) cc_final: 0.8860 (pt) REVERT: A 383 ASP cc_start: 0.7657 (t0) cc_final: 0.7383 (t0) REVERT: A 385 SER cc_start: 0.9092 (t) cc_final: 0.8760 (m) REVERT: A 393 MET cc_start: 0.8580 (mmm) cc_final: 0.8144 (mtt) REVERT: B 47 ASP cc_start: 0.8624 (t0) cc_final: 0.7209 (t70) REVERT: B 50 LEU cc_start: 0.9139 (mp) cc_final: 0.8744 (mt) REVERT: B 180 GLU cc_start: 0.8136 (mp0) cc_final: 0.7687 (mm-30) REVERT: B 308 ILE cc_start: 0.9484 (mt) cc_final: 0.9253 (mm) REVERT: B 321 LEU cc_start: 0.8871 (tp) cc_final: 0.8412 (tp) REVERT: B 339 GLN cc_start: 0.9313 (tp40) cc_final: 0.8815 (tp40) REVERT: B 385 SER cc_start: 0.9131 (t) cc_final: 0.8760 (m) REVERT: C 47 ASP cc_start: 0.8686 (t0) cc_final: 0.7975 (t70) REVERT: C 50 LEU cc_start: 0.9232 (mp) cc_final: 0.8932 (mt) REVERT: C 54 ASP cc_start: 0.8532 (m-30) cc_final: 0.8115 (p0) REVERT: C 180 GLU cc_start: 0.8234 (mp0) cc_final: 0.7940 (mm-30) REVERT: C 308 ILE cc_start: 0.9308 (mt) cc_final: 0.9108 (mm) REVERT: C 314 ILE cc_start: 0.9060 (tt) cc_final: 0.8625 (pt) REVERT: C 339 GLN cc_start: 0.9254 (tp40) cc_final: 0.8957 (tp40) REVERT: C 383 ASP cc_start: 0.7713 (t0) cc_final: 0.7479 (t0) REVERT: C 385 SER cc_start: 0.9394 (t) cc_final: 0.8847 (t) REVERT: C 393 MET cc_start: 0.8480 (mmm) cc_final: 0.7873 (mtp) REVERT: D 47 ASP cc_start: 0.8557 (t0) cc_final: 0.7821 (t70) REVERT: D 49 LEU cc_start: 0.9019 (tp) cc_final: 0.8376 (mp) REVERT: D 125 TYR cc_start: 0.9298 (t80) cc_final: 0.9079 (t80) REVERT: D 126 GLU cc_start: 0.8436 (pt0) cc_final: 0.8113 (pt0) REVERT: D 180 GLU cc_start: 0.7876 (mp0) cc_final: 0.7387 (mm-30) REVERT: D 237 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8081 (tt0) REVERT: D 303 TYR cc_start: 0.9130 (t80) cc_final: 0.8890 (t80) REVERT: D 314 ILE cc_start: 0.9336 (tt) cc_final: 0.8864 (pt) REVERT: D 383 ASP cc_start: 0.7650 (t0) cc_final: 0.7385 (t0) REVERT: D 385 SER cc_start: 0.9092 (t) cc_final: 0.8761 (m) REVERT: D 393 MET cc_start: 0.8573 (mmm) cc_final: 0.8135 (mtt) REVERT: E 47 ASP cc_start: 0.8627 (t0) cc_final: 0.7205 (t70) REVERT: E 50 LEU cc_start: 0.9139 (mp) cc_final: 0.8746 (mt) REVERT: E 180 GLU cc_start: 0.8130 (mp0) cc_final: 0.7683 (mm-30) REVERT: E 308 ILE cc_start: 0.9480 (mt) cc_final: 0.9260 (mm) REVERT: E 321 LEU cc_start: 0.8874 (tp) cc_final: 0.8413 (tp) REVERT: E 339 GLN cc_start: 0.9299 (tp40) cc_final: 0.8806 (tp40) REVERT: E 385 SER cc_start: 0.9131 (t) cc_final: 0.8757 (m) REVERT: F 47 ASP cc_start: 0.8690 (t0) cc_final: 0.7985 (t70) REVERT: F 50 LEU cc_start: 0.9225 (mp) cc_final: 0.8930 (mt) REVERT: F 54 ASP cc_start: 0.8528 (m-30) cc_final: 0.8112 (p0) REVERT: F 180 GLU cc_start: 0.8242 (mp0) cc_final: 0.7944 (mm-30) REVERT: F 314 ILE cc_start: 0.9061 (tt) cc_final: 0.8622 (pt) REVERT: F 339 GLN cc_start: 0.9259 (tp40) cc_final: 0.8953 (tp40) REVERT: F 383 ASP cc_start: 0.7710 (t0) cc_final: 0.7484 (t0) REVERT: F 385 SER cc_start: 0.9397 (t) cc_final: 0.8852 (t) REVERT: F 393 MET cc_start: 0.8477 (mmm) cc_final: 0.7874 (mtp) REVERT: G 47 ASP cc_start: 0.8559 (t0) cc_final: 0.7826 (t70) REVERT: G 49 LEU cc_start: 0.9018 (tp) cc_final: 0.8374 (mp) REVERT: G 125 TYR cc_start: 0.9300 (t80) cc_final: 0.9080 (t80) REVERT: G 126 GLU cc_start: 0.8441 (pt0) cc_final: 0.8115 (pt0) REVERT: G 180 GLU cc_start: 0.7876 (mp0) cc_final: 0.7388 (mm-30) REVERT: G 237 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8082 (tt0) REVERT: G 314 ILE cc_start: 0.9335 (tt) cc_final: 0.8867 (pt) REVERT: G 383 ASP cc_start: 0.7664 (t0) cc_final: 0.7391 (t0) REVERT: G 385 SER cc_start: 0.9093 (t) cc_final: 0.8762 (m) REVERT: G 393 MET cc_start: 0.8578 (mmm) cc_final: 0.8140 (mtt) REVERT: H 47 ASP cc_start: 0.8622 (t0) cc_final: 0.7205 (t70) REVERT: H 50 LEU cc_start: 0.9138 (mp) cc_final: 0.8739 (mt) REVERT: H 180 GLU cc_start: 0.8132 (mp0) cc_final: 0.7683 (mm-30) REVERT: H 308 ILE cc_start: 0.9477 (mt) cc_final: 0.9246 (mm) REVERT: H 321 LEU cc_start: 0.8881 (tp) cc_final: 0.8420 (tp) REVERT: H 339 GLN cc_start: 0.9296 (tp40) cc_final: 0.8809 (tp40) REVERT: H 385 SER cc_start: 0.9130 (t) cc_final: 0.8759 (m) REVERT: I 47 ASP cc_start: 0.8686 (t0) cc_final: 0.7977 (t70) REVERT: I 50 LEU cc_start: 0.9233 (mp) cc_final: 0.8933 (mt) REVERT: I 54 ASP cc_start: 0.8534 (m-30) cc_final: 0.8115 (p0) REVERT: I 180 GLU cc_start: 0.8238 (mp0) cc_final: 0.7948 (mm-30) REVERT: I 308 ILE cc_start: 0.9323 (mt) cc_final: 0.9123 (mm) REVERT: I 314 ILE cc_start: 0.9062 (tt) cc_final: 0.8624 (pt) REVERT: I 339 GLN cc_start: 0.9266 (tp40) cc_final: 0.8955 (tp40) REVERT: I 383 ASP cc_start: 0.7704 (t0) cc_final: 0.7482 (t0) REVERT: I 385 SER cc_start: 0.9396 (t) cc_final: 0.8849 (t) REVERT: I 393 MET cc_start: 0.8480 (mmm) cc_final: 0.7875 (mtp) REVERT: J 47 ASP cc_start: 0.8559 (t0) cc_final: 0.7825 (t70) REVERT: J 49 LEU cc_start: 0.9016 (tp) cc_final: 0.8371 (mp) REVERT: J 125 TYR cc_start: 0.9302 (t80) cc_final: 0.9084 (t80) REVERT: J 126 GLU cc_start: 0.8442 (pt0) cc_final: 0.8112 (pt0) REVERT: J 180 GLU cc_start: 0.7871 (mp0) cc_final: 0.7382 (mm-30) REVERT: J 237 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8083 (tt0) REVERT: J 314 ILE cc_start: 0.9335 (tt) cc_final: 0.8863 (pt) REVERT: J 383 ASP cc_start: 0.7661 (t0) cc_final: 0.7388 (t0) REVERT: J 385 SER cc_start: 0.9091 (t) cc_final: 0.8759 (m) REVERT: J 393 MET cc_start: 0.8576 (mmm) cc_final: 0.8142 (mtt) REVERT: K 47 ASP cc_start: 0.8626 (t0) cc_final: 0.7207 (t70) REVERT: K 50 LEU cc_start: 0.9137 (mp) cc_final: 0.8742 (mt) REVERT: K 180 GLU cc_start: 0.8132 (mp0) cc_final: 0.7681 (mm-30) REVERT: K 308 ILE cc_start: 0.9477 (mt) cc_final: 0.9236 (mm) REVERT: K 321 LEU cc_start: 0.8887 (tp) cc_final: 0.8424 (tp) REVERT: K 339 GLN cc_start: 0.9312 (tp40) cc_final: 0.8821 (tp40) REVERT: K 385 SER cc_start: 0.9131 (t) cc_final: 0.8760 (m) REVERT: K 393 MET cc_start: 0.8567 (mmm) cc_final: 0.8366 (mtp) REVERT: L 47 ASP cc_start: 0.8684 (t0) cc_final: 0.7978 (t70) REVERT: L 50 LEU cc_start: 0.9234 (mp) cc_final: 0.8935 (mt) REVERT: L 54 ASP cc_start: 0.8538 (m-30) cc_final: 0.8116 (p0) REVERT: L 180 GLU cc_start: 0.8236 (mp0) cc_final: 0.7949 (mm-30) REVERT: L 308 ILE cc_start: 0.9312 (mt) cc_final: 0.9110 (mm) REVERT: L 314 ILE cc_start: 0.9064 (tt) cc_final: 0.8628 (pt) REVERT: L 339 GLN cc_start: 0.9259 (tp40) cc_final: 0.8960 (tp40) REVERT: L 383 ASP cc_start: 0.7709 (t0) cc_final: 0.7484 (t0) REVERT: L 385 SER cc_start: 0.9393 (t) cc_final: 0.8849 (t) REVERT: L 393 MET cc_start: 0.8477 (mmm) cc_final: 0.7872 (mtp) outliers start: 0 outliers final: 0 residues processed: 920 average time/residue: 0.2326 time to fit residues: 344.9766 Evaluate side-chains 484 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.0370 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 5.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 389 ASN B 320 GLN C 320 GLN D 320 GLN D 389 ASN E 320 GLN F 320 GLN G 320 GLN G 389 ASN H 320 GLN I 320 GLN J 275 HIS J 320 GLN J 389 ASN K 320 GLN L 320 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.061980 restraints weight = 109436.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064339 restraints weight = 55358.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065861 restraints weight = 36189.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066849 restraints weight = 27640.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067484 restraints weight = 23253.568| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39312 Z= 0.186 Angle : 0.640 9.800 53400 Z= 0.320 Chirality : 0.044 0.147 6060 Planarity : 0.005 0.066 6888 Dihedral : 4.783 21.977 5280 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.93 % Allowed : 7.87 % Favored : 89.20 % 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: -1.06 (0.12), residues: 4908 helix: 0.29 (0.11), residues: 2172 sheet: -2.01 (0.17), residues: 660 loop : -1.23 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 80 TYR 0.011 0.002 TYR G 303 PHE 0.028 0.002 PHE E 76 TRP 0.006 0.001 TRP J 365 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00414 (39312) covalent geometry : angle 0.63958 (53400) hydrogen bonds : bond 0.04065 ( 1800) hydrogen bonds : angle 5.30304 ( 5328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 555 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8676 (t0) cc_final: 0.8367 (t70) REVERT: A 91 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8539 (m) REVERT: A 121 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9262 (mp) REVERT: A 314 ILE cc_start: 0.9333 (tt) cc_final: 0.8917 (pt) REVERT: A 383 ASP cc_start: 0.7520 (t0) cc_final: 0.7131 (t0) REVERT: A 385 SER cc_start: 0.8871 (t) cc_final: 0.8630 (p) REVERT: A 393 MET cc_start: 0.8612 (mmm) cc_final: 0.7976 (mtt) REVERT: B 240 MET cc_start: 0.9043 (mmm) cc_final: 0.8721 (mmm) REVERT: B 333 PHE cc_start: 0.7397 (t80) cc_final: 0.7088 (t80) REVERT: B 383 ASP cc_start: 0.6764 (t0) cc_final: 0.6079 (t0) REVERT: C 47 ASP cc_start: 0.8497 (t0) cc_final: 0.8137 (t70) REVERT: C 54 ASP cc_start: 0.8384 (m-30) cc_final: 0.7873 (p0) REVERT: C 308 ILE cc_start: 0.9327 (mt) cc_final: 0.9073 (mm) REVERT: C 314 ILE cc_start: 0.9064 (tt) cc_final: 0.8633 (pt) REVERT: C 315 ASP cc_start: 0.8764 (p0) cc_final: 0.8286 (p0) REVERT: C 383 ASP cc_start: 0.7643 (t0) cc_final: 0.7387 (t0) REVERT: C 393 MET cc_start: 0.8572 (mmm) cc_final: 0.8162 (mtt) REVERT: D 47 ASP cc_start: 0.8669 (t0) cc_final: 0.8358 (t70) REVERT: D 91 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8540 (m) REVERT: D 121 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9262 (mp) REVERT: D 314 ILE cc_start: 0.9331 (tt) cc_final: 0.8921 (pt) REVERT: D 383 ASP cc_start: 0.7520 (t0) cc_final: 0.7147 (t0) REVERT: D 385 SER cc_start: 0.8867 (t) cc_final: 0.8631 (p) REVERT: D 393 MET cc_start: 0.8606 (mmm) cc_final: 0.7888 (mtt) REVERT: E 240 MET cc_start: 0.9057 (mmm) cc_final: 0.8727 (mmm) REVERT: E 333 PHE cc_start: 0.7392 (t80) cc_final: 0.7084 (t80) REVERT: E 383 ASP cc_start: 0.6773 (t0) cc_final: 0.6082 (t0) REVERT: F 47 ASP cc_start: 0.8503 (t0) cc_final: 0.8139 (t70) REVERT: F 54 ASP cc_start: 0.8377 (m-30) cc_final: 0.7874 (p0) REVERT: F 314 ILE cc_start: 0.9046 (tt) cc_final: 0.8639 (pt) REVERT: F 315 ASP cc_start: 0.8757 (p0) cc_final: 0.8281 (p0) REVERT: F 383 ASP cc_start: 0.7654 (t0) cc_final: 0.7399 (t0) REVERT: F 393 MET cc_start: 0.8580 (mmm) cc_final: 0.8168 (mtt) REVERT: G 47 ASP cc_start: 0.8679 (t0) cc_final: 0.8358 (t70) REVERT: G 91 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8545 (m) REVERT: G 121 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9257 (mp) REVERT: G 126 GLU cc_start: 0.8699 (pt0) cc_final: 0.8498 (pt0) REVERT: G 314 ILE cc_start: 0.9336 (tt) cc_final: 0.8931 (pt) REVERT: G 383 ASP cc_start: 0.7542 (t0) cc_final: 0.7156 (t0) REVERT: G 385 SER cc_start: 0.8875 (t) cc_final: 0.8638 (p) REVERT: G 393 MET cc_start: 0.8608 (mmm) cc_final: 0.7890 (mtt) REVERT: H 240 MET cc_start: 0.9051 (mmm) cc_final: 0.8722 (mmm) REVERT: H 333 PHE cc_start: 0.7397 (t80) cc_final: 0.7088 (t80) REVERT: H 383 ASP cc_start: 0.6765 (t0) cc_final: 0.6083 (t0) REVERT: I 47 ASP cc_start: 0.8493 (t0) cc_final: 0.8134 (t70) REVERT: I 54 ASP cc_start: 0.8383 (m-30) cc_final: 0.7876 (p0) REVERT: I 308 ILE cc_start: 0.9344 (mt) cc_final: 0.9087 (mm) REVERT: I 314 ILE cc_start: 0.9070 (tt) cc_final: 0.8642 (pt) REVERT: I 315 ASP cc_start: 0.8740 (p0) cc_final: 0.8263 (p0) REVERT: I 383 ASP cc_start: 0.7634 (t0) cc_final: 0.7392 (t0) REVERT: I 393 MET cc_start: 0.8578 (mmm) cc_final: 0.8169 (mtt) REVERT: J 47 ASP cc_start: 0.8683 (t0) cc_final: 0.8369 (t70) REVERT: J 91 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8542 (m) REVERT: J 121 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9260 (mp) REVERT: J 314 ILE cc_start: 0.9337 (tt) cc_final: 0.8927 (pt) REVERT: J 383 ASP cc_start: 0.7535 (t0) cc_final: 0.7151 (t0) REVERT: J 385 SER cc_start: 0.8866 (t) cc_final: 0.8634 (p) REVERT: J 393 MET cc_start: 0.8622 (mmm) cc_final: 0.7901 (mtt) REVERT: K 240 MET cc_start: 0.9050 (mmm) cc_final: 0.8723 (mmm) REVERT: K 333 PHE cc_start: 0.7399 (t80) cc_final: 0.7098 (t80) REVERT: K 383 ASP cc_start: 0.6769 (t0) cc_final: 0.6082 (t0) REVERT: K 393 MET cc_start: 0.8665 (mmm) cc_final: 0.8321 (mtp) REVERT: L 47 ASP cc_start: 0.8493 (t0) cc_final: 0.8134 (t70) REVERT: L 54 ASP cc_start: 0.8402 (m-30) cc_final: 0.7880 (p0) REVERT: L 308 ILE cc_start: 0.9328 (mt) cc_final: 0.9070 (mm) REVERT: L 314 ILE cc_start: 0.9069 (tt) cc_final: 0.8638 (pt) REVERT: L 315 ASP cc_start: 0.8756 (p0) cc_final: 0.8276 (p0) REVERT: L 383 ASP cc_start: 0.7644 (t0) cc_final: 0.7394 (t0) REVERT: L 393 MET cc_start: 0.8593 (mmm) cc_final: 0.7780 (mtp) outliers start: 120 outliers final: 76 residues processed: 635 average time/residue: 0.2110 time to fit residues: 227.8922 Evaluate side-chains 476 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 392 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 62 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 chunk 448 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 377 optimal weight: 6.9990 chunk 473 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN E 127 ASN H 127 ASN K 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.079516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.059650 restraints weight = 110227.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.061929 restraints weight = 56739.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.063406 restraints weight = 37610.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064365 restraints weight = 28989.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064945 restraints weight = 24635.244| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 39312 Z= 0.227 Angle : 0.651 9.299 53400 Z= 0.323 Chirality : 0.044 0.153 6060 Planarity : 0.005 0.072 6888 Dihedral : 4.627 20.777 5280 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.96 % Allowed : 10.65 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4908 helix: 1.18 (0.11), residues: 2196 sheet: -1.60 (0.18), residues: 660 loop : -0.92 (0.15), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 78 TYR 0.015 0.002 TYR B 125 PHE 0.034 0.002 PHE H 76 TRP 0.006 0.001 TRP A 84 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00504 (39312) covalent geometry : angle 0.65098 (53400) hydrogen bonds : bond 0.03990 ( 1800) hydrogen bonds : angle 5.09852 ( 5328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 389 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8438 (m) REVERT: A 121 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9324 (mp) REVERT: A 314 ILE cc_start: 0.9329 (tt) cc_final: 0.8978 (pt) REVERT: A 383 ASP cc_start: 0.7648 (t0) cc_final: 0.7297 (t0) REVERT: A 385 SER cc_start: 0.8774 (t) cc_final: 0.8516 (p) REVERT: A 393 MET cc_start: 0.8748 (mmm) cc_final: 0.8039 (mtt) REVERT: B 240 MET cc_start: 0.9208 (mmm) cc_final: 0.8970 (mmm) REVERT: C 54 ASP cc_start: 0.8434 (m-30) cc_final: 0.7895 (p0) REVERT: C 240 MET cc_start: 0.9223 (mmm) cc_final: 0.8888 (mmm) REVERT: C 314 ILE cc_start: 0.9193 (tt) cc_final: 0.8880 (pt) REVERT: C 315 ASP cc_start: 0.8750 (p0) cc_final: 0.8539 (p0) REVERT: C 333 PHE cc_start: 0.7354 (m-10) cc_final: 0.7107 (m-10) REVERT: C 393 MET cc_start: 0.8613 (mmm) cc_final: 0.7875 (mtp) REVERT: D 91 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8440 (m) REVERT: D 121 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9329 (mp) REVERT: D 314 ILE cc_start: 0.9331 (tt) cc_final: 0.8991 (pt) REVERT: D 383 ASP cc_start: 0.7656 (t0) cc_final: 0.7300 (t0) REVERT: D 385 SER cc_start: 0.8801 (t) cc_final: 0.8569 (p) REVERT: D 393 MET cc_start: 0.8744 (mmm) cc_final: 0.8012 (mtt) REVERT: E 240 MET cc_start: 0.9206 (mmm) cc_final: 0.8970 (mmm) REVERT: F 54 ASP cc_start: 0.8428 (m-30) cc_final: 0.7897 (p0) REVERT: F 240 MET cc_start: 0.9220 (mmm) cc_final: 0.8885 (mmm) REVERT: F 314 ILE cc_start: 0.9126 (tt) cc_final: 0.8788 (pt) REVERT: F 315 ASP cc_start: 0.8743 (p0) cc_final: 0.8537 (p0) REVERT: F 333 PHE cc_start: 0.7345 (m-10) cc_final: 0.7096 (m-10) REVERT: F 393 MET cc_start: 0.8614 (mmm) cc_final: 0.7880 (mtp) REVERT: G 91 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8438 (m) REVERT: G 121 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9314 (mp) REVERT: G 126 GLU cc_start: 0.8538 (pt0) cc_final: 0.8189 (pt0) REVERT: G 314 ILE cc_start: 0.9322 (tt) cc_final: 0.8967 (pt) REVERT: G 383 ASP cc_start: 0.7680 (t0) cc_final: 0.7312 (t0) REVERT: G 385 SER cc_start: 0.8806 (t) cc_final: 0.8574 (p) REVERT: G 393 MET cc_start: 0.8739 (mmm) cc_final: 0.8010 (mtt) REVERT: H 240 MET cc_start: 0.9206 (mmm) cc_final: 0.8967 (mmm) REVERT: I 54 ASP cc_start: 0.8423 (m-30) cc_final: 0.7890 (p0) REVERT: I 240 MET cc_start: 0.9224 (mmm) cc_final: 0.8893 (mmm) REVERT: I 314 ILE cc_start: 0.9195 (tt) cc_final: 0.8883 (pt) REVERT: I 315 ASP cc_start: 0.8732 (p0) cc_final: 0.8522 (p0) REVERT: I 333 PHE cc_start: 0.7345 (m-10) cc_final: 0.7088 (m-10) REVERT: I 393 MET cc_start: 0.8617 (mmm) cc_final: 0.7882 (mtp) REVERT: J 91 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8438 (m) REVERT: J 121 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9321 (mp) REVERT: J 314 ILE cc_start: 0.9316 (tt) cc_final: 0.8961 (pt) REVERT: J 383 ASP cc_start: 0.7668 (t0) cc_final: 0.7304 (t0) REVERT: J 385 SER cc_start: 0.8800 (t) cc_final: 0.8569 (p) REVERT: J 393 MET cc_start: 0.8749 (mmm) cc_final: 0.8020 (mtt) REVERT: K 240 MET cc_start: 0.9205 (mmm) cc_final: 0.8963 (mmm) REVERT: K 393 MET cc_start: 0.8678 (mmm) cc_final: 0.8238 (mtp) REVERT: K 419 MET cc_start: 0.8719 (mpp) cc_final: 0.8519 (pmm) REVERT: L 54 ASP cc_start: 0.8426 (m-30) cc_final: 0.7889 (p0) REVERT: L 240 MET cc_start: 0.9226 (mmm) cc_final: 0.8921 (mmm) REVERT: L 314 ILE cc_start: 0.9200 (tt) cc_final: 0.8881 (pt) REVERT: L 315 ASP cc_start: 0.8739 (p0) cc_final: 0.8533 (p0) REVERT: L 393 MET cc_start: 0.8640 (mmm) cc_final: 0.7850 (mtp) outliers start: 162 outliers final: 127 residues processed: 508 average time/residue: 0.1938 time to fit residues: 171.7240 Evaluate side-chains 503 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 368 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 127 ASN Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 177 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 488 optimal weight: 30.0000 chunk 204 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN E 127 ASN H 127 ASN K 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.060143 restraints weight = 109848.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062426 restraints weight = 55921.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.063918 restraints weight = 36907.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064877 restraints weight = 28397.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065485 restraints weight = 24087.504| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39312 Z= 0.160 Angle : 0.613 10.216 53400 Z= 0.299 Chirality : 0.043 0.144 6060 Planarity : 0.004 0.070 6888 Dihedral : 4.540 20.213 5280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.54 % Allowed : 12.85 % Favored : 83.60 % 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: 0.28 (0.13), residues: 4908 helix: 1.57 (0.11), residues: 2196 sheet: -1.37 (0.18), residues: 660 loop : -0.76 (0.15), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.014 0.002 TYR A 125 PHE 0.031 0.001 PHE F 76 TRP 0.004 0.001 TRP G 84 HIS 0.003 0.001 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00359 (39312) covalent geometry : angle 0.61304 (53400) hydrogen bonds : bond 0.03599 ( 1800) hydrogen bonds : angle 4.86936 ( 5328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 397 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8472 (m) REVERT: A 121 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9234 (mp) REVERT: A 314 ILE cc_start: 0.9286 (tt) cc_final: 0.8935 (pt) REVERT: A 383 ASP cc_start: 0.7610 (t0) cc_final: 0.7339 (t0) REVERT: A 385 SER cc_start: 0.8765 (t) cc_final: 0.8476 (p) REVERT: A 393 MET cc_start: 0.8791 (mmm) cc_final: 0.7934 (mtt) REVERT: B 240 MET cc_start: 0.9305 (mmm) cc_final: 0.9074 (mmm) REVERT: B 323 MET cc_start: 0.7718 (mmm) cc_final: 0.7502 (mmm) REVERT: B 419 MET cc_start: 0.9271 (mpp) cc_final: 0.8715 (pmm) REVERT: C 49 LEU cc_start: 0.9271 (mp) cc_final: 0.8837 (mt) REVERT: C 54 ASP cc_start: 0.8391 (m-30) cc_final: 0.7845 (p0) REVERT: C 314 ILE cc_start: 0.9164 (tt) cc_final: 0.8830 (pt) REVERT: C 315 ASP cc_start: 0.8850 (p0) cc_final: 0.8636 (p0) REVERT: C 391 MET cc_start: 0.9391 (tpt) cc_final: 0.9185 (tpt) REVERT: C 393 MET cc_start: 0.8595 (mmm) cc_final: 0.8032 (mmm) REVERT: D 91 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8475 (m) REVERT: D 121 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9229 (mp) REVERT: D 314 ILE cc_start: 0.9282 (tt) cc_final: 0.8944 (pt) REVERT: D 383 ASP cc_start: 0.7642 (t0) cc_final: 0.7381 (t0) REVERT: D 385 SER cc_start: 0.8753 (t) cc_final: 0.8484 (p) REVERT: D 393 MET cc_start: 0.8769 (mmm) cc_final: 0.7906 (mtt) REVERT: E 240 MET cc_start: 0.9301 (mmm) cc_final: 0.9079 (mmm) REVERT: E 294 MET cc_start: 0.8254 (tmm) cc_final: 0.8021 (tmm) REVERT: E 323 MET cc_start: 0.7716 (mmm) cc_final: 0.7503 (mmm) REVERT: E 419 MET cc_start: 0.9267 (mpp) cc_final: 0.8715 (pmm) REVERT: F 49 LEU cc_start: 0.9268 (mp) cc_final: 0.8833 (mt) REVERT: F 54 ASP cc_start: 0.8378 (m-30) cc_final: 0.7844 (p0) REVERT: F 314 ILE cc_start: 0.9146 (tt) cc_final: 0.8813 (pt) REVERT: F 315 ASP cc_start: 0.8765 (p0) cc_final: 0.8545 (p0) REVERT: F 391 MET cc_start: 0.9390 (tpt) cc_final: 0.9182 (tpt) REVERT: F 393 MET cc_start: 0.8601 (mmm) cc_final: 0.8040 (mmm) REVERT: G 91 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8476 (m) REVERT: G 121 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9242 (mp) REVERT: G 126 GLU cc_start: 0.8520 (pt0) cc_final: 0.8221 (pt0) REVERT: G 314 ILE cc_start: 0.9292 (tt) cc_final: 0.8950 (pt) REVERT: G 383 ASP cc_start: 0.7659 (t0) cc_final: 0.7389 (t0) REVERT: G 385 SER cc_start: 0.8759 (t) cc_final: 0.8488 (p) REVERT: G 393 MET cc_start: 0.8758 (mmm) cc_final: 0.7894 (mtt) REVERT: H 240 MET cc_start: 0.9296 (mmm) cc_final: 0.9070 (mmm) REVERT: H 294 MET cc_start: 0.8251 (tmm) cc_final: 0.8016 (tmm) REVERT: H 323 MET cc_start: 0.7701 (mmm) cc_final: 0.7495 (mmm) REVERT: H 419 MET cc_start: 0.9270 (mpp) cc_final: 0.8711 (pmm) REVERT: I 49 LEU cc_start: 0.9269 (mp) cc_final: 0.8833 (mt) REVERT: I 54 ASP cc_start: 0.8375 (m-30) cc_final: 0.7834 (p0) REVERT: I 314 ILE cc_start: 0.9170 (tt) cc_final: 0.8828 (pt) REVERT: I 315 ASP cc_start: 0.8817 (p0) cc_final: 0.8615 (p0) REVERT: I 391 MET cc_start: 0.9389 (tpt) cc_final: 0.9181 (tpt) REVERT: I 393 MET cc_start: 0.8603 (mmm) cc_final: 0.8041 (mmm) REVERT: J 91 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8477 (m) REVERT: J 121 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9231 (mp) REVERT: J 314 ILE cc_start: 0.9288 (tt) cc_final: 0.8946 (pt) REVERT: J 383 ASP cc_start: 0.7646 (t0) cc_final: 0.7388 (t0) REVERT: J 385 SER cc_start: 0.8750 (t) cc_final: 0.8489 (p) REVERT: J 393 MET cc_start: 0.8770 (mmm) cc_final: 0.7909 (mtt) REVERT: K 240 MET cc_start: 0.9303 (mmm) cc_final: 0.9070 (mmm) REVERT: K 294 MET cc_start: 0.8248 (tmm) cc_final: 0.8018 (tmm) REVERT: K 323 MET cc_start: 0.7723 (mmm) cc_final: 0.7511 (mmm) REVERT: K 391 MET cc_start: 0.9197 (tpp) cc_final: 0.8979 (ttt) REVERT: K 393 MET cc_start: 0.8662 (mmm) cc_final: 0.8234 (mtp) REVERT: L 49 LEU cc_start: 0.9271 (mp) cc_final: 0.8837 (mt) REVERT: L 54 ASP cc_start: 0.8383 (m-30) cc_final: 0.7836 (p0) REVERT: L 314 ILE cc_start: 0.9174 (tt) cc_final: 0.8832 (pt) REVERT: L 315 ASP cc_start: 0.8821 (p0) cc_final: 0.8619 (p0) REVERT: L 393 MET cc_start: 0.8619 (mmm) cc_final: 0.7985 (mmm) outliers start: 145 outliers final: 106 residues processed: 502 average time/residue: 0.1922 time to fit residues: 169.9739 Evaluate side-chains 488 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 374 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 171 optimal weight: 6.9990 chunk 257 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 375 optimal weight: 20.0000 chunk 430 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 164 optimal weight: 30.0000 overall best weight: 6.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.058605 restraints weight = 110126.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060844 restraints weight = 56772.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062269 restraints weight = 37778.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.063206 restraints weight = 29353.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063784 restraints weight = 25025.361| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 39312 Z= 0.237 Angle : 0.654 10.530 53400 Z= 0.320 Chirality : 0.044 0.149 6060 Planarity : 0.004 0.065 6888 Dihedral : 4.532 19.655 5280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.89 % Allowed : 13.03 % Favored : 83.09 % 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: 0.45 (0.13), residues: 4908 helix: 1.73 (0.11), residues: 2196 sheet: -1.26 (0.18), residues: 660 loop : -0.70 (0.15), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.019 0.002 TYR J 125 PHE 0.024 0.001 PHE L 76 TRP 0.004 0.001 TRP G 84 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00528 (39312) covalent geometry : angle 0.65399 (53400) hydrogen bonds : bond 0.03790 ( 1800) hydrogen bonds : angle 4.89129 ( 5328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 365 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8526 (m) REVERT: A 314 ILE cc_start: 0.9332 (tt) cc_final: 0.8989 (pt) REVERT: A 383 ASP cc_start: 0.7688 (t0) cc_final: 0.7407 (t0) REVERT: A 385 SER cc_start: 0.8802 (t) cc_final: 0.8506 (p) REVERT: A 393 MET cc_start: 0.8827 (mmm) cc_final: 0.7960 (mtt) REVERT: B 240 MET cc_start: 0.9273 (mmm) cc_final: 0.9036 (mmm) REVERT: B 323 MET cc_start: 0.8026 (mmm) cc_final: 0.7685 (mmm) REVERT: B 393 MET cc_start: 0.8068 (mtp) cc_final: 0.7795 (mtt) REVERT: B 415 LEU cc_start: 0.9255 (tp) cc_final: 0.8921 (tp) REVERT: B 419 MET cc_start: 0.9214 (mpp) cc_final: 0.8730 (mpp) REVERT: C 54 ASP cc_start: 0.8440 (m-30) cc_final: 0.7892 (p0) REVERT: C 314 ILE cc_start: 0.9197 (tt) cc_final: 0.8850 (pt) REVERT: C 393 MET cc_start: 0.8677 (mmm) cc_final: 0.8362 (mmm) REVERT: D 91 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8524 (m) REVERT: D 314 ILE cc_start: 0.9334 (tt) cc_final: 0.9000 (pt) REVERT: D 383 ASP cc_start: 0.7691 (t0) cc_final: 0.7407 (t0) REVERT: D 385 SER cc_start: 0.8775 (t) cc_final: 0.8495 (p) REVERT: D 393 MET cc_start: 0.8821 (mmm) cc_final: 0.8167 (mmm) REVERT: E 61 LYS cc_start: 0.9621 (mttt) cc_final: 0.9276 (mttm) REVERT: E 240 MET cc_start: 0.9272 (mmm) cc_final: 0.9045 (mmm) REVERT: E 323 MET cc_start: 0.8025 (mmm) cc_final: 0.7685 (mmm) REVERT: E 393 MET cc_start: 0.8064 (mtp) cc_final: 0.7593 (mtt) REVERT: E 415 LEU cc_start: 0.9254 (tp) cc_final: 0.8921 (tp) REVERT: E 419 MET cc_start: 0.9215 (mpp) cc_final: 0.8727 (mpp) REVERT: F 54 ASP cc_start: 0.8421 (m-30) cc_final: 0.7895 (p0) REVERT: F 314 ILE cc_start: 0.9186 (tt) cc_final: 0.8840 (pt) REVERT: F 393 MET cc_start: 0.8676 (mmm) cc_final: 0.8364 (mmm) REVERT: G 91 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8524 (m) REVERT: G 126 GLU cc_start: 0.8584 (pt0) cc_final: 0.8158 (pt0) REVERT: G 314 ILE cc_start: 0.9342 (tt) cc_final: 0.9006 (pt) REVERT: G 383 ASP cc_start: 0.7702 (t0) cc_final: 0.7414 (t0) REVERT: G 385 SER cc_start: 0.8778 (t) cc_final: 0.8497 (p) REVERT: G 393 MET cc_start: 0.8814 (mmm) cc_final: 0.8157 (mmm) REVERT: H 61 LYS cc_start: 0.9619 (mttt) cc_final: 0.9275 (mttm) REVERT: H 240 MET cc_start: 0.9272 (mmm) cc_final: 0.9045 (mmm) REVERT: H 323 MET cc_start: 0.8017 (mmm) cc_final: 0.7681 (mmm) REVERT: H 393 MET cc_start: 0.8071 (mtp) cc_final: 0.7593 (mtt) REVERT: H 415 LEU cc_start: 0.9253 (tp) cc_final: 0.8911 (tp) REVERT: H 419 MET cc_start: 0.9215 (mpp) cc_final: 0.8731 (mpp) REVERT: I 54 ASP cc_start: 0.8415 (m-30) cc_final: 0.7880 (p0) REVERT: I 314 ILE cc_start: 0.9205 (tt) cc_final: 0.8847 (pt) REVERT: I 393 MET cc_start: 0.8685 (mmm) cc_final: 0.8367 (mmm) REVERT: J 91 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8523 (m) REVERT: J 314 ILE cc_start: 0.9338 (tt) cc_final: 0.9001 (pt) REVERT: J 383 ASP cc_start: 0.7696 (t0) cc_final: 0.7406 (t0) REVERT: J 385 SER cc_start: 0.8770 (t) cc_final: 0.8505 (p) REVERT: J 393 MET cc_start: 0.8821 (mmm) cc_final: 0.7950 (mtt) REVERT: K 61 LYS cc_start: 0.9629 (mttt) cc_final: 0.9290 (mttm) REVERT: K 240 MET cc_start: 0.9276 (mmm) cc_final: 0.9044 (mmm) REVERT: K 323 MET cc_start: 0.8030 (mmm) cc_final: 0.7690 (mmm) REVERT: K 393 MET cc_start: 0.8772 (mmm) cc_final: 0.8379 (mtp) REVERT: L 54 ASP cc_start: 0.8433 (m-30) cc_final: 0.7886 (p0) REVERT: L 314 ILE cc_start: 0.9209 (tt) cc_final: 0.8847 (pt) REVERT: L 393 MET cc_start: 0.8702 (mmm) cc_final: 0.8232 (mmm) REVERT: L 419 MET cc_start: 0.9090 (mpp) cc_final: 0.8572 (pmm) outliers start: 159 outliers final: 133 residues processed: 487 average time/residue: 0.1954 time to fit residues: 166.6508 Evaluate side-chains 492 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 355 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 82 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 437 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 379 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 470 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 439 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.058481 restraints weight = 110011.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.060714 restraints weight = 56632.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.062157 restraints weight = 37621.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.063074 restraints weight = 29154.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063643 restraints weight = 24900.431| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 39312 Z= 0.214 Angle : 0.648 10.315 53400 Z= 0.315 Chirality : 0.044 0.163 6060 Planarity : 0.004 0.064 6888 Dihedral : 4.532 18.828 5280 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.55 % Allowed : 13.00 % Favored : 82.45 % 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: 0.47 (0.13), residues: 4908 helix: 1.75 (0.11), residues: 2208 sheet: -1.16 (0.18), residues: 660 loop : -0.73 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 78 TYR 0.023 0.002 TYR A 125 PHE 0.024 0.001 PHE C 76 TRP 0.005 0.001 TRP J 283 HIS 0.004 0.001 HIS L 221 Details of bonding type rmsd covalent geometry : bond 0.00481 (39312) covalent geometry : angle 0.64805 (53400) hydrogen bonds : bond 0.03714 ( 1800) hydrogen bonds : angle 4.82513 ( 5328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 397 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8521 (m) REVERT: A 314 ILE cc_start: 0.9313 (tt) cc_final: 0.8943 (pt) REVERT: A 383 ASP cc_start: 0.7611 (t0) cc_final: 0.7312 (t0) REVERT: A 385 SER cc_start: 0.8699 (t) cc_final: 0.8305 (p) REVERT: A 393 MET cc_start: 0.8808 (mmm) cc_final: 0.7923 (mtt) REVERT: B 61 LYS cc_start: 0.9635 (mttt) cc_final: 0.9282 (mttm) REVERT: B 240 MET cc_start: 0.9281 (mmm) cc_final: 0.9065 (mmm) REVERT: B 323 MET cc_start: 0.8190 (mmm) cc_final: 0.7822 (mmm) REVERT: B 415 LEU cc_start: 0.8989 (tp) cc_final: 0.8490 (tp) REVERT: C 54 ASP cc_start: 0.8460 (m-30) cc_final: 0.7918 (p0) REVERT: C 314 ILE cc_start: 0.9145 (tt) cc_final: 0.8771 (pt) REVERT: C 393 MET cc_start: 0.8472 (mmm) cc_final: 0.8222 (mmm) REVERT: D 91 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8527 (m) REVERT: D 314 ILE cc_start: 0.9317 (tt) cc_final: 0.8956 (pt) REVERT: D 383 ASP cc_start: 0.7699 (t0) cc_final: 0.7398 (t0) REVERT: D 385 SER cc_start: 0.8784 (t) cc_final: 0.8441 (p) REVERT: D 393 MET cc_start: 0.8844 (mmm) cc_final: 0.8170 (mmm) REVERT: E 61 LYS cc_start: 0.9635 (mttt) cc_final: 0.9284 (mttm) REVERT: E 240 MET cc_start: 0.9281 (mmm) cc_final: 0.9072 (mmm) REVERT: E 323 MET cc_start: 0.8183 (mmm) cc_final: 0.7819 (mmm) REVERT: E 393 MET cc_start: 0.8065 (mtp) cc_final: 0.7575 (mtt) REVERT: E 415 LEU cc_start: 0.8987 (tp) cc_final: 0.8484 (tp) REVERT: F 54 ASP cc_start: 0.8441 (m-30) cc_final: 0.7920 (p0) REVERT: F 314 ILE cc_start: 0.9131 (tt) cc_final: 0.8763 (pt) REVERT: F 393 MET cc_start: 0.8473 (mmm) cc_final: 0.8226 (mmm) REVERT: G 91 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8531 (m) REVERT: G 126 GLU cc_start: 0.8677 (pt0) cc_final: 0.8255 (pt0) REVERT: G 314 ILE cc_start: 0.9320 (tt) cc_final: 0.8958 (pt) REVERT: G 383 ASP cc_start: 0.7717 (t0) cc_final: 0.7407 (t0) REVERT: G 385 SER cc_start: 0.8787 (t) cc_final: 0.8441 (p) REVERT: G 393 MET cc_start: 0.8844 (mmm) cc_final: 0.8166 (mmm) REVERT: H 61 LYS cc_start: 0.9633 (mttt) cc_final: 0.9282 (mttm) REVERT: H 240 MET cc_start: 0.9354 (mmm) cc_final: 0.9134 (mmm) REVERT: H 323 MET cc_start: 0.7968 (mmm) cc_final: 0.7632 (mmm) REVERT: H 393 MET cc_start: 0.8067 (mtp) cc_final: 0.7578 (mtt) REVERT: H 415 LEU cc_start: 0.8983 (tp) cc_final: 0.8475 (tp) REVERT: I 54 ASP cc_start: 0.8432 (m-30) cc_final: 0.7908 (p0) REVERT: I 314 ILE cc_start: 0.9146 (tt) cc_final: 0.8772 (pt) REVERT: I 393 MET cc_start: 0.8480 (mmm) cc_final: 0.8231 (mmm) REVERT: J 91 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8530 (m) REVERT: J 314 ILE cc_start: 0.9313 (tt) cc_final: 0.8953 (pt) REVERT: J 383 ASP cc_start: 0.7706 (t0) cc_final: 0.7406 (t0) REVERT: J 385 SER cc_start: 0.8779 (t) cc_final: 0.8448 (p) REVERT: J 393 MET cc_start: 0.8857 (mmm) cc_final: 0.7972 (mtt) REVERT: K 61 LYS cc_start: 0.9635 (mttt) cc_final: 0.9283 (mttm) REVERT: K 240 MET cc_start: 0.9357 (mmm) cc_final: 0.9130 (mmm) REVERT: K 323 MET cc_start: 0.7978 (mmm) cc_final: 0.7643 (mmm) REVERT: K 393 MET cc_start: 0.8780 (mmm) cc_final: 0.8337 (mtp) REVERT: L 54 ASP cc_start: 0.8453 (m-30) cc_final: 0.7914 (p0) REVERT: L 314 ILE cc_start: 0.9151 (tt) cc_final: 0.8777 (pt) REVERT: L 393 MET cc_start: 0.8701 (mmm) cc_final: 0.8277 (mmm) outliers start: 186 outliers final: 140 residues processed: 540 average time/residue: 0.1920 time to fit residues: 182.2730 Evaluate side-chains 495 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 351 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 207 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 380 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 402 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 chunk 387 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.059125 restraints weight = 109264.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.061383 restraints weight = 56098.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062847 restraints weight = 37172.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063756 restraints weight = 28750.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.064336 restraints weight = 24588.038| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39312 Z= 0.175 Angle : 0.639 13.992 53400 Z= 0.308 Chirality : 0.044 0.187 6060 Planarity : 0.004 0.062 6888 Dihedral : 4.523 18.311 5280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.67 % Allowed : 14.39 % Favored : 81.94 % 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: 0.45 (0.13), residues: 4908 helix: 1.85 (0.11), residues: 2124 sheet: -1.08 (0.18), residues: 660 loop : -0.83 (0.15), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 78 TYR 0.023 0.002 TYR A 125 PHE 0.028 0.001 PHE H 76 TRP 0.004 0.001 TRP D 283 HIS 0.003 0.001 HIS L 60 Details of bonding type rmsd covalent geometry : bond 0.00397 (39312) covalent geometry : angle 0.63863 (53400) hydrogen bonds : bond 0.03601 ( 1800) hydrogen bonds : angle 4.74547 ( 5328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 388 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 314 ILE cc_start: 0.9354 (tt) cc_final: 0.8962 (pt) REVERT: A 315 ASP cc_start: 0.8673 (p0) cc_final: 0.8391 (p0) REVERT: A 383 ASP cc_start: 0.7696 (t0) cc_final: 0.7470 (t0) REVERT: A 385 SER cc_start: 0.8786 (t) cc_final: 0.8355 (p) REVERT: A 393 MET cc_start: 0.8748 (mmm) cc_final: 0.8013 (mmm) REVERT: B 61 LYS cc_start: 0.9631 (mttt) cc_final: 0.9275 (mttm) REVERT: B 240 MET cc_start: 0.9323 (mmm) cc_final: 0.9095 (mmm) REVERT: B 323 MET cc_start: 0.8025 (mmm) cc_final: 0.7661 (mmm) REVERT: B 393 MET cc_start: 0.7958 (mtp) cc_final: 0.7550 (mtt) REVERT: B 415 LEU cc_start: 0.8743 (tp) cc_final: 0.8407 (tp) REVERT: C 54 ASP cc_start: 0.8430 (m-30) cc_final: 0.7907 (p0) REVERT: C 314 ILE cc_start: 0.9122 (tt) cc_final: 0.8772 (pt) REVERT: C 393 MET cc_start: 0.8389 (mmm) cc_final: 0.8138 (mmm) REVERT: D 91 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8610 (m) REVERT: D 314 ILE cc_start: 0.9355 (tt) cc_final: 0.8973 (pt) REVERT: D 383 ASP cc_start: 0.7662 (t0) cc_final: 0.7335 (t0) REVERT: D 385 SER cc_start: 0.8780 (t) cc_final: 0.8416 (p) REVERT: D 393 MET cc_start: 0.8837 (mmm) cc_final: 0.8159 (mmm) REVERT: E 61 LYS cc_start: 0.9630 (mttt) cc_final: 0.9279 (mttm) REVERT: E 240 MET cc_start: 0.9324 (mmm) cc_final: 0.9104 (mmm) REVERT: E 323 MET cc_start: 0.8019 (mmm) cc_final: 0.7655 (mmm) REVERT: E 415 LEU cc_start: 0.8743 (tp) cc_final: 0.8406 (tp) REVERT: F 54 ASP cc_start: 0.8422 (m-30) cc_final: 0.7908 (p0) REVERT: F 314 ILE cc_start: 0.9106 (tt) cc_final: 0.8759 (pt) REVERT: F 393 MET cc_start: 0.8384 (mmm) cc_final: 0.8127 (mmm) REVERT: G 91 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8607 (m) REVERT: G 126 GLU cc_start: 0.8676 (pt0) cc_final: 0.8247 (pt0) REVERT: G 314 ILE cc_start: 0.9357 (tt) cc_final: 0.8975 (pt) REVERT: G 383 ASP cc_start: 0.7686 (t0) cc_final: 0.7351 (t0) REVERT: G 385 SER cc_start: 0.8777 (t) cc_final: 0.8419 (p) REVERT: G 393 MET cc_start: 0.8836 (mmm) cc_final: 0.8152 (mmm) REVERT: H 61 LYS cc_start: 0.9629 (mttt) cc_final: 0.9276 (mttm) REVERT: H 240 MET cc_start: 0.9324 (mmm) cc_final: 0.9109 (mmm) REVERT: H 323 MET cc_start: 0.8010 (mmm) cc_final: 0.7649 (mmm) REVERT: H 415 LEU cc_start: 0.8738 (tp) cc_final: 0.8399 (tp) REVERT: I 54 ASP cc_start: 0.8406 (m-30) cc_final: 0.7897 (p0) REVERT: I 314 ILE cc_start: 0.9124 (tt) cc_final: 0.8772 (pt) REVERT: I 393 MET cc_start: 0.8396 (mmm) cc_final: 0.8140 (mmm) REVERT: J 91 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8610 (m) REVERT: J 314 ILE cc_start: 0.9350 (tt) cc_final: 0.8969 (pt) REVERT: J 383 ASP cc_start: 0.7662 (t0) cc_final: 0.7333 (t0) REVERT: J 385 SER cc_start: 0.8772 (t) cc_final: 0.8410 (p) REVERT: J 393 MET cc_start: 0.8849 (mmm) cc_final: 0.8190 (mmm) REVERT: K 61 LYS cc_start: 0.9632 (mttt) cc_final: 0.9276 (mttm) REVERT: K 240 MET cc_start: 0.9320 (mmm) cc_final: 0.9103 (mmm) REVERT: K 323 MET cc_start: 0.8021 (mmm) cc_final: 0.7661 (mmm) REVERT: K 393 MET cc_start: 0.8756 (mmm) cc_final: 0.8371 (mtp) REVERT: L 54 ASP cc_start: 0.8423 (m-30) cc_final: 0.7898 (p0) REVERT: L 314 ILE cc_start: 0.9131 (tt) cc_final: 0.8767 (pt) REVERT: L 393 MET cc_start: 0.8607 (mmm) cc_final: 0.8220 (mmm) outliers start: 150 outliers final: 135 residues processed: 507 average time/residue: 0.1968 time to fit residues: 175.5045 Evaluate side-chains 519 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 380 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 112 optimal weight: 6.9990 chunk 401 optimal weight: 20.0000 chunk 74 optimal weight: 0.0070 chunk 36 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 467 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.059874 restraints weight = 108525.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062157 restraints weight = 55415.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.063636 restraints weight = 36612.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064572 restraints weight = 28287.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065100 restraints weight = 24115.202| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39312 Z= 0.145 Angle : 0.631 15.205 53400 Z= 0.300 Chirality : 0.043 0.166 6060 Planarity : 0.004 0.059 6888 Dihedral : 4.445 17.712 5280 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.96 % Allowed : 14.71 % Favored : 81.33 % 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: 0.50 (0.13), residues: 4908 helix: 1.83 (0.11), residues: 2172 sheet: -0.99 (0.19), residues: 660 loop : -0.80 (0.15), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 381 TYR 0.025 0.001 TYR A 125 PHE 0.028 0.001 PHE E 76 TRP 0.005 0.001 TRP K 259 HIS 0.003 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00331 (39312) covalent geometry : angle 0.63117 (53400) hydrogen bonds : bond 0.03412 ( 1800) hydrogen bonds : angle 4.64029 ( 5328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 391 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8601 (m) REVERT: A 314 ILE cc_start: 0.9299 (tt) cc_final: 0.8901 (pt) REVERT: A 383 ASP cc_start: 0.7717 (t0) cc_final: 0.7404 (t0) REVERT: A 385 SER cc_start: 0.8855 (t) cc_final: 0.8543 (p) REVERT: A 393 MET cc_start: 0.8608 (mmm) cc_final: 0.8365 (mmt) REVERT: B 61 LYS cc_start: 0.9642 (mttt) cc_final: 0.9292 (mttm) REVERT: B 240 MET cc_start: 0.9299 (mmm) cc_final: 0.9089 (mmm) REVERT: B 323 MET cc_start: 0.8307 (mmm) cc_final: 0.7848 (mmm) REVERT: B 415 LEU cc_start: 0.8605 (tp) cc_final: 0.8154 (tp) REVERT: C 54 ASP cc_start: 0.8422 (m-30) cc_final: 0.7887 (p0) REVERT: C 314 ILE cc_start: 0.8926 (tt) cc_final: 0.8605 (pt) REVERT: C 393 MET cc_start: 0.8378 (mmm) cc_final: 0.8145 (mmm) REVERT: D 91 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8612 (m) REVERT: D 314 ILE cc_start: 0.9342 (tt) cc_final: 0.8926 (pt) REVERT: D 383 ASP cc_start: 0.7604 (t0) cc_final: 0.7248 (t0) REVERT: D 385 SER cc_start: 0.8765 (t) cc_final: 0.8396 (p) REVERT: D 393 MET cc_start: 0.8837 (mmm) cc_final: 0.8156 (mmm) REVERT: E 61 LYS cc_start: 0.9632 (mttt) cc_final: 0.9266 (mttm) REVERT: E 240 MET cc_start: 0.9297 (mmm) cc_final: 0.9058 (mmm) REVERT: E 323 MET cc_start: 0.8302 (mmm) cc_final: 0.7846 (mmm) REVERT: E 393 MET cc_start: 0.7970 (mtp) cc_final: 0.7579 (mtt) REVERT: E 415 LEU cc_start: 0.8599 (tp) cc_final: 0.8151 (tp) REVERT: F 54 ASP cc_start: 0.8402 (m-30) cc_final: 0.7887 (p0) REVERT: F 314 ILE cc_start: 0.8889 (tt) cc_final: 0.8562 (pt) REVERT: F 393 MET cc_start: 0.8373 (mmm) cc_final: 0.8137 (mmm) REVERT: G 91 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8612 (m) REVERT: G 126 GLU cc_start: 0.8688 (pt0) cc_final: 0.8243 (pt0) REVERT: G 314 ILE cc_start: 0.9346 (tt) cc_final: 0.8925 (pt) REVERT: G 383 ASP cc_start: 0.7631 (t0) cc_final: 0.7266 (t0) REVERT: G 385 SER cc_start: 0.8771 (t) cc_final: 0.8401 (p) REVERT: G 393 MET cc_start: 0.8834 (mmm) cc_final: 0.8155 (mmm) REVERT: H 61 LYS cc_start: 0.9630 (mttt) cc_final: 0.9263 (mttm) REVERT: H 240 MET cc_start: 0.9288 (mmm) cc_final: 0.9058 (mmm) REVERT: H 323 MET cc_start: 0.8294 (mmm) cc_final: 0.7841 (mmm) REVERT: H 415 LEU cc_start: 0.8592 (tp) cc_final: 0.8139 (tp) REVERT: I 54 ASP cc_start: 0.8398 (m-30) cc_final: 0.7875 (p0) REVERT: I 314 ILE cc_start: 0.8931 (tt) cc_final: 0.8610 (pt) REVERT: I 393 MET cc_start: 0.8378 (mmm) cc_final: 0.8132 (mmm) REVERT: J 91 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8612 (m) REVERT: J 314 ILE cc_start: 0.9339 (tt) cc_final: 0.8923 (pt) REVERT: J 383 ASP cc_start: 0.7612 (t0) cc_final: 0.7254 (t0) REVERT: J 385 SER cc_start: 0.8767 (t) cc_final: 0.8399 (p) REVERT: J 393 MET cc_start: 0.8829 (mmm) cc_final: 0.7911 (mtt) REVERT: K 61 LYS cc_start: 0.9634 (mttt) cc_final: 0.9264 (mttm) REVERT: K 240 MET cc_start: 0.9297 (mmm) cc_final: 0.9060 (mmm) REVERT: K 323 MET cc_start: 0.8304 (mmm) cc_final: 0.7845 (mmm) REVERT: K 393 MET cc_start: 0.8756 (mmm) cc_final: 0.8400 (mtp) REVERT: L 54 ASP cc_start: 0.8417 (m-30) cc_final: 0.7881 (p0) REVERT: L 314 ILE cc_start: 0.8942 (tt) cc_final: 0.8616 (pt) REVERT: L 333 PHE cc_start: 0.6764 (t80) cc_final: 0.6312 (t80) REVERT: L 393 MET cc_start: 0.8599 (mmm) cc_final: 0.8226 (mmm) outliers start: 162 outliers final: 127 residues processed: 509 average time/residue: 0.1915 time to fit residues: 171.6451 Evaluate side-chains 500 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 369 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 399 optimal weight: 30.0000 chunk 154 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 438 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 480 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 353 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 460 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.079063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059014 restraints weight = 109511.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.061249 restraints weight = 56319.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062706 restraints weight = 37371.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063599 restraints weight = 28970.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.064173 restraints weight = 24828.059| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39312 Z= 0.196 Angle : 0.677 15.558 53400 Z= 0.323 Chirality : 0.044 0.164 6060 Planarity : 0.004 0.060 6888 Dihedral : 4.478 17.703 5280 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.57 % Allowed : 15.52 % Favored : 80.91 % 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: 0.57 (0.13), residues: 4908 helix: 1.79 (0.11), residues: 2244 sheet: -0.99 (0.19), residues: 660 loop : -0.73 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 381 TYR 0.029 0.002 TYR A 125 PHE 0.028 0.001 PHE E 76 TRP 0.005 0.001 TRP D 283 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00444 (39312) covalent geometry : angle 0.67707 (53400) hydrogen bonds : bond 0.03633 ( 1800) hydrogen bonds : angle 4.70692 ( 5328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 362 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 383 ASP cc_start: 0.7736 (t0) cc_final: 0.7447 (t0) REVERT: A 385 SER cc_start: 0.8809 (t) cc_final: 0.8465 (p) REVERT: A 391 MET cc_start: 0.9433 (ttm) cc_final: 0.7733 (ttp) REVERT: B 61 LYS cc_start: 0.9626 (mttt) cc_final: 0.9266 (mttm) REVERT: B 240 MET cc_start: 0.9355 (mmm) cc_final: 0.9133 (mmm) REVERT: B 323 MET cc_start: 0.8293 (mmm) cc_final: 0.7958 (mmm) REVERT: B 415 LEU cc_start: 0.8458 (tp) cc_final: 0.7953 (tp) REVERT: C 54 ASP cc_start: 0.8437 (m-30) cc_final: 0.7894 (p0) REVERT: C 237 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: C 314 ILE cc_start: 0.8979 (tt) cc_final: 0.8670 (pt) REVERT: C 323 MET cc_start: 0.7734 (mmm) cc_final: 0.7496 (mmm) REVERT: C 393 MET cc_start: 0.8399 (mmm) cc_final: 0.8145 (mmm) REVERT: D 91 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8628 (m) REVERT: D 383 ASP cc_start: 0.7583 (t0) cc_final: 0.7244 (t0) REVERT: D 385 SER cc_start: 0.8870 (t) cc_final: 0.8443 (p) REVERT: D 393 MET cc_start: 0.8628 (mmm) cc_final: 0.7808 (mtt) REVERT: E 61 LYS cc_start: 0.9629 (mttt) cc_final: 0.9272 (mttm) REVERT: E 240 MET cc_start: 0.9352 (mmm) cc_final: 0.9135 (mmm) REVERT: E 323 MET cc_start: 0.8285 (mmm) cc_final: 0.7954 (mmm) REVERT: E 415 LEU cc_start: 0.8453 (tp) cc_final: 0.7954 (tp) REVERT: F 54 ASP cc_start: 0.8422 (m-30) cc_final: 0.7887 (p0) REVERT: F 314 ILE cc_start: 0.8974 (tt) cc_final: 0.8666 (pt) REVERT: F 323 MET cc_start: 0.7741 (mmm) cc_final: 0.7500 (mmm) REVERT: F 393 MET cc_start: 0.8378 (mmm) cc_final: 0.8140 (mmm) REVERT: G 91 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8629 (m) REVERT: G 126 GLU cc_start: 0.8686 (pt0) cc_final: 0.8390 (pt0) REVERT: G 383 ASP cc_start: 0.7607 (t0) cc_final: 0.7253 (t0) REVERT: G 385 SER cc_start: 0.8874 (t) cc_final: 0.8448 (p) REVERT: G 393 MET cc_start: 0.8629 (mmm) cc_final: 0.7812 (mtt) REVERT: H 61 LYS cc_start: 0.9627 (mttt) cc_final: 0.9270 (mttm) REVERT: H 240 MET cc_start: 0.9341 (mmm) cc_final: 0.9133 (mmm) REVERT: H 323 MET cc_start: 0.8324 (mmm) cc_final: 0.7880 (mmm) REVERT: H 415 LEU cc_start: 0.8451 (tp) cc_final: 0.7949 (tp) REVERT: I 54 ASP cc_start: 0.8416 (m-30) cc_final: 0.7884 (p0) REVERT: I 314 ILE cc_start: 0.8987 (tt) cc_final: 0.8673 (pt) REVERT: I 323 MET cc_start: 0.7748 (mmm) cc_final: 0.7512 (mmm) REVERT: I 393 MET cc_start: 0.8378 (mmm) cc_final: 0.8149 (mmm) REVERT: J 91 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8628 (m) REVERT: J 383 ASP cc_start: 0.7590 (t0) cc_final: 0.7243 (t0) REVERT: J 385 SER cc_start: 0.8861 (t) cc_final: 0.8434 (p) REVERT: J 393 MET cc_start: 0.8634 (mmm) cc_final: 0.7833 (mtt) REVERT: K 61 LYS cc_start: 0.9627 (mttt) cc_final: 0.9269 (mttm) REVERT: K 240 MET cc_start: 0.9346 (mmm) cc_final: 0.9132 (mmm) REVERT: K 323 MET cc_start: 0.8202 (mmm) cc_final: 0.7907 (mmm) REVERT: K 393 MET cc_start: 0.8766 (mmm) cc_final: 0.8408 (mtp) REVERT: L 54 ASP cc_start: 0.8438 (m-30) cc_final: 0.7886 (p0) REVERT: L 314 ILE cc_start: 0.9013 (tt) cc_final: 0.8706 (pt) REVERT: L 323 MET cc_start: 0.7741 (mmm) cc_final: 0.7505 (mmm) REVERT: L 393 MET cc_start: 0.8609 (mmm) cc_final: 0.8235 (mmm) REVERT: L 415 LEU cc_start: 0.9150 (tp) cc_final: 0.8933 (tp) outliers start: 146 outliers final: 131 residues processed: 483 average time/residue: 0.1851 time to fit residues: 159.9772 Evaluate side-chains 484 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 348 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 287 optimal weight: 30.0000 chunk 234 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 392 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060206 restraints weight = 107938.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.062453 restraints weight = 55078.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063922 restraints weight = 36369.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.064855 restraints weight = 28059.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.065390 restraints weight = 23900.495| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39312 Z= 0.139 Angle : 0.673 18.551 53400 Z= 0.314 Chirality : 0.044 0.186 6060 Planarity : 0.004 0.060 6888 Dihedral : 4.451 19.590 5280 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.27 % Allowed : 16.15 % Favored : 80.57 % 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: 0.61 (0.13), residues: 4908 helix: 1.92 (0.12), residues: 2172 sheet: -0.93 (0.19), residues: 660 loop : -0.76 (0.15), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 381 TYR 0.029 0.001 TYR A 125 PHE 0.024 0.001 PHE E 76 TRP 0.004 0.001 TRP J 283 HIS 0.003 0.001 HIS L 60 Details of bonding type rmsd covalent geometry : bond 0.00320 (39312) covalent geometry : angle 0.67349 (53400) hydrogen bonds : bond 0.03403 ( 1800) hydrogen bonds : angle 4.63087 ( 5328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 379 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 91 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 270 VAL cc_start: 0.9268 (t) cc_final: 0.8956 (p) REVERT: A 383 ASP cc_start: 0.7634 (t0) cc_final: 0.7225 (t0) REVERT: A 385 SER cc_start: 0.8845 (t) cc_final: 0.8503 (p) REVERT: A 393 MET cc_start: 0.8464 (mmt) cc_final: 0.7811 (mmm) REVERT: B 240 MET cc_start: 0.9321 (mmm) cc_final: 0.9092 (mmm) REVERT: B 323 MET cc_start: 0.8404 (mmm) cc_final: 0.8047 (mmm) REVERT: B 415 LEU cc_start: 0.8389 (tp) cc_final: 0.7924 (tp) REVERT: C 54 ASP cc_start: 0.8417 (m-30) cc_final: 0.7866 (p0) REVERT: C 237 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: C 270 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 314 ILE cc_start: 0.8951 (tt) cc_final: 0.8612 (pt) REVERT: C 323 MET cc_start: 0.7721 (mmm) cc_final: 0.7479 (mmm) REVERT: C 393 MET cc_start: 0.8397 (mmm) cc_final: 0.8142 (mmm) REVERT: D 91 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8625 (m) REVERT: D 270 VAL cc_start: 0.9270 (t) cc_final: 0.8965 (p) REVERT: D 383 ASP cc_start: 0.7575 (t0) cc_final: 0.7365 (t0) REVERT: D 385 SER cc_start: 0.8838 (t) cc_final: 0.8388 (p) REVERT: D 391 MET cc_start: 0.9588 (tpp) cc_final: 0.9379 (tpp) REVERT: D 393 MET cc_start: 0.8691 (mmm) cc_final: 0.7802 (mtt) REVERT: E 240 MET cc_start: 0.9312 (mmm) cc_final: 0.9088 (mmm) REVERT: E 323 MET cc_start: 0.8391 (mmm) cc_final: 0.8038 (mmm) REVERT: E 415 LEU cc_start: 0.8382 (tp) cc_final: 0.7918 (tp) REVERT: F 54 ASP cc_start: 0.8394 (m-30) cc_final: 0.7861 (p0) REVERT: F 270 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8612 (p) REVERT: F 314 ILE cc_start: 0.8915 (tt) cc_final: 0.8564 (pt) REVERT: F 323 MET cc_start: 0.7726 (mmm) cc_final: 0.7483 (mmm) REVERT: F 393 MET cc_start: 0.8393 (mmm) cc_final: 0.8133 (mmm) REVERT: G 91 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8614 (m) REVERT: G 126 GLU cc_start: 0.8679 (pt0) cc_final: 0.8195 (pt0) REVERT: G 270 VAL cc_start: 0.9274 (t) cc_final: 0.8962 (p) REVERT: G 383 ASP cc_start: 0.7601 (t0) cc_final: 0.7380 (t0) REVERT: G 385 SER cc_start: 0.8841 (t) cc_final: 0.8401 (p) REVERT: G 391 MET cc_start: 0.9590 (tpp) cc_final: 0.9386 (tpp) REVERT: G 393 MET cc_start: 0.8614 (mmm) cc_final: 0.7836 (mtt) REVERT: H 240 MET cc_start: 0.9309 (mmm) cc_final: 0.9084 (mmm) REVERT: H 323 MET cc_start: 0.8391 (mmm) cc_final: 0.8035 (mmm) REVERT: H 415 LEU cc_start: 0.8375 (tp) cc_final: 0.7908 (tp) REVERT: I 54 ASP cc_start: 0.8385 (m-30) cc_final: 0.7851 (p0) REVERT: I 270 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8609 (p) REVERT: I 314 ILE cc_start: 0.8958 (tt) cc_final: 0.8614 (pt) REVERT: I 323 MET cc_start: 0.7734 (mmm) cc_final: 0.7493 (mmm) REVERT: I 393 MET cc_start: 0.8394 (mmm) cc_final: 0.8141 (mmm) REVERT: J 91 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8630 (m) REVERT: J 270 VAL cc_start: 0.9273 (t) cc_final: 0.8959 (p) REVERT: J 383 ASP cc_start: 0.7582 (t0) cc_final: 0.7366 (t0) REVERT: J 385 SER cc_start: 0.8835 (t) cc_final: 0.8393 (p) REVERT: J 391 MET cc_start: 0.9585 (tpp) cc_final: 0.9376 (tpp) REVERT: J 393 MET cc_start: 0.8727 (mmm) cc_final: 0.7870 (mtt) REVERT: K 240 MET cc_start: 0.9312 (mmm) cc_final: 0.9083 (mmm) REVERT: K 323 MET cc_start: 0.8394 (mmm) cc_final: 0.8042 (mmm) REVERT: K 393 MET cc_start: 0.8760 (mmm) cc_final: 0.8408 (mtp) REVERT: L 54 ASP cc_start: 0.8417 (m-30) cc_final: 0.7858 (p0) REVERT: L 270 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8604 (p) REVERT: L 314 ILE cc_start: 0.8960 (tt) cc_final: 0.8614 (pt) REVERT: L 323 MET cc_start: 0.7730 (mmm) cc_final: 0.7490 (mmm) REVERT: L 333 PHE cc_start: 0.6711 (t80) cc_final: 0.6037 (t80) REVERT: L 393 MET cc_start: 0.8545 (mmm) cc_final: 0.8099 (mmm) REVERT: L 415 LEU cc_start: 0.9316 (tp) cc_final: 0.9064 (tp) REVERT: L 419 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9003 (pmm) outliers start: 134 outliers final: 120 residues processed: 477 average time/residue: 0.1856 time to fit residues: 159.1708 Evaluate side-chains 489 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 359 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 268 optimal weight: 20.0000 chunk 269 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 487 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.058826 restraints weight = 109024.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.061040 restraints weight = 56297.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062478 restraints weight = 37525.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063389 restraints weight = 29173.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.063931 restraints weight = 24975.426| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 39312 Z= 0.203 Angle : 0.695 15.392 53400 Z= 0.328 Chirality : 0.044 0.175 6060 Planarity : 0.004 0.062 6888 Dihedral : 4.497 24.551 5280 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.45 % Allowed : 16.32 % Favored : 80.23 % 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: 0.62 (0.13), residues: 4908 helix: 1.82 (0.11), residues: 2244 sheet: -0.95 (0.19), residues: 660 loop : -0.70 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 78 TYR 0.032 0.002 TYR D 125 PHE 0.027 0.002 PHE F 76 TRP 0.006 0.001 TRP J 283 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00464 (39312) covalent geometry : angle 0.69536 (53400) hydrogen bonds : bond 0.03630 ( 1800) hydrogen bonds : angle 4.70246 ( 5328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5381.38 seconds wall clock time: 94 minutes 3.26 seconds (5643.26 seconds total)