Starting phenix.real_space_refine on Sat Mar 7 13:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uol_26649/03_2026/7uol_26649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uol_26649/03_2026/7uol_26649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uol_26649/03_2026/7uol_26649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uol_26649/03_2026/7uol_26649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uol_26649/03_2026/7uol_26649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uol_26649/03_2026/7uol_26649.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 288 5.16 5 C 28008 2.51 5 N 8016 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.05s 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: 44496 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Restraints were copied for chains: E, F, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d Time building chain proxies: 3.85, per 1000 atoms: 0.09 Number of scatterers: 44496 At special positions: 0 Unit cell: (148.24, 148.24, 148.24, 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 288 16.00 O 8184 8.00 N 8016 7.00 C 28008 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: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10656 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 96 sheets defined 49.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'D' and resid 230 through 247 Processing helix chain 'D' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN D 301 " --> pdb=" O GLN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR D 339 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 377 through 380 Processing helix chain 'D' and resid 430 through 447 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'E' and resid 230 through 247 Processing helix chain 'E' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG E 267 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA E 271 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN E 301 " --> pdb=" O GLN E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR E 339 " --> pdb=" O ASN E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'E' and resid 377 through 380 Processing helix chain 'E' and resid 430 through 447 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'F' and resid 230 through 247 Processing helix chain 'F' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN F 301 " --> pdb=" O GLN F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR F 339 " --> pdb=" O ASN F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS F 358 " --> pdb=" O GLU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 Processing helix chain 'F' and resid 377 through 380 Processing helix chain 'F' and resid 430 through 447 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'J' and resid 230 through 247 Processing helix chain 'J' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG J 267 " --> pdb=" O GLU J 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP J 270 " --> pdb=" O ALA J 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA J 271 " --> pdb=" O ARG J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN J 301 " --> pdb=" O GLN J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR J 339 " --> pdb=" O ASN J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS J 358 " --> pdb=" O GLU J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 366 Processing helix chain 'J' and resid 377 through 380 Processing helix chain 'J' and resid 430 through 447 Processing helix chain 'J' and resid 449 through 454 Processing helix chain 'K' and resid 230 through 247 Processing helix chain 'K' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG K 267 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP K 270 " --> pdb=" O ALA K 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA K 271 " --> pdb=" O ARG K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN K 301 " --> pdb=" O GLN K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR K 339 " --> pdb=" O ASN K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS K 358 " --> pdb=" O GLU K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 366 Processing helix chain 'K' and resid 377 through 380 Processing helix chain 'K' and resid 430 through 447 Processing helix chain 'K' and resid 449 through 454 Processing helix chain 'L' and resid 230 through 247 Processing helix chain 'L' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG L 267 " --> pdb=" O GLU L 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP L 270 " --> pdb=" O ALA L 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA L 271 " --> pdb=" O ARG L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN L 301 " --> pdb=" O GLN L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR L 339 " --> pdb=" O ASN L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 341 through 358 removed outlier: 3.666A pdb=" N LYS L 358 " --> pdb=" O GLU L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 366 Processing helix chain 'L' and resid 377 through 380 Processing helix chain 'L' and resid 430 through 447 Processing helix chain 'L' and resid 449 through 454 Processing helix chain 'M' and resid 230 through 247 Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP M 270 " --> pdb=" O ALA M 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA M 271 " --> pdb=" O ARG M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN M 301 " --> pdb=" O GLN M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR M 339 " --> pdb=" O ASN M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 366 Processing helix chain 'M' and resid 377 through 380 Processing helix chain 'M' and resid 430 through 447 Processing helix chain 'M' and resid 449 through 454 Processing helix chain 'N' and resid 230 through 247 Processing helix chain 'N' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP N 270 " --> pdb=" O ALA N 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA N 271 " --> pdb=" O ARG N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN N 301 " --> pdb=" O GLN N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR N 339 " --> pdb=" O ASN N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS N 358 " --> pdb=" O GLU N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 366 Processing helix chain 'N' and resid 377 through 380 Processing helix chain 'N' and resid 430 through 447 Processing helix chain 'N' and resid 449 through 454 Processing helix chain 'O' and resid 230 through 247 Processing helix chain 'O' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG O 267 " --> pdb=" O GLU O 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP O 270 " --> pdb=" O ALA O 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA O 271 " --> pdb=" O ARG O 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 297 Processing helix chain 'O' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN O 301 " --> pdb=" O GLN O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR O 339 " --> pdb=" O ASN O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS O 358 " --> pdb=" O GLU O 354 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 366 Processing helix chain 'O' and resid 377 through 380 Processing helix chain 'O' and resid 430 through 447 Processing helix chain 'O' and resid 449 through 454 Processing helix chain 'P' and resid 230 through 247 Processing helix chain 'P' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG P 267 " --> pdb=" O GLU P 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA P 271 " --> pdb=" O ARG P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 297 Processing helix chain 'P' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN P 301 " --> pdb=" O GLN P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR P 339 " --> pdb=" O ASN P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS P 358 " --> pdb=" O GLU P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 366 Processing helix chain 'P' and resid 377 through 380 Processing helix chain 'P' and resid 430 through 447 Processing helix chain 'P' and resid 449 through 454 Processing helix chain 'Q' and resid 230 through 247 Processing helix chain 'Q' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG Q 267 " --> pdb=" O GLU Q 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP Q 270 " --> pdb=" O ALA Q 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA Q 271 " --> pdb=" O ARG Q 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 297 Processing helix chain 'Q' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN Q 301 " --> pdb=" O GLN Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR Q 339 " --> pdb=" O ASN Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 358 removed outlier: 3.663A pdb=" N LYS Q 358 " --> pdb=" O GLU Q 354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 362 through 366 Processing helix chain 'Q' and resid 377 through 380 Processing helix chain 'Q' and resid 430 through 447 Processing helix chain 'Q' and resid 449 through 454 Processing helix chain 'R' and resid 230 through 247 Processing helix chain 'R' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG R 267 " --> pdb=" O GLU R 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 297 Processing helix chain 'R' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN R 301 " --> pdb=" O GLN R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR R 339 " --> pdb=" O ASN R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS R 358 " --> pdb=" O GLU R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 377 through 380 Processing helix chain 'R' and resid 430 through 447 Processing helix chain 'R' and resid 449 through 454 Processing helix chain 'S' and resid 230 through 247 Processing helix chain 'S' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG S 267 " --> pdb=" O GLU S 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP S 270 " --> pdb=" O ALA S 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA S 271 " --> pdb=" O ARG S 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 282 through 297 Processing helix chain 'S' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN S 301 " --> pdb=" O GLN S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR S 339 " --> pdb=" O ASN S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS S 358 " --> pdb=" O GLU S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 362 through 366 Processing helix chain 'S' and resid 377 through 380 Processing helix chain 'S' and resid 430 through 447 Processing helix chain 'S' and resid 449 through 454 Processing helix chain 'T' and resid 230 through 247 Processing helix chain 'T' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG T 267 " --> pdb=" O GLU T 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP T 270 " --> pdb=" O ALA T 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA T 271 " --> pdb=" O ARG T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN T 301 " --> pdb=" O GLN T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR T 339 " --> pdb=" O ASN T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS T 358 " --> pdb=" O GLU T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 362 through 366 Processing helix chain 'T' and resid 377 through 380 Processing helix chain 'T' and resid 430 through 447 Processing helix chain 'T' and resid 449 through 454 Processing helix chain 'U' and resid 230 through 247 Processing helix chain 'U' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG U 267 " --> pdb=" O GLU U 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP U 270 " --> pdb=" O ALA U 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA U 271 " --> pdb=" O ARG U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 282 through 297 Processing helix chain 'U' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN U 301 " --> pdb=" O GLN U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR U 339 " --> pdb=" O ASN U 336 " (cutoff:3.500A) Processing helix chain 'U' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS U 358 " --> pdb=" O GLU U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 366 Processing helix chain 'U' and resid 377 through 380 Processing helix chain 'U' and resid 430 through 447 Processing helix chain 'U' and resid 449 through 454 Processing helix chain 'V' and resid 230 through 247 Processing helix chain 'V' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG V 267 " --> pdb=" O GLU V 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP V 270 " --> pdb=" O ALA V 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA V 271 " --> pdb=" O ARG V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN V 301 " --> pdb=" O GLN V 297 " (cutoff:3.500A) Processing helix chain 'V' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR V 339 " --> pdb=" O ASN V 336 " (cutoff:3.500A) Processing helix chain 'V' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS V 358 " --> pdb=" O GLU V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 362 through 366 Processing helix chain 'V' and resid 377 through 380 Processing helix chain 'V' and resid 430 through 447 Processing helix chain 'V' and resid 449 through 454 Processing helix chain 'W' and resid 230 through 247 Processing helix chain 'W' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG W 267 " --> pdb=" O GLU W 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP W 270 " --> pdb=" O ALA W 266 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA W 271 " --> pdb=" O ARG W 267 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 297 Processing helix chain 'W' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN W 301 " --> pdb=" O GLN W 297 " (cutoff:3.500A) Processing helix chain 'W' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR W 339 " --> pdb=" O ASN W 336 " (cutoff:3.500A) Processing helix chain 'W' and resid 341 through 358 removed outlier: 3.663A pdb=" N LYS W 358 " --> pdb=" O GLU W 354 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 366 Processing helix chain 'W' and resid 377 through 380 Processing helix chain 'W' and resid 430 through 447 Processing helix chain 'W' and resid 449 through 454 Processing helix chain 'X' and resid 230 through 247 Processing helix chain 'X' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG X 267 " --> pdb=" O GLU X 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP X 270 " --> pdb=" O ALA X 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA X 271 " --> pdb=" O ARG X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 297 through 302 removed outlier: 3.894A pdb=" N ASN X 301 " --> pdb=" O GLN X 297 " (cutoff:3.500A) Processing helix chain 'X' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR X 339 " --> pdb=" O ASN X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS X 358 " --> pdb=" O GLU X 354 " (cutoff:3.500A) Processing helix chain 'X' and resid 362 through 366 Processing helix chain 'X' and resid 377 through 380 Processing helix chain 'X' and resid 430 through 447 Processing helix chain 'X' and resid 449 through 454 Processing helix chain 'Y' and resid 230 through 247 Processing helix chain 'Y' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG Y 267 " --> pdb=" O GLU Y 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP Y 270 " --> pdb=" O ALA Y 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA Y 271 " --> pdb=" O ARG Y 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 297 Processing helix chain 'Y' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN Y 301 " --> pdb=" O GLN Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR Y 339 " --> pdb=" O ASN Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS Y 358 " --> pdb=" O GLU Y 354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 362 through 366 Processing helix chain 'Y' and resid 377 through 380 Processing helix chain 'Y' and resid 430 through 447 Processing helix chain 'Y' and resid 449 through 454 Processing helix chain 'Z' and resid 230 through 247 Processing helix chain 'Z' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP Z 270 " --> pdb=" O ALA Z 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA Z 271 " --> pdb=" O ARG Z 267 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 297 Processing helix chain 'Z' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN Z 301 " --> pdb=" O GLN Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR Z 339 " --> pdb=" O ASN Z 336 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS Z 358 " --> pdb=" O GLU Z 354 " (cutoff:3.500A) Processing helix chain 'Z' and resid 362 through 366 Processing helix chain 'Z' and resid 377 through 380 Processing helix chain 'Z' and resid 430 through 447 Processing helix chain 'Z' and resid 449 through 454 Processing helix chain 'a' and resid 230 through 247 Processing helix chain 'a' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG a 267 " --> pdb=" O GLU a 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP a 270 " --> pdb=" O ALA a 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA a 271 " --> pdb=" O ARG a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 282 through 297 Processing helix chain 'a' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN a 301 " --> pdb=" O GLN a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR a 339 " --> pdb=" O ASN a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS a 358 " --> pdb=" O GLU a 354 " (cutoff:3.500A) Processing helix chain 'a' and resid 362 through 366 Processing helix chain 'a' and resid 377 through 380 Processing helix chain 'a' and resid 430 through 447 Processing helix chain 'a' and resid 449 through 454 Processing helix chain 'b' and resid 230 through 247 Processing helix chain 'b' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG b 267 " --> pdb=" O GLU b 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP b 270 " --> pdb=" O ALA b 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA b 271 " --> pdb=" O ARG b 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 297 Processing helix chain 'b' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN b 301 " --> pdb=" O GLN b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR b 339 " --> pdb=" O ASN b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS b 358 " --> pdb=" O GLU b 354 " (cutoff:3.500A) Processing helix chain 'b' and resid 362 through 366 Processing helix chain 'b' and resid 377 through 380 Processing helix chain 'b' and resid 430 through 447 Processing helix chain 'b' and resid 449 through 454 Processing helix chain 'c' and resid 230 through 247 Processing helix chain 'c' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG c 267 " --> pdb=" O GLU c 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP c 270 " --> pdb=" O ALA c 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA c 271 " --> pdb=" O ARG c 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 282 through 297 Processing helix chain 'c' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN c 301 " --> pdb=" O GLN c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR c 339 " --> pdb=" O ASN c 336 " (cutoff:3.500A) Processing helix chain 'c' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS c 358 " --> pdb=" O GLU c 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 362 through 366 Processing helix chain 'c' and resid 377 through 380 Processing helix chain 'c' and resid 430 through 447 Processing helix chain 'c' and resid 449 through 454 Processing helix chain 'd' and resid 230 through 247 Processing helix chain 'd' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG d 267 " --> pdb=" O GLU d 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP d 270 " --> pdb=" O ALA d 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA d 271 " --> pdb=" O ARG d 267 " (cutoff:3.500A) Processing helix chain 'd' and resid 282 through 297 Processing helix chain 'd' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN d 301 " --> pdb=" O GLN d 297 " (cutoff:3.500A) Processing helix chain 'd' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR d 339 " --> pdb=" O ASN d 336 " (cutoff:3.500A) Processing helix chain 'd' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS d 358 " --> pdb=" O GLU d 354 " (cutoff:3.500A) Processing helix chain 'd' and resid 362 through 366 Processing helix chain 'd' and resid 377 through 380 Processing helix chain 'd' and resid 430 through 447 Processing helix chain 'd' and resid 449 through 454 Processing sheet with id=AA1, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA2, first strand: chain 'D' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR D 372 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR D 372 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 383 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AA5, first strand: chain 'D' and resid 323 through 325 Processing sheet with id=AA6, first strand: chain 'D' and resid 383 through 384 removed outlier: 3.926A pdb=" N PHE D 383 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E 372 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 383 through 384 removed outlier: 3.926A pdb=" N PHE D 383 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 226 through 228 Processing sheet with id=AA9, first strand: chain 'E' and resid 323 through 325 Processing sheet with id=AB1, first strand: chain 'E' and resid 383 through 384 removed outlier: 3.937A pdb=" N PHE E 383 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 372 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 383 through 384 removed outlier: 3.937A pdb=" N PHE E 383 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 323 through 325 Processing sheet with id=AB4, first strand: chain 'J' and resid 226 through 228 Processing sheet with id=AB5, first strand: chain 'J' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR J 372 " --> pdb=" O ALA J 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR J 372 " --> pdb=" O ALA J 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE K 383 " --> pdb=" O PHE J 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 303 through 305 Processing sheet with id=AB8, first strand: chain 'J' and resid 323 through 325 Processing sheet with id=AB9, first strand: chain 'J' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE J 383 " --> pdb=" O PHE L 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR L 372 " --> pdb=" O ALA L 394 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE J 383 " --> pdb=" O PHE L 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR K 372 " --> pdb=" O ALA K 394 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR K 372 " --> pdb=" O ALA K 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE L 383 " --> pdb=" O PHE K 253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 303 through 305 Processing sheet with id=AC5, first strand: chain 'K' and resid 323 through 325 Processing sheet with id=AC6, first strand: chain 'L' and resid 323 through 325 Processing sheet with id=AC7, first strand: chain 'M' and resid 226 through 228 Processing sheet with id=AC8, first strand: chain 'M' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR M 372 " --> pdb=" O ALA M 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR M 372 " --> pdb=" O ALA M 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE N 383 " --> pdb=" O PHE M 253 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 303 through 305 Processing sheet with id=AD2, first strand: chain 'M' and resid 323 through 325 Processing sheet with id=AD3, first strand: chain 'M' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE M 383 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR O 372 " --> pdb=" O ALA O 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE M 383 " --> pdb=" O PHE O 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR N 372 " --> pdb=" O ALA N 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR N 372 " --> pdb=" O ALA N 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE O 383 " --> pdb=" O PHE N 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 303 through 305 Processing sheet with id=AD8, first strand: chain 'N' and resid 323 through 325 Processing sheet with id=AD9, first strand: chain 'O' and resid 323 through 325 Processing sheet with id=AE1, first strand: chain 'P' and resid 226 through 228 Processing sheet with id=AE2, first strand: chain 'P' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR P 372 " --> pdb=" O ALA P 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR P 372 " --> pdb=" O ALA P 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE Q 383 " --> pdb=" O PHE P 253 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 303 through 305 Processing sheet with id=AE5, first strand: chain 'P' and resid 323 through 325 Processing sheet with id=AE6, first strand: chain 'P' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE P 383 " --> pdb=" O PHE R 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR R 372 " --> pdb=" O ALA R 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE P 383 " --> pdb=" O PHE R 253 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Q 372 " --> pdb=" O ALA Q 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Q 372 " --> pdb=" O ALA Q 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE R 383 " --> pdb=" O PHE Q 253 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 303 through 305 Processing sheet with id=AF2, first strand: chain 'Q' and resid 323 through 325 Processing sheet with id=AF3, first strand: chain 'R' and resid 323 through 325 Processing sheet with id=AF4, first strand: chain 'S' and resid 226 through 228 Processing sheet with id=AF5, first strand: chain 'S' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR S 372 " --> pdb=" O ALA S 394 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR S 372 " --> pdb=" O ALA S 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE T 383 " --> pdb=" O PHE S 253 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 303 through 305 Processing sheet with id=AF8, first strand: chain 'S' and resid 323 through 325 Processing sheet with id=AF9, first strand: chain 'S' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE S 383 " --> pdb=" O PHE U 253 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR U 372 " --> pdb=" O ALA U 394 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE S 383 " --> pdb=" O PHE U 253 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 333 through 334 removed outlier: 4.208A pdb=" N THR T 372 " --> pdb=" O ALA T 394 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 333 through 334 removed outlier: 4.208A pdb=" N THR T 372 " --> pdb=" O ALA T 394 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE U 383 " --> pdb=" O PHE T 253 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 303 through 305 Processing sheet with id=AG5, first strand: chain 'T' and resid 323 through 325 Processing sheet with id=AG6, first strand: chain 'U' and resid 323 through 325 Processing sheet with id=AG7, first strand: chain 'V' and resid 226 through 228 Processing sheet with id=AG8, first strand: chain 'V' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR V 372 " --> pdb=" O ALA V 394 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR V 372 " --> pdb=" O ALA V 394 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE W 383 " --> pdb=" O PHE V 253 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 303 through 305 Processing sheet with id=AH2, first strand: chain 'V' and resid 323 through 325 Processing sheet with id=AH3, first strand: chain 'V' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE V 383 " --> pdb=" O PHE X 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR X 372 " --> pdb=" O ALA X 394 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE V 383 " --> pdb=" O PHE X 253 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR W 372 " --> pdb=" O ALA W 394 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR W 372 " --> pdb=" O ALA W 394 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE X 383 " --> pdb=" O PHE W 253 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 303 through 305 Processing sheet with id=AH8, first strand: chain 'W' and resid 323 through 325 Processing sheet with id=AH9, first strand: chain 'X' and resid 323 through 325 Processing sheet with id=AI1, first strand: chain 'Y' and resid 226 through 228 Processing sheet with id=AI2, first strand: chain 'Y' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR Y 372 " --> pdb=" O ALA Y 394 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR Y 372 " --> pdb=" O ALA Y 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE Z 383 " --> pdb=" O PHE Y 253 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 303 through 305 Processing sheet with id=AI5, first strand: chain 'Y' and resid 323 through 325 Processing sheet with id=AI6, first strand: chain 'Y' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE Y 383 " --> pdb=" O PHE a 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR a 372 " --> pdb=" O ALA a 394 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Y' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE Y 383 " --> pdb=" O PHE a 253 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Z' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Z 372 " --> pdb=" O ALA Z 394 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Z' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Z 372 " --> pdb=" O ALA Z 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE a 383 " --> pdb=" O PHE Z 253 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Z' and resid 303 through 305 Processing sheet with id=AJ2, first strand: chain 'Z' and resid 323 through 325 Processing sheet with id=AJ3, first strand: chain 'a' and resid 323 through 325 Processing sheet with id=AJ4, first strand: chain 'b' and resid 226 through 228 Processing sheet with id=AJ5, first strand: chain 'b' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR b 372 " --> pdb=" O ALA b 394 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'b' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR b 372 " --> pdb=" O ALA b 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE c 383 " --> pdb=" O PHE b 253 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'b' and resid 303 through 305 Processing sheet with id=AJ8, first strand: chain 'b' and resid 323 through 325 Processing sheet with id=AJ9, first strand: chain 'b' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE b 383 " --> pdb=" O PHE d 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR d 372 " --> pdb=" O ALA d 394 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'b' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE b 383 " --> pdb=" O PHE d 253 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'c' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR c 372 " --> pdb=" O ALA c 394 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'c' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR c 372 " --> pdb=" O ALA c 394 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE d 383 " --> pdb=" O PHE c 253 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'c' and resid 303 through 305 Processing sheet with id=AK5, first strand: chain 'c' and resid 323 through 325 Processing sheet with id=AK6, first strand: chain 'd' and resid 323 through 325 2910 hydrogen bonds defined for protein. 7893 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: 13.17 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15216 1.34 - 1.46: 8723 1.46 - 1.58: 20653 1.58 - 1.70: 0 1.70 - 1.82: 552 Bond restraints: 45144 Sorted by residual: bond pdb=" N GLY U 220 " pdb=" CA GLY U 220 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.23e+00 bond pdb=" N GLY X 220 " pdb=" CA GLY X 220 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" N GLY L 220 " pdb=" CA GLY L 220 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY V 220 " pdb=" CA GLY V 220 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.07e+00 bond pdb=" N GLY J 220 " pdb=" CA GLY J 220 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.07e+00 ... (remaining 45139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 58779 1.33 - 2.67: 1679 2.67 - 4.00: 353 4.00 - 5.33: 53 5.33 - 6.67: 24 Bond angle restraints: 60888 Sorted by residual: angle pdb=" N ASN M 359 " pdb=" CA ASN M 359 " pdb=" C ASN M 359 " ideal model delta sigma weight residual 113.01 117.12 -4.11 1.20e+00 6.94e-01 1.17e+01 angle pdb=" N ASN S 359 " pdb=" CA ASN S 359 " pdb=" C ASN S 359 " ideal model delta sigma weight residual 113.01 117.11 -4.10 1.20e+00 6.94e-01 1.17e+01 angle pdb=" N ASN V 359 " pdb=" CA ASN V 359 " pdb=" C ASN V 359 " ideal model delta sigma weight residual 113.01 117.08 -4.07 1.20e+00 6.94e-01 1.15e+01 angle pdb=" N ASN T 359 " pdb=" CA ASN T 359 " pdb=" C ASN T 359 " ideal model delta sigma weight residual 113.01 117.08 -4.07 1.20e+00 6.94e-01 1.15e+01 angle pdb=" N ASN D 359 " pdb=" CA ASN D 359 " pdb=" C ASN D 359 " ideal model delta sigma weight residual 113.01 117.08 -4.07 1.20e+00 6.94e-01 1.15e+01 ... (remaining 60883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 24912 15.99 - 31.99: 2328 31.99 - 47.98: 576 47.98 - 63.97: 144 63.97 - 79.97: 48 Dihedral angle restraints: 28008 sinusoidal: 11592 harmonic: 16416 Sorted by residual: dihedral pdb=" CA ASN R 389 " pdb=" C ASN R 389 " pdb=" N PRO R 390 " pdb=" CA PRO R 390 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN O 389 " pdb=" C ASN O 389 " pdb=" N PRO O 390 " pdb=" CA PRO O 390 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN X 389 " pdb=" C ASN X 389 " pdb=" N PRO X 390 " pdb=" CA PRO X 390 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 28005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 4043 0.025 - 0.051: 1740 0.051 - 0.076: 519 0.076 - 0.101: 230 0.101 - 0.126: 500 Chirality restraints: 7032 Sorted by residual: chirality pdb=" CA ILE R 408 " pdb=" N ILE R 408 " pdb=" C ILE R 408 " pdb=" CB ILE R 408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE d 408 " pdb=" N ILE d 408 " pdb=" C ILE d 408 " pdb=" CB ILE d 408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE U 408 " pdb=" N ILE U 408 " pdb=" C ILE U 408 " pdb=" CB ILE U 408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 7029 not shown) Planarity restraints: 7944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS a 358 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C LYS a 358 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS a 358 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN a 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 358 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LYS E 358 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS E 358 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN E 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 358 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LYS R 358 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS R 358 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN R 359 " 0.009 2.00e-02 2.50e+03 ... (remaining 7941 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 16288 2.88 - 3.39: 43373 3.39 - 3.89: 69534 3.89 - 4.40: 76849 4.40 - 4.90: 136016 Nonbonded interactions: 342060 Sorted by model distance: nonbonded pdb=" OE2 GLU a 242 " pdb=" OG1 THR a 246 " model vdw 2.380 3.040 nonbonded pdb=" OE2 GLU c 242 " pdb=" OG1 THR c 246 " model vdw 2.380 3.040 nonbonded pdb=" OE2 GLU T 242 " pdb=" OG1 THR T 246 " model vdw 2.380 3.040 nonbonded pdb=" OE2 GLU K 242 " pdb=" OG1 THR K 246 " model vdw 2.380 3.040 nonbonded pdb=" OE2 GLU b 242 " pdb=" OG1 THR b 246 " model vdw 2.380 3.040 ... (remaining 342055 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: 0.15 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 37.790 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.100 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45144 Z= 0.162 Angle : 0.579 6.668 60888 Z= 0.343 Chirality : 0.042 0.126 7032 Planarity : 0.003 0.023 7944 Dihedral : 14.152 79.967 17352 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.50 % Allowed : 7.42 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.11), residues: 5616 helix: 1.88 (0.11), residues: 2256 sheet: 0.08 (0.18), residues: 864 loop : -0.98 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 314 TYR 0.006 0.001 TYR V 419 PHE 0.010 0.001 PHE b 437 HIS 0.004 0.001 HIS c 225 Details of bonding type rmsd covalent geometry : bond 0.00318 (45144) covalent geometry : angle 0.57919 (60888) hydrogen bonds : bond 0.19821 ( 2664) hydrogen bonds : angle 7.14372 ( 7893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 569 time to evaluate : 1.658 Fit side-chains REVERT: Q 238 GLN cc_start: 0.7798 (tp40) cc_final: 0.7591 (tm-30) outliers start: 24 outliers final: 24 residues processed: 593 average time/residue: 0.2443 time to fit residues: 248.4761 Evaluate side-chains 433 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 409 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 0.8980 chunk 430 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.131966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111215 restraints weight = 58353.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113717 restraints weight = 36399.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115288 restraints weight = 26969.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116490 restraints weight = 22240.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117258 restraints weight = 19498.908| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45144 Z= 0.145 Angle : 0.521 4.748 60888 Z= 0.291 Chirality : 0.043 0.144 7032 Planarity : 0.004 0.030 7944 Dihedral : 5.636 38.800 6288 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.33 % Allowed : 10.46 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.11), residues: 5616 helix: 2.23 (0.11), residues: 2304 sheet: 0.06 (0.16), residues: 912 loop : -0.61 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 314 TYR 0.006 0.001 TYR O 313 PHE 0.013 0.002 PHE Y 437 HIS 0.002 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00362 (45144) covalent geometry : angle 0.52079 (60888) hydrogen bonds : bond 0.04320 ( 2664) hydrogen bonds : angle 5.30518 ( 7893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 458 time to evaluate : 1.364 Fit side-chains REVERT: F 309 LYS cc_start: 0.7869 (mppt) cc_final: 0.7665 (tppt) REVERT: K 229 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7936 (mtt) REVERT: L 309 LYS cc_start: 0.7807 (mppt) cc_final: 0.7596 (tppt) REVERT: M 309 LYS cc_start: 0.7866 (mppt) cc_final: 0.7649 (tppt) REVERT: N 229 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7878 (mtt) REVERT: O 309 LYS cc_start: 0.7868 (mppt) cc_final: 0.7627 (tppt) REVERT: Q 238 GLN cc_start: 0.7703 (tp40) cc_final: 0.7444 (tm-30) REVERT: R 309 LYS cc_start: 0.7868 (mppt) cc_final: 0.7656 (tppt) REVERT: T 229 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7784 (mtt) REVERT: U 309 LYS cc_start: 0.7864 (mppt) cc_final: 0.7635 (tppt) REVERT: V 309 LYS cc_start: 0.7881 (mppt) cc_final: 0.7579 (tppt) REVERT: W 229 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: X 229 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: Y 309 LYS cc_start: 0.7856 (mppt) cc_final: 0.7649 (tppt) REVERT: Z 229 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7865 (mtt) REVERT: a 309 LYS cc_start: 0.7859 (mppt) cc_final: 0.7618 (tppt) REVERT: b 309 LYS cc_start: 0.7850 (mppt) cc_final: 0.7624 (tppt) REVERT: c 229 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: d 309 LYS cc_start: 0.7857 (mppt) cc_final: 0.7647 (tppt) outliers start: 112 outliers final: 24 residues processed: 546 average time/residue: 0.2768 time to fit residues: 241.2885 Evaluate side-chains 425 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 394 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 229 MET Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 229 MET Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 229 MET Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 229 MET Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 415 optimal weight: 3.9990 chunk 462 optimal weight: 1.9990 chunk 322 optimal weight: 0.6980 chunk 275 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 545 optimal weight: 0.6980 chunk 360 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 533 optimal weight: 2.9990 chunk 491 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 392 GLN T 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110337 restraints weight = 57437.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112907 restraints weight = 35747.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114602 restraints weight = 26183.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115570 restraints weight = 21318.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116383 restraints weight = 18788.211| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45144 Z= 0.139 Angle : 0.494 4.876 60888 Z= 0.273 Chirality : 0.043 0.142 7032 Planarity : 0.004 0.035 7944 Dihedral : 5.507 37.744 6288 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.52 % Allowed : 12.35 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.11), residues: 5616 helix: 2.36 (0.11), residues: 2304 sheet: -0.32 (0.19), residues: 768 loop : -0.61 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 314 TYR 0.006 0.001 TYR O 419 PHE 0.012 0.002 PHE E 437 HIS 0.002 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00353 (45144) covalent geometry : angle 0.49372 (60888) hydrogen bonds : bond 0.03800 ( 2664) hydrogen bonds : angle 4.99843 ( 7893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 447 time to evaluate : 1.771 Fit side-chains REVERT: F 242 GLU cc_start: 0.7426 (tp30) cc_final: 0.7210 (tp30) REVERT: K 231 ARG cc_start: 0.7592 (tpp-160) cc_final: 0.6912 (mpt-90) REVERT: L 242 GLU cc_start: 0.7373 (tp30) cc_final: 0.7163 (tp30) REVERT: M 242 GLU cc_start: 0.7390 (tp30) cc_final: 0.7188 (tp30) REVERT: N 231 ARG cc_start: 0.7636 (tpp-160) cc_final: 0.6989 (mpt-90) REVERT: O 242 GLU cc_start: 0.7368 (tp30) cc_final: 0.7155 (tp30) REVERT: Q 238 GLN cc_start: 0.7660 (tp40) cc_final: 0.7386 (tm-30) REVERT: R 242 GLU cc_start: 0.7360 (tp30) cc_final: 0.7159 (tp30) REVERT: S 242 GLU cc_start: 0.7448 (tp30) cc_final: 0.7236 (tp30) REVERT: T 283 MET cc_start: 0.9020 (tpp) cc_final: 0.8424 (tpp) REVERT: U 242 GLU cc_start: 0.7359 (tp30) cc_final: 0.7150 (tp30) REVERT: W 231 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7026 (mpt-90) REVERT: Y 242 GLU cc_start: 0.7399 (tp30) cc_final: 0.7197 (tp30) REVERT: Z 231 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.7015 (mpt-90) REVERT: a 242 GLU cc_start: 0.7376 (tp30) cc_final: 0.7161 (tp30) REVERT: c 231 ARG cc_start: 0.7653 (tpp-160) cc_final: 0.6981 (mpt-90) REVERT: d 242 GLU cc_start: 0.7371 (tp30) cc_final: 0.7163 (tp30) outliers start: 121 outliers final: 55 residues processed: 559 average time/residue: 0.2431 time to fit residues: 231.2185 Evaluate side-chains 463 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 408 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 304 ILE Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 304 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 181 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 370 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 492 optimal weight: 0.8980 chunk 491 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 392 GLN M 392 GLN N 392 GLN S 392 GLN T 392 GLN Y 392 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111199 restraints weight = 57788.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113853 restraints weight = 35714.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115563 restraints weight = 25987.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116569 restraints weight = 21145.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117427 restraints weight = 18585.160| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 45144 Z= 0.140 Angle : 0.496 5.050 60888 Z= 0.272 Chirality : 0.043 0.142 7032 Planarity : 0.004 0.039 7944 Dihedral : 5.451 37.078 6288 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.96 % Allowed : 12.54 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.11), residues: 5616 helix: 2.38 (0.11), residues: 2304 sheet: -0.36 (0.19), residues: 768 loop : -0.62 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 314 TYR 0.007 0.001 TYR c 419 PHE 0.011 0.002 PHE E 437 HIS 0.002 0.001 HIS V 399 Details of bonding type rmsd covalent geometry : bond 0.00357 (45144) covalent geometry : angle 0.49646 (60888) hydrogen bonds : bond 0.03574 ( 2664) hydrogen bonds : angle 4.84159 ( 7893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 403 time to evaluate : 1.786 Fit side-chains REVERT: D 283 MET cc_start: 0.8949 (tpp) cc_final: 0.8464 (tpp) REVERT: E 283 MET cc_start: 0.8987 (tpp) cc_final: 0.8535 (tpp) REVERT: F 283 MET cc_start: 0.8989 (tpp) cc_final: 0.8562 (tpp) REVERT: K 283 MET cc_start: 0.8975 (tpp) cc_final: 0.8482 (tpp) REVERT: L 283 MET cc_start: 0.8990 (tpp) cc_final: 0.8536 (tpp) REVERT: N 283 MET cc_start: 0.8969 (tpp) cc_final: 0.8475 (tpp) REVERT: O 242 GLU cc_start: 0.7384 (tp30) cc_final: 0.7167 (tp30) REVERT: O 283 MET cc_start: 0.8985 (tpp) cc_final: 0.8551 (tpp) REVERT: P 283 MET cc_start: 0.8965 (tpp) cc_final: 0.8522 (tpp) REVERT: Q 238 GLN cc_start: 0.7622 (tp40) cc_final: 0.7334 (tm-30) REVERT: Q 283 MET cc_start: 0.8981 (tpp) cc_final: 0.8547 (tpp) REVERT: R 242 GLU cc_start: 0.7365 (tp30) cc_final: 0.7156 (tp30) REVERT: R 283 MET cc_start: 0.8973 (tpp) cc_final: 0.8527 (tpp) REVERT: T 283 MET cc_start: 0.8971 (tpp) cc_final: 0.8426 (tpp) REVERT: U 242 GLU cc_start: 0.7309 (tp30) cc_final: 0.7097 (tp30) REVERT: U 283 MET cc_start: 0.8991 (tpp) cc_final: 0.8558 (tpp) REVERT: V 283 MET cc_start: 0.8937 (tpp) cc_final: 0.8543 (tpp) REVERT: W 283 MET cc_start: 0.8979 (tpp) cc_final: 0.8480 (tpp) REVERT: Z 283 MET cc_start: 0.8976 (tpp) cc_final: 0.8556 (tpp) REVERT: a 242 GLU cc_start: 0.7381 (tp30) cc_final: 0.7164 (tp30) REVERT: a 283 MET cc_start: 0.8977 (tpp) cc_final: 0.8552 (tpp) REVERT: c 283 MET cc_start: 0.8957 (tpp) cc_final: 0.8454 (tpp) outliers start: 94 outliers final: 63 residues processed: 474 average time/residue: 0.2360 time to fit residues: 191.2798 Evaluate side-chains 471 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 408 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain U residue 418 MET Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 304 ILE Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 304 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 211 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 505 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 427 optimal weight: 0.8980 chunk 398 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 521 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 412 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 392 GLN J 392 GLN N 392 GLN O 392 GLN P 392 GLN S 392 GLN X 392 GLN Y 392 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110539 restraints weight = 57832.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113182 restraints weight = 35775.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114728 restraints weight = 25915.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115959 restraints weight = 21226.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116662 restraints weight = 18480.987| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45144 Z= 0.152 Angle : 0.498 5.425 60888 Z= 0.270 Chirality : 0.043 0.144 7032 Planarity : 0.004 0.041 7944 Dihedral : 5.419 37.037 6288 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.90 % Allowed : 13.08 % Favored : 85.02 % 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: 1.01 (0.12), residues: 5616 helix: 2.42 (0.11), residues: 2304 sheet: -0.53 (0.19), residues: 744 loop : -0.59 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 314 TYR 0.008 0.001 TYR b 419 PHE 0.010 0.002 PHE M 383 HIS 0.004 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00387 (45144) covalent geometry : angle 0.49777 (60888) hydrogen bonds : bond 0.03629 ( 2664) hydrogen bonds : angle 4.79121 ( 7893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 408 time to evaluate : 1.555 Fit side-chains REVERT: D 283 MET cc_start: 0.8944 (tpp) cc_final: 0.8484 (tpp) REVERT: E 283 MET cc_start: 0.8950 (tpp) cc_final: 0.8527 (tpp) REVERT: F 283 MET cc_start: 0.8998 (tpp) cc_final: 0.8529 (tpp) REVERT: J 283 MET cc_start: 0.8982 (tpp) cc_final: 0.8502 (tpp) REVERT: K 283 MET cc_start: 0.8976 (tpp) cc_final: 0.8483 (tpp) REVERT: L 283 MET cc_start: 0.8948 (tpp) cc_final: 0.8518 (tpp) REVERT: L 305 ASP cc_start: 0.7329 (t0) cc_final: 0.7085 (t0) REVERT: M 283 MET cc_start: 0.8974 (tpp) cc_final: 0.8487 (tpp) REVERT: N 283 MET cc_start: 0.8983 (tpp) cc_final: 0.8498 (tpp) REVERT: O 242 GLU cc_start: 0.7464 (tp30) cc_final: 0.7217 (tp30) REVERT: O 283 MET cc_start: 0.8996 (tpp) cc_final: 0.8533 (tpp) REVERT: O 305 ASP cc_start: 0.7227 (t0) cc_final: 0.6947 (t0) REVERT: P 283 MET cc_start: 0.8940 (tpp) cc_final: 0.8521 (tpp) REVERT: Q 238 GLN cc_start: 0.7644 (tp40) cc_final: 0.7328 (tm-30) REVERT: Q 283 MET cc_start: 0.8984 (tpp) cc_final: 0.8522 (tpp) REVERT: R 242 GLU cc_start: 0.7453 (tp30) cc_final: 0.7207 (tp30) REVERT: R 283 MET cc_start: 0.8936 (tpp) cc_final: 0.8506 (tpp) REVERT: S 283 MET cc_start: 0.8985 (tpp) cc_final: 0.8505 (tpp) REVERT: T 283 MET cc_start: 0.8962 (tpp) cc_final: 0.8459 (tpp) REVERT: U 242 GLU cc_start: 0.7459 (tp30) cc_final: 0.7209 (tp30) REVERT: U 283 MET cc_start: 0.8995 (tpp) cc_final: 0.8538 (tpp) REVERT: U 305 ASP cc_start: 0.7323 (t0) cc_final: 0.7070 (t0) REVERT: V 283 MET cc_start: 0.8955 (tpp) cc_final: 0.8566 (tpp) REVERT: W 283 MET cc_start: 0.8982 (tpp) cc_final: 0.8492 (tpp) REVERT: X 283 MET cc_start: 0.8976 (tpp) cc_final: 0.8476 (tpp) REVERT: Y 283 MET cc_start: 0.8964 (tpp) cc_final: 0.8472 (tpp) REVERT: Z 283 MET cc_start: 0.8979 (tpp) cc_final: 0.8531 (tpp) REVERT: a 242 GLU cc_start: 0.7469 (tp30) cc_final: 0.7229 (tp30) REVERT: a 283 MET cc_start: 0.8985 (tpp) cc_final: 0.8530 (tpp) REVERT: b 283 MET cc_start: 0.8969 (tpp) cc_final: 0.8478 (tpp) REVERT: c 283 MET cc_start: 0.8951 (tpp) cc_final: 0.8475 (tpp) REVERT: d 242 GLU cc_start: 0.7454 (tp30) cc_final: 0.7214 (tp30) REVERT: d 283 MET cc_start: 0.8977 (tpp) cc_final: 0.8477 (tpp) REVERT: d 305 ASP cc_start: 0.7230 (t0) cc_final: 0.6953 (t0) outliers start: 91 outliers final: 78 residues processed: 474 average time/residue: 0.2311 time to fit residues: 189.1829 Evaluate side-chains 475 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 397 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain U residue 418 MET Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 290 optimal weight: 0.0870 chunk 417 optimal weight: 2.9990 chunk 532 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 324 optimal weight: 2.9990 chunk 241 optimal weight: 0.0770 chunk 401 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 392 GLN O 392 GLN P 392 GLN ** Q 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 392 GLN ** T 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 392 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110186 restraints weight = 58163.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112784 restraints weight = 35668.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114432 restraints weight = 25930.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115598 restraints weight = 21104.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116319 restraints weight = 18395.125| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45144 Z= 0.162 Angle : 0.506 6.109 60888 Z= 0.273 Chirality : 0.043 0.144 7032 Planarity : 0.004 0.042 7944 Dihedral : 5.409 36.916 6288 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.73 % Allowed : 12.62 % Favored : 84.65 % 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: 0.93 (0.12), residues: 5616 helix: 2.49 (0.11), residues: 2280 sheet: -1.22 (0.16), residues: 984 loop : -0.40 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 314 TYR 0.009 0.001 TYR R 419 PHE 0.010 0.002 PHE P 383 HIS 0.005 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00412 (45144) covalent geometry : angle 0.50641 (60888) hydrogen bonds : bond 0.03678 ( 2664) hydrogen bonds : angle 4.78446 ( 7893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 414 time to evaluate : 1.764 Fit side-chains REVERT: E 283 MET cc_start: 0.8956 (tpp) cc_final: 0.8554 (tpp) REVERT: F 283 MET cc_start: 0.8961 (tpp) cc_final: 0.8519 (tpp) REVERT: F 305 ASP cc_start: 0.7392 (t0) cc_final: 0.6808 (p0) REVERT: J 283 MET cc_start: 0.8981 (tpp) cc_final: 0.8509 (tpp) REVERT: K 283 MET cc_start: 0.8978 (tpp) cc_final: 0.8522 (tpp) REVERT: L 283 MET cc_start: 0.8961 (tpp) cc_final: 0.8549 (tpp) REVERT: L 305 ASP cc_start: 0.7388 (t0) cc_final: 0.6818 (p0) REVERT: M 283 MET cc_start: 0.8979 (tpp) cc_final: 0.8498 (tpp) REVERT: N 283 MET cc_start: 0.8987 (tpp) cc_final: 0.8510 (tpp) REVERT: O 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8520 (tpp) REVERT: O 305 ASP cc_start: 0.7392 (t0) cc_final: 0.6795 (p0) REVERT: P 283 MET cc_start: 0.8951 (tpp) cc_final: 0.8556 (tpp) REVERT: Q 238 GLN cc_start: 0.7686 (tp40) cc_final: 0.7331 (tm-30) REVERT: Q 283 MET cc_start: 0.8965 (tpp) cc_final: 0.8533 (tpp) REVERT: R 283 MET cc_start: 0.8952 (tpp) cc_final: 0.8542 (tpp) REVERT: R 305 ASP cc_start: 0.7391 (t0) cc_final: 0.6814 (p0) REVERT: S 283 MET cc_start: 0.8991 (tpp) cc_final: 0.8513 (tpp) REVERT: T 283 MET cc_start: 0.8972 (tpp) cc_final: 0.8505 (tpp) REVERT: U 283 MET cc_start: 0.8997 (tpp) cc_final: 0.8523 (tpp) REVERT: U 305 ASP cc_start: 0.7378 (t0) cc_final: 0.6816 (p0) REVERT: V 283 MET cc_start: 0.8965 (tpp) cc_final: 0.8591 (tpp) REVERT: W 283 MET cc_start: 0.8983 (tpp) cc_final: 0.8503 (tpp) REVERT: X 283 MET cc_start: 0.8982 (tpp) cc_final: 0.8488 (tpp) REVERT: X 305 ASP cc_start: 0.7348 (t0) cc_final: 0.6759 (p0) REVERT: Y 283 MET cc_start: 0.8963 (tpp) cc_final: 0.8505 (tpp) REVERT: Z 283 MET cc_start: 0.8973 (tpp) cc_final: 0.8562 (tpp) REVERT: a 283 MET cc_start: 0.8963 (tpp) cc_final: 0.8523 (tpp) REVERT: a 305 ASP cc_start: 0.7400 (t0) cc_final: 0.6815 (p0) REVERT: b 283 MET cc_start: 0.8968 (tpp) cc_final: 0.8508 (tpp) REVERT: c 283 MET cc_start: 0.8963 (tpp) cc_final: 0.8519 (tpp) REVERT: d 283 MET cc_start: 0.8981 (tpp) cc_final: 0.8484 (tpp) REVERT: d 305 ASP cc_start: 0.7385 (t0) cc_final: 0.6814 (p0) outliers start: 131 outliers final: 79 residues processed: 520 average time/residue: 0.2357 time to fit residues: 211.7571 Evaluate side-chains 491 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 412 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 317 ILE Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain U residue 418 MET Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 304 ILE Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 317 ILE Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 317 ILE Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 434 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 472 optimal weight: 0.6980 chunk 138 optimal weight: 8.9990 chunk 359 optimal weight: 0.8980 chunk 362 optimal weight: 0.0370 chunk 393 optimal weight: 0.0060 chunk 145 optimal weight: 2.9990 overall best weight: 0.4874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 426 HIS F 426 HIS J 392 GLN M 392 GLN O 426 HIS P 392 GLN S 392 GLN S 426 HIS V 392 GLN Y 392 GLN Y 426 HIS b 426 HIS d 426 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113307 restraints weight = 57460.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115946 restraints weight = 35241.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117691 restraints weight = 25623.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118739 restraints weight = 20762.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119240 restraints weight = 18197.830| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45144 Z= 0.108 Angle : 0.470 6.546 60888 Z= 0.253 Chirality : 0.042 0.137 7032 Planarity : 0.004 0.041 7944 Dihedral : 5.229 36.585 6288 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.81 % Allowed : 12.96 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 5616 helix: 2.69 (0.11), residues: 2280 sheet: -1.20 (0.16), residues: 984 loop : -0.31 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 314 TYR 0.005 0.001 TYR U 419 PHE 0.011 0.001 PHE P 437 HIS 0.005 0.000 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00275 (45144) covalent geometry : angle 0.47027 (60888) hydrogen bonds : bond 0.02983 ( 2664) hydrogen bonds : angle 4.59385 ( 7893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 436 time to evaluate : 1.789 Fit side-chains REVERT: D 283 MET cc_start: 0.8912 (tpp) cc_final: 0.8507 (tpp) REVERT: E 283 MET cc_start: 0.8932 (tpp) cc_final: 0.8566 (tpp) REVERT: F 283 MET cc_start: 0.8924 (tpp) cc_final: 0.8482 (tpp) REVERT: F 305 ASP cc_start: 0.7263 (t0) cc_final: 0.6701 (p0) REVERT: J 283 MET cc_start: 0.8954 (tpp) cc_final: 0.8482 (tpp) REVERT: K 283 MET cc_start: 0.8929 (tpp) cc_final: 0.8489 (tpp) REVERT: L 283 MET cc_start: 0.8922 (tpp) cc_final: 0.8549 (tpp) REVERT: L 305 ASP cc_start: 0.7485 (t0) cc_final: 0.6947 (p0) REVERT: M 283 MET cc_start: 0.8953 (tpp) cc_final: 0.8472 (tpp) REVERT: N 283 MET cc_start: 0.8967 (tpp) cc_final: 0.8496 (tpp) REVERT: O 283 MET cc_start: 0.8961 (tpp) cc_final: 0.8487 (tpp) REVERT: O 305 ASP cc_start: 0.7259 (t0) cc_final: 0.6699 (p0) REVERT: P 283 MET cc_start: 0.8926 (tpp) cc_final: 0.8533 (tpp) REVERT: Q 238 GLN cc_start: 0.7613 (tp40) cc_final: 0.7264 (tm-30) REVERT: Q 283 MET cc_start: 0.8964 (tpp) cc_final: 0.8494 (tpp) REVERT: R 283 MET cc_start: 0.8930 (tpp) cc_final: 0.8526 (tpp) REVERT: R 305 ASP cc_start: 0.7265 (t0) cc_final: 0.6716 (p0) REVERT: S 283 MET cc_start: 0.8963 (tpp) cc_final: 0.8489 (tpp) REVERT: T 283 MET cc_start: 0.8918 (tpp) cc_final: 0.8450 (tpp) REVERT: U 283 MET cc_start: 0.8964 (tpp) cc_final: 0.8487 (tpp) REVERT: U 305 ASP cc_start: 0.7358 (t0) cc_final: 0.6830 (p0) REVERT: V 283 MET cc_start: 0.8913 (tpp) cc_final: 0.8546 (tpp) REVERT: W 283 MET cc_start: 0.8960 (tpp) cc_final: 0.8489 (tpp) REVERT: X 283 MET cc_start: 0.8957 (tpp) cc_final: 0.8474 (tpp) REVERT: X 305 ASP cc_start: 0.7270 (t0) cc_final: 0.6707 (p0) REVERT: Y 283 MET cc_start: 0.8918 (tpp) cc_final: 0.8480 (tpp) REVERT: Z 283 MET cc_start: 0.8958 (tpp) cc_final: 0.8497 (tpp) REVERT: a 283 MET cc_start: 0.8956 (tpp) cc_final: 0.8482 (tpp) REVERT: a 305 ASP cc_start: 0.7500 (t0) cc_final: 0.6950 (p0) REVERT: b 283 MET cc_start: 0.8922 (tpp) cc_final: 0.8483 (tpp) REVERT: c 283 MET cc_start: 0.8912 (tpp) cc_final: 0.8476 (tpp) REVERT: d 283 MET cc_start: 0.8948 (tpp) cc_final: 0.8460 (tpp) REVERT: d 305 ASP cc_start: 0.7262 (t0) cc_final: 0.6719 (p0) outliers start: 135 outliers final: 75 residues processed: 547 average time/residue: 0.2374 time to fit residues: 226.2929 Evaluate side-chains 489 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 414 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 317 ILE Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 317 ILE Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 317 ILE Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 317 ILE Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain U residue 418 MET Chi-restraints excluded: chain V residue 317 ILE Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 308 THR Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 317 ILE Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 317 ILE Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 317 ILE Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 376 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 504 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 526 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 405 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 427 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 392 GLN M 392 GLN O 392 GLN P 392 GLN S 392 GLN V 392 GLN Y 392 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110286 restraints weight = 57930.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112798 restraints weight = 36084.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114427 restraints weight = 26385.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115575 restraints weight = 21463.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116213 restraints weight = 18728.521| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45144 Z= 0.156 Angle : 0.517 6.942 60888 Z= 0.279 Chirality : 0.044 0.143 7032 Planarity : 0.004 0.044 7944 Dihedral : 5.291 36.315 6286 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.50 % Allowed : 13.17 % Favored : 84.33 % 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: 0.98 (0.12), residues: 5616 helix: 2.57 (0.11), residues: 2280 sheet: -1.21 (0.16), residues: 984 loop : -0.40 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 404 TYR 0.009 0.001 TYR F 419 PHE 0.010 0.002 PHE S 383 HIS 0.003 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00396 (45144) covalent geometry : angle 0.51744 (60888) hydrogen bonds : bond 0.03464 ( 2664) hydrogen bonds : angle 4.71027 ( 7893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 407 time to evaluate : 1.747 Fit side-chains REVERT: D 283 MET cc_start: 0.8945 (tpp) cc_final: 0.8525 (tpp) REVERT: E 283 MET cc_start: 0.8983 (tpp) cc_final: 0.8520 (tpp) REVERT: F 283 MET cc_start: 0.8956 (tpp) cc_final: 0.8516 (tpp) REVERT: F 305 ASP cc_start: 0.7474 (t0) cc_final: 0.7027 (p0) REVERT: J 283 MET cc_start: 0.8981 (tpp) cc_final: 0.8500 (tpp) REVERT: K 283 MET cc_start: 0.8951 (tpp) cc_final: 0.8512 (tpp) REVERT: L 283 MET cc_start: 0.8973 (tpp) cc_final: 0.8510 (tpp) REVERT: L 305 ASP cc_start: 0.7496 (t0) cc_final: 0.7010 (p0) REVERT: M 283 MET cc_start: 0.8981 (tpp) cc_final: 0.8496 (tpp) REVERT: N 283 MET cc_start: 0.8986 (tpp) cc_final: 0.8501 (tpp) REVERT: N 308 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8368 (m) REVERT: O 283 MET cc_start: 0.8991 (tpp) cc_final: 0.8488 (tpp) REVERT: O 305 ASP cc_start: 0.7455 (t0) cc_final: 0.6981 (p0) REVERT: P 283 MET cc_start: 0.8926 (tpp) cc_final: 0.8531 (tpp) REVERT: Q 238 GLN cc_start: 0.7604 (tp40) cc_final: 0.7263 (tm-30) REVERT: Q 283 MET cc_start: 0.9003 (tpp) cc_final: 0.8529 (tpp) REVERT: R 242 GLU cc_start: 0.7359 (tp30) cc_final: 0.7131 (tp30) REVERT: R 283 MET cc_start: 0.8917 (tpp) cc_final: 0.8501 (tpp) REVERT: R 305 ASP cc_start: 0.7478 (t0) cc_final: 0.7036 (p0) REVERT: S 283 MET cc_start: 0.8987 (tpp) cc_final: 0.8493 (tpp) REVERT: T 283 MET cc_start: 0.8942 (tpp) cc_final: 0.8492 (tpp) REVERT: U 283 MET cc_start: 0.8992 (tpp) cc_final: 0.8494 (tpp) REVERT: U 305 ASP cc_start: 0.7473 (t0) cc_final: 0.7039 (p0) REVERT: V 283 MET cc_start: 0.8975 (tpp) cc_final: 0.8615 (tpp) REVERT: W 283 MET cc_start: 0.8984 (tpp) cc_final: 0.8494 (tpp) REVERT: X 283 MET cc_start: 0.8978 (tpp) cc_final: 0.8475 (tpp) REVERT: X 305 ASP cc_start: 0.7478 (t0) cc_final: 0.7014 (p0) REVERT: Y 283 MET cc_start: 0.8943 (tpp) cc_final: 0.8508 (tpp) REVERT: Z 283 MET cc_start: 0.8997 (tpp) cc_final: 0.8534 (tpp) REVERT: Z 308 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8373 (m) REVERT: a 283 MET cc_start: 0.8984 (tpp) cc_final: 0.8481 (tpp) REVERT: a 305 ASP cc_start: 0.7509 (t0) cc_final: 0.7012 (p0) REVERT: b 283 MET cc_start: 0.8948 (tpp) cc_final: 0.8507 (tpp) REVERT: c 283 MET cc_start: 0.8934 (tpp) cc_final: 0.8504 (tpp) REVERT: d 283 MET cc_start: 0.8959 (tpp) cc_final: 0.8462 (tpp) REVERT: d 305 ASP cc_start: 0.7477 (t0) cc_final: 0.7035 (p0) outliers start: 120 outliers final: 109 residues processed: 502 average time/residue: 0.2345 time to fit residues: 205.3038 Evaluate side-chains 529 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 418 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 309 LYS Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 317 ILE Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 317 ILE Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 317 ILE Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 308 THR Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 317 ILE Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 317 ILE Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 317 ILE Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 308 THR Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 317 ILE Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 317 ILE Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 308 THR Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 317 ILE Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 304 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 317 ILE Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 317 ILE Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 439 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 330 optimal weight: 0.5980 chunk 266 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 460 optimal weight: 2.9990 chunk 501 optimal weight: 0.7980 chunk 400 optimal weight: 2.9990 chunk 499 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 426 HIS O 392 GLN Q 426 HIS S 392 GLN W 426 HIS ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 426 HIS c 426 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112096 restraints weight = 57663.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114655 restraints weight = 35623.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116324 restraints weight = 25955.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117453 restraints weight = 21067.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118105 restraints weight = 18373.789| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45144 Z= 0.133 Angle : 0.506 7.664 60888 Z= 0.270 Chirality : 0.043 0.140 7032 Planarity : 0.004 0.045 7944 Dihedral : 5.251 36.288 6286 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.33 % Allowed : 13.25 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 5616 helix: 2.63 (0.11), residues: 2280 sheet: -1.27 (0.16), residues: 984 loop : -0.39 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 404 TYR 0.007 0.001 TYR J 419 PHE 0.010 0.001 PHE M 383 HIS 0.003 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00338 (45144) covalent geometry : angle 0.50560 (60888) hydrogen bonds : bond 0.03213 ( 2664) hydrogen bonds : angle 4.64779 ( 7893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 410 time to evaluate : 1.404 Fit side-chains REVERT: D 283 MET cc_start: 0.8960 (tpp) cc_final: 0.8567 (tpp) REVERT: E 283 MET cc_start: 0.8992 (tpp) cc_final: 0.8627 (tpp) REVERT: F 242 GLU cc_start: 0.7359 (tp30) cc_final: 0.7116 (tp30) REVERT: F 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8550 (tpp) REVERT: F 305 ASP cc_start: 0.7478 (t0) cc_final: 0.7030 (p0) REVERT: J 283 MET cc_start: 0.8970 (tpp) cc_final: 0.8495 (tpp) REVERT: K 242 GLU cc_start: 0.7360 (tp30) cc_final: 0.7109 (tp30) REVERT: K 283 MET cc_start: 0.8955 (tpp) cc_final: 0.8544 (tpp) REVERT: L 242 GLU cc_start: 0.7373 (tp30) cc_final: 0.7128 (tp30) REVERT: L 283 MET cc_start: 0.8987 (tpp) cc_final: 0.8612 (tpp) REVERT: M 242 GLU cc_start: 0.7357 (tp30) cc_final: 0.7121 (tp30) REVERT: M 283 MET cc_start: 0.8991 (tpp) cc_final: 0.8530 (tpp) REVERT: N 283 MET cc_start: 0.8996 (tpp) cc_final: 0.8540 (tpp) REVERT: N 308 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8426 (m) REVERT: O 242 GLU cc_start: 0.7367 (tp30) cc_final: 0.7117 (tp30) REVERT: O 283 MET cc_start: 0.8972 (tpp) cc_final: 0.8477 (tpp) REVERT: O 305 ASP cc_start: 0.7483 (t0) cc_final: 0.7023 (p0) REVERT: P 242 GLU cc_start: 0.7357 (tp30) cc_final: 0.7109 (tp30) REVERT: P 283 MET cc_start: 0.8954 (tpp) cc_final: 0.8590 (tpp) REVERT: Q 238 GLN cc_start: 0.7575 (tp40) cc_final: 0.7239 (tm-30) REVERT: Q 283 MET cc_start: 0.8975 (tpp) cc_final: 0.8495 (tpp) REVERT: R 283 MET cc_start: 0.8944 (tpp) cc_final: 0.8556 (tpp) REVERT: R 305 ASP cc_start: 0.7485 (t0) cc_final: 0.7033 (p0) REVERT: S 242 GLU cc_start: 0.7368 (tp30) cc_final: 0.7129 (tp30) REVERT: S 283 MET cc_start: 0.8973 (tpp) cc_final: 0.8497 (tpp) REVERT: T 283 MET cc_start: 0.8919 (tpp) cc_final: 0.8492 (tpp) REVERT: U 283 MET cc_start: 0.9016 (tpp) cc_final: 0.8539 (tpp) REVERT: U 305 ASP cc_start: 0.7474 (t0) cc_final: 0.7038 (p0) REVERT: V 283 MET cc_start: 0.8938 (tpp) cc_final: 0.8586 (tpp) REVERT: W 283 MET cc_start: 0.8969 (tpp) cc_final: 0.8490 (tpp) REVERT: X 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8468 (tpp) REVERT: X 305 ASP cc_start: 0.7482 (t0) cc_final: 0.7006 (p0) REVERT: Y 242 GLU cc_start: 0.7360 (tp30) cc_final: 0.7126 (tp30) REVERT: Y 283 MET cc_start: 0.8951 (tpp) cc_final: 0.8541 (tpp) REVERT: Z 283 MET cc_start: 0.8985 (tpp) cc_final: 0.8571 (tpp) REVERT: Z 308 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8437 (m) REVERT: a 283 MET cc_start: 0.8969 (tpp) cc_final: 0.8476 (tpp) REVERT: a 305 ASP cc_start: 0.7397 (t0) cc_final: 0.6972 (p0) REVERT: b 242 GLU cc_start: 0.7348 (tp30) cc_final: 0.7097 (tp30) REVERT: b 283 MET cc_start: 0.8958 (tpp) cc_final: 0.8543 (tpp) REVERT: c 283 MET cc_start: 0.8954 (tpp) cc_final: 0.8552 (tpp) REVERT: d 283 MET cc_start: 0.8937 (tpp) cc_final: 0.8459 (tpp) REVERT: d 305 ASP cc_start: 0.7477 (t0) cc_final: 0.7027 (p0) outliers start: 112 outliers final: 109 residues processed: 498 average time/residue: 0.2306 time to fit residues: 201.3959 Evaluate side-chains 494 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 383 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 317 ILE Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 317 ILE Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 317 ILE Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 308 THR Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 317 ILE Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 317 ILE Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 317 ILE Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 304 ILE Chi-restraints excluded: chain W residue 308 THR Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 317 ILE Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 317 ILE Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 308 THR Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 317 ILE Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 317 ILE Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 317 ILE Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 94 optimal weight: 0.7980 chunk 446 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 330 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 chunk 412 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110987 restraints weight = 58487.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113625 restraints weight = 36126.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115358 restraints weight = 26221.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116358 restraints weight = 21243.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117166 restraints weight = 18682.641| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45144 Z= 0.155 Angle : 0.521 7.147 60888 Z= 0.278 Chirality : 0.044 0.144 7032 Planarity : 0.004 0.045 7944 Dihedral : 5.294 36.448 6286 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.33 % Allowed : 13.08 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 5616 helix: 2.56 (0.11), residues: 2280 sheet: -1.28 (0.16), residues: 984 loop : -0.44 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 404 TYR 0.011 0.001 TYR D 419 PHE 0.010 0.002 PHE D 383 HIS 0.002 0.001 HIS T 399 Details of bonding type rmsd covalent geometry : bond 0.00396 (45144) covalent geometry : angle 0.52120 (60888) hydrogen bonds : bond 0.03479 ( 2664) hydrogen bonds : angle 4.68488 ( 7893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 387 time to evaluate : 1.705 Fit side-chains REVERT: D 283 MET cc_start: 0.8996 (tpp) cc_final: 0.8603 (tpp) REVERT: E 283 MET cc_start: 0.9045 (tpp) cc_final: 0.8612 (tpp) REVERT: F 283 MET cc_start: 0.8943 (tpp) cc_final: 0.8518 (tpp) REVERT: J 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8500 (tpp) REVERT: K 283 MET cc_start: 0.8981 (tpp) cc_final: 0.8582 (tpp) REVERT: L 283 MET cc_start: 0.9038 (tpp) cc_final: 0.8606 (tpp) REVERT: M 283 MET cc_start: 0.9007 (tpp) cc_final: 0.8543 (tpp) REVERT: N 283 MET cc_start: 0.9007 (tpp) cc_final: 0.8554 (tpp) REVERT: N 308 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8454 (m) REVERT: O 283 MET cc_start: 0.8978 (tpp) cc_final: 0.8544 (tpp) REVERT: P 283 MET cc_start: 0.8956 (tpp) cc_final: 0.8605 (tpp) REVERT: Q 238 GLN cc_start: 0.7558 (tp40) cc_final: 0.7256 (tm-30) REVERT: Q 283 MET cc_start: 0.8976 (tpp) cc_final: 0.8557 (tpp) REVERT: R 283 MET cc_start: 0.8937 (tpp) cc_final: 0.8560 (tpp) REVERT: S 283 MET cc_start: 0.8967 (tpp) cc_final: 0.8500 (tpp) REVERT: T 283 MET cc_start: 0.8986 (tpp) cc_final: 0.8583 (tpp) REVERT: U 283 MET cc_start: 0.8982 (tpp) cc_final: 0.8544 (tpp) REVERT: V 283 MET cc_start: 0.8965 (tpp) cc_final: 0.8626 (tpp) REVERT: W 283 MET cc_start: 0.8968 (tpp) cc_final: 0.8495 (tpp) REVERT: X 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8475 (tpp) REVERT: X 305 ASP cc_start: 0.7411 (t0) cc_final: 0.6979 (p0) REVERT: Y 283 MET cc_start: 0.8967 (tpp) cc_final: 0.8562 (tpp) REVERT: Z 283 MET cc_start: 0.8978 (tpp) cc_final: 0.8561 (tpp) REVERT: a 283 MET cc_start: 0.8988 (tpp) cc_final: 0.8563 (tpp) REVERT: a 305 ASP cc_start: 0.7452 (t0) cc_final: 0.7000 (p0) REVERT: b 283 MET cc_start: 0.8973 (tpp) cc_final: 0.8567 (tpp) REVERT: c 283 MET cc_start: 0.8959 (tpp) cc_final: 0.8550 (tpp) REVERT: d 283 MET cc_start: 0.8946 (tpp) cc_final: 0.8479 (tpp) outliers start: 112 outliers final: 108 residues processed: 475 average time/residue: 0.2259 time to fit residues: 189.7111 Evaluate side-chains 497 residues out of total 4800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 388 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 308 THR Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 317 ILE Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 317 ILE Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 317 ILE Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 308 THR Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 317 ILE Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 317 ILE Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 317 ILE Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 304 ILE Chi-restraints excluded: chain W residue 308 THR Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 317 ILE Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 317 ILE Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 317 ILE Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 317 ILE Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 304 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 317 ILE Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 317 ILE Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 161 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 437 optimal weight: 4.9990 chunk 547 optimal weight: 0.8980 chunk 361 optimal weight: 0.9980 chunk 330 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 543 optimal weight: 0.0770 chunk 150 optimal weight: 0.5980 chunk 465 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 392 GLN K 426 HIS N 392 GLN R 426 HIS S 392 GLN ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 426 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112223 restraints weight = 57941.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114798 restraints weight = 35719.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116296 restraints weight = 25879.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117548 restraints weight = 21253.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118016 restraints weight = 18462.205| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45144 Z= 0.130 Angle : 0.500 7.942 60888 Z= 0.268 Chirality : 0.043 0.140 7032 Planarity : 0.004 0.044 7944 Dihedral : 5.239 36.230 6286 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.25 % Allowed : 13.23 % Favored : 84.52 % 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: 0.99 (0.12), residues: 5616 helix: 2.64 (0.11), residues: 2280 sheet: -1.30 (0.16), residues: 984 loop : -0.41 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG d 404 TYR 0.006 0.001 TYR D 419 PHE 0.010 0.001 PHE M 383 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00331 (45144) covalent geometry : angle 0.50029 (60888) hydrogen bonds : bond 0.03161 ( 2664) hydrogen bonds : angle 4.57118 ( 7893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6119.61 seconds wall clock time: 107 minutes 53.08 seconds (6473.08 seconds total)