Starting phenix.real_space_refine on Thu Nov 20 22:32:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w68_8778/11_2025/5w68_8778.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w68_8778/11_2025/5w68_8778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w68_8778/11_2025/5w68_8778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w68_8778/11_2025/5w68_8778.map" model { file = "/net/cci-nas-00/data/ceres_data/5w68_8778/11_2025/5w68_8778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w68_8778/11_2025/5w68_8778.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.050 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 165 5.16 5 C 24735 2.51 5 N 6750 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39390 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2626 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 4.22, per 1000 atoms: 0.11 Number of scatterers: 39390 At special positions: 0 Unit cell: (159, 160.06, 130.38, 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 165 16.00 O 7740 8.00 N 6750 7.00 C 24735 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: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 76 sheets defined 23.4% alpha, 55.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 605 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN A 652 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 removed outlier: 3.570A pdb=" N GLN B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU B 603 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 652 removed outlier: 3.715A pdb=" N GLN B 652 " --> pdb=" O TYR B 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 411 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 652 removed outlier: 3.717A pdb=" N GLN C 652 " --> pdb=" O TYR C 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 307 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 411 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU D 603 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 605 " --> pdb=" O ASN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN D 652 " --> pdb=" O TYR D 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 304 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR E 307 " --> pdb=" O GLN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN E 347 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 348 " --> pdb=" O ASP E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 411 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS E 605 " --> pdb=" O ASN E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN E 652 " --> pdb=" O TYR E 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 307 " --> pdb=" O GLN F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 357 removed outlier: 3.572A pdb=" N GLN F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER F 348 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 411 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU F 603 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 605 " --> pdb=" O ASN F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN F 652 " --> pdb=" O TYR F 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY G 306 " --> pdb=" O LYS G 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 348 " --> pdb=" O ASP G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 411 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G 605 " --> pdb=" O ASN G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN G 652 " --> pdb=" O TYR G 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU H 297 " --> pdb=" O LYS H 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN H 303 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL H 304 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY H 306 " --> pdb=" O LYS H 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR H 307 " --> pdb=" O GLN H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 357 removed outlier: 3.570A pdb=" N GLN H 347 " --> pdb=" O GLN H 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 411 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU H 603 " --> pdb=" O ILE H 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS H 605 " --> pdb=" O ASN H 602 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN H 652 " --> pdb=" O TYR H 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU I 297 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN I 303 " --> pdb=" O ASP I 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL I 304 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER I 305 " --> pdb=" O LEU I 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY I 306 " --> pdb=" O LYS I 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR I 307 " --> pdb=" O GLN I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN I 347 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER I 348 " --> pdb=" O ASP I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 411 Processing helix chain 'I' and resid 439 through 444 Processing helix chain 'I' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU I 603 " --> pdb=" O ILE I 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 605 " --> pdb=" O ASN I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN I 652 " --> pdb=" O TYR I 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU J 297 " --> pdb=" O LYS J 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN J 303 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL J 304 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER J 305 " --> pdb=" O LEU J 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY J 306 " --> pdb=" O LYS J 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR J 307 " --> pdb=" O GLN J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN J 347 " --> pdb=" O GLN J 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER J 348 " --> pdb=" O ASP J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 411 Processing helix chain 'J' and resid 439 through 444 Processing helix chain 'J' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU J 603 " --> pdb=" O ILE J 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS J 605 " --> pdb=" O ASN J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN J 652 " --> pdb=" O TYR J 648 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 309 removed outlier: 3.742A pdb=" N LEU K 297 " --> pdb=" O LYS K 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN K 303 " --> pdb=" O ASP K 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL K 304 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY K 306 " --> pdb=" O LYS K 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR K 307 " --> pdb=" O GLN K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN K 347 " --> pdb=" O GLN K 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER K 348 " --> pdb=" O ASP K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 411 Processing helix chain 'K' and resid 439 through 444 Processing helix chain 'K' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU K 603 " --> pdb=" O ILE K 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 605 " --> pdb=" O ASN K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN K 652 " --> pdb=" O TYR K 648 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU L 297 " --> pdb=" O LYS L 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN L 303 " --> pdb=" O ASP L 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL L 304 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER L 305 " --> pdb=" O LEU L 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY L 306 " --> pdb=" O LYS L 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR L 307 " --> pdb=" O GLN L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN L 347 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER L 348 " --> pdb=" O ASP L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 411 Processing helix chain 'L' and resid 439 through 444 Processing helix chain 'L' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU L 603 " --> pdb=" O ILE L 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS L 605 " --> pdb=" O ASN L 602 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN L 652 " --> pdb=" O TYR L 648 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU M 297 " --> pdb=" O LYS M 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN M 303 " --> pdb=" O ASP M 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL M 304 " --> pdb=" O VAL M 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY M 306 " --> pdb=" O LYS M 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR M 307 " --> pdb=" O GLN M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN M 347 " --> pdb=" O GLN M 343 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER M 348 " --> pdb=" O ASP M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 401 through 411 Processing helix chain 'M' and resid 439 through 444 Processing helix chain 'M' and resid 600 through 605 removed outlier: 3.578A pdb=" N LEU M 603 " --> pdb=" O ILE M 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS M 605 " --> pdb=" O ASN M 602 " (cutoff:3.500A) Processing helix chain 'M' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN M 652 " --> pdb=" O TYR M 648 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU N 297 " --> pdb=" O LYS N 293 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN N 303 " --> pdb=" O ASP N 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL N 304 " --> pdb=" O VAL N 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER N 305 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR N 307 " --> pdb=" O GLN N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN N 347 " --> pdb=" O GLN N 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER N 348 " --> pdb=" O ASP N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 401 through 411 Processing helix chain 'N' and resid 439 through 444 Processing helix chain 'N' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU N 603 " --> pdb=" O ILE N 600 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS N 605 " --> pdb=" O ASN N 602 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN N 652 " --> pdb=" O TYR N 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 309 removed outlier: 3.743A pdb=" N LEU O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN O 303 " --> pdb=" O ASP O 299 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL O 304 " --> pdb=" O VAL O 300 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER O 305 " --> pdb=" O LEU O 301 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY O 306 " --> pdb=" O LYS O 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR O 307 " --> pdb=" O GLN O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 357 removed outlier: 3.571A pdb=" N GLN O 347 " --> pdb=" O GLN O 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER O 348 " --> pdb=" O ASP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 411 Processing helix chain 'O' and resid 439 through 444 Processing helix chain 'O' and resid 600 through 605 removed outlier: 3.577A pdb=" N LEU O 603 " --> pdb=" O ILE O 600 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS O 605 " --> pdb=" O ASN O 602 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 652 removed outlier: 3.716A pdb=" N GLN O 652 " --> pdb=" O TYR O 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 284 through 288 Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER A 587 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS O 467 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN O 468 " --> pdb=" O ASN O 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN O 377 " --> pdb=" O ASN O 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN O 362 " --> pdb=" O LEU O 625 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 576 " --> pdb=" O THR O 481 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N LEU O 483 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 15.547A pdb=" N ILE A 574 " --> pdb=" O LEU O 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER O 587 " --> pdb=" O ALA O 608 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS N 467 " --> pdb=" O LYS O 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN N 468 " --> pdb=" O ASN N 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN N 377 " --> pdb=" O ASN N 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN N 362 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU O 576 " --> pdb=" O THR N 481 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU N 483 " --> pdb=" O ILE O 574 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE O 574 " --> pdb=" O LEU N 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER N 587 " --> pdb=" O ALA N 608 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS M 467 " --> pdb=" O LYS N 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN M 468 " --> pdb=" O ASN M 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN M 377 " --> pdb=" O ASN M 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN M 362 " --> pdb=" O LEU M 625 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 576 " --> pdb=" O THR M 481 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N LEU M 483 " --> pdb=" O ILE N 574 " (cutoff:3.500A) removed outlier: 15.546A pdb=" N ILE N 574 " --> pdb=" O LEU M 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER M 587 " --> pdb=" O ALA M 608 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS L 467 " --> pdb=" O LYS M 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN L 468 " --> pdb=" O ASN L 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN L 377 " --> pdb=" O ASN L 468 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN L 362 " --> pdb=" O LEU L 625 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU M 576 " --> pdb=" O THR L 481 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N LEU L 483 " --> pdb=" O ILE M 574 " (cutoff:3.500A) removed outlier: 15.545A pdb=" N ILE M 574 " --> pdb=" O LEU L 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER L 587 " --> pdb=" O ALA L 608 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 467 " --> pdb=" O LYS L 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN K 468 " --> pdb=" O ASN K 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN K 377 " --> pdb=" O ASN K 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 362 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 576 " --> pdb=" O THR K 481 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N LEU K 483 " --> pdb=" O ILE L 574 " (cutoff:3.500A) removed outlier: 15.548A pdb=" N ILE L 574 " --> pdb=" O LEU K 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER K 587 " --> pdb=" O ALA K 608 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS J 467 " --> pdb=" O LYS K 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN J 468 " --> pdb=" O ASN J 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN J 377 " --> pdb=" O ASN J 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 362 " --> pdb=" O LEU J 625 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU K 576 " --> pdb=" O THR J 481 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N LEU J 483 " --> pdb=" O ILE K 574 " (cutoff:3.500A) removed outlier: 15.542A pdb=" N ILE K 574 " --> pdb=" O LEU J 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER J 587 " --> pdb=" O ALA J 608 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS I 467 " --> pdb=" O LYS J 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN I 468 " --> pdb=" O ASN I 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN I 377 " --> pdb=" O ASN I 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 362 " --> pdb=" O LEU I 625 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU J 576 " --> pdb=" O THR I 481 " (cutoff:3.500A) removed outlier: 12.220A pdb=" N LEU I 483 " --> pdb=" O ILE J 574 " (cutoff:3.500A) removed outlier: 15.532A pdb=" N ILE J 574 " --> pdb=" O LEU I 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER I 587 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS H 467 " --> pdb=" O LYS I 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN H 468 " --> pdb=" O ASN H 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN H 377 " --> pdb=" O ASN H 468 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN H 362 " --> pdb=" O LEU H 625 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU I 576 " --> pdb=" O THR H 481 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N LEU H 483 " --> pdb=" O ILE I 574 " (cutoff:3.500A) removed outlier: 15.567A pdb=" N ILE I 574 " --> pdb=" O LEU H 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER H 587 " --> pdb=" O ALA H 608 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS G 467 " --> pdb=" O LYS H 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN G 468 " --> pdb=" O ASN G 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN G 377 " --> pdb=" O ASN G 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN G 362 " --> pdb=" O LEU G 625 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU H 576 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N LEU G 483 " --> pdb=" O ILE H 574 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N ILE H 574 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER G 587 " --> pdb=" O ALA G 608 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 467 " --> pdb=" O LYS G 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN F 468 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN F 377 " --> pdb=" O ASN F 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 362 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 576 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU F 483 " --> pdb=" O ILE G 574 " (cutoff:3.500A) removed outlier: 15.569A pdb=" N ILE G 574 " --> pdb=" O LEU F 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER F 587 " --> pdb=" O ALA F 608 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 467 " --> pdb=" O LYS F 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 468 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E 377 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN E 362 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 576 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU E 483 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 15.541A pdb=" N ILE F 574 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER E 587 " --> pdb=" O ALA E 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 467 " --> pdb=" O LYS E 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN D 468 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 377 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 362 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 576 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N LEU D 483 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 15.568A pdb=" N ILE E 574 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER D 587 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 467 " --> pdb=" O LYS D 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 468 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 377 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 362 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 576 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 12.216A pdb=" N LEU C 483 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 15.530A pdb=" N ILE D 574 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 608 through 609 removed outlier: 3.826A pdb=" N SER C 587 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 467 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 468 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 377 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 362 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 576 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 12.237A pdb=" N LEU B 483 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 15.555A pdb=" N ILE C 574 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 608 through 609 removed outlier: 3.827A pdb=" N SER B 587 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 467 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 468 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 377 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 362 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 576 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU A 483 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE B 574 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 574 through 583 removed outlier: 15.547A pdb=" N ILE A 574 " --> pdb=" O LEU O 483 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N LEU O 483 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 576 " --> pdb=" O THR O 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN O 362 " --> pdb=" O LEU O 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU O 612 " --> pdb=" O ASP O 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP O 582 " --> pdb=" O GLU O 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG O 614 " --> pdb=" O MET O 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET O 580 " --> pdb=" O ARG O 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU O 616 " --> pdb=" O GLY O 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY O 578 " --> pdb=" O LEU O 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL O 618 " --> pdb=" O LEU O 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE O 574 " --> pdb=" O ILE O 620 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE O 574 " --> pdb=" O LEU N 483 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU N 483 " --> pdb=" O ILE O 574 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU O 576 " --> pdb=" O THR N 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN N 362 " --> pdb=" O LEU N 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU N 612 " --> pdb=" O ASP N 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP N 582 " --> pdb=" O GLU N 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG N 614 " --> pdb=" O MET N 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET N 580 " --> pdb=" O ARG N 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU N 616 " --> pdb=" O GLY N 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY N 578 " --> pdb=" O LEU N 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL N 618 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE N 574 " --> pdb=" O ILE N 620 " (cutoff:3.500A) removed outlier: 15.546A pdb=" N ILE N 574 " --> pdb=" O LEU M 483 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N LEU M 483 " --> pdb=" O ILE N 574 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 576 " --> pdb=" O THR M 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN M 362 " --> pdb=" O LEU M 625 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU M 612 " --> pdb=" O ASP M 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP M 582 " --> pdb=" O GLU M 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG M 614 " --> pdb=" O MET M 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET M 580 " --> pdb=" O ARG M 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU M 616 " --> pdb=" O GLY M 578 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY M 578 " --> pdb=" O LEU M 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL M 618 " --> pdb=" O LEU M 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE M 574 " --> pdb=" O ILE M 620 " (cutoff:3.500A) removed outlier: 15.545A pdb=" N ILE M 574 " --> pdb=" O LEU L 483 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N LEU L 483 " --> pdb=" O ILE M 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU M 576 " --> pdb=" O THR L 481 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN L 362 " --> pdb=" O LEU L 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU L 612 " --> pdb=" O ASP L 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP L 582 " --> pdb=" O GLU L 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG L 614 " --> pdb=" O MET L 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET L 580 " --> pdb=" O ARG L 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU L 616 " --> pdb=" O GLY L 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY L 578 " --> pdb=" O LEU L 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL L 618 " --> pdb=" O LEU L 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) removed outlier: 15.548A pdb=" N ILE L 574 " --> pdb=" O LEU K 483 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N LEU K 483 " --> pdb=" O ILE L 574 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 576 " --> pdb=" O THR K 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 362 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 612 " --> pdb=" O ASP K 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP K 582 " --> pdb=" O GLU K 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG K 614 " --> pdb=" O MET K 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET K 580 " --> pdb=" O ARG K 614 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU K 616 " --> pdb=" O GLY K 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY K 578 " --> pdb=" O LEU K 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL K 618 " --> pdb=" O LEU K 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) removed outlier: 15.542A pdb=" N ILE K 574 " --> pdb=" O LEU J 483 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N LEU J 483 " --> pdb=" O ILE K 574 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU K 576 " --> pdb=" O THR J 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 362 " --> pdb=" O LEU J 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU J 612 " --> pdb=" O ASP J 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP J 582 " --> pdb=" O GLU J 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG J 614 " --> pdb=" O MET J 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET J 580 " --> pdb=" O ARG J 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU J 616 " --> pdb=" O GLY J 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY J 578 " --> pdb=" O LEU J 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL J 618 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) removed outlier: 15.532A pdb=" N ILE J 574 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 12.220A pdb=" N LEU I 483 " --> pdb=" O ILE J 574 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU J 576 " --> pdb=" O THR I 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 362 " --> pdb=" O LEU I 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU I 612 " --> pdb=" O ASP I 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP I 582 " --> pdb=" O GLU I 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG I 614 " --> pdb=" O MET I 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET I 580 " --> pdb=" O ARG I 614 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU I 616 " --> pdb=" O GLY I 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY I 578 " --> pdb=" O LEU I 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 618 " --> pdb=" O LEU I 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) removed outlier: 15.567A pdb=" N ILE I 574 " --> pdb=" O LEU H 483 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N LEU H 483 " --> pdb=" O ILE I 574 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU I 576 " --> pdb=" O THR H 481 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN H 362 " --> pdb=" O LEU H 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU H 612 " --> pdb=" O ASP H 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP H 582 " --> pdb=" O GLU H 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG H 614 " --> pdb=" O MET H 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET H 580 " --> pdb=" O ARG H 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU H 616 " --> pdb=" O GLY H 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY H 578 " --> pdb=" O LEU H 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL H 618 " --> pdb=" O LEU H 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N ILE H 574 " --> pdb=" O LEU G 483 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N LEU G 483 " --> pdb=" O ILE H 574 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU H 576 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN G 362 " --> pdb=" O LEU G 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU G 612 " --> pdb=" O ASP G 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP G 582 " --> pdb=" O GLU G 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG G 614 " --> pdb=" O MET G 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET G 580 " --> pdb=" O ARG G 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 616 " --> pdb=" O GLY G 578 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY G 578 " --> pdb=" O LEU G 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL G 618 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 15.569A pdb=" N ILE G 574 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU F 483 " --> pdb=" O ILE G 574 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 576 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 362 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU F 612 " --> pdb=" O ASP F 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP F 582 " --> pdb=" O GLU F 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG F 614 " --> pdb=" O MET F 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET F 580 " --> pdb=" O ARG F 614 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU F 616 " --> pdb=" O GLY F 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY F 578 " --> pdb=" O LEU F 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL F 618 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 15.541A pdb=" N ILE F 574 " --> pdb=" O LEU E 483 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU E 483 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 576 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN E 362 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU E 612 " --> pdb=" O ASP E 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP E 582 " --> pdb=" O GLU E 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG E 614 " --> pdb=" O MET E 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET E 580 " --> pdb=" O ARG E 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU E 616 " --> pdb=" O GLY E 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY E 578 " --> pdb=" O LEU E 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 15.568A pdb=" N ILE E 574 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N LEU D 483 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU E 576 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 362 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU D 612 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP D 582 " --> pdb=" O GLU D 612 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG D 614 " --> pdb=" O MET D 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET D 580 " --> pdb=" O ARG D 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 616 " --> pdb=" O GLY D 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY D 578 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL D 618 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 15.530A pdb=" N ILE D 574 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 12.216A pdb=" N LEU C 483 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 576 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 362 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU C 612 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP C 582 " --> pdb=" O GLU C 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG C 614 " --> pdb=" O MET C 580 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET C 580 " --> pdb=" O ARG C 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 616 " --> pdb=" O GLY C 578 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY C 578 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 15.555A pdb=" N ILE C 574 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 12.237A pdb=" N LEU B 483 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 576 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 362 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU B 612 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP B 582 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 614 " --> pdb=" O MET B 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 580 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 616 " --> pdb=" O GLY B 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY B 578 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 618 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 15.540A pdb=" N ILE B 574 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU A 483 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 576 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 362 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 612 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP A 582 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG A 614 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET A 580 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 616 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY A 578 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 515 through 519 removed outlier: 3.671A pdb=" N ASP A 495 " --> pdb=" O PHE B 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 556 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AC2, first strand: chain 'A' and resid 523 through 525 Processing sheet with id=AC3, first strand: chain 'A' and resid 546 through 548 removed outlier: 3.772A pdb=" N VAL A 556 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP O 495 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 288 Processing sheet with id=AC5, first strand: chain 'B' and resid 515 through 519 removed outlier: 3.680A pdb=" N ASP B 495 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 556 " --> pdb=" O GLU C 548 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 523 through 525 Processing sheet with id=AC7, first strand: chain 'B' and resid 523 through 525 Processing sheet with id=AC8, first strand: chain 'C' and resid 284 through 288 Processing sheet with id=AC9, first strand: chain 'C' and resid 515 through 519 removed outlier: 3.663A pdb=" N ASP C 495 " --> pdb=" O PHE D 557 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 556 " --> pdb=" O GLU D 548 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 523 through 525 Processing sheet with id=AD2, first strand: chain 'C' and resid 523 through 525 Processing sheet with id=AD3, first strand: chain 'D' and resid 284 through 288 Processing sheet with id=AD4, first strand: chain 'D' and resid 515 through 519 removed outlier: 3.695A pdb=" N ASP D 495 " --> pdb=" O PHE E 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 556 " --> pdb=" O GLU E 548 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 523 through 525 Processing sheet with id=AD6, first strand: chain 'D' and resid 523 through 525 Processing sheet with id=AD7, first strand: chain 'E' and resid 284 through 288 Processing sheet with id=AD8, first strand: chain 'E' and resid 515 through 519 removed outlier: 3.660A pdb=" N ASP E 495 " --> pdb=" O PHE F 557 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 556 " --> pdb=" O GLU F 548 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 523 through 525 Processing sheet with id=AE1, first strand: chain 'E' and resid 523 through 525 Processing sheet with id=AE2, first strand: chain 'F' and resid 284 through 288 Processing sheet with id=AE3, first strand: chain 'F' and resid 515 through 519 removed outlier: 3.635A pdb=" N ASP F 495 " --> pdb=" O PHE G 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 556 " --> pdb=" O GLU G 548 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 523 through 525 Processing sheet with id=AE5, first strand: chain 'F' and resid 523 through 525 Processing sheet with id=AE6, first strand: chain 'G' and resid 284 through 288 Processing sheet with id=AE7, first strand: chain 'G' and resid 515 through 519 removed outlier: 3.748A pdb=" N ASP G 495 " --> pdb=" O PHE H 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL H 556 " --> pdb=" O GLU H 548 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 523 through 525 Processing sheet with id=AE9, first strand: chain 'G' and resid 523 through 525 Processing sheet with id=AF1, first strand: chain 'H' and resid 284 through 288 Processing sheet with id=AF2, first strand: chain 'H' and resid 515 through 519 removed outlier: 3.684A pdb=" N ASP H 495 " --> pdb=" O PHE I 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 556 " --> pdb=" O GLU I 548 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 523 through 525 Processing sheet with id=AF4, first strand: chain 'H' and resid 523 through 525 Processing sheet with id=AF5, first strand: chain 'I' and resid 284 through 288 Processing sheet with id=AF6, first strand: chain 'I' and resid 515 through 519 removed outlier: 3.669A pdb=" N ASP I 495 " --> pdb=" O PHE J 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL J 556 " --> pdb=" O GLU J 548 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 523 through 525 Processing sheet with id=AF8, first strand: chain 'I' and resid 523 through 525 Processing sheet with id=AF9, first strand: chain 'J' and resid 284 through 288 Processing sheet with id=AG1, first strand: chain 'J' and resid 515 through 519 removed outlier: 3.670A pdb=" N ASP J 495 " --> pdb=" O PHE K 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL K 556 " --> pdb=" O GLU K 548 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 523 through 525 Processing sheet with id=AG3, first strand: chain 'J' and resid 523 through 525 Processing sheet with id=AG4, first strand: chain 'K' and resid 284 through 288 Processing sheet with id=AG5, first strand: chain 'K' and resid 515 through 519 removed outlier: 3.681A pdb=" N ASP K 495 " --> pdb=" O PHE L 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 556 " --> pdb=" O GLU L 548 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 523 through 525 Processing sheet with id=AG7, first strand: chain 'K' and resid 523 through 525 Processing sheet with id=AG8, first strand: chain 'L' and resid 284 through 288 Processing sheet with id=AG9, first strand: chain 'L' and resid 515 through 519 removed outlier: 3.671A pdb=" N ASP L 495 " --> pdb=" O PHE M 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 556 " --> pdb=" O GLU M 548 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 523 through 525 Processing sheet with id=AH2, first strand: chain 'L' and resid 523 through 525 Processing sheet with id=AH3, first strand: chain 'M' and resid 284 through 288 Processing sheet with id=AH4, first strand: chain 'M' and resid 515 through 519 removed outlier: 3.676A pdb=" N ASP M 495 " --> pdb=" O PHE N 557 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL N 556 " --> pdb=" O GLU N 548 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 523 through 525 Processing sheet with id=AH6, first strand: chain 'M' and resid 523 through 525 Processing sheet with id=AH7, first strand: chain 'N' and resid 284 through 288 Processing sheet with id=AH8, first strand: chain 'N' and resid 515 through 519 removed outlier: 3.673A pdb=" N ASP N 495 " --> pdb=" O PHE O 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL O 556 " --> pdb=" O GLU O 548 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 523 through 525 Processing sheet with id=AI1, first strand: chain 'N' and resid 523 through 525 Processing sheet with id=AI2, first strand: chain 'O' and resid 284 through 288 Processing sheet with id=AI3, first strand: chain 'O' and resid 523 through 525 Processing sheet with id=AI4, first strand: chain 'O' and resid 523 through 525 2370 hydrogen bonds defined for protein. 6345 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: 12.05 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 12562 1.33 - 1.45: 4156 1.45 - 1.57: 22792 1.57 - 1.69: 0 1.69 - 1.80: 330 Bond restraints: 39840 Sorted by residual: bond pdb=" C ASN E 430 " pdb=" N PRO E 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.67e+01 bond pdb=" C ASN L 430 " pdb=" N PRO L 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.66e+01 bond pdb=" C ASN K 430 " pdb=" N PRO K 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.65e+01 bond pdb=" C ASN G 430 " pdb=" N PRO G 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.64e+01 bond pdb=" C ASN J 430 " pdb=" N PRO J 431 " ideal model delta sigma weight residual 1.329 1.380 -0.051 1.25e-02 6.40e+03 1.63e+01 ... (remaining 39835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 51599 1.92 - 3.84: 1883 3.84 - 5.75: 323 5.75 - 7.67: 45 7.67 - 9.59: 45 Bond angle restraints: 53895 Sorted by residual: angle pdb=" N PRO O 592 " pdb=" CA PRO O 592 " pdb=" C PRO O 592 " ideal model delta sigma weight residual 113.47 119.10 -5.63 1.43e+00 4.89e-01 1.55e+01 angle pdb=" N PRO C 592 " pdb=" CA PRO C 592 " pdb=" C PRO C 592 " ideal model delta sigma weight residual 113.47 119.08 -5.61 1.43e+00 4.89e-01 1.54e+01 angle pdb=" N PRO G 592 " pdb=" CA PRO G 592 " pdb=" C PRO G 592 " ideal model delta sigma weight residual 113.47 119.07 -5.60 1.43e+00 4.89e-01 1.54e+01 angle pdb=" N PRO D 592 " pdb=" CA PRO D 592 " pdb=" C PRO D 592 " ideal model delta sigma weight residual 113.47 119.07 -5.60 1.43e+00 4.89e-01 1.53e+01 angle pdb=" N PRO H 592 " pdb=" CA PRO H 592 " pdb=" C PRO H 592 " ideal model delta sigma weight residual 113.47 119.06 -5.59 1.43e+00 4.89e-01 1.53e+01 ... (remaining 53890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 23370 16.16 - 32.31: 805 32.31 - 48.47: 140 48.47 - 64.63: 0 64.63 - 80.79: 75 Dihedral angle restraints: 24390 sinusoidal: 9525 harmonic: 14865 Sorted by residual: dihedral pdb=" CA VAL A 591 " pdb=" C VAL A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL J 591 " pdb=" C VAL J 591 " pdb=" N PRO J 592 " pdb=" CA PRO J 592 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL L 591 " pdb=" C VAL L 591 " pdb=" N PRO L 592 " pdb=" CA PRO L 592 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 24387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4793 0.057 - 0.114: 1272 0.114 - 0.171: 340 0.171 - 0.228: 45 0.228 - 0.285: 30 Chirality restraints: 6480 Sorted by residual: chirality pdb=" CB ILE J 400 " pdb=" CA ILE J 400 " pdb=" CG1 ILE J 400 " pdb=" CG2 ILE J 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 400 " pdb=" CA ILE B 400 " pdb=" CG1 ILE B 400 " pdb=" CG2 ILE B 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE H 400 " pdb=" CA ILE H 400 " pdb=" CG1 ILE H 400 " pdb=" CG2 ILE H 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 6477 not shown) Planarity restraints: 6990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 549 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C GLY A 549 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 549 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 550 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 549 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C GLY C 549 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY C 549 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 550 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 549 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C GLY B 549 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY B 549 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN B 550 " -0.013 2.00e-02 2.50e+03 ... (remaining 6987 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3838 2.75 - 3.28: 35257 3.28 - 3.82: 60712 3.82 - 4.36: 68437 4.36 - 4.90: 130206 Nonbonded interactions: 298450 Sorted by model distance: nonbonded pdb=" OG SER G 327 " pdb=" OG1 THR H 307 " model vdw 2.206 3.040 nonbonded pdb=" OG SER I 327 " pdb=" OG1 THR J 307 " model vdw 2.231 3.040 nonbonded pdb=" OG SER K 327 " pdb=" OG1 THR L 307 " model vdw 2.233 3.040 nonbonded pdb=" OG SER D 327 " pdb=" OG1 THR E 307 " model vdw 2.234 3.040 nonbonded pdb=" OG SER J 327 " pdb=" OG1 THR K 307 " model vdw 2.235 3.040 ... (remaining 298445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.490 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 36.840 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.006 0.052 39840 Z= 0.276 Angle : 0.890 9.589 53895 Z= 0.479 Chirality : 0.059 0.285 6480 Planarity : 0.006 0.048 6990 Dihedral : 10.333 80.787 14790 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.69 % Allowed : 4.34 % Favored : 94.97 % 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: -5.31 (0.10), residues: 5130 helix: -3.94 (0.07), residues: 1245 sheet: -2.88 (0.10), residues: 2505 loop : -3.56 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 643 TYR 0.020 0.002 TYR M 648 PHE 0.025 0.002 PHE G 489 TRP 0.008 0.001 TRP C 459 HIS 0.003 0.001 HIS F 659 Details of bonding type rmsd covalent geometry : bond 0.00575 (39840) covalent geometry : angle 0.88976 (53895) hydrogen bonds : bond 0.21910 ( 2010) hydrogen bonds : angle 12.21241 ( 6345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1137 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8370 (tptp) REVERT: A 346 MET cc_start: 0.8663 (tpp) cc_final: 0.8424 (mmm) REVERT: A 350 GLN cc_start: 0.8939 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 359 ARG cc_start: 0.7769 (tpt-90) cc_final: 0.7567 (tpt-90) REVERT: A 392 MET cc_start: 0.7226 (mpt) cc_final: 0.6996 (mpp) REVERT: A 462 LEU cc_start: 0.9066 (tp) cc_final: 0.8844 (tp) REVERT: A 540 ILE cc_start: 0.8744 (tt) cc_final: 0.8483 (mp) REVERT: A 541 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7341 (tm-30) REVERT: A 649 ARG cc_start: 0.8429 (mmt180) cc_final: 0.8214 (mmm-85) REVERT: B 291 TYR cc_start: 0.9246 (m-80) cc_final: 0.9037 (m-80) REVERT: B 302 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8352 (tptt) REVERT: B 346 MET cc_start: 0.8878 (tpp) cc_final: 0.8444 (mmm) REVERT: B 350 GLN cc_start: 0.8991 (tt0) cc_final: 0.8663 (tm-30) REVERT: B 359 ARG cc_start: 0.8000 (tpt-90) cc_final: 0.7774 (tpt-90) REVERT: B 392 MET cc_start: 0.7303 (mpt) cc_final: 0.7006 (mpp) REVERT: B 447 PHE cc_start: 0.8480 (t80) cc_final: 0.7966 (t80) REVERT: B 462 LEU cc_start: 0.8992 (tp) cc_final: 0.8504 (tt) REVERT: B 540 ILE cc_start: 0.8667 (tt) cc_final: 0.8407 (mp) REVERT: B 541 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7016 (tm-30) REVERT: B 639 TYR cc_start: 0.8300 (t80) cc_final: 0.7916 (t80) REVERT: B 643 ARG cc_start: 0.8390 (ttt180) cc_final: 0.7924 (ttt-90) REVERT: B 649 ARG cc_start: 0.8676 (mmt180) cc_final: 0.8366 (mmm-85) REVERT: C 346 MET cc_start: 0.8502 (tpp) cc_final: 0.8241 (mmm) REVERT: C 392 MET cc_start: 0.7510 (mpt) cc_final: 0.7221 (mpp) REVERT: C 462 LEU cc_start: 0.9134 (tp) cc_final: 0.8675 (tt) REVERT: C 540 ILE cc_start: 0.8693 (tt) cc_final: 0.8451 (mp) REVERT: C 541 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7496 (tm-30) REVERT: C 639 TYR cc_start: 0.8459 (t80) cc_final: 0.8243 (t80) REVERT: C 649 ARG cc_start: 0.8552 (mmt180) cc_final: 0.8237 (mmm-85) REVERT: D 291 TYR cc_start: 0.9264 (m-80) cc_final: 0.9047 (m-80) REVERT: D 346 MET cc_start: 0.8818 (tpp) cc_final: 0.8440 (mmm) REVERT: D 350 GLN cc_start: 0.8911 (tt0) cc_final: 0.8471 (tm-30) REVERT: D 392 MET cc_start: 0.7149 (mpt) cc_final: 0.6835 (mpp) REVERT: D 447 PHE cc_start: 0.8521 (t80) cc_final: 0.8310 (t80) REVERT: D 460 MET cc_start: 0.7891 (ttp) cc_final: 0.7545 (ttm) REVERT: D 462 LEU cc_start: 0.8904 (tp) cc_final: 0.8424 (tt) REVERT: D 487 GLU cc_start: 0.7897 (pt0) cc_final: 0.7663 (pt0) REVERT: D 519 LYS cc_start: 0.8850 (mttm) cc_final: 0.8607 (mmtm) REVERT: D 523 MET cc_start: 0.7033 (ttm) cc_final: 0.6602 (mtp) REVERT: D 540 ILE cc_start: 0.8739 (tt) cc_final: 0.8499 (mp) REVERT: D 541 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7045 (tm-30) REVERT: D 649 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8275 (mmm-85) REVERT: E 291 TYR cc_start: 0.9340 (m-80) cc_final: 0.9138 (m-80) REVERT: E 346 MET cc_start: 0.8576 (tpp) cc_final: 0.8297 (mmm) REVERT: E 350 GLN cc_start: 0.8833 (tt0) cc_final: 0.8486 (tm-30) REVERT: E 392 MET cc_start: 0.7255 (mpt) cc_final: 0.6964 (mpp) REVERT: E 462 LEU cc_start: 0.9028 (tp) cc_final: 0.8510 (tt) REVERT: E 541 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7326 (tm-30) REVERT: E 612 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 649 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8276 (mmm-85) REVERT: F 346 MET cc_start: 0.8639 (tpp) cc_final: 0.8332 (mmm) REVERT: F 350 GLN cc_start: 0.9033 (tt0) cc_final: 0.8731 (tm-30) REVERT: F 392 MET cc_start: 0.7343 (mpt) cc_final: 0.7117 (mpp) REVERT: F 462 LEU cc_start: 0.9055 (tp) cc_final: 0.8561 (tt) REVERT: F 540 ILE cc_start: 0.8743 (tt) cc_final: 0.8518 (mp) REVERT: F 643 ARG cc_start: 0.8373 (ttt180) cc_final: 0.8085 (tpt-90) REVERT: G 346 MET cc_start: 0.8724 (tpp) cc_final: 0.8331 (mmm) REVERT: G 350 GLN cc_start: 0.8948 (tt0) cc_final: 0.8588 (tm-30) REVERT: G 359 ARG cc_start: 0.8065 (tpt-90) cc_final: 0.7823 (tpt-90) REVERT: G 392 MET cc_start: 0.7279 (mpt) cc_final: 0.7052 (mpp) REVERT: G 462 LEU cc_start: 0.8983 (tp) cc_final: 0.8677 (tp) REVERT: G 541 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7166 (tm-30) REVERT: G 643 ARG cc_start: 0.8281 (ttt180) cc_final: 0.8057 (ttt-90) REVERT: G 649 ARG cc_start: 0.8586 (mmt180) cc_final: 0.8231 (mmm-85) REVERT: H 291 TYR cc_start: 0.9316 (m-80) cc_final: 0.9042 (m-80) REVERT: H 302 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8369 (tptt) REVERT: H 346 MET cc_start: 0.8681 (tpp) cc_final: 0.8380 (mmm) REVERT: H 350 GLN cc_start: 0.8977 (tt0) cc_final: 0.8758 (tm-30) REVERT: H 392 MET cc_start: 0.7124 (mpt) cc_final: 0.6915 (mpp) REVERT: H 541 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7201 (tm-30) REVERT: I 302 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8227 (tptt) REVERT: I 346 MET cc_start: 0.8575 (tpp) cc_final: 0.8238 (mmm) REVERT: I 350 GLN cc_start: 0.8968 (tt0) cc_final: 0.8762 (tm-30) REVERT: I 460 MET cc_start: 0.8036 (ttp) cc_final: 0.7638 (ttm) REVERT: I 462 LEU cc_start: 0.9051 (tp) cc_final: 0.8478 (mp) REVERT: I 541 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7487 (tm-30) REVERT: J 291 TYR cc_start: 0.9278 (m-80) cc_final: 0.9053 (m-80) REVERT: J 346 MET cc_start: 0.8763 (tpp) cc_final: 0.8419 (mmm) REVERT: J 350 GLN cc_start: 0.9008 (tt0) cc_final: 0.8668 (tm-30) REVERT: J 392 MET cc_start: 0.7244 (mpt) cc_final: 0.6923 (mpp) REVERT: J 462 LEU cc_start: 0.8964 (tp) cc_final: 0.8652 (tp) REVERT: J 487 GLU cc_start: 0.7850 (pt0) cc_final: 0.7616 (pt0) REVERT: J 491 MET cc_start: 0.7497 (ttt) cc_final: 0.7241 (ttm) REVERT: J 541 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7253 (tm-30) REVERT: J 643 ARG cc_start: 0.8394 (ttt180) cc_final: 0.8019 (tpt-90) REVERT: J 649 ARG cc_start: 0.8611 (mmt180) cc_final: 0.8313 (mmm-85) REVERT: K 291 TYR cc_start: 0.9260 (m-80) cc_final: 0.9042 (m-80) REVERT: K 346 MET cc_start: 0.8704 (tpp) cc_final: 0.8486 (mmm) REVERT: K 350 GLN cc_start: 0.8997 (tt0) cc_final: 0.8677 (tm-30) REVERT: K 357 ASP cc_start: 0.7202 (t0) cc_final: 0.6984 (t0) REVERT: K 392 MET cc_start: 0.7265 (mpt) cc_final: 0.6779 (mpp) REVERT: K 541 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7084 (tm-30) REVERT: K 639 TYR cc_start: 0.8437 (t80) cc_final: 0.7920 (t80) REVERT: K 643 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8188 (ttt-90) REVERT: L 291 TYR cc_start: 0.9265 (m-80) cc_final: 0.9007 (m-80) REVERT: L 346 MET cc_start: 0.8568 (tpp) cc_final: 0.8225 (mmm) REVERT: L 350 GLN cc_start: 0.8980 (tt0) cc_final: 0.8631 (tm-30) REVERT: L 541 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7359 (tm-30) REVERT: L 639 TYR cc_start: 0.8251 (t80) cc_final: 0.7825 (t80) REVERT: L 643 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7876 (ttt-90) REVERT: M 291 TYR cc_start: 0.9291 (m-80) cc_final: 0.9089 (m-80) REVERT: M 346 MET cc_start: 0.8787 (tpp) cc_final: 0.8493 (mmm) REVERT: M 350 GLN cc_start: 0.8886 (tt0) cc_final: 0.8667 (tm-30) REVERT: M 392 MET cc_start: 0.7443 (mpt) cc_final: 0.7155 (mpp) REVERT: M 462 LEU cc_start: 0.8988 (tp) cc_final: 0.8541 (tt) REVERT: M 541 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7413 (tm-30) REVERT: N 346 MET cc_start: 0.8657 (tpp) cc_final: 0.8393 (mmm) REVERT: N 350 GLN cc_start: 0.8932 (tt0) cc_final: 0.8636 (tm-30) REVERT: N 392 MET cc_start: 0.7469 (mpt) cc_final: 0.7257 (mpp) REVERT: N 541 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7324 (tm-30) REVERT: O 291 TYR cc_start: 0.9300 (m-80) cc_final: 0.9016 (m-80) REVERT: O 346 MET cc_start: 0.8633 (tpp) cc_final: 0.8398 (mmm) REVERT: O 350 GLN cc_start: 0.8963 (tt0) cc_final: 0.8683 (tm-30) REVERT: O 460 MET cc_start: 0.7921 (ttp) cc_final: 0.7520 (ttm) REVERT: O 462 LEU cc_start: 0.9050 (tp) cc_final: 0.8503 (mp) REVERT: O 541 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7480 (tm-30) REVERT: O 649 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8203 (mmm-85) outliers start: 30 outliers final: 15 residues processed: 1167 average time/residue: 0.2910 time to fit residues: 522.5205 Evaluate side-chains 650 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 635 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain O residue 477 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 364 HIS ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 364 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 364 HIS ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN D 364 HIS ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN E 335 ASN E 364 HIS ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 335 ASN F 364 HIS ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN G 335 ASN G 364 HIS ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 364 HIS ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 ASN I 364 HIS ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 ASN J 364 HIS ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN K 364 HIS ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 ASN L 364 HIS ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 ASN M 364 HIS ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 ASN N 335 ASN N 364 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 ASN O 364 HIS ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097764 restraints weight = 56372.567| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.28 r_work: 0.3444 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 39840 Z= 0.279 Angle : 0.729 8.384 53895 Z= 0.385 Chirality : 0.050 0.157 6480 Planarity : 0.006 0.042 6990 Dihedral : 5.928 28.186 5430 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.15 % Allowed : 13.36 % Favored : 83.49 % 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: -4.11 (0.10), residues: 5130 helix: -1.63 (0.12), residues: 1155 sheet: -2.70 (0.09), residues: 2535 loop : -3.08 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 626 TYR 0.022 0.002 TYR O 639 PHE 0.024 0.003 PHE D 619 TRP 0.005 0.001 TRP K 459 HIS 0.004 0.001 HIS I 364 Details of bonding type rmsd covalent geometry : bond 0.00620 (39840) covalent geometry : angle 0.72916 (53895) hydrogen bonds : bond 0.04301 ( 2010) hydrogen bonds : angle 6.51777 ( 6345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 664 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8321 (tptt) REVERT: A 332 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8706 (tmtt) REVERT: A 333 HIS cc_start: 0.8607 (m90) cc_final: 0.8289 (m90) REVERT: A 346 MET cc_start: 0.8898 (tpp) cc_final: 0.8430 (mmm) REVERT: A 350 GLN cc_start: 0.9085 (tt0) cc_final: 0.8635 (pp30) REVERT: A 392 MET cc_start: 0.7910 (mpt) cc_final: 0.7484 (mpp) REVERT: A 462 LEU cc_start: 0.9074 (tp) cc_final: 0.8762 (tp) REVERT: A 541 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7688 (tm-30) REVERT: A 553 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7317 (tp) REVERT: A 554 ASP cc_start: 0.8147 (t0) cc_final: 0.7895 (m-30) REVERT: A 639 TYR cc_start: 0.8260 (t80) cc_final: 0.7858 (t80) REVERT: A 649 ARG cc_start: 0.8459 (mmt180) cc_final: 0.8193 (mmm-85) REVERT: B 302 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8247 (tptt) REVERT: B 346 MET cc_start: 0.8987 (tpp) cc_final: 0.8332 (tpp) REVERT: B 350 GLN cc_start: 0.9114 (tt0) cc_final: 0.8654 (pp30) REVERT: B 359 ARG cc_start: 0.8240 (tpt-90) cc_final: 0.7930 (tpt-90) REVERT: B 392 MET cc_start: 0.7891 (mpt) cc_final: 0.7412 (mpp) REVERT: B 462 LEU cc_start: 0.8996 (tp) cc_final: 0.8778 (tp) REVERT: B 541 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7830 (tm-30) REVERT: B 554 ASP cc_start: 0.8032 (t0) cc_final: 0.7524 (m-30) REVERT: B 639 TYR cc_start: 0.8419 (t80) cc_final: 0.8186 (t80) REVERT: B 649 ARG cc_start: 0.8663 (mmt180) cc_final: 0.8316 (mmm-85) REVERT: C 332 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8793 (tmtt) REVERT: C 333 HIS cc_start: 0.8686 (m-70) cc_final: 0.7906 (m90) REVERT: C 392 MET cc_start: 0.7963 (mpt) cc_final: 0.7509 (mpp) REVERT: C 462 LEU cc_start: 0.8994 (tp) cc_final: 0.8785 (tp) REVERT: C 541 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7759 (tm-30) REVERT: C 639 TYR cc_start: 0.8407 (t80) cc_final: 0.8145 (t80) REVERT: C 649 ARG cc_start: 0.8618 (mmt180) cc_final: 0.8240 (mmm-85) REVERT: D 332 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8868 (tmtt) REVERT: D 333 HIS cc_start: 0.8606 (m90) cc_final: 0.7919 (m-70) REVERT: D 346 MET cc_start: 0.8910 (tpp) cc_final: 0.8520 (tpp) REVERT: D 350 GLN cc_start: 0.9033 (tt0) cc_final: 0.8801 (pp30) REVERT: D 359 ARG cc_start: 0.7989 (tpt-90) cc_final: 0.7662 (tpt-90) REVERT: D 392 MET cc_start: 0.7941 (mpt) cc_final: 0.7428 (mpp) REVERT: D 460 MET cc_start: 0.7763 (ttp) cc_final: 0.7441 (ttm) REVERT: D 462 LEU cc_start: 0.8958 (tp) cc_final: 0.8699 (tp) REVERT: D 541 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7528 (tm-30) REVERT: D 649 ARG cc_start: 0.8329 (mmt180) cc_final: 0.8104 (mmm-85) REVERT: E 346 MET cc_start: 0.9045 (tpp) cc_final: 0.8528 (tpp) REVERT: E 350 GLN cc_start: 0.8966 (tt0) cc_final: 0.8539 (pp30) REVERT: E 354 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8527 (mt-10) REVERT: E 359 ARG cc_start: 0.8066 (tpt-90) cc_final: 0.7749 (tpt-90) REVERT: E 392 MET cc_start: 0.8050 (mpt) cc_final: 0.7835 (mpt) REVERT: E 442 GLN cc_start: 0.9318 (pp30) cc_final: 0.8994 (pp30) REVERT: E 462 LEU cc_start: 0.9012 (tp) cc_final: 0.8456 (mp) REVERT: E 523 MET cc_start: 0.7800 (ttm) cc_final: 0.7579 (ttm) REVERT: E 541 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7714 (tm-30) REVERT: E 580 MET cc_start: 0.8729 (mpp) cc_final: 0.8469 (mpp) REVERT: E 612 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7721 (tm-30) REVERT: E 639 TYR cc_start: 0.8360 (t80) cc_final: 0.7938 (t80) REVERT: E 649 ARG cc_start: 0.8536 (mmt180) cc_final: 0.8313 (mmm-85) REVERT: F 299 ASP cc_start: 0.8285 (m-30) cc_final: 0.7934 (m-30) REVERT: F 346 MET cc_start: 0.8912 (tpp) cc_final: 0.8530 (tpp) REVERT: F 350 GLN cc_start: 0.9045 (tt0) cc_final: 0.8489 (pp30) REVERT: F 359 ARG cc_start: 0.7945 (tpt-90) cc_final: 0.7642 (tpt-90) REVERT: F 392 MET cc_start: 0.7995 (mpt) cc_final: 0.7555 (mpp) REVERT: F 462 LEU cc_start: 0.8934 (tp) cc_final: 0.8712 (tp) REVERT: F 554 ASP cc_start: 0.8147 (t0) cc_final: 0.7787 (m-30) REVERT: G 332 LYS cc_start: 0.8764 (tmtt) cc_final: 0.8215 (ttmm) REVERT: G 350 GLN cc_start: 0.9110 (tt0) cc_final: 0.8617 (pp30) REVERT: G 359 ARG cc_start: 0.8277 (tpt-90) cc_final: 0.7934 (tpt-90) REVERT: G 392 MET cc_start: 0.8018 (mpt) cc_final: 0.7519 (mpp) REVERT: G 462 LEU cc_start: 0.9098 (tp) cc_final: 0.8799 (tp) REVERT: G 491 MET cc_start: 0.8600 (ttm) cc_final: 0.8393 (ttm) REVERT: G 541 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7739 (tm-30) REVERT: G 554 ASP cc_start: 0.8049 (t0) cc_final: 0.7837 (m-30) REVERT: G 649 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8114 (mmm160) REVERT: H 302 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8278 (tptt) REVERT: H 346 MET cc_start: 0.8805 (tpp) cc_final: 0.8252 (tpp) REVERT: H 350 GLN cc_start: 0.9145 (tt0) cc_final: 0.8648 (pp30) REVERT: H 541 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7717 (tm-30) REVERT: H 554 ASP cc_start: 0.7844 (t0) cc_final: 0.7632 (m-30) REVERT: H 580 MET cc_start: 0.8615 (mpp) cc_final: 0.8390 (mpp) REVERT: H 639 TYR cc_start: 0.8572 (t80) cc_final: 0.8319 (t80) REVERT: I 332 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8718 (tmtt) REVERT: I 346 MET cc_start: 0.8926 (tpp) cc_final: 0.8385 (mmm) REVERT: I 350 GLN cc_start: 0.9119 (tt0) cc_final: 0.8602 (pp30) REVERT: I 359 ARG cc_start: 0.8053 (tpt-90) cc_final: 0.7589 (tpt-90) REVERT: I 366 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: I 371 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7976 (tm-30) REVERT: I 460 MET cc_start: 0.7835 (ttp) cc_final: 0.7310 (ttm) REVERT: I 462 LEU cc_start: 0.9045 (tp) cc_final: 0.8541 (mp) REVERT: I 541 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7850 (tm-30) REVERT: I 554 ASP cc_start: 0.7879 (t0) cc_final: 0.7557 (m-30) REVERT: I 614 ARG cc_start: 0.8651 (tmm-80) cc_final: 0.8394 (tmm-80) REVERT: I 639 TYR cc_start: 0.8533 (t80) cc_final: 0.8220 (t80) REVERT: J 332 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8771 (tmtt) REVERT: J 346 MET cc_start: 0.8893 (tpp) cc_final: 0.8600 (tpp) REVERT: J 350 GLN cc_start: 0.9035 (tt0) cc_final: 0.8503 (pp30) REVERT: J 359 ARG cc_start: 0.8076 (tpt-90) cc_final: 0.7791 (tpt-90) REVERT: J 392 MET cc_start: 0.7800 (mpt) cc_final: 0.7275 (mpp) REVERT: J 462 LEU cc_start: 0.9002 (tp) cc_final: 0.8743 (tp) REVERT: J 541 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7559 (tm-30) REVERT: J 554 ASP cc_start: 0.7923 (t0) cc_final: 0.7562 (m-30) REVERT: J 639 TYR cc_start: 0.8542 (t80) cc_final: 0.8328 (t80) REVERT: J 649 ARG cc_start: 0.8643 (mmt180) cc_final: 0.8306 (mmm-85) REVERT: K 346 MET cc_start: 0.8897 (tpp) cc_final: 0.8417 (mmm) REVERT: K 350 GLN cc_start: 0.9066 (tt0) cc_final: 0.8503 (pp30) REVERT: K 392 MET cc_start: 0.7719 (mpt) cc_final: 0.7230 (mpp) REVERT: K 462 LEU cc_start: 0.9007 (tp) cc_final: 0.8754 (tp) REVERT: K 516 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: K 523 MET cc_start: 0.7803 (ttt) cc_final: 0.7565 (ttt) REVERT: K 541 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7886 (tm-30) REVERT: K 554 ASP cc_start: 0.8034 (t0) cc_final: 0.7678 (m-30) REVERT: K 610 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8285 (ttmm) REVERT: K 639 TYR cc_start: 0.8503 (t80) cc_final: 0.7708 (t80) REVERT: L 346 MET cc_start: 0.8725 (tpp) cc_final: 0.8197 (mmm) REVERT: L 350 GLN cc_start: 0.9083 (tt0) cc_final: 0.8485 (pp30) REVERT: L 442 GLN cc_start: 0.9356 (pp30) cc_final: 0.9002 (pp30) REVERT: L 516 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: L 541 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7760 (tm-30) REVERT: L 639 TYR cc_start: 0.8249 (t80) cc_final: 0.8001 (t80) REVERT: M 299 ASP cc_start: 0.8280 (m-30) cc_final: 0.8045 (m-30) REVERT: M 332 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8737 (tmtt) REVERT: M 346 MET cc_start: 0.8957 (tpp) cc_final: 0.8404 (tpp) REVERT: M 350 GLN cc_start: 0.9003 (tt0) cc_final: 0.8608 (pp30) REVERT: M 460 MET cc_start: 0.6739 (ttm) cc_final: 0.6411 (ttm) REVERT: M 462 LEU cc_start: 0.8943 (tp) cc_final: 0.8679 (tp) REVERT: M 541 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7640 (tm-30) REVERT: M 626 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.6277 (mmm-85) REVERT: N 332 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8833 (tmtt) REVERT: N 350 GLN cc_start: 0.9071 (tt0) cc_final: 0.8753 (pp30) REVERT: N 392 MET cc_start: 0.7882 (mpt) cc_final: 0.7477 (mpp) REVERT: N 460 MET cc_start: 0.7120 (ttm) cc_final: 0.6697 (ttm) REVERT: N 487 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: N 541 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7717 (tm-30) REVERT: N 553 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7205 (tp) REVERT: N 554 ASP cc_start: 0.7954 (t0) cc_final: 0.7584 (m-30) REVERT: O 346 MET cc_start: 0.8933 (tpp) cc_final: 0.8487 (mmm) REVERT: O 350 GLN cc_start: 0.9067 (tt0) cc_final: 0.8579 (pp30) REVERT: O 359 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7709 (tpt-90) REVERT: O 460 MET cc_start: 0.7743 (ttp) cc_final: 0.7273 (ttm) REVERT: O 462 LEU cc_start: 0.8985 (tp) cc_final: 0.8463 (mp) REVERT: O 541 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7984 (tm-30) REVERT: O 643 ARG cc_start: 0.8386 (ttt180) cc_final: 0.8122 (ttt180) outliers start: 137 outliers final: 85 residues processed: 777 average time/residue: 0.2606 time to fit residues: 319.9725 Evaluate side-chains 634 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 543 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 664 ILE Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 480 ILE Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 664 ILE Chi-restraints excluded: chain L residue 402 ILE Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 516 GLU Chi-restraints excluded: chain L residue 546 LYS Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 402 ILE Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 664 ILE Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 487 GLU Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain N residue 664 ILE Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 664 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 235 optimal weight: 0.9980 chunk 505 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 448 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 283 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 GLN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN H 652 GLN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 GLN ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 652 GLN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 ASN O 652 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.140328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097370 restraints weight = 56158.189| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.28 r_work: 0.3354 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 39840 Z= 0.230 Angle : 0.645 9.380 53895 Z= 0.339 Chirality : 0.048 0.161 6480 Planarity : 0.005 0.039 6990 Dihedral : 5.502 25.731 5430 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.52 % Allowed : 14.60 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.11), residues: 5130 helix: -0.64 (0.14), residues: 1155 sheet: -2.47 (0.10), residues: 2505 loop : -2.92 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 626 TYR 0.020 0.002 TYR O 639 PHE 0.020 0.002 PHE D 619 TRP 0.005 0.001 TRP K 459 HIS 0.007 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00507 (39840) covalent geometry : angle 0.64490 (53895) hydrogen bonds : bond 0.03797 ( 2010) hydrogen bonds : angle 5.82753 ( 6345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 588 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8721 (tmtt) REVERT: A 333 HIS cc_start: 0.8628 (m90) cc_final: 0.8387 (m90) REVERT: A 346 MET cc_start: 0.8900 (tpp) cc_final: 0.8400 (mmm) REVERT: A 392 MET cc_start: 0.8036 (mpt) cc_final: 0.7604 (mpp) REVERT: A 462 LEU cc_start: 0.9024 (tp) cc_final: 0.8763 (tp) REVERT: A 541 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7773 (tm-30) REVERT: A 553 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 554 ASP cc_start: 0.8178 (t0) cc_final: 0.7935 (m-30) REVERT: A 649 ARG cc_start: 0.8558 (mmt180) cc_final: 0.8209 (mmm-85) REVERT: B 346 MET cc_start: 0.8989 (tpp) cc_final: 0.8365 (tpp) REVERT: B 350 GLN cc_start: 0.9154 (tt0) cc_final: 0.8680 (pp30) REVERT: B 359 ARG cc_start: 0.8237 (tpt-90) cc_final: 0.7946 (tpt-90) REVERT: B 392 MET cc_start: 0.7912 (mpt) cc_final: 0.7380 (mpp) REVERT: B 462 LEU cc_start: 0.9025 (tp) cc_final: 0.8551 (mp) REVERT: B 541 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7974 (mp0) REVERT: B 554 ASP cc_start: 0.8034 (t0) cc_final: 0.7594 (m-30) REVERT: B 649 ARG cc_start: 0.8693 (mmt180) cc_final: 0.8419 (mmt90) REVERT: C 328 ILE cc_start: 0.9042 (mm) cc_final: 0.8755 (mm) REVERT: C 359 ARG cc_start: 0.8058 (tpt-90) cc_final: 0.7845 (tpt-90) REVERT: C 392 MET cc_start: 0.8025 (mpt) cc_final: 0.7578 (mpp) REVERT: C 541 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7695 (tm-30) REVERT: C 580 MET cc_start: 0.8692 (mpp) cc_final: 0.8465 (mpp) REVERT: C 626 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.6309 (mmm-85) REVERT: C 649 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8244 (mmm-85) REVERT: D 346 MET cc_start: 0.8911 (tpp) cc_final: 0.8484 (tpp) REVERT: D 350 GLN cc_start: 0.9215 (tt0) cc_final: 0.8804 (tm-30) REVERT: D 392 MET cc_start: 0.8024 (mpt) cc_final: 0.7572 (mpp) REVERT: D 460 MET cc_start: 0.7729 (ttp) cc_final: 0.7447 (ttm) REVERT: D 541 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7643 (tm-30) REVERT: D 554 ASP cc_start: 0.8115 (t0) cc_final: 0.7894 (m-30) REVERT: D 649 ARG cc_start: 0.8548 (mmt180) cc_final: 0.8235 (mmm-85) REVERT: E 346 MET cc_start: 0.9042 (tpp) cc_final: 0.8534 (tpp) REVERT: E 359 ARG cc_start: 0.8035 (tpt-90) cc_final: 0.7652 (tpt-90) REVERT: E 392 MET cc_start: 0.8130 (mpt) cc_final: 0.7701 (mpp) REVERT: E 462 LEU cc_start: 0.8978 (tp) cc_final: 0.8464 (mp) REVERT: E 523 MET cc_start: 0.7774 (ttm) cc_final: 0.7529 (ttm) REVERT: E 541 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7816 (tm-30) REVERT: E 580 MET cc_start: 0.8731 (mpp) cc_final: 0.8416 (mpp) REVERT: E 612 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7682 (tm-30) REVERT: E 626 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.6587 (mmm160) REVERT: E 639 TYR cc_start: 0.8356 (t80) cc_final: 0.8118 (t80) REVERT: E 649 ARG cc_start: 0.8621 (mmt180) cc_final: 0.8291 (mmm-85) REVERT: F 346 MET cc_start: 0.8961 (tpp) cc_final: 0.8637 (tpp) REVERT: F 350 GLN cc_start: 0.9096 (tt0) cc_final: 0.8868 (pp30) REVERT: F 359 ARG cc_start: 0.7955 (tpt-90) cc_final: 0.7653 (tpt-90) REVERT: F 392 MET cc_start: 0.7953 (mpt) cc_final: 0.7463 (mpp) REVERT: F 462 LEU cc_start: 0.8983 (tp) cc_final: 0.8756 (tp) REVERT: G 332 LYS cc_start: 0.8854 (tmtt) cc_final: 0.8530 (tmtt) REVERT: G 350 GLN cc_start: 0.9155 (tt0) cc_final: 0.8657 (pp30) REVERT: G 359 ARG cc_start: 0.8248 (tpt-90) cc_final: 0.7875 (tpt-90) REVERT: G 462 LEU cc_start: 0.9051 (tp) cc_final: 0.8575 (mp) REVERT: G 491 MET cc_start: 0.8454 (ttm) cc_final: 0.8241 (ttm) REVERT: G 541 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7871 (tm-30) REVERT: G 649 ARG cc_start: 0.8774 (mmt180) cc_final: 0.8341 (mmm160) REVERT: H 328 ILE cc_start: 0.8989 (mm) cc_final: 0.8758 (mm) REVERT: H 346 MET cc_start: 0.8814 (tpp) cc_final: 0.8263 (tpp) REVERT: H 350 GLN cc_start: 0.9215 (tt0) cc_final: 0.8703 (pp30) REVERT: H 541 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7658 (tm-30) REVERT: H 554 ASP cc_start: 0.8042 (t0) cc_final: 0.7580 (m-30) REVERT: H 580 MET cc_start: 0.8649 (mpp) cc_final: 0.8328 (mpp) REVERT: I 346 MET cc_start: 0.8949 (tpp) cc_final: 0.8441 (mmm) REVERT: I 350 GLN cc_start: 0.9154 (tt0) cc_final: 0.8567 (pp30) REVERT: I 366 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: I 371 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8153 (tm-30) REVERT: I 460 MET cc_start: 0.7884 (ttp) cc_final: 0.7382 (ttm) REVERT: I 462 LEU cc_start: 0.9073 (tp) cc_final: 0.8593 (mp) REVERT: I 541 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7927 (tm-30) REVERT: J 332 LYS cc_start: 0.8970 (ttmm) cc_final: 0.8763 (tmtt) REVERT: J 346 MET cc_start: 0.8904 (tpp) cc_final: 0.8668 (tpp) REVERT: J 350 GLN cc_start: 0.9112 (tt0) cc_final: 0.8545 (pp30) REVERT: J 366 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: J 392 MET cc_start: 0.7841 (mpt) cc_final: 0.7293 (mpp) REVERT: J 462 LEU cc_start: 0.9010 (tp) cc_final: 0.8734 (tp) REVERT: J 541 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7647 (tm-30) REVERT: J 649 ARG cc_start: 0.8681 (mmt180) cc_final: 0.8335 (mmm-85) REVERT: K 346 MET cc_start: 0.8893 (tpp) cc_final: 0.8372 (tpp) REVERT: K 350 GLN cc_start: 0.9121 (tt0) cc_final: 0.8496 (pp30) REVERT: K 462 LEU cc_start: 0.8915 (tp) cc_final: 0.8397 (mp) REVERT: K 541 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8014 (tm-30) REVERT: K 554 ASP cc_start: 0.8055 (t0) cc_final: 0.7680 (m-30) REVERT: K 610 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8485 (ttmm) REVERT: L 346 MET cc_start: 0.8673 (tpp) cc_final: 0.8231 (mmm) REVERT: L 350 GLN cc_start: 0.9133 (tt0) cc_final: 0.8496 (pp30) REVERT: L 392 MET cc_start: 0.7380 (mpp) cc_final: 0.7096 (mpp) REVERT: L 491 MET cc_start: 0.8727 (ttm) cc_final: 0.8301 (mtp) REVERT: L 541 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7813 (tm-30) REVERT: L 554 ASP cc_start: 0.8047 (t0) cc_final: 0.7578 (m-30) REVERT: L 639 TYR cc_start: 0.8286 (t80) cc_final: 0.8039 (t80) REVERT: M 299 ASP cc_start: 0.8448 (m-30) cc_final: 0.8241 (m-30) REVERT: M 332 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8660 (tmtt) REVERT: M 346 MET cc_start: 0.8956 (tpp) cc_final: 0.8454 (tpp) REVERT: M 350 GLN cc_start: 0.9066 (tt0) cc_final: 0.8657 (pp30) REVERT: M 462 LEU cc_start: 0.8894 (tp) cc_final: 0.8331 (mp) REVERT: M 541 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7748 (tm-30) REVERT: N 350 GLN cc_start: 0.9226 (tt0) cc_final: 0.8789 (tm-30) REVERT: N 392 MET cc_start: 0.8036 (mpt) cc_final: 0.7639 (mpp) REVERT: N 460 MET cc_start: 0.6891 (ttm) cc_final: 0.6480 (ttm) REVERT: N 541 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7764 (tm-30) REVERT: N 553 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7268 (tp) REVERT: N 554 ASP cc_start: 0.7975 (t0) cc_final: 0.7631 (m-30) REVERT: O 346 MET cc_start: 0.8868 (tpp) cc_final: 0.8360 (mmm) REVERT: O 350 GLN cc_start: 0.9121 (tt0) cc_final: 0.8558 (pp30) REVERT: O 460 MET cc_start: 0.7743 (ttp) cc_final: 0.7261 (ttm) REVERT: O 462 LEU cc_start: 0.8955 (tp) cc_final: 0.8434 (mp) REVERT: O 541 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7900 (tm-30) outliers start: 153 outliers final: 110 residues processed: 712 average time/residue: 0.2664 time to fit residues: 299.4470 Evaluate side-chains 635 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 521 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 366 GLU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 480 ILE Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 553 LEU Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 415 optimal weight: 1.9990 chunk 488 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 401 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 293 optimal weight: 2.9990 chunk 384 optimal weight: 0.0970 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN H 652 GLN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN ** L 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 ASN N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.141580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098725 restraints weight = 55695.862| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.29 r_work: 0.3380 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39840 Z= 0.171 Angle : 0.603 10.060 53895 Z= 0.313 Chirality : 0.047 0.165 6480 Planarity : 0.004 0.037 6990 Dihedral : 5.178 23.959 5430 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.61 % Allowed : 15.82 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.11), residues: 5130 helix: -0.11 (0.15), residues: 1155 sheet: -2.32 (0.10), residues: 2535 loop : -2.70 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 626 TYR 0.023 0.001 TYR G 639 PHE 0.015 0.002 PHE H 619 TRP 0.006 0.001 TRP A 384 HIS 0.005 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00374 (39840) covalent geometry : angle 0.60299 (53895) hydrogen bonds : bond 0.03455 ( 2010) hydrogen bonds : angle 5.28134 ( 6345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 594 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8621 (tmtt) REVERT: A 333 HIS cc_start: 0.8587 (m90) cc_final: 0.8257 (m-70) REVERT: A 346 MET cc_start: 0.8808 (tpp) cc_final: 0.8400 (mmm) REVERT: A 392 MET cc_start: 0.8049 (mpt) cc_final: 0.7612 (mpp) REVERT: A 462 LEU cc_start: 0.9010 (tp) cc_final: 0.8541 (mp) REVERT: A 540 ILE cc_start: 0.8864 (tt) cc_final: 0.8361 (pt) REVERT: A 541 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7751 (tm-30) REVERT: A 553 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 554 ASP cc_start: 0.8233 (t0) cc_final: 0.8002 (m-30) REVERT: A 649 ARG cc_start: 0.8509 (mmt180) cc_final: 0.8235 (mmm-85) REVERT: B 346 MET cc_start: 0.8937 (tpp) cc_final: 0.8322 (tpp) REVERT: B 350 GLN cc_start: 0.9147 (tt0) cc_final: 0.8674 (pp30) REVERT: B 359 ARG cc_start: 0.8187 (tpt-90) cc_final: 0.7784 (tpt-90) REVERT: B 392 MET cc_start: 0.7953 (mpt) cc_final: 0.7445 (mpp) REVERT: B 462 LEU cc_start: 0.8994 (tp) cc_final: 0.8783 (tp) REVERT: B 487 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 649 ARG cc_start: 0.8672 (mmt180) cc_final: 0.8301 (mmm-85) REVERT: C 328 ILE cc_start: 0.9066 (mm) cc_final: 0.8750 (mm) REVERT: C 346 MET cc_start: 0.8859 (tpp) cc_final: 0.8331 (mmm) REVERT: C 359 ARG cc_start: 0.8055 (tpt-90) cc_final: 0.7695 (tpt-90) REVERT: C 371 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8068 (tm-30) REVERT: C 392 MET cc_start: 0.8036 (mpt) cc_final: 0.7582 (mpp) REVERT: C 462 LEU cc_start: 0.8950 (tp) cc_final: 0.8350 (mp) REVERT: C 487 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8017 (tt0) REVERT: C 540 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8360 (pt) REVERT: C 541 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7620 (tm-30) REVERT: C 614 ARG cc_start: 0.8521 (tmm-80) cc_final: 0.8167 (mtp-110) REVERT: C 649 ARG cc_start: 0.8561 (mmt180) cc_final: 0.8155 (mmm-85) REVERT: D 332 LYS cc_start: 0.8727 (tmtt) cc_final: 0.8295 (ttmt) REVERT: D 346 MET cc_start: 0.8901 (tpp) cc_final: 0.8520 (tpp) REVERT: D 350 GLN cc_start: 0.9231 (tt0) cc_final: 0.8838 (tm-30) REVERT: D 392 MET cc_start: 0.7993 (mpt) cc_final: 0.7521 (mpp) REVERT: D 460 MET cc_start: 0.7829 (ttp) cc_final: 0.7149 (ttm) REVERT: D 462 LEU cc_start: 0.8933 (tp) cc_final: 0.8438 (mp) REVERT: D 541 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7671 (tm-30) REVERT: D 610 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8467 (tttm) REVERT: D 649 ARG cc_start: 0.8459 (mmt180) cc_final: 0.8236 (mmm-85) REVERT: E 346 MET cc_start: 0.8967 (tpp) cc_final: 0.8538 (mmm) REVERT: E 350 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8809 (tm-30) REVERT: E 359 ARG cc_start: 0.8016 (tpt-90) cc_final: 0.7655 (tpt-90) REVERT: E 392 MET cc_start: 0.8065 (mpt) cc_final: 0.7649 (mpp) REVERT: E 462 LEU cc_start: 0.8948 (tp) cc_final: 0.8474 (mp) REVERT: E 523 MET cc_start: 0.7727 (ttm) cc_final: 0.7450 (ttm) REVERT: E 540 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8421 (pt) REVERT: E 541 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7808 (tm-30) REVERT: E 580 MET cc_start: 0.8842 (mpp) cc_final: 0.8563 (mpp) REVERT: E 612 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7680 (tm-30) REVERT: E 614 ARG cc_start: 0.8491 (tmm-80) cc_final: 0.8052 (mtp-110) REVERT: E 649 ARG cc_start: 0.8620 (mmt180) cc_final: 0.8336 (mmm-85) REVERT: F 299 ASP cc_start: 0.8263 (m-30) cc_final: 0.7954 (m-30) REVERT: F 333 HIS cc_start: 0.8597 (m90) cc_final: 0.8029 (m-70) REVERT: F 346 MET cc_start: 0.8919 (tpp) cc_final: 0.8610 (tpp) REVERT: F 350 GLN cc_start: 0.9250 (tt0) cc_final: 0.8882 (tm-30) REVERT: F 359 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7595 (tpt-90) REVERT: F 392 MET cc_start: 0.8005 (mpt) cc_final: 0.7472 (mpp) REVERT: F 462 LEU cc_start: 0.8872 (tp) cc_final: 0.8615 (tp) REVERT: F 487 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8159 (tm-30) REVERT: F 540 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8207 (pt) REVERT: F 554 ASP cc_start: 0.8196 (t0) cc_final: 0.7868 (m-30) REVERT: G 332 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8476 (tmtt) REVERT: G 350 GLN cc_start: 0.9172 (tt0) cc_final: 0.8683 (pp30) REVERT: G 359 ARG cc_start: 0.8216 (tpt-90) cc_final: 0.7800 (tpt-90) REVERT: G 392 MET cc_start: 0.8136 (mpt) cc_final: 0.7648 (mpp) REVERT: G 462 LEU cc_start: 0.9007 (tp) cc_final: 0.8551 (mp) REVERT: G 541 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7955 (mp0) REVERT: G 649 ARG cc_start: 0.8679 (mmt180) cc_final: 0.8337 (mmm-85) REVERT: H 328 ILE cc_start: 0.8990 (mm) cc_final: 0.8729 (mm) REVERT: H 346 MET cc_start: 0.8755 (tpp) cc_final: 0.8242 (tpp) REVERT: H 350 GLN cc_start: 0.9182 (tt0) cc_final: 0.8704 (pp30) REVERT: H 541 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7822 (tm-30) REVERT: H 554 ASP cc_start: 0.8026 (t0) cc_final: 0.7720 (m-30) REVERT: H 580 MET cc_start: 0.8655 (mpp) cc_final: 0.8289 (mpp) REVERT: I 346 MET cc_start: 0.9020 (tpp) cc_final: 0.8468 (mmm) REVERT: I 350 GLN cc_start: 0.9151 (tt0) cc_final: 0.8562 (pp30) REVERT: I 366 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: I 371 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8130 (tm-30) REVERT: I 460 MET cc_start: 0.7912 (ttp) cc_final: 0.7409 (ttm) REVERT: I 462 LEU cc_start: 0.8992 (tp) cc_final: 0.8520 (mp) REVERT: I 541 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7894 (tm-30) REVERT: J 332 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8745 (tmtt) REVERT: J 346 MET cc_start: 0.8898 (tpp) cc_final: 0.8605 (tpp) REVERT: J 350 GLN cc_start: 0.9125 (tt0) cc_final: 0.8548 (pp30) REVERT: J 359 ARG cc_start: 0.8092 (tpt-90) cc_final: 0.7783 (tpt-90) REVERT: J 392 MET cc_start: 0.7847 (mpt) cc_final: 0.7299 (mpp) REVERT: J 462 LEU cc_start: 0.8999 (tp) cc_final: 0.8691 (tp) REVERT: J 541 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7671 (tm-30) REVERT: J 649 ARG cc_start: 0.8828 (mmt180) cc_final: 0.8457 (mmm-85) REVERT: K 346 MET cc_start: 0.8843 (tpp) cc_final: 0.8308 (tpp) REVERT: K 350 GLN cc_start: 0.9121 (tt0) cc_final: 0.8497 (pp30) REVERT: K 462 LEU cc_start: 0.8939 (tp) cc_final: 0.8451 (mp) REVERT: K 541 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7982 (tm-30) REVERT: K 554 ASP cc_start: 0.8029 (t0) cc_final: 0.7661 (m-30) REVERT: K 581 ASP cc_start: 0.8898 (t0) cc_final: 0.8533 (t70) REVERT: K 610 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8383 (ttmm) REVERT: L 346 MET cc_start: 0.8713 (tpp) cc_final: 0.8266 (mmm) REVERT: L 350 GLN cc_start: 0.9089 (tt0) cc_final: 0.8485 (pp30) REVERT: L 392 MET cc_start: 0.7464 (mpp) cc_final: 0.7239 (mpp) REVERT: L 487 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7955 (tm-30) REVERT: L 491 MET cc_start: 0.8661 (ttm) cc_final: 0.8283 (mtp) REVERT: L 541 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7839 (tm-30) REVERT: L 546 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (ttpp) REVERT: L 554 ASP cc_start: 0.8086 (t0) cc_final: 0.7731 (m-30) REVERT: M 299 ASP cc_start: 0.8402 (m-30) cc_final: 0.8181 (m-30) REVERT: M 332 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8540 (tmtt) REVERT: M 346 MET cc_start: 0.8953 (tpp) cc_final: 0.8434 (tpp) REVERT: M 350 GLN cc_start: 0.9086 (tt0) cc_final: 0.8659 (pp30) REVERT: M 462 LEU cc_start: 0.8873 (tp) cc_final: 0.8589 (tp) REVERT: M 541 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7734 (tm-30) REVERT: N 332 LYS cc_start: 0.8915 (tmtt) cc_final: 0.8403 (ttmt) REVERT: N 346 MET cc_start: 0.8954 (tpp) cc_final: 0.8437 (mmm) REVERT: N 350 GLN cc_start: 0.9235 (tt0) cc_final: 0.8819 (tm-30) REVERT: N 392 MET cc_start: 0.8076 (mpt) cc_final: 0.7669 (mpp) REVERT: N 460 MET cc_start: 0.6825 (ttm) cc_final: 0.6459 (ttm) REVERT: N 541 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7782 (tm-30) REVERT: N 553 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7213 (tp) REVERT: N 554 ASP cc_start: 0.8010 (t0) cc_final: 0.7649 (m-30) REVERT: O 328 ILE cc_start: 0.9002 (mm) cc_final: 0.8578 (mm) REVERT: O 346 MET cc_start: 0.8917 (tpp) cc_final: 0.8438 (mmm) REVERT: O 350 GLN cc_start: 0.9116 (tt0) cc_final: 0.8585 (pp30) REVERT: O 359 ARG cc_start: 0.8165 (tpt-90) cc_final: 0.7895 (tpt-90) REVERT: O 460 MET cc_start: 0.7723 (ttp) cc_final: 0.7068 (ttm) REVERT: O 462 LEU cc_start: 0.8953 (tp) cc_final: 0.8448 (mp) REVERT: O 541 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7938 (tm-30) REVERT: O 626 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.6336 (mmm160) outliers start: 157 outliers final: 114 residues processed: 722 average time/residue: 0.2510 time to fit residues: 290.9699 Evaluate side-chains 661 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 539 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 600 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 620 ILE Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 546 LYS Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 17 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 381 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 334 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN L 485 ASN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.099271 restraints weight = 56311.634| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.29 r_work: 0.3391 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 39840 Z= 0.231 Angle : 0.634 10.283 53895 Z= 0.331 Chirality : 0.048 0.184 6480 Planarity : 0.004 0.068 6990 Dihedral : 5.272 24.644 5430 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.48 % Allowed : 16.21 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.11), residues: 5130 helix: 0.18 (0.16), residues: 1155 sheet: -2.29 (0.10), residues: 2490 loop : -2.96 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 626 TYR 0.023 0.001 TYR G 639 PHE 0.017 0.002 PHE G 489 TRP 0.008 0.001 TRP A 384 HIS 0.006 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00516 (39840) covalent geometry : angle 0.63389 (53895) hydrogen bonds : bond 0.03554 ( 2010) hydrogen bonds : angle 5.22044 ( 6345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 569 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8659 (tmtt) REVERT: A 333 HIS cc_start: 0.8661 (m90) cc_final: 0.8351 (m-70) REVERT: A 346 MET cc_start: 0.8828 (tpp) cc_final: 0.8502 (tpp) REVERT: A 392 MET cc_start: 0.8073 (mpt) cc_final: 0.7685 (mpp) REVERT: A 462 LEU cc_start: 0.8977 (tp) cc_final: 0.8500 (mp) REVERT: A 540 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8400 (pt) REVERT: A 541 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7682 (tm-30) REVERT: A 553 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 554 ASP cc_start: 0.8196 (t0) cc_final: 0.7930 (m-30) REVERT: A 629 MET cc_start: 0.6412 (tmm) cc_final: 0.6193 (tmm) REVERT: A 649 ARG cc_start: 0.8609 (mmt180) cc_final: 0.8062 (mmm160) REVERT: B 346 MET cc_start: 0.8947 (tpp) cc_final: 0.8327 (tpp) REVERT: B 350 GLN cc_start: 0.9162 (tt0) cc_final: 0.8670 (pp30) REVERT: B 359 ARG cc_start: 0.8115 (tpt-90) cc_final: 0.7908 (tpt-90) REVERT: B 392 MET cc_start: 0.7984 (mpt) cc_final: 0.7430 (mpp) REVERT: B 462 LEU cc_start: 0.8959 (tp) cc_final: 0.8491 (mp) REVERT: B 487 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 519 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8764 (mmtm) REVERT: B 639 TYR cc_start: 0.8450 (t80) cc_final: 0.8134 (t80) REVERT: B 649 ARG cc_start: 0.8713 (mmt180) cc_final: 0.8240 (mmm-85) REVERT: C 359 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7829 (tpt-90) REVERT: C 462 LEU cc_start: 0.8914 (tp) cc_final: 0.8681 (tp) REVERT: C 540 ILE cc_start: 0.8879 (tt) cc_final: 0.8492 (pt) REVERT: C 541 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7650 (tm-30) REVERT: C 580 MET cc_start: 0.8686 (mpp) cc_final: 0.8469 (mpp) REVERT: C 639 TYR cc_start: 0.8616 (t80) cc_final: 0.8273 (t80) REVERT: C 649 ARG cc_start: 0.8630 (mmt180) cc_final: 0.8257 (mmt90) REVERT: D 332 LYS cc_start: 0.8649 (tmtt) cc_final: 0.8296 (ttmt) REVERT: D 346 MET cc_start: 0.8811 (tpp) cc_final: 0.8407 (tpp) REVERT: D 350 GLN cc_start: 0.9214 (tt0) cc_final: 0.8798 (tm-30) REVERT: D 392 MET cc_start: 0.8009 (mpt) cc_final: 0.7576 (mpp) REVERT: D 460 MET cc_start: 0.7743 (ttp) cc_final: 0.7147 (ttm) REVERT: D 462 LEU cc_start: 0.8890 (tp) cc_final: 0.8442 (mp) REVERT: D 541 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7686 (tm-30) REVERT: D 554 ASP cc_start: 0.8115 (t0) cc_final: 0.7752 (m-30) REVERT: D 610 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8449 (tttm) REVERT: D 649 ARG cc_start: 0.8532 (mmt180) cc_final: 0.8208 (mmm-85) REVERT: E 346 MET cc_start: 0.8955 (tpp) cc_final: 0.8469 (tpp) REVERT: E 350 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8796 (tm-30) REVERT: E 359 ARG cc_start: 0.8032 (tpt-90) cc_final: 0.7649 (tpt-90) REVERT: E 392 MET cc_start: 0.8126 (mpt) cc_final: 0.7689 (mpp) REVERT: E 462 LEU cc_start: 0.8895 (tp) cc_final: 0.8396 (mp) REVERT: E 523 MET cc_start: 0.7822 (ttm) cc_final: 0.7538 (ttm) REVERT: E 541 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7758 (tm-30) REVERT: E 580 MET cc_start: 0.8772 (mpp) cc_final: 0.8469 (mpp) REVERT: E 612 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7719 (tm-30) REVERT: E 614 ARG cc_start: 0.8542 (tmm-80) cc_final: 0.8104 (mtp-110) REVERT: E 649 ARG cc_start: 0.8665 (mmt180) cc_final: 0.8279 (mmm-85) REVERT: F 299 ASP cc_start: 0.8379 (m-30) cc_final: 0.8050 (m-30) REVERT: F 332 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8360 (ptmt) REVERT: F 346 MET cc_start: 0.8916 (tpp) cc_final: 0.8571 (tpp) REVERT: F 350 GLN cc_start: 0.9324 (tt0) cc_final: 0.8908 (tm-30) REVERT: F 359 ARG cc_start: 0.7994 (tpt-90) cc_final: 0.7607 (tpt-90) REVERT: F 392 MET cc_start: 0.7954 (mpt) cc_final: 0.7405 (mpp) REVERT: F 462 LEU cc_start: 0.8907 (tp) cc_final: 0.8665 (tp) REVERT: F 487 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 540 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8151 (pt) REVERT: F 541 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8145 (tm-30) REVERT: F 554 ASP cc_start: 0.8240 (t0) cc_final: 0.7886 (m-30) REVERT: G 332 LYS cc_start: 0.8792 (tmtt) cc_final: 0.8458 (tmtt) REVERT: G 350 GLN cc_start: 0.9095 (tt0) cc_final: 0.8878 (pp30) REVERT: G 359 ARG cc_start: 0.8300 (tpt-90) cc_final: 0.7883 (tpt-90) REVERT: G 392 MET cc_start: 0.8183 (mpt) cc_final: 0.7680 (mpp) REVERT: G 462 LEU cc_start: 0.8940 (tp) cc_final: 0.8458 (mp) REVERT: G 541 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7899 (mp0) REVERT: G 649 ARG cc_start: 0.8749 (mmt180) cc_final: 0.8336 (mmm-85) REVERT: H 332 LYS cc_start: 0.8813 (tmtt) cc_final: 0.8370 (ttmt) REVERT: H 346 MET cc_start: 0.8710 (tpp) cc_final: 0.8161 (tpp) REVERT: H 350 GLN cc_start: 0.9172 (tt0) cc_final: 0.8971 (pp30) REVERT: H 541 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7708 (tm-30) REVERT: H 580 MET cc_start: 0.8561 (mpp) cc_final: 0.8181 (mpp) REVERT: I 308 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8213 (tt) REVERT: I 346 MET cc_start: 0.9056 (tpp) cc_final: 0.8709 (tpp) REVERT: I 350 GLN cc_start: 0.9160 (tt0) cc_final: 0.8554 (pp30) REVERT: I 366 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: I 371 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8096 (tm-30) REVERT: I 460 MET cc_start: 0.7852 (ttp) cc_final: 0.7328 (ttm) REVERT: I 462 LEU cc_start: 0.8981 (tp) cc_final: 0.8491 (mp) REVERT: I 541 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7862 (tm-30) REVERT: I 560 ARG cc_start: 0.8724 (mpt-90) cc_final: 0.8424 (mtt90) REVERT: J 346 MET cc_start: 0.8847 (tpp) cc_final: 0.8574 (tpp) REVERT: J 350 GLN cc_start: 0.9102 (tt0) cc_final: 0.8471 (pp30) REVERT: J 392 MET cc_start: 0.7830 (mpt) cc_final: 0.7230 (mpp) REVERT: J 460 MET cc_start: 0.6416 (ttm) cc_final: 0.6113 (ttm) REVERT: J 462 LEU cc_start: 0.8972 (tp) cc_final: 0.8490 (mp) REVERT: J 499 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8001 (pp) REVERT: J 541 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7655 (tm-30) REVERT: J 649 ARG cc_start: 0.8860 (mmt180) cc_final: 0.8398 (mmm-85) REVERT: K 346 MET cc_start: 0.8831 (tpp) cc_final: 0.8229 (tpp) REVERT: K 350 GLN cc_start: 0.9098 (tt0) cc_final: 0.8483 (pp30) REVERT: K 460 MET cc_start: 0.6604 (ttm) cc_final: 0.6310 (ttm) REVERT: K 462 LEU cc_start: 0.8836 (tp) cc_final: 0.8608 (tp) REVERT: K 541 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7875 (tm-30) REVERT: K 554 ASP cc_start: 0.8029 (t0) cc_final: 0.7634 (m-30) REVERT: K 581 ASP cc_start: 0.8859 (t0) cc_final: 0.8442 (t70) REVERT: K 639 TYR cc_start: 0.8563 (t80) cc_final: 0.8275 (t80) REVERT: L 346 MET cc_start: 0.8816 (tpp) cc_final: 0.8293 (mmm) REVERT: L 350 GLN cc_start: 0.9067 (tt0) cc_final: 0.8445 (pp30) REVERT: L 392 MET cc_start: 0.7496 (mpp) cc_final: 0.7273 (mpp) REVERT: L 491 MET cc_start: 0.8804 (ttm) cc_final: 0.8438 (mtp) REVERT: L 541 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7819 (tm-30) REVERT: L 546 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8273 (ttpp) REVERT: L 554 ASP cc_start: 0.8155 (t0) cc_final: 0.7761 (m-30) REVERT: L 614 ARG cc_start: 0.8690 (tmm-80) cc_final: 0.8328 (tmm-80) REVERT: M 299 ASP cc_start: 0.8439 (m-30) cc_final: 0.8222 (m-30) REVERT: M 332 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8645 (tmtt) REVERT: M 346 MET cc_start: 0.8923 (tpp) cc_final: 0.8320 (tpp) REVERT: M 350 GLN cc_start: 0.9072 (tt0) cc_final: 0.8639 (pp30) REVERT: M 462 LEU cc_start: 0.8843 (tp) cc_final: 0.8286 (mp) REVERT: M 487 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8101 (tm-30) REVERT: M 540 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8364 (pt) REVERT: M 541 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7691 (tm-30) REVERT: N 332 LYS cc_start: 0.8917 (tmtt) cc_final: 0.8415 (ttmt) REVERT: N 350 GLN cc_start: 0.9282 (tt0) cc_final: 0.8848 (tm-30) REVERT: N 392 MET cc_start: 0.8054 (mpt) cc_final: 0.7673 (mpp) REVERT: N 460 MET cc_start: 0.6727 (ttm) cc_final: 0.6291 (ttm) REVERT: N 541 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7780 (tm-30) REVERT: O 332 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8796 (tmtt) REVERT: O 346 MET cc_start: 0.8803 (tpp) cc_final: 0.8268 (tpp) REVERT: O 350 GLN cc_start: 0.9092 (tt0) cc_final: 0.8819 (pp30) REVERT: O 460 MET cc_start: 0.7654 (ttp) cc_final: 0.6917 (ttm) REVERT: O 462 LEU cc_start: 0.8887 (tp) cc_final: 0.8341 (mp) REVERT: O 540 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8343 (pt) REVERT: O 541 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7829 (tm-30) REVERT: O 610 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8293 (tttm) outliers start: 195 outliers final: 137 residues processed: 725 average time/residue: 0.2508 time to fit residues: 291.2286 Evaluate side-chains 688 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 540 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 600 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 620 ILE Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 546 LYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 220 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 chunk 405 optimal weight: 1.9990 chunk 467 optimal weight: 20.0000 chunk 291 optimal weight: 6.9990 chunk 521 optimal weight: 20.0000 chunk 487 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 440 optimal weight: 5.9990 chunk 517 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 ASN G 602 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 ASN L 602 ASN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 ASN N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 602 ASN ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.139890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096903 restraints weight = 57272.357| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.30 r_work: 0.3433 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 39840 Z= 0.293 Angle : 0.699 12.169 53895 Z= 0.358 Chirality : 0.049 0.187 6480 Planarity : 0.004 0.043 6990 Dihedral : 5.484 25.071 5430 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.43 % Favored : 90.35 % Rotamer: Outliers : 4.64 % Allowed : 16.57 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.11), residues: 5130 helix: -0.02 (0.15), residues: 1245 sheet: -2.42 (0.10), residues: 2580 loop : -3.02 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 626 TYR 0.024 0.001 TYR G 639 PHE 0.021 0.002 PHE G 489 TRP 0.009 0.001 TRP A 384 HIS 0.006 0.002 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00658 (39840) covalent geometry : angle 0.69857 (53895) hydrogen bonds : bond 0.03679 ( 2010) hydrogen bonds : angle 5.25743 ( 6345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 565 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 HIS cc_start: 0.8701 (m90) cc_final: 0.8374 (m-70) REVERT: A 346 MET cc_start: 0.8720 (tpp) cc_final: 0.8409 (tpp) REVERT: A 392 MET cc_start: 0.8231 (mpt) cc_final: 0.7804 (mpp) REVERT: A 462 LEU cc_start: 0.8968 (tp) cc_final: 0.8486 (mp) REVERT: A 540 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8392 (pt) REVERT: A 541 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7671 (tm-30) REVERT: A 553 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7352 (tp) REVERT: A 554 ASP cc_start: 0.8195 (t0) cc_final: 0.7908 (m-30) REVERT: A 649 ARG cc_start: 0.8619 (mmt180) cc_final: 0.7989 (mmm160) REVERT: B 346 MET cc_start: 0.8929 (tpp) cc_final: 0.8339 (tpp) REVERT: B 350 GLN cc_start: 0.9155 (tt0) cc_final: 0.8639 (pp30) REVERT: B 359 ARG cc_start: 0.8164 (tpt-90) cc_final: 0.7891 (tpt-90) REVERT: B 392 MET cc_start: 0.8096 (mpt) cc_final: 0.7470 (mpp) REVERT: B 462 LEU cc_start: 0.8939 (tp) cc_final: 0.8459 (mp) REVERT: B 487 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8166 (tt0) REVERT: B 519 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8703 (mmtm) REVERT: B 649 ARG cc_start: 0.8775 (mmt180) cc_final: 0.8137 (mmm160) REVERT: C 359 ARG cc_start: 0.8057 (tpt-90) cc_final: 0.7795 (tpt-90) REVERT: C 540 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8446 (pt) REVERT: C 541 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7622 (tm-30) REVERT: C 649 ARG cc_start: 0.8687 (mmt180) cc_final: 0.8231 (mmt90) REVERT: D 346 MET cc_start: 0.8817 (tpp) cc_final: 0.8332 (tpp) REVERT: D 350 GLN cc_start: 0.9247 (tt0) cc_final: 0.8808 (tm-30) REVERT: D 392 MET cc_start: 0.8058 (mpt) cc_final: 0.7615 (mpp) REVERT: D 460 MET cc_start: 0.7763 (ttp) cc_final: 0.7162 (ttm) REVERT: D 462 LEU cc_start: 0.8857 (tp) cc_final: 0.8385 (mp) REVERT: D 541 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7663 (tm-30) REVERT: D 554 ASP cc_start: 0.8166 (t0) cc_final: 0.7765 (m-30) REVERT: D 649 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8180 (mmm-85) REVERT: E 346 MET cc_start: 0.8941 (tpp) cc_final: 0.8408 (tpp) REVERT: E 350 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8824 (tm-30) REVERT: E 392 MET cc_start: 0.8174 (mpt) cc_final: 0.7716 (mpp) REVERT: E 462 LEU cc_start: 0.8880 (tp) cc_final: 0.8368 (mp) REVERT: E 519 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8659 (mmmm) REVERT: E 523 MET cc_start: 0.7843 (ttm) cc_final: 0.7493 (ttm) REVERT: E 541 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7732 (tm-30) REVERT: E 580 MET cc_start: 0.8729 (mpp) cc_final: 0.8340 (mpp) REVERT: E 649 ARG cc_start: 0.8825 (mmt180) cc_final: 0.8321 (mmm-85) REVERT: F 299 ASP cc_start: 0.8399 (m-30) cc_final: 0.8073 (m-30) REVERT: F 332 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8301 (ttmt) REVERT: F 346 MET cc_start: 0.8916 (tpp) cc_final: 0.8578 (tpp) REVERT: F 350 GLN cc_start: 0.9332 (tt0) cc_final: 0.8911 (tm-30) REVERT: F 359 ARG cc_start: 0.8009 (tpt-90) cc_final: 0.7483 (tpt-90) REVERT: F 392 MET cc_start: 0.8056 (mpt) cc_final: 0.7583 (mpp) REVERT: F 462 LEU cc_start: 0.8863 (tp) cc_final: 0.8386 (mp) REVERT: F 540 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8186 (pt) REVERT: F 541 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8143 (tm-30) REVERT: F 554 ASP cc_start: 0.8219 (t0) cc_final: 0.7915 (m-30) REVERT: G 332 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8458 (tmtt) REVERT: G 350 GLN cc_start: 0.9297 (tt0) cc_final: 0.8919 (tm-30) REVERT: G 359 ARG cc_start: 0.8210 (tpt-90) cc_final: 0.7892 (tpt-90) REVERT: G 392 MET cc_start: 0.8163 (mpt) cc_final: 0.7618 (mpp) REVERT: G 462 LEU cc_start: 0.8917 (tp) cc_final: 0.8422 (mp) REVERT: G 541 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7691 (tm-30) REVERT: G 554 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: G 610 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8438 (ttmm) REVERT: G 649 ARG cc_start: 0.8758 (mmt180) cc_final: 0.8237 (mmm-85) REVERT: H 332 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8326 (ttmt) REVERT: H 346 MET cc_start: 0.8674 (tpp) cc_final: 0.8128 (tpp) REVERT: H 350 GLN cc_start: 0.9319 (tt0) cc_final: 0.8916 (tm-30) REVERT: H 462 LEU cc_start: 0.8987 (tp) cc_final: 0.8313 (mp) REVERT: H 541 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7629 (tm-30) REVERT: H 580 MET cc_start: 0.8614 (mpp) cc_final: 0.8186 (mpp) REVERT: H 642 MET cc_start: 0.9164 (mmt) cc_final: 0.8715 (mmt) REVERT: I 308 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8228 (tt) REVERT: I 346 MET cc_start: 0.9033 (tpp) cc_final: 0.8609 (tpp) REVERT: I 350 GLN cc_start: 0.9153 (tt0) cc_final: 0.8529 (pp30) REVERT: I 366 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: I 371 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8071 (tm-30) REVERT: I 460 MET cc_start: 0.7909 (ttp) cc_final: 0.7363 (ttm) REVERT: I 462 LEU cc_start: 0.8960 (tp) cc_final: 0.8452 (mp) REVERT: I 541 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7821 (tm-30) REVERT: J 332 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8236 (ttmt) REVERT: J 346 MET cc_start: 0.8797 (tpp) cc_final: 0.8546 (tpp) REVERT: J 350 GLN cc_start: 0.9099 (tt0) cc_final: 0.8461 (pp30) REVERT: J 359 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.7740 (tpt-90) REVERT: J 460 MET cc_start: 0.6471 (ttm) cc_final: 0.6047 (ttm) REVERT: J 462 LEU cc_start: 0.8958 (tp) cc_final: 0.8474 (mp) REVERT: J 499 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7857 (pp) REVERT: J 541 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7565 (tm-30) REVERT: J 649 ARG cc_start: 0.8915 (mmt180) cc_final: 0.8371 (mmm-85) REVERT: K 333 HIS cc_start: 0.8596 (m-70) cc_final: 0.8313 (m90) REVERT: K 346 MET cc_start: 0.8820 (tpp) cc_final: 0.8254 (tpp) REVERT: K 350 GLN cc_start: 0.9094 (tt0) cc_final: 0.8478 (pp30) REVERT: K 462 LEU cc_start: 0.8857 (tp) cc_final: 0.8347 (mp) REVERT: K 541 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7850 (tm-30) REVERT: K 581 ASP cc_start: 0.8848 (t0) cc_final: 0.8414 (t70) REVERT: K 629 MET cc_start: 0.6992 (tmm) cc_final: 0.6755 (tmm) REVERT: K 639 TYR cc_start: 0.8597 (t80) cc_final: 0.8303 (t80) REVERT: L 346 MET cc_start: 0.8780 (tpp) cc_final: 0.8297 (tpp) REVERT: L 350 GLN cc_start: 0.9059 (tt0) cc_final: 0.8531 (pp30) REVERT: L 354 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8388 (mt-10) REVERT: L 392 MET cc_start: 0.7595 (mpp) cc_final: 0.7368 (mpp) REVERT: L 541 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7670 (tm-30) REVERT: L 546 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8255 (ttpp) REVERT: L 554 ASP cc_start: 0.8219 (t0) cc_final: 0.7865 (m-30) REVERT: L 639 TYR cc_start: 0.8049 (t80) cc_final: 0.7788 (t80) REVERT: M 299 ASP cc_start: 0.8432 (m-30) cc_final: 0.8201 (m-30) REVERT: M 333 HIS cc_start: 0.8729 (m90) cc_final: 0.8264 (m-70) REVERT: M 346 MET cc_start: 0.8893 (tpp) cc_final: 0.8294 (tpp) REVERT: M 350 GLN cc_start: 0.9066 (tt0) cc_final: 0.8650 (pp30) REVERT: M 354 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8324 (mt-10) REVERT: M 462 LEU cc_start: 0.8837 (tp) cc_final: 0.8284 (mp) REVERT: M 541 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7699 (tm-30) REVERT: M 594 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8611 (pt) REVERT: N 332 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8346 (ttmt) REVERT: N 350 GLN cc_start: 0.9260 (tt0) cc_final: 0.8832 (tm-30) REVERT: N 392 MET cc_start: 0.8041 (mpt) cc_final: 0.7657 (mpp) REVERT: N 460 MET cc_start: 0.6766 (ttm) cc_final: 0.6340 (ttm) REVERT: N 541 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7720 (tm-30) REVERT: O 346 MET cc_start: 0.8813 (tpp) cc_final: 0.8323 (mmm) REVERT: O 350 GLN cc_start: 0.9280 (tt0) cc_final: 0.8811 (tm-30) REVERT: O 460 MET cc_start: 0.7772 (ttp) cc_final: 0.7029 (ttm) REVERT: O 462 LEU cc_start: 0.8849 (tp) cc_final: 0.8366 (mp) REVERT: O 540 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8311 (pt) REVERT: O 541 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7823 (tm-30) REVERT: O 629 MET cc_start: 0.6727 (tmm) cc_final: 0.6478 (tmm) outliers start: 202 outliers final: 151 residues processed: 727 average time/residue: 0.2579 time to fit residues: 300.0496 Evaluate side-chains 697 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 532 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 519 LYS Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 553 LEU Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 620 ILE Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 553 LEU Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 499 LEU Chi-restraints excluded: chain K residue 553 LEU Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 546 LYS Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 366 GLU Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 402 ILE Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 170 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 142 optimal weight: 0.0270 chunk 330 optimal weight: 9.9990 chunk 508 optimal weight: 6.9990 chunk 503 optimal weight: 4.9990 chunk 414 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 473 optimal weight: 3.9990 chunk 460 optimal weight: 5.9990 chunk 472 optimal weight: 0.8980 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 615 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.144662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101621 restraints weight = 56151.722| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.32 r_work: 0.3501 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39840 Z= 0.135 Angle : 0.614 12.505 53895 Z= 0.310 Chirality : 0.047 0.173 6480 Planarity : 0.004 0.044 6990 Dihedral : 4.958 21.440 5430 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.18 % Favored : 93.55 % Rotamer: Outliers : 3.68 % Allowed : 17.91 % Favored : 78.41 % 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: -2.81 (0.12), residues: 5130 helix: 0.67 (0.16), residues: 1155 sheet: -2.27 (0.10), residues: 2580 loop : -2.78 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 626 TYR 0.023 0.001 TYR G 639 PHE 0.012 0.001 PHE L 447 TRP 0.009 0.001 TRP A 384 HIS 0.004 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00296 (39840) covalent geometry : angle 0.61406 (53895) hydrogen bonds : bond 0.03258 ( 2010) hydrogen bonds : angle 4.81900 ( 6345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 619 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8257 (ttmm) REVERT: A 333 HIS cc_start: 0.8605 (m90) cc_final: 0.8157 (m-70) REVERT: A 346 MET cc_start: 0.8667 (tpp) cc_final: 0.8159 (mmm) REVERT: A 359 ARG cc_start: 0.8120 (tpt-90) cc_final: 0.7480 (tpt-90) REVERT: A 384 TRP cc_start: 0.8296 (m100) cc_final: 0.7928 (m100) REVERT: A 392 MET cc_start: 0.8049 (mpt) cc_final: 0.7587 (mpp) REVERT: A 462 LEU cc_start: 0.8902 (tp) cc_final: 0.8611 (tp) REVERT: A 541 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7696 (tm-30) REVERT: A 542 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 553 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 554 ASP cc_start: 0.8212 (t0) cc_final: 0.7951 (m-30) REVERT: A 649 ARG cc_start: 0.8575 (mmt180) cc_final: 0.7914 (mmm160) REVERT: B 332 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8312 (ptmt) REVERT: B 346 MET cc_start: 0.8890 (tpp) cc_final: 0.8305 (mmm) REVERT: B 350 GLN cc_start: 0.9133 (tt0) cc_final: 0.8567 (pp30) REVERT: B 359 ARG cc_start: 0.8169 (tpt-90) cc_final: 0.7923 (tpt-90) REVERT: B 392 MET cc_start: 0.8049 (mpt) cc_final: 0.7601 (mpp) REVERT: B 462 LEU cc_start: 0.8825 (tp) cc_final: 0.8616 (tp) REVERT: B 487 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 519 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (mmtm) REVERT: B 540 ILE cc_start: 0.8773 (tt) cc_final: 0.8292 (pt) REVERT: B 554 ASP cc_start: 0.8117 (t0) cc_final: 0.7724 (m-30) REVERT: B 649 ARG cc_start: 0.8668 (mmt180) cc_final: 0.8174 (mmm-85) REVERT: C 332 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8336 (ttmt) REVERT: C 359 ARG cc_start: 0.8025 (tpt-90) cc_final: 0.7756 (tpt-90) REVERT: C 540 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8495 (pt) REVERT: C 541 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7605 (tm-30) REVERT: C 614 ARG cc_start: 0.8359 (tmm-80) cc_final: 0.8044 (mtp-110) REVERT: C 649 ARG cc_start: 0.8603 (mmt180) cc_final: 0.8183 (mmm-85) REVERT: D 332 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8268 (ptmt) REVERT: D 346 MET cc_start: 0.8748 (tpp) cc_final: 0.8205 (mmm) REVERT: D 350 GLN cc_start: 0.9183 (tt0) cc_final: 0.8837 (tm-30) REVERT: D 354 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8842 (tp30) REVERT: D 392 MET cc_start: 0.8065 (mpt) cc_final: 0.7673 (mpp) REVERT: D 460 MET cc_start: 0.7649 (ttp) cc_final: 0.7318 (ttm) REVERT: D 540 ILE cc_start: 0.8779 (tt) cc_final: 0.8346 (pt) REVERT: D 541 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7535 (tm-30) REVERT: D 554 ASP cc_start: 0.8194 (t0) cc_final: 0.7976 (m-30) REVERT: D 581 ASP cc_start: 0.8792 (t0) cc_final: 0.8566 (t0) REVERT: D 614 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8158 (mtp-110) REVERT: D 649 ARG cc_start: 0.8592 (mmt180) cc_final: 0.8215 (mmm-85) REVERT: E 346 MET cc_start: 0.8906 (tpp) cc_final: 0.8353 (tpp) REVERT: E 350 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8838 (tm-30) REVERT: E 359 ARG cc_start: 0.8119 (tpt-90) cc_final: 0.7706 (tpt-90) REVERT: E 392 MET cc_start: 0.8069 (mpt) cc_final: 0.7696 (mpp) REVERT: E 462 LEU cc_start: 0.8815 (tp) cc_final: 0.8310 (mp) REVERT: E 519 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8725 (mmmm) REVERT: E 523 MET cc_start: 0.7794 (ttm) cc_final: 0.7519 (ttm) REVERT: E 540 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8269 (pt) REVERT: E 541 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7669 (tm-30) REVERT: E 580 MET cc_start: 0.8703 (mpp) cc_final: 0.8438 (mpp) REVERT: E 586 GLU cc_start: 0.7421 (tp30) cc_final: 0.7052 (tp30) REVERT: E 629 MET cc_start: 0.6202 (tmm) cc_final: 0.5996 (tmm) REVERT: E 649 ARG cc_start: 0.8710 (mmt180) cc_final: 0.8290 (mmm-85) REVERT: F 299 ASP cc_start: 0.8353 (m-30) cc_final: 0.8016 (m-30) REVERT: F 332 LYS cc_start: 0.8726 (tmtt) cc_final: 0.8296 (ptmt) REVERT: F 346 MET cc_start: 0.8852 (tpp) cc_final: 0.8535 (tpp) REVERT: F 350 GLN cc_start: 0.9307 (tt0) cc_final: 0.8879 (tm-30) REVERT: F 359 ARG cc_start: 0.7953 (tpt-90) cc_final: 0.7546 (tpt-90) REVERT: F 392 MET cc_start: 0.7999 (mpt) cc_final: 0.7536 (mpp) REVERT: F 462 LEU cc_start: 0.8818 (tp) cc_final: 0.8562 (tp) REVERT: F 540 ILE cc_start: 0.8736 (tt) cc_final: 0.8226 (pt) REVERT: F 541 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8041 (tm-30) REVERT: F 554 ASP cc_start: 0.8256 (t0) cc_final: 0.7928 (m-30) REVERT: F 580 MET cc_start: 0.8589 (mpp) cc_final: 0.7945 (mpp) REVERT: G 332 LYS cc_start: 0.8730 (tmtt) cc_final: 0.8408 (tmtt) REVERT: G 350 GLN cc_start: 0.9273 (tt0) cc_final: 0.8918 (tm-30) REVERT: G 359 ARG cc_start: 0.8171 (tpt-90) cc_final: 0.7886 (tpt-90) REVERT: G 392 MET cc_start: 0.8111 (mpt) cc_final: 0.7594 (mpp) REVERT: G 462 LEU cc_start: 0.8869 (tp) cc_final: 0.8629 (tp) REVERT: G 540 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8418 (pt) REVERT: G 541 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7793 (mp0) REVERT: G 554 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: G 614 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.8097 (mtp-110) REVERT: G 649 ARG cc_start: 0.8704 (mmt180) cc_final: 0.8315 (mmm-85) REVERT: H 332 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8338 (ptmt) REVERT: H 346 MET cc_start: 0.8640 (tpp) cc_final: 0.8139 (tpp) REVERT: H 350 GLN cc_start: 0.9291 (tt0) cc_final: 0.8801 (tm-30) REVERT: H 462 LEU cc_start: 0.8955 (tp) cc_final: 0.8352 (mp) REVERT: H 541 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7659 (tm-30) REVERT: H 554 ASP cc_start: 0.8147 (t0) cc_final: 0.7709 (m-30) REVERT: H 580 MET cc_start: 0.8619 (mpp) cc_final: 0.8258 (mpp) REVERT: H 614 ARG cc_start: 0.8553 (tmm-80) cc_final: 0.8157 (mtp-110) REVERT: H 642 MET cc_start: 0.9144 (mmt) cc_final: 0.8768 (mmt) REVERT: I 308 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8317 (tt) REVERT: I 346 MET cc_start: 0.9020 (tpp) cc_final: 0.8683 (tpp) REVERT: I 350 GLN cc_start: 0.9107 (tt0) cc_final: 0.8577 (pp30) REVERT: I 354 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8558 (mt-10) REVERT: I 359 ARG cc_start: 0.7957 (tpt-90) cc_final: 0.7546 (tpt-90) REVERT: I 366 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: I 371 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8030 (tm-30) REVERT: I 462 LEU cc_start: 0.8863 (tp) cc_final: 0.8572 (tp) REVERT: I 541 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7804 (tm-30) REVERT: I 560 ARG cc_start: 0.8663 (mpt-90) cc_final: 0.8360 (mtt90) REVERT: J 332 LYS cc_start: 0.8693 (tmtt) cc_final: 0.8230 (ptmt) REVERT: J 346 MET cc_start: 0.8745 (tpp) cc_final: 0.8520 (tpp) REVERT: J 350 GLN cc_start: 0.9075 (tt0) cc_final: 0.8427 (pp30) REVERT: J 359 ARG cc_start: 0.8033 (tpt-90) cc_final: 0.7697 (tpt-90) REVERT: J 392 MET cc_start: 0.7860 (mpt) cc_final: 0.7277 (mpp) REVERT: J 460 MET cc_start: 0.6336 (ttm) cc_final: 0.5890 (ttm) REVERT: J 462 LEU cc_start: 0.8861 (tp) cc_final: 0.8340 (mp) REVERT: J 487 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8332 (tm-30) REVERT: J 499 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7958 (pp) REVERT: J 541 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7578 (tm-30) REVERT: J 649 ARG cc_start: 0.8794 (mmt180) cc_final: 0.8316 (mmm-85) REVERT: K 332 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8268 (ttmt) REVERT: K 346 MET cc_start: 0.8738 (tpp) cc_final: 0.8168 (tpp) REVERT: K 350 GLN cc_start: 0.9052 (tt0) cc_final: 0.8428 (pp30) REVERT: K 392 MET cc_start: 0.7839 (mpt) cc_final: 0.7390 (mpp) REVERT: K 462 LEU cc_start: 0.8768 (tp) cc_final: 0.8282 (mp) REVERT: K 541 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7746 (tm-30) REVERT: K 581 ASP cc_start: 0.8857 (t0) cc_final: 0.8367 (t70) REVERT: K 639 TYR cc_start: 0.8519 (t80) cc_final: 0.8251 (t80) REVERT: L 346 MET cc_start: 0.8744 (tpp) cc_final: 0.8253 (mmm) REVERT: L 350 GLN cc_start: 0.9041 (tt0) cc_final: 0.8625 (pp30) REVERT: L 354 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8317 (pt0) REVERT: L 392 MET cc_start: 0.7488 (mpp) cc_final: 0.7271 (mpp) REVERT: L 541 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7746 (tm-30) REVERT: L 615 ASN cc_start: 0.8585 (m-40) cc_final: 0.8341 (m-40) REVERT: M 299 ASP cc_start: 0.8396 (m-30) cc_final: 0.8175 (m-30) REVERT: M 332 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8275 (ptmt) REVERT: M 346 MET cc_start: 0.8900 (tpp) cc_final: 0.8374 (mmm) REVERT: M 350 GLN cc_start: 0.9043 (tt0) cc_final: 0.8639 (pp30) REVERT: M 354 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8420 (mt-10) REVERT: M 462 LEU cc_start: 0.8743 (tp) cc_final: 0.8444 (tp) REVERT: M 541 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7614 (tm-30) REVERT: M 581 ASP cc_start: 0.8906 (t0) cc_final: 0.8652 (t0) REVERT: M 594 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8364 (pt) REVERT: N 332 LYS cc_start: 0.8831 (tmtt) cc_final: 0.8271 (ttmt) REVERT: N 350 GLN cc_start: 0.9245 (tt0) cc_final: 0.8807 (tm-30) REVERT: N 392 MET cc_start: 0.7950 (mpt) cc_final: 0.7571 (mpp) REVERT: N 460 MET cc_start: 0.6643 (ttm) cc_final: 0.6253 (ttm) REVERT: N 541 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7687 (tm-30) REVERT: N 580 MET cc_start: 0.8431 (mpp) cc_final: 0.7957 (mpp) REVERT: O 346 MET cc_start: 0.8779 (tpp) cc_final: 0.8235 (mmm) REVERT: O 350 GLN cc_start: 0.9246 (tt0) cc_final: 0.8814 (tm-30) REVERT: O 460 MET cc_start: 0.7494 (ttp) cc_final: 0.7294 (ttm) REVERT: O 462 LEU cc_start: 0.8826 (tp) cc_final: 0.8580 (tp) REVERT: O 483 LEU cc_start: 0.9117 (mt) cc_final: 0.8849 (mt) REVERT: O 540 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8307 (pt) REVERT: O 541 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7731 (tm-30) REVERT: O 542 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8049 (tm-30) REVERT: O 581 ASP cc_start: 0.8828 (t0) cc_final: 0.8531 (t0) REVERT: O 586 GLU cc_start: 0.7749 (tp30) cc_final: 0.7145 (tp30) REVERT: O 629 MET cc_start: 0.6774 (tmm) cc_final: 0.6481 (tmm) outliers start: 160 outliers final: 123 residues processed: 754 average time/residue: 0.2519 time to fit residues: 305.4608 Evaluate side-chains 700 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 564 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 519 LYS Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 620 ILE Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 499 LEU Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Chi-restraints excluded: chain O residue 600 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 471 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 419 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 415 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 515 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 485 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 333 HIS ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 HIS ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 HIS ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.142331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.099392 restraints weight = 56491.222| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.29 r_work: 0.3466 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39840 Z= 0.213 Angle : 0.659 11.805 53895 Z= 0.334 Chirality : 0.047 0.168 6480 Planarity : 0.004 0.043 6990 Dihedral : 5.099 23.975 5430 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.07 % Favored : 91.64 % Rotamer: Outliers : 3.75 % Allowed : 18.60 % Favored : 77.66 % 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: -2.82 (0.12), residues: 5130 helix: 0.68 (0.16), residues: 1155 sheet: -2.28 (0.10), residues: 2580 loop : -2.79 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 626 TYR 0.025 0.001 TYR G 639 PHE 0.016 0.001 PHE G 489 TRP 0.018 0.001 TRP I 384 HIS 0.005 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00480 (39840) covalent geometry : angle 0.65910 (53895) hydrogen bonds : bond 0.03431 ( 2010) hydrogen bonds : angle 4.92129 ( 6345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 568 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 HIS cc_start: 0.8713 (m90) cc_final: 0.8385 (m-70) REVERT: A 346 MET cc_start: 0.8691 (tpp) cc_final: 0.8169 (mmm) REVERT: A 392 MET cc_start: 0.8225 (mpt) cc_final: 0.7788 (mpp) REVERT: A 462 LEU cc_start: 0.8942 (tp) cc_final: 0.8476 (mp) REVERT: A 540 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8397 (pt) REVERT: A 541 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7640 (tm-30) REVERT: A 553 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7405 (tp) REVERT: A 554 ASP cc_start: 0.8242 (t0) cc_final: 0.8006 (m-30) REVERT: A 649 ARG cc_start: 0.8586 (mmt180) cc_final: 0.7929 (mmm160) REVERT: B 332 LYS cc_start: 0.8741 (tmtt) cc_final: 0.8314 (ptmt) REVERT: B 346 MET cc_start: 0.8916 (tpp) cc_final: 0.8328 (mmm) REVERT: B 350 GLN cc_start: 0.9151 (tt0) cc_final: 0.8630 (pp30) REVERT: B 359 ARG cc_start: 0.8215 (tpt-90) cc_final: 0.7969 (tpt-90) REVERT: B 392 MET cc_start: 0.8104 (mpt) cc_final: 0.7606 (mpp) REVERT: B 487 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8122 (tt0) REVERT: B 519 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8762 (mmtm) REVERT: B 649 ARG cc_start: 0.8720 (mmt180) cc_final: 0.8210 (mmm160) REVERT: C 332 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8387 (ptmt) REVERT: C 359 ARG cc_start: 0.8032 (tpt-90) cc_final: 0.7751 (tpt-90) REVERT: C 371 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7990 (tm-30) REVERT: C 540 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8440 (pt) REVERT: C 541 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7615 (tm-30) REVERT: C 612 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7375 (tm-30) REVERT: C 614 ARG cc_start: 0.8414 (tmm-80) cc_final: 0.7909 (mtp-110) REVERT: C 629 MET cc_start: 0.6677 (tmm) cc_final: 0.6365 (tmm) REVERT: C 649 ARG cc_start: 0.8634 (mmt180) cc_final: 0.8216 (mmt90) REVERT: D 332 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8253 (ttmt) REVERT: D 346 MET cc_start: 0.8775 (tpp) cc_final: 0.8375 (tpp) REVERT: D 350 GLN cc_start: 0.9216 (tt0) cc_final: 0.8860 (tm-30) REVERT: D 354 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8868 (tp30) REVERT: D 392 MET cc_start: 0.8102 (mpt) cc_final: 0.7662 (mpp) REVERT: D 460 MET cc_start: 0.7699 (ttp) cc_final: 0.7123 (ttm) REVERT: D 462 LEU cc_start: 0.8832 (tp) cc_final: 0.8381 (mp) REVERT: D 540 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8346 (pt) REVERT: D 541 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7583 (tm-30) REVERT: D 554 ASP cc_start: 0.8244 (t0) cc_final: 0.7984 (m-30) REVERT: D 581 ASP cc_start: 0.8848 (t0) cc_final: 0.8618 (t0) REVERT: D 612 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7588 (tm-30) REVERT: D 649 ARG cc_start: 0.8621 (mmt180) cc_final: 0.8223 (mmm-85) REVERT: E 346 MET cc_start: 0.8923 (tpp) cc_final: 0.8341 (tpp) REVERT: E 359 ARG cc_start: 0.8176 (tpt-90) cc_final: 0.7783 (tpt-90) REVERT: E 392 MET cc_start: 0.8152 (mpt) cc_final: 0.7771 (mpp) REVERT: E 462 LEU cc_start: 0.8828 (tp) cc_final: 0.8323 (mp) REVERT: E 519 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8711 (mmmm) REVERT: E 523 MET cc_start: 0.7893 (ttm) cc_final: 0.7629 (ttm) REVERT: E 540 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8397 (pt) REVERT: E 541 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7703 (tm-30) REVERT: E 580 MET cc_start: 0.8742 (mpp) cc_final: 0.8439 (mpp) REVERT: E 629 MET cc_start: 0.6524 (tmm) cc_final: 0.6115 (tmm) REVERT: E 649 ARG cc_start: 0.8722 (mmt180) cc_final: 0.8257 (mmm-85) REVERT: F 299 ASP cc_start: 0.8407 (m-30) cc_final: 0.8078 (m-30) REVERT: F 332 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8351 (ptmt) REVERT: F 346 MET cc_start: 0.8893 (tpp) cc_final: 0.8542 (tpp) REVERT: F 350 GLN cc_start: 0.9331 (tt0) cc_final: 0.8889 (tm-30) REVERT: F 359 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7504 (tpt-90) REVERT: F 392 MET cc_start: 0.8070 (mpt) cc_final: 0.7595 (mpp) REVERT: F 462 LEU cc_start: 0.8830 (tp) cc_final: 0.8581 (tp) REVERT: F 540 ILE cc_start: 0.8750 (tt) cc_final: 0.8186 (pt) REVERT: F 541 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8114 (tm-30) REVERT: F 554 ASP cc_start: 0.8260 (t0) cc_final: 0.7910 (m-30) REVERT: G 332 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8431 (tmtt) REVERT: G 350 GLN cc_start: 0.9286 (tt0) cc_final: 0.8894 (tm-30) REVERT: G 359 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7838 (tpt-90) REVERT: G 392 MET cc_start: 0.8166 (mpt) cc_final: 0.7623 (mpp) REVERT: G 462 LEU cc_start: 0.8907 (tp) cc_final: 0.8661 (tp) REVERT: G 540 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8399 (pt) REVERT: G 541 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7613 (tm-30) REVERT: G 554 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: G 614 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8150 (mtp-110) REVERT: G 649 ARG cc_start: 0.8707 (mmt180) cc_final: 0.8293 (mmm-85) REVERT: H 332 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8206 (ttmt) REVERT: H 346 MET cc_start: 0.8654 (tpp) cc_final: 0.8135 (tpp) REVERT: H 350 GLN cc_start: 0.9244 (tt0) cc_final: 0.8772 (tm-30) REVERT: H 462 LEU cc_start: 0.8928 (tp) cc_final: 0.8162 (mp) REVERT: H 541 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7662 (tm-30) REVERT: H 554 ASP cc_start: 0.8160 (t0) cc_final: 0.7662 (m-30) REVERT: H 580 MET cc_start: 0.8585 (mpp) cc_final: 0.8163 (mpp) REVERT: H 642 MET cc_start: 0.9170 (mmt) cc_final: 0.8810 (mmt) REVERT: I 308 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8282 (tt) REVERT: I 346 MET cc_start: 0.9013 (tpp) cc_final: 0.8593 (tpp) REVERT: I 350 GLN cc_start: 0.9151 (tt0) cc_final: 0.8665 (pp30) REVERT: I 354 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8596 (mt-10) REVERT: I 366 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: I 371 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8019 (tm-30) REVERT: I 462 LEU cc_start: 0.8930 (tp) cc_final: 0.8635 (tp) REVERT: I 541 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7810 (tm-30) REVERT: J 332 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8173 (ttmt) REVERT: J 346 MET cc_start: 0.8773 (tpp) cc_final: 0.8517 (tpp) REVERT: J 350 GLN cc_start: 0.9101 (tt0) cc_final: 0.8462 (pp30) REVERT: J 460 MET cc_start: 0.6452 (ttm) cc_final: 0.6011 (ttm) REVERT: J 462 LEU cc_start: 0.8892 (tp) cc_final: 0.8418 (mp) REVERT: J 541 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7561 (tm-30) REVERT: J 649 ARG cc_start: 0.8816 (mmt180) cc_final: 0.8298 (mmm-85) REVERT: K 332 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8211 (ttmt) REVERT: K 346 MET cc_start: 0.8771 (tpp) cc_final: 0.8175 (tpp) REVERT: K 350 GLN cc_start: 0.9076 (tt0) cc_final: 0.8449 (pp30) REVERT: K 462 LEU cc_start: 0.8851 (tp) cc_final: 0.8380 (mp) REVERT: K 541 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7810 (tm-30) REVERT: K 581 ASP cc_start: 0.8879 (t0) cc_final: 0.8403 (t70) REVERT: K 610 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8299 (ttmm) REVERT: K 639 TYR cc_start: 0.8519 (t80) cc_final: 0.8225 (t80) REVERT: L 333 HIS cc_start: 0.8664 (m-70) cc_final: 0.8356 (m-70) REVERT: L 346 MET cc_start: 0.8751 (tpp) cc_final: 0.8258 (mmm) REVERT: L 350 GLN cc_start: 0.9064 (tt0) cc_final: 0.8267 (pp30) REVERT: L 354 GLU cc_start: 0.8813 (mt-10) cc_final: 0.7749 (pt0) REVERT: L 541 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7795 (tm-30) REVERT: L 554 ASP cc_start: 0.8228 (t0) cc_final: 0.7771 (m-30) REVERT: L 580 MET cc_start: 0.8529 (mpp) cc_final: 0.8130 (mpp) REVERT: M 299 ASP cc_start: 0.8427 (m-30) cc_final: 0.8186 (m-30) REVERT: M 332 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8218 (ptmt) REVERT: M 346 MET cc_start: 0.8888 (tpp) cc_final: 0.8313 (mmm) REVERT: M 350 GLN cc_start: 0.9056 (tt0) cc_final: 0.8637 (pp30) REVERT: M 354 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8294 (mt-10) REVERT: M 460 MET cc_start: 0.6634 (ttm) cc_final: 0.6340 (ttm) REVERT: M 462 LEU cc_start: 0.8785 (tp) cc_final: 0.8517 (tp) REVERT: M 541 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7645 (tm-30) REVERT: M 594 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8460 (pt) REVERT: N 332 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8247 (ttmm) REVERT: N 350 GLN cc_start: 0.9269 (tt0) cc_final: 0.8763 (tm-30) REVERT: N 392 MET cc_start: 0.8037 (mpt) cc_final: 0.7654 (mpp) REVERT: N 460 MET cc_start: 0.6698 (ttm) cc_final: 0.6311 (ttm) REVERT: N 541 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7747 (tm-30) REVERT: O 346 MET cc_start: 0.8777 (tpp) cc_final: 0.8301 (mmm) REVERT: O 350 GLN cc_start: 0.9269 (tt0) cc_final: 0.8891 (tm-30) REVERT: O 460 MET cc_start: 0.7597 (ttp) cc_final: 0.7261 (ttm) REVERT: O 462 LEU cc_start: 0.8852 (tp) cc_final: 0.8614 (tp) REVERT: O 483 LEU cc_start: 0.9165 (mt) cc_final: 0.8907 (mt) REVERT: O 540 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8296 (pt) REVERT: O 541 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7779 (tm-30) REVERT: O 581 ASP cc_start: 0.8827 (t0) cc_final: 0.8537 (t0) REVERT: O 629 MET cc_start: 0.6967 (tmm) cc_final: 0.6492 (tmm) outliers start: 163 outliers final: 139 residues processed: 699 average time/residue: 0.2615 time to fit residues: 293.0572 Evaluate side-chains 702 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 550 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 519 LYS Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 523 MET Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 593 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Chi-restraints excluded: chain O residue 600 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 352 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 488 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 HIS ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 662 GLN M 333 HIS ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.139149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096248 restraints weight = 57373.114| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.28 r_work: 0.3421 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 39840 Z= 0.313 Angle : 0.734 10.617 53895 Z= 0.376 Chirality : 0.049 0.192 6480 Planarity : 0.005 0.045 6990 Dihedral : 5.510 25.696 5430 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.82 % Favored : 89.88 % Rotamer: Outliers : 3.89 % Allowed : 18.92 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.11), residues: 5130 helix: 0.50 (0.16), residues: 1155 sheet: -2.42 (0.10), residues: 2580 loop : -2.85 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 626 TYR 0.025 0.002 TYR G 639 PHE 0.022 0.002 PHE G 489 TRP 0.023 0.002 TRP L 384 HIS 0.007 0.002 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00708 (39840) covalent geometry : angle 0.73364 (53895) hydrogen bonds : bond 0.03709 ( 2010) hydrogen bonds : angle 5.21771 ( 6345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 549 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8700 (tpp) cc_final: 0.8139 (mmm) REVERT: A 359 ARG cc_start: 0.8173 (tpt-90) cc_final: 0.7559 (tpt-90) REVERT: A 392 MET cc_start: 0.8306 (mpt) cc_final: 0.7824 (mpp) REVERT: A 462 LEU cc_start: 0.8974 (tp) cc_final: 0.8498 (mp) REVERT: A 540 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8419 (pt) REVERT: A 541 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7674 (tm-30) REVERT: A 553 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7435 (tp) REVERT: A 554 ASP cc_start: 0.8193 (t0) cc_final: 0.7954 (m-30) REVERT: A 649 ARG cc_start: 0.8600 (mmt180) cc_final: 0.8078 (mmm-85) REVERT: B 332 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8167 (ttmt) REVERT: B 346 MET cc_start: 0.8932 (tpp) cc_final: 0.8355 (tpp) REVERT: B 350 GLN cc_start: 0.9153 (tt0) cc_final: 0.8637 (pp30) REVERT: B 359 ARG cc_start: 0.8088 (tpt-90) cc_final: 0.7812 (tpt-90) REVERT: B 392 MET cc_start: 0.8178 (mpt) cc_final: 0.7607 (mpp) REVERT: B 519 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8717 (mmtm) REVERT: B 649 ARG cc_start: 0.8747 (mmt180) cc_final: 0.8159 (mmm-85) REVERT: C 332 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8370 (ttmt) REVERT: C 359 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7699 (tpt-90) REVERT: C 371 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8071 (tm-30) REVERT: C 540 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8306 (pt) REVERT: C 541 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7604 (tm-30) REVERT: C 612 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7552 (tm-30) REVERT: C 614 ARG cc_start: 0.8500 (tmm-80) cc_final: 0.7978 (mtp-110) REVERT: C 629 MET cc_start: 0.6853 (tmm) cc_final: 0.6552 (tmm) REVERT: C 649 ARG cc_start: 0.8709 (mmt180) cc_final: 0.8186 (mmm-85) REVERT: D 332 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8267 (ttmt) REVERT: D 346 MET cc_start: 0.8779 (tpp) cc_final: 0.8286 (tpp) REVERT: D 350 GLN cc_start: 0.9248 (tt0) cc_final: 0.8882 (tm-30) REVERT: D 354 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8900 (tp30) REVERT: D 359 ARG cc_start: 0.7889 (tpt-90) cc_final: 0.7635 (tpt-90) REVERT: D 392 MET cc_start: 0.8189 (mpt) cc_final: 0.7732 (mpp) REVERT: D 460 MET cc_start: 0.7750 (ttp) cc_final: 0.7181 (ttm) REVERT: D 462 LEU cc_start: 0.8849 (tp) cc_final: 0.8366 (mp) REVERT: D 540 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8371 (pt) REVERT: D 541 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7581 (tm-30) REVERT: D 554 ASP cc_start: 0.8279 (t0) cc_final: 0.7967 (m-30) REVERT: D 581 ASP cc_start: 0.8889 (t0) cc_final: 0.8661 (t0) REVERT: D 612 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7781 (tm-30) REVERT: D 649 ARG cc_start: 0.8659 (mmt180) cc_final: 0.8094 (mmm-85) REVERT: E 332 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8682 (tmtt) REVERT: E 346 MET cc_start: 0.8920 (tpp) cc_final: 0.8349 (tpp) REVERT: E 392 MET cc_start: 0.8289 (mpt) cc_final: 0.7864 (mpp) REVERT: E 462 LEU cc_start: 0.8868 (tp) cc_final: 0.8346 (mp) REVERT: E 523 MET cc_start: 0.7888 (ttm) cc_final: 0.7609 (ttm) REVERT: E 540 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8404 (pt) REVERT: E 541 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7728 (tm-30) REVERT: E 629 MET cc_start: 0.6581 (tmm) cc_final: 0.6202 (tmm) REVERT: E 649 ARG cc_start: 0.8837 (mmt180) cc_final: 0.8185 (mmm160) REVERT: F 332 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8355 (ttmt) REVERT: F 346 MET cc_start: 0.8893 (tpp) cc_final: 0.8499 (tpp) REVERT: F 350 GLN cc_start: 0.9350 (tt0) cc_final: 0.8965 (tm-30) REVERT: F 392 MET cc_start: 0.8213 (mpt) cc_final: 0.7774 (mpp) REVERT: F 462 LEU cc_start: 0.8866 (tp) cc_final: 0.8643 (tp) REVERT: F 540 ILE cc_start: 0.8797 (tt) cc_final: 0.8177 (pt) REVERT: F 541 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 554 ASP cc_start: 0.8263 (t0) cc_final: 0.7889 (m-30) REVERT: G 332 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8539 (tmtt) REVERT: G 350 GLN cc_start: 0.9308 (tt0) cc_final: 0.8923 (tm-30) REVERT: G 359 ARG cc_start: 0.8096 (tpt-90) cc_final: 0.7805 (tpt-90) REVERT: G 462 LEU cc_start: 0.8913 (tp) cc_final: 0.8431 (mp) REVERT: G 541 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7700 (tm-30) REVERT: G 554 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: G 610 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8443 (ttmm) REVERT: G 614 ARG cc_start: 0.8669 (tmm-80) cc_final: 0.8196 (mtp-110) REVERT: G 649 ARG cc_start: 0.8705 (mmt180) cc_final: 0.8183 (mmm-85) REVERT: H 332 LYS cc_start: 0.8739 (tmtt) cc_final: 0.8267 (ttmt) REVERT: H 346 MET cc_start: 0.8651 (tpp) cc_final: 0.8150 (tpp) REVERT: H 350 GLN cc_start: 0.9258 (tt0) cc_final: 0.8798 (tm-30) REVERT: H 462 LEU cc_start: 0.8962 (tp) cc_final: 0.8323 (mp) REVERT: H 541 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7605 (tm-30) REVERT: H 554 ASP cc_start: 0.8147 (t0) cc_final: 0.7680 (m-30) REVERT: H 580 MET cc_start: 0.8633 (mpp) cc_final: 0.8221 (mpp) REVERT: H 614 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.8156 (mtp-110) REVERT: H 642 MET cc_start: 0.9217 (mmt) cc_final: 0.8886 (mmt) REVERT: I 308 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8261 (tt) REVERT: I 346 MET cc_start: 0.9023 (tpp) cc_final: 0.8608 (tpp) REVERT: I 350 GLN cc_start: 0.9180 (tt0) cc_final: 0.8650 (pp30) REVERT: I 354 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8588 (mt-10) REVERT: I 359 ARG cc_start: 0.7920 (tpt-90) cc_final: 0.7563 (tpt-90) REVERT: I 366 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: I 371 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8103 (tm-30) REVERT: I 462 LEU cc_start: 0.8924 (tp) cc_final: 0.8640 (tp) REVERT: I 541 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7827 (tm-30) REVERT: J 332 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8270 (ttmt) REVERT: J 346 MET cc_start: 0.8801 (tpp) cc_final: 0.8554 (tpp) REVERT: J 350 GLN cc_start: 0.9117 (tt0) cc_final: 0.8482 (pp30) REVERT: J 460 MET cc_start: 0.6599 (ttm) cc_final: 0.6134 (ttm) REVERT: J 462 LEU cc_start: 0.8959 (tp) cc_final: 0.8465 (mp) REVERT: J 541 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7541 (tm-30) REVERT: J 649 ARG cc_start: 0.8890 (mmt180) cc_final: 0.8315 (mmm-85) REVERT: K 332 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8199 (ttmt) REVERT: K 333 HIS cc_start: 0.8615 (m90) cc_final: 0.8303 (m-70) REVERT: K 346 MET cc_start: 0.8874 (tpp) cc_final: 0.8298 (tpp) REVERT: K 350 GLN cc_start: 0.9101 (tt0) cc_final: 0.8477 (pp30) REVERT: K 462 LEU cc_start: 0.8880 (tp) cc_final: 0.8648 (tp) REVERT: K 487 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8056 (tm-30) REVERT: K 541 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7823 (tm-30) REVERT: K 581 ASP cc_start: 0.8867 (t0) cc_final: 0.8394 (t70) REVERT: K 639 TYR cc_start: 0.8591 (t80) cc_final: 0.8353 (t80) REVERT: L 333 HIS cc_start: 0.8729 (m-70) cc_final: 0.8410 (m-70) REVERT: L 346 MET cc_start: 0.8783 (tpp) cc_final: 0.8534 (tpp) REVERT: L 350 GLN cc_start: 0.9076 (tt0) cc_final: 0.8501 (pp30) REVERT: L 354 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8228 (mt-10) REVERT: L 359 ARG cc_start: 0.8113 (tpt-90) cc_final: 0.7832 (tpt-90) REVERT: L 541 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7703 (tm-30) REVERT: L 554 ASP cc_start: 0.8279 (t0) cc_final: 0.7811 (m-30) REVERT: L 580 MET cc_start: 0.8595 (mpp) cc_final: 0.8188 (mpp) REVERT: M 299 ASP cc_start: 0.8435 (m-30) cc_final: 0.8196 (m-30) REVERT: M 332 LYS cc_start: 0.8757 (tmtt) cc_final: 0.8272 (ptmt) REVERT: M 346 MET cc_start: 0.8861 (tpp) cc_final: 0.8264 (tpp) REVERT: M 359 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7691 (tpt-90) REVERT: M 460 MET cc_start: 0.6610 (ttm) cc_final: 0.6286 (ttm) REVERT: M 462 LEU cc_start: 0.8816 (tp) cc_final: 0.8562 (tp) REVERT: M 541 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7719 (tm-30) REVERT: M 594 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8553 (pt) REVERT: N 332 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8245 (ttmm) REVERT: N 350 GLN cc_start: 0.9272 (tt0) cc_final: 0.8808 (tm-30) REVERT: N 392 MET cc_start: 0.8084 (mpt) cc_final: 0.7663 (mpp) REVERT: N 460 MET cc_start: 0.6723 (ttm) cc_final: 0.6280 (ttm) REVERT: N 519 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8813 (mmmm) REVERT: N 541 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7704 (tm-30) REVERT: O 332 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8690 (tmtt) REVERT: O 346 MET cc_start: 0.8791 (tpp) cc_final: 0.8283 (mmm) REVERT: O 350 GLN cc_start: 0.9286 (tt0) cc_final: 0.8892 (tm-30) REVERT: O 460 MET cc_start: 0.7677 (ttp) cc_final: 0.7338 (ttm) REVERT: O 462 LEU cc_start: 0.8873 (tp) cc_final: 0.8649 (tp) REVERT: O 540 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8329 (pt) REVERT: O 541 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7829 (tm-30) REVERT: O 629 MET cc_start: 0.6903 (tmm) cc_final: 0.6316 (tmm) outliers start: 169 outliers final: 146 residues processed: 682 average time/residue: 0.2605 time to fit residues: 283.9897 Evaluate side-chains 690 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 532 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 546 LYS Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 576 LEU Chi-restraints excluded: chain I residue 620 ILE Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 523 MET Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 482 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 519 LYS Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 482 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 594 LEU Chi-restraints excluded: chain O residue 600 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 357 optimal weight: 5.9990 chunk 473 optimal weight: 2.9990 chunk 438 optimal weight: 4.9990 chunk 493 optimal weight: 0.1980 chunk 415 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 505 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS C 333 HIS ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 ASN N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.143871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100963 restraints weight = 55930.938| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.28 r_work: 0.3412 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39840 Z= 0.151 Angle : 0.654 14.314 53895 Z= 0.327 Chirality : 0.047 0.176 6480 Planarity : 0.004 0.044 6990 Dihedral : 5.020 21.787 5430 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.06 % Favored : 92.65 % Rotamer: Outliers : 3.26 % Allowed : 19.82 % Favored : 76.92 % 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: -2.80 (0.12), residues: 5130 helix: 0.73 (0.16), residues: 1155 sheet: -2.31 (0.10), residues: 2610 loop : -2.69 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 626 TYR 0.024 0.001 TYR O 639 PHE 0.014 0.001 PHE G 490 TRP 0.021 0.001 TRP I 384 HIS 0.005 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00335 (39840) covalent geometry : angle 0.65404 (53895) hydrogen bonds : bond 0.03281 ( 2010) hydrogen bonds : angle 4.83680 ( 6345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 577 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8706 (tpp) cc_final: 0.8202 (mmm) REVERT: A 359 ARG cc_start: 0.8168 (tpt-90) cc_final: 0.7617 (tpt-90) REVERT: A 392 MET cc_start: 0.8234 (mpt) cc_final: 0.7790 (mpp) REVERT: A 462 LEU cc_start: 0.8918 (tp) cc_final: 0.8626 (tp) REVERT: A 540 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8356 (pt) REVERT: A 541 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7702 (tm-30) REVERT: A 542 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 554 ASP cc_start: 0.8222 (t0) cc_final: 0.7985 (m-30) REVERT: A 576 LEU cc_start: 0.9045 (mt) cc_final: 0.8783 (mt) REVERT: A 649 ARG cc_start: 0.8561 (mmt180) cc_final: 0.7862 (mmm160) REVERT: B 332 LYS cc_start: 0.8637 (tmtt) cc_final: 0.8210 (ptmt) REVERT: B 346 MET cc_start: 0.8927 (tpp) cc_final: 0.8373 (mmm) REVERT: B 350 GLN cc_start: 0.9147 (tt0) cc_final: 0.8587 (pp30) REVERT: B 359 ARG cc_start: 0.8075 (tpt-90) cc_final: 0.7813 (tpt-90) REVERT: B 392 MET cc_start: 0.8154 (mpt) cc_final: 0.7668 (mpp) REVERT: B 487 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 519 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8839 (mmtm) REVERT: B 540 ILE cc_start: 0.8794 (tt) cc_final: 0.8305 (pt) REVERT: B 649 ARG cc_start: 0.8641 (mmt180) cc_final: 0.8123 (mmm160) REVERT: C 332 LYS cc_start: 0.8759 (tmtt) cc_final: 0.8274 (ptmt) REVERT: C 359 ARG cc_start: 0.8049 (tpt-90) cc_final: 0.7769 (tpt-90) REVERT: C 371 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 540 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8379 (pt) REVERT: C 541 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7653 (tm-30) REVERT: C 612 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 639 TYR cc_start: 0.8600 (t80) cc_final: 0.8303 (t80) REVERT: C 649 ARG cc_start: 0.8603 (mmt180) cc_final: 0.8049 (mmm-85) REVERT: D 332 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8116 (ttmt) REVERT: D 346 MET cc_start: 0.8793 (tpp) cc_final: 0.8423 (tpp) REVERT: D 350 GLN cc_start: 0.9219 (tt0) cc_final: 0.8875 (tm-30) REVERT: D 354 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8861 (tp30) REVERT: D 359 ARG cc_start: 0.7912 (tpt-90) cc_final: 0.7670 (tpt-90) REVERT: D 392 MET cc_start: 0.8120 (mpt) cc_final: 0.7676 (mpp) REVERT: D 460 MET cc_start: 0.7732 (ttp) cc_final: 0.7393 (ttm) REVERT: D 540 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8376 (pt) REVERT: D 541 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7572 (tm-30) REVERT: D 554 ASP cc_start: 0.8268 (t0) cc_final: 0.7989 (m-30) REVERT: D 581 ASP cc_start: 0.8820 (t0) cc_final: 0.8611 (t0) REVERT: D 612 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 649 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8012 (mmm160) REVERT: E 346 MET cc_start: 0.8935 (tpp) cc_final: 0.8375 (tpp) REVERT: E 359 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7838 (tpt-90) REVERT: E 384 TRP cc_start: 0.8358 (m100) cc_final: 0.8069 (m100) REVERT: E 392 MET cc_start: 0.8185 (mpt) cc_final: 0.7770 (mpp) REVERT: E 462 LEU cc_start: 0.8873 (tp) cc_final: 0.8367 (mp) REVERT: E 519 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8768 (mmmm) REVERT: E 523 MET cc_start: 0.7763 (ttm) cc_final: 0.7502 (ttm) REVERT: E 540 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8298 (pt) REVERT: E 541 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7758 (tm-30) REVERT: E 580 MET cc_start: 0.8660 (mpp) cc_final: 0.8385 (mpp) REVERT: E 649 ARG cc_start: 0.8732 (mmt180) cc_final: 0.8224 (mmm-85) REVERT: F 299 ASP cc_start: 0.8432 (m-30) cc_final: 0.8110 (m-30) REVERT: F 332 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8324 (ptmt) REVERT: F 346 MET cc_start: 0.8906 (tpp) cc_final: 0.8562 (tpp) REVERT: F 350 GLN cc_start: 0.9335 (tt0) cc_final: 0.8908 (tm-30) REVERT: F 392 MET cc_start: 0.8092 (mpt) cc_final: 0.7599 (mpp) REVERT: F 462 LEU cc_start: 0.8868 (tp) cc_final: 0.8582 (tp) REVERT: F 540 ILE cc_start: 0.8746 (tt) cc_final: 0.8183 (pt) REVERT: F 541 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8071 (tm-30) REVERT: F 580 MET cc_start: 0.8571 (mpp) cc_final: 0.7928 (mpp) REVERT: F 586 GLU cc_start: 0.7773 (tp30) cc_final: 0.7398 (tp30) REVERT: G 332 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8476 (tmtt) REVERT: G 350 GLN cc_start: 0.9327 (tt0) cc_final: 0.8941 (tm-30) REVERT: G 359 ARG cc_start: 0.8083 (tpt-90) cc_final: 0.7801 (tpt-90) REVERT: G 462 LEU cc_start: 0.8899 (tp) cc_final: 0.8463 (mp) REVERT: G 540 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8429 (pt) REVERT: G 541 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7632 (tm-30) REVERT: G 554 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: G 614 ARG cc_start: 0.8576 (tmm-80) cc_final: 0.8181 (mtp-110) REVERT: G 649 ARG cc_start: 0.8658 (mmt180) cc_final: 0.8170 (mmm160) REVERT: H 332 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8211 (ttmt) REVERT: H 346 MET cc_start: 0.8670 (tpp) cc_final: 0.8166 (tpp) REVERT: H 350 GLN cc_start: 0.9246 (tt0) cc_final: 0.8799 (tm-30) REVERT: H 462 LEU cc_start: 0.8961 (tp) cc_final: 0.8375 (mp) REVERT: H 541 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7693 (tm-30) REVERT: H 554 ASP cc_start: 0.8137 (t0) cc_final: 0.7725 (m-30) REVERT: H 580 MET cc_start: 0.8674 (mpp) cc_final: 0.8328 (mpp) REVERT: H 614 ARG cc_start: 0.8549 (tmm-80) cc_final: 0.8137 (mtp-110) REVERT: I 308 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8308 (tt) REVERT: I 346 MET cc_start: 0.9032 (tpp) cc_final: 0.8675 (tpp) REVERT: I 350 GLN cc_start: 0.9160 (tt0) cc_final: 0.8549 (pp30) REVERT: I 359 ARG cc_start: 0.7998 (tpt-90) cc_final: 0.7630 (tpt-90) REVERT: I 366 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: I 371 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8102 (tm-30) REVERT: I 462 LEU cc_start: 0.8875 (tp) cc_final: 0.8596 (tp) REVERT: I 541 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7835 (tm-30) REVERT: I 580 MET cc_start: 0.8651 (mpp) cc_final: 0.8338 (mpp) REVERT: I 617 MET cc_start: 0.8507 (mmt) cc_final: 0.8299 (mmt) REVERT: J 332 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8234 (ptmt) REVERT: J 346 MET cc_start: 0.8762 (tpp) cc_final: 0.8305 (mmm) REVERT: J 350 GLN cc_start: 0.9114 (tt0) cc_final: 0.8472 (pp30) REVERT: J 392 MET cc_start: 0.8005 (mpt) cc_final: 0.7434 (mpp) REVERT: J 460 MET cc_start: 0.6408 (ttm) cc_final: 0.5975 (ttm) REVERT: J 462 LEU cc_start: 0.8899 (tp) cc_final: 0.8360 (mp) REVERT: J 541 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7870 (mp0) REVERT: J 649 ARG cc_start: 0.8809 (mmt180) cc_final: 0.8283 (mmm-85) REVERT: K 332 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8179 (ttmt) REVERT: K 346 MET cc_start: 0.8777 (tpp) cc_final: 0.8201 (mmm) REVERT: K 350 GLN cc_start: 0.9079 (tt0) cc_final: 0.8429 (pp30) REVERT: K 392 MET cc_start: 0.7891 (mpt) cc_final: 0.7415 (mpp) REVERT: K 462 LEU cc_start: 0.8882 (tp) cc_final: 0.8631 (tp) REVERT: K 541 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7791 (tm-30) REVERT: K 581 ASP cc_start: 0.8879 (t0) cc_final: 0.8408 (t70) REVERT: K 639 TYR cc_start: 0.8534 (t80) cc_final: 0.8269 (t80) REVERT: L 333 HIS cc_start: 0.8602 (m-70) cc_final: 0.8311 (m-70) REVERT: L 346 MET cc_start: 0.8795 (tpp) cc_final: 0.8321 (mmm) REVERT: L 350 GLN cc_start: 0.9075 (tt0) cc_final: 0.8656 (pp30) REVERT: L 354 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8316 (pt0) REVERT: L 359 ARG cc_start: 0.8123 (tpt-90) cc_final: 0.7848 (tpt-90) REVERT: L 541 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7832 (tm-30) REVERT: L 554 ASP cc_start: 0.8277 (t0) cc_final: 0.7830 (m-30) REVERT: L 615 ASN cc_start: 0.8605 (m-40) cc_final: 0.8350 (m-40) REVERT: M 299 ASP cc_start: 0.8407 (m-30) cc_final: 0.8200 (m-30) REVERT: M 332 LYS cc_start: 0.8633 (tmtt) cc_final: 0.8155 (ptmt) REVERT: M 346 MET cc_start: 0.8877 (tpp) cc_final: 0.8337 (mmm) REVERT: M 359 ARG cc_start: 0.7947 (tpt-90) cc_final: 0.7703 (tpt-90) REVERT: M 460 MET cc_start: 0.6531 (ttm) cc_final: 0.6198 (ttm) REVERT: M 462 LEU cc_start: 0.8816 (tp) cc_final: 0.8532 (tp) REVERT: M 541 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7669 (tm-30) REVERT: M 594 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8475 (pt) REVERT: N 332 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8192 (ttmm) REVERT: N 350 GLN cc_start: 0.9269 (tt0) cc_final: 0.8752 (tm-30) REVERT: N 392 MET cc_start: 0.8066 (mpt) cc_final: 0.7665 (mpp) REVERT: N 460 MET cc_start: 0.6739 (ttm) cc_final: 0.6321 (ttm) REVERT: N 519 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8914 (mmmm) REVERT: N 541 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7722 (tm-30) REVERT: O 346 MET cc_start: 0.8812 (tpp) cc_final: 0.8282 (mmm) REVERT: O 350 GLN cc_start: 0.9273 (tt0) cc_final: 0.8847 (tm-30) REVERT: O 353 ILE cc_start: 0.9335 (mt) cc_final: 0.9124 (mp) REVERT: O 460 MET cc_start: 0.7570 (ttp) cc_final: 0.7221 (ttm) REVERT: O 462 LEU cc_start: 0.8869 (tp) cc_final: 0.8632 (tp) REVERT: O 483 LEU cc_start: 0.9173 (mt) cc_final: 0.8894 (mt) REVERT: O 540 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8332 (pt) REVERT: O 541 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7790 (tm-30) REVERT: O 542 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8080 (tm-30) REVERT: O 580 MET cc_start: 0.8587 (mpp) cc_final: 0.8204 (mpp) REVERT: O 581 ASP cc_start: 0.8866 (t0) cc_final: 0.8568 (t0) REVERT: O 586 GLU cc_start: 0.7825 (tp30) cc_final: 0.7262 (tp30) REVERT: O 629 MET cc_start: 0.6781 (tmm) cc_final: 0.6287 (tmm) outliers start: 142 outliers final: 123 residues processed: 688 average time/residue: 0.2643 time to fit residues: 289.3751 Evaluate side-chains 683 residues out of total 4350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 547 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 519 LYS Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 496 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 575 VAL Chi-restraints excluded: chain G residue 576 LEU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 575 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 593 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 575 VAL Chi-restraints excluded: chain I residue 576 LEU Chi-restraints excluded: chain I residue 620 ILE Chi-restraints excluded: chain J residue 366 GLU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 477 THR Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 482 THR Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 551 THR Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 482 THR Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 593 LEU Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 575 VAL Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain M residue 366 GLU Chi-restraints excluded: chain M residue 433 THR Chi-restraints excluded: chain M residue 477 THR Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 496 VAL Chi-restraints excluded: chain M residue 540 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 593 LEU Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 629 MET Chi-restraints excluded: chain N residue 433 THR Chi-restraints excluded: chain N residue 477 THR Chi-restraints excluded: chain N residue 496 VAL Chi-restraints excluded: chain N residue 519 LYS Chi-restraints excluded: chain N residue 551 THR Chi-restraints excluded: chain N residue 575 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 366 GLU Chi-restraints excluded: chain O residue 433 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 499 LEU Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain O residue 540 ILE Chi-restraints excluded: chain O residue 575 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 193 optimal weight: 0.9980 chunk 467 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 440 optimal weight: 6.9990 chunk 425 optimal weight: 4.9990 chunk 377 optimal weight: 7.9990 chunk 506 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS C 333 HIS ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 HIS ** K 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 HIS ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 HIS ** N 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.143202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100132 restraints weight = 56605.876| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.30 r_work: 0.3401 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39840 Z= 0.180 Angle : 0.666 13.969 53895 Z= 0.334 Chirality : 0.047 0.169 6480 Planarity : 0.004 0.043 6990 Dihedral : 5.014 23.164 5430 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.41 % Favored : 92.30 % Rotamer: Outliers : 3.38 % Allowed : 20.07 % Favored : 76.55 % 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: -2.74 (0.12), residues: 5130 helix: 0.76 (0.16), residues: 1155 sheet: -2.22 (0.10), residues: 2580 loop : -2.79 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 626 TYR 0.025 0.001 TYR O 639 PHE 0.014 0.001 PHE J 489 TRP 0.026 0.002 TRP L 384 HIS 0.005 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00402 (39840) covalent geometry : angle 0.66593 (53895) hydrogen bonds : bond 0.03338 ( 2010) hydrogen bonds : angle 4.82000 ( 6345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9939.03 seconds wall clock time: 170 minutes 54.49 seconds (10254.49 seconds total)