Starting phenix.real_space_refine on Sat Aug 8 02:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdp_64991/08_2026/9vdp_64991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdp_64991/08_2026/9vdp_64991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vdp_64991/08_2026/9vdp_64991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdp_64991/08_2026/9vdp_64991.map" model { file = "/net/cci-nas-00/data/ceres_data/9vdp_64991/08_2026/9vdp_64991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdp_64991/08_2026/9vdp_64991.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 132 5.16 5 C 15816 2.51 5 N 4134 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4049 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Chain: "I" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Restraints were copied for chains: B, D, F, H, K, C, E, G, J, L Time building chain proxies: 4.64, per 1000 atoms: 0.19 Number of scatterers: 24888 At special positions: 0 Unit cell: (135.85, 129.2, 105.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 30 15.00 O 4776 8.00 N 4134 7.00 C 15816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 60.4% alpha, 5.5% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 160 through 168 removed outlier: 4.365A pdb=" N TRP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.751A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.553A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 3.843A pdb=" N TYR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.516A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 350 through 365 Processing helix chain 'A' and resid 366 through 374 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 385 through 402 Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.771A pdb=" N MET A 407 " --> pdb=" O CYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.502A pdb=" N ASP A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.757A pdb=" N ASP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 160 through 168 removed outlier: 4.365A pdb=" N TRP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.751A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.553A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.843A pdb=" N TYR B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.517A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 366 through 374 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 385 through 402 Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.770A pdb=" N MET B 407 " --> pdb=" O CYS B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.502A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.757A pdb=" N ASP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 127 through 139 Processing helix chain 'D' and resid 160 through 168 removed outlier: 4.364A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.751A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.553A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 266 removed outlier: 3.843A pdb=" N TYR D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.517A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 350 through 365 Processing helix chain 'D' and resid 366 through 374 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 385 through 402 Processing helix chain 'D' and resid 403 through 417 removed outlier: 3.771A pdb=" N MET D 407 " --> pdb=" O CYS D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 434 through 445 removed outlier: 3.502A pdb=" N ASP D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.757A pdb=" N ASP D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 127 through 139 Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.364A pdb=" N TRP F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.750A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 3.553A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 3.844A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.516A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 350 through 365 Processing helix chain 'F' and resid 366 through 374 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 385 through 402 Processing helix chain 'F' and resid 403 through 417 removed outlier: 3.771A pdb=" N MET F 407 " --> pdb=" O CYS F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 434 through 445 removed outlier: 3.503A pdb=" N ASP F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.757A pdb=" N ASP F 462 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 95 through 100 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 127 through 139 Processing helix chain 'H' and resid 160 through 168 removed outlier: 4.364A pdb=" N TRP H 164 " --> pdb=" O HIS H 160 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 166 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 176 Processing helix chain 'H' and resid 186 through 199 removed outlier: 3.751A pdb=" N LYS H 199 " --> pdb=" O GLN H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 231 removed outlier: 3.553A pdb=" N SER H 214 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA H 223 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL H 224 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP H 231 " --> pdb=" O ARG H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 266 removed outlier: 3.843A pdb=" N TYR H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.517A pdb=" N SER H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 329 Processing helix chain 'H' and resid 333 through 343 Processing helix chain 'H' and resid 350 through 365 Processing helix chain 'H' and resid 366 through 374 Proline residue: H 370 - end of helix Processing helix chain 'H' and resid 385 through 402 Processing helix chain 'H' and resid 403 through 417 removed outlier: 3.771A pdb=" N MET H 407 " --> pdb=" O CYS H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 434 through 445 removed outlier: 3.502A pdb=" N ASP H 445 " --> pdb=" O LEU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 462 removed outlier: 3.757A pdb=" N ASP H 462 " --> pdb=" O ILE H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 469 Processing helix chain 'H' and resid 470 through 480 Processing helix chain 'H' and resid 490 through 498 Processing helix chain 'K' and resid 6 through 17 Processing helix chain 'K' and resid 40 through 50 Processing helix chain 'K' and resid 81 through 95 Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 101 through 103 No H-bonds generated for 'chain 'K' and resid 101 through 103' Processing helix chain 'K' and resid 127 through 139 Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.365A pdb=" N TRP K 164 " --> pdb=" O HIS K 160 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL K 166 " --> pdb=" O ILE K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.751A pdb=" N LYS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 231 removed outlier: 3.554A pdb=" N SER K 214 " --> pdb=" O PRO K 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA K 223 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 266 removed outlier: 3.843A pdb=" N TYR K 266 " --> pdb=" O GLU K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 295 removed outlier: 3.515A pdb=" N SER K 290 " --> pdb=" O ASP K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 329 Processing helix chain 'K' and resid 333 through 343 Processing helix chain 'K' and resid 350 through 365 Processing helix chain 'K' and resid 366 through 374 Proline residue: K 370 - end of helix Processing helix chain 'K' and resid 385 through 402 Processing helix chain 'K' and resid 403 through 417 removed outlier: 3.771A pdb=" N MET K 407 " --> pdb=" O CYS K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 422 through 433 Processing helix chain 'K' and resid 434 through 445 removed outlier: 3.503A pdb=" N ASP K 445 " --> pdb=" O LEU K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 447 through 462 removed outlier: 3.757A pdb=" N ASP K 462 " --> pdb=" O ILE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 469 Processing helix chain 'K' and resid 470 through 480 Processing helix chain 'K' and resid 490 through 498 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.632A pdb=" N LEU A 234 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.631A pdb=" N LEU B 234 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 63 through 68 Processing sheet with id=AA6, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.632A pdb=" N LEU D 234 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 63 through 68 Processing sheet with id=AA8, first strand: chain 'F' and resid 234 through 238 removed outlier: 4.631A pdb=" N LEU F 234 " --> pdb=" O TYR F 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 63 through 68 Processing sheet with id=AB1, first strand: chain 'H' and resid 234 through 238 removed outlier: 4.631A pdb=" N LEU H 234 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 63 through 68 Processing sheet with id=AB3, first strand: chain 'K' and resid 234 through 238 removed outlier: 4.631A pdb=" N LEU K 234 " --> pdb=" O TYR K 245 " (cutoff:3.500A) 1261 hydrogen bonds defined for protein. 3657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7962 1.35 - 1.46: 6327 1.46 - 1.58: 11007 1.58 - 1.70: 54 1.70 - 1.82: 186 Bond restraints: 25536 Sorted by residual: bond pdb=" C3' DC C 5 " pdb=" O3' DC C 5 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" C3' DC E 5 " pdb=" O3' DC E 5 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" C3' DC I 5 " pdb=" O3' DC I 5 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.49e+01 bond pdb=" C3' DC G 5 " pdb=" O3' DC G 5 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.49e+01 bond pdb=" C3' DC J 5 " pdb=" O3' DC J 5 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.48e+01 ... (remaining 25531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 33793 2.02 - 4.04: 737 4.04 - 6.06: 96 6.06 - 8.08: 36 8.08 - 10.10: 6 Bond angle restraints: 34668 Sorted by residual: angle pdb=" C ASP H 383 " pdb=" CA ASP H 383 " pdb=" CB ASP H 383 " ideal model delta sigma weight residual 116.54 109.59 6.95 1.15e+00 7.56e-01 3.66e+01 angle pdb=" C ASP A 383 " pdb=" CA ASP A 383 " pdb=" CB ASP A 383 " ideal model delta sigma weight residual 116.54 109.59 6.95 1.15e+00 7.56e-01 3.65e+01 angle pdb=" C ASP F 383 " pdb=" CA ASP F 383 " pdb=" CB ASP F 383 " ideal model delta sigma weight residual 116.54 109.61 6.93 1.15e+00 7.56e-01 3.63e+01 angle pdb=" C ASP D 383 " pdb=" CA ASP D 383 " pdb=" CB ASP D 383 " ideal model delta sigma weight residual 116.54 109.62 6.92 1.15e+00 7.56e-01 3.62e+01 angle pdb=" C ASP K 383 " pdb=" CA ASP K 383 " pdb=" CB ASP K 383 " ideal model delta sigma weight residual 116.54 109.62 6.92 1.15e+00 7.56e-01 3.62e+01 ... (remaining 34663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 14664 35.33 - 70.67: 504 70.67 - 106.00: 24 106.00 - 141.34: 0 141.34 - 176.67: 12 Dihedral angle restraints: 15204 sinusoidal: 6402 harmonic: 8802 Sorted by residual: dihedral pdb=" C4' DC G 6 " pdb=" C3' DC G 6 " pdb=" O3' DC G 6 " pdb=" P DC G 7 " ideal model delta sinusoidal sigma weight residual -140.00 36.67 -176.67 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 6 " pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " pdb=" P DC J 7 " ideal model delta sinusoidal sigma weight residual -140.00 36.63 -176.63 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC C 6 " pdb=" C3' DC C 6 " pdb=" O3' DC C 6 " pdb=" P DC C 7 " ideal model delta sinusoidal sigma weight residual -140.00 36.61 -176.61 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 15201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2447 0.041 - 0.082: 946 0.082 - 0.123: 250 0.123 - 0.164: 74 0.164 - 0.204: 27 Chirality restraints: 3744 Sorted by residual: chirality pdb=" C3' DC L 5 " pdb=" C4' DC L 5 " pdb=" O3' DC L 5 " pdb=" C2' DC L 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' DC I 5 " pdb=" C4' DC I 5 " pdb=" O3' DC I 5 " pdb=" C2' DC I 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' DC J 5 " pdb=" C4' DC J 5 " pdb=" O3' DC J 5 " pdb=" C2' DC J 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3741 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 20 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO D 21 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 21 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 21 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 20 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 21 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 20 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 21 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.032 5.00e-02 4.00e+02 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4602 2.77 - 3.30: 24419 3.30 - 3.83: 45289 3.83 - 4.37: 54418 4.37 - 4.90: 91145 Nonbonded interactions: 219873 Sorted by model distance: nonbonded pdb=" O LEU F 15 " pdb=" OG SER F 36 " model vdw 2.234 3.040 nonbonded pdb=" O LEU D 15 " pdb=" OG SER D 36 " model vdw 2.234 3.040 nonbonded pdb=" O LEU H 15 " pdb=" OG SER H 36 " model vdw 2.234 3.040 nonbonded pdb=" O LEU K 15 " pdb=" OG SER K 36 " model vdw 2.234 3.040 nonbonded pdb=" O LEU B 15 " pdb=" OG SER B 36 " model vdw 2.234 3.040 ... (remaining 219868 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.220 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25536 Z= 0.228 Angle : 0.725 10.101 34668 Z= 0.426 Chirality : 0.049 0.204 3744 Planarity : 0.006 0.058 4350 Dihedral : 17.877 176.673 9540 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.47 % Favored : 96.33 % Rotamer: Outliers : 3.17 % Allowed : 20.06 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 2940 helix: -0.29 (0.11), residues: 1650 sheet: -0.42 (0.33), residues: 210 loop : -0.65 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 37 TYR 0.026 0.002 TYR D 11 PHE 0.012 0.001 PHE H 39 TRP 0.010 0.002 TRP B 471 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.23 (25536) covalent geometry : angle 0.72488 / 0.43 (34668) hydrogen bonds : bond 0.14232 / 9.68 ( 1261) hydrogen bonds : angle 6.68494 / 4.85 ( 3657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 552 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6860 (mt-10) REVERT: A 27 ILE cc_start: 0.6505 (pt) cc_final: 0.6284 (pp) REVERT: A 54 ARG cc_start: 0.6489 (ttp80) cc_final: 0.6075 (ttt-90) REVERT: A 56 SER cc_start: 0.7821 (m) cc_final: 0.7591 (p) REVERT: A 64 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7279 (mm-30) REVERT: A 66 TYR cc_start: 0.7587 (m-80) cc_final: 0.7170 (m-80) REVERT: A 69 ARG cc_start: 0.6537 (mtm-85) cc_final: 0.6102 (mtm-85) REVERT: A 98 GLU cc_start: 0.6678 (mp0) cc_final: 0.6214 (mm-30) REVERT: A 104 GLU cc_start: 0.6759 (pp20) cc_final: 0.6026 (mp0) REVERT: A 135 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5605 (tt0) REVERT: A 137 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6097 (t0) REVERT: A 189 ASP cc_start: 0.5657 (t70) cc_final: 0.5141 (m-30) REVERT: A 190 LYS cc_start: 0.6560 (mmmm) cc_final: 0.6247 (mmmt) REVERT: A 197 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7261 (mm-40) REVERT: A 199 LYS cc_start: 0.6728 (ttpp) cc_final: 0.6428 (ttmm) REVERT: A 226 LYS cc_start: 0.6570 (ttpt) cc_final: 0.5963 (tttp) REVERT: A 227 ARG cc_start: 0.6198 (mmm160) cc_final: 0.5535 (tpt-90) REVERT: A 247 LYS cc_start: 0.7195 (mttt) cc_final: 0.6891 (mttm) REVERT: A 254 GLU cc_start: 0.5945 (tp30) cc_final: 0.5599 (tp30) REVERT: A 272 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6499 (mt) REVERT: A 274 LYS cc_start: 0.6049 (mmtm) cc_final: 0.5655 (mmtm) REVERT: A 276 LYS cc_start: 0.7334 (pttm) cc_final: 0.7108 (pttp) REVERT: A 386 GLU cc_start: 0.5293 (tp30) cc_final: 0.5016 (tp30) REVERT: A 397 MET cc_start: 0.6770 (tmm) cc_final: 0.6198 (tmm) REVERT: A 401 ASN cc_start: 0.7227 (m-40) cc_final: 0.6939 (m110) REVERT: A 402 LYS cc_start: 0.6501 (mmtp) cc_final: 0.6036 (mptp) REVERT: A 407 MET cc_start: 0.7562 (tpp) cc_final: 0.7329 (tpp) REVERT: A 423 ASP cc_start: 0.5829 (m-30) cc_final: 0.5414 (m-30) REVERT: A 427 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: A 452 ASN cc_start: 0.6584 (t0) cc_final: 0.6259 (t0) REVERT: A 457 ASP cc_start: 0.6768 (m-30) cc_final: 0.6411 (m-30) REVERT: A 459 ILE cc_start: 0.7401 (mm) cc_final: 0.7196 (mt) REVERT: A 460 LYS cc_start: 0.6637 (ptpp) cc_final: 0.5643 (pptt) REVERT: A 462 ASP cc_start: 0.6782 (t0) cc_final: 0.6535 (t70) REVERT: B 12 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 27 ILE cc_start: 0.6453 (pt) cc_final: 0.6238 (pp) REVERT: B 54 ARG cc_start: 0.6555 (ttp80) cc_final: 0.6229 (ttt-90) REVERT: B 64 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7193 (mm-30) REVERT: B 66 TYR cc_start: 0.7629 (m-80) cc_final: 0.7288 (m-80) REVERT: B 69 ARG cc_start: 0.6576 (mtm-85) cc_final: 0.6080 (mtm-85) REVERT: B 98 GLU cc_start: 0.6614 (mp0) cc_final: 0.6116 (mm-30) REVERT: B 104 GLU cc_start: 0.6667 (pp20) cc_final: 0.5930 (mp0) REVERT: B 135 GLU cc_start: 0.6449 (mt-10) cc_final: 0.5568 (tt0) REVERT: B 137 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6170 (t0) REVERT: B 171 ASN cc_start: 0.5684 (m-40) cc_final: 0.5468 (m110) REVERT: B 189 ASP cc_start: 0.6066 (t70) cc_final: 0.5343 (m-30) REVERT: B 190 LYS cc_start: 0.6474 (mmmm) cc_final: 0.6213 (mmmt) REVERT: B 197 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7137 (mm-40) REVERT: B 199 LYS cc_start: 0.6422 (ttpp) cc_final: 0.6102 (ttmm) REVERT: B 226 LYS cc_start: 0.6504 (ttpt) cc_final: 0.5933 (tttp) REVERT: B 227 ARG cc_start: 0.6141 (mmm160) cc_final: 0.5525 (tpt-90) REVERT: B 241 ASP cc_start: 0.6635 (t70) cc_final: 0.6386 (t70) REVERT: B 247 LYS cc_start: 0.7215 (mttt) cc_final: 0.6895 (mttm) REVERT: B 254 GLU cc_start: 0.5956 (tp30) cc_final: 0.5629 (tp30) REVERT: B 272 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6590 (mt) REVERT: B 274 LYS cc_start: 0.5957 (mmtm) cc_final: 0.5617 (mmtm) REVERT: B 276 LYS cc_start: 0.7282 (pttm) cc_final: 0.7060 (pttp) REVERT: B 386 GLU cc_start: 0.5103 (tp30) cc_final: 0.4810 (tp30) REVERT: B 397 MET cc_start: 0.6667 (tmm) cc_final: 0.6178 (tmm) REVERT: B 401 ASN cc_start: 0.7119 (m-40) cc_final: 0.6886 (m110) REVERT: B 402 LYS cc_start: 0.6594 (mmtp) cc_final: 0.6003 (mptp) REVERT: B 423 ASP cc_start: 0.5561 (m-30) cc_final: 0.5156 (m-30) REVERT: B 427 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: B 442 ASP cc_start: 0.6612 (t70) cc_final: 0.6314 (t70) REVERT: B 452 ASN cc_start: 0.6424 (t0) cc_final: 0.6151 (t0) REVERT: B 457 ASP cc_start: 0.6830 (m-30) cc_final: 0.6412 (m-30) REVERT: B 460 LYS cc_start: 0.6851 (ptpp) cc_final: 0.5830 (pptt) REVERT: B 462 ASP cc_start: 0.6652 (t0) cc_final: 0.6145 (m-30) REVERT: D 42 GLU cc_start: 0.7303 (mp0) cc_final: 0.7096 (mp0) REVERT: D 54 ARG cc_start: 0.6571 (ttp80) cc_final: 0.6279 (ttp-110) REVERT: D 64 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6876 (mm-30) REVERT: D 75 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.6522 (ttp-110) REVERT: D 98 GLU cc_start: 0.6469 (mp0) cc_final: 0.6029 (mm-30) REVERT: D 104 GLU cc_start: 0.6591 (pp20) cc_final: 0.5760 (mp0) REVERT: D 113 ASP cc_start: 0.6330 (t0) cc_final: 0.6104 (t0) REVERT: D 137 ASN cc_start: 0.6820 (OUTLIER) cc_final: 0.6022 (t0) REVERT: D 149 ASP cc_start: 0.6498 (m-30) cc_final: 0.5531 (t70) REVERT: D 189 ASP cc_start: 0.5769 (t70) cc_final: 0.5309 (m-30) REVERT: D 197 GLN cc_start: 0.7596 (mm-40) cc_final: 0.6969 (mm-40) REVERT: D 199 LYS cc_start: 0.6786 (ttpp) cc_final: 0.6436 (ttmm) REVERT: D 226 LYS cc_start: 0.6457 (ttpt) cc_final: 0.5948 (tttp) REVERT: D 227 ARG cc_start: 0.6089 (mmm160) cc_final: 0.5723 (tpt-90) REVERT: D 272 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6328 (mt) REVERT: D 276 LYS cc_start: 0.7394 (pttm) cc_final: 0.7192 (pttp) REVERT: D 287 ASN cc_start: 0.6691 (p0) cc_final: 0.6450 (p0) REVERT: D 304 ASP cc_start: 0.6117 (p0) cc_final: 0.5877 (p0) REVERT: D 313 SER cc_start: 0.6858 (OUTLIER) cc_final: 0.6586 (t) REVERT: D 347 ASP cc_start: 0.6647 (p0) cc_final: 0.6374 (p0) REVERT: D 367 MET cc_start: 0.7155 (ptm) cc_final: 0.6919 (ptm) REVERT: D 385 ASP cc_start: 0.6069 (OUTLIER) cc_final: 0.5743 (p0) REVERT: D 386 GLU cc_start: 0.5587 (tp30) cc_final: 0.5215 (tp30) REVERT: D 393 GLU cc_start: 0.6463 (tp30) cc_final: 0.5954 (tp30) REVERT: D 397 MET cc_start: 0.6861 (tmm) cc_final: 0.6001 (tmm) REVERT: D 401 ASN cc_start: 0.6949 (m-40) cc_final: 0.6749 (m110) REVERT: D 402 LYS cc_start: 0.6568 (mmtp) cc_final: 0.6135 (mptp) REVERT: D 407 MET cc_start: 0.7478 (tpp) cc_final: 0.6838 (tpp) REVERT: D 424 ASP cc_start: 0.6651 (t70) cc_final: 0.6104 (p0) REVERT: D 427 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: D 452 ASN cc_start: 0.6510 (t0) cc_final: 0.6281 (t0) REVERT: D 462 ASP cc_start: 0.6850 (t0) cc_final: 0.6626 (t70) REVERT: D 490 LYS cc_start: 0.5881 (mmmt) cc_final: 0.4858 (mttm) REVERT: F 12 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7007 (mt-10) REVERT: F 27 ILE cc_start: 0.6371 (pt) cc_final: 0.6158 (pp) REVERT: F 54 ARG cc_start: 0.6719 (ttp80) cc_final: 0.6404 (ttt-90) REVERT: F 64 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6782 (mm-30) REVERT: F 69 ARG cc_start: 0.6617 (mtm-85) cc_final: 0.6262 (mpp80) REVERT: F 98 GLU cc_start: 0.6293 (mp0) cc_final: 0.5915 (mm-30) REVERT: F 104 GLU cc_start: 0.6588 (pp20) cc_final: 0.5967 (mp0) REVERT: F 113 ASP cc_start: 0.6399 (t0) cc_final: 0.6190 (t70) REVERT: F 137 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.5996 (t0) REVERT: F 149 ASP cc_start: 0.6716 (m-30) cc_final: 0.5496 (t70) REVERT: F 189 ASP cc_start: 0.5811 (t70) cc_final: 0.5262 (m-30) REVERT: F 190 LYS cc_start: 0.6708 (mmmm) cc_final: 0.6504 (mmmm) REVERT: F 197 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7164 (mm-40) REVERT: F 199 LYS cc_start: 0.6579 (ttpp) cc_final: 0.6210 (ttmm) REVERT: F 226 LYS cc_start: 0.6635 (ttpt) cc_final: 0.6049 (tttp) REVERT: F 227 ARG cc_start: 0.6062 (mmm160) cc_final: 0.5646 (tpt-90) REVERT: F 247 LYS cc_start: 0.7118 (mttt) cc_final: 0.6809 (mttp) REVERT: F 272 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6438 (mt) REVERT: F 274 LYS cc_start: 0.5967 (mmtm) cc_final: 0.5663 (mptm) REVERT: F 276 LYS cc_start: 0.7370 (pttm) cc_final: 0.7081 (pttp) REVERT: F 313 SER cc_start: 0.6881 (OUTLIER) cc_final: 0.6638 (t) REVERT: F 345 ASN cc_start: 0.7589 (m-40) cc_final: 0.7308 (m110) REVERT: F 367 MET cc_start: 0.7324 (ptm) cc_final: 0.7066 (ptm) REVERT: F 393 GLU cc_start: 0.6217 (tp30) cc_final: 0.5786 (tp30) REVERT: F 397 MET cc_start: 0.6647 (tmm) cc_final: 0.6227 (tmm) REVERT: F 402 LYS cc_start: 0.6708 (mmtp) cc_final: 0.6109 (mptp) REVERT: F 423 ASP cc_start: 0.5807 (m-30) cc_final: 0.4560 (t70) REVERT: F 427 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: F 457 ASP cc_start: 0.6583 (m-30) cc_final: 0.6272 (m-30) REVERT: F 460 LYS cc_start: 0.6533 (ptpp) cc_final: 0.5641 (pptt) REVERT: H 12 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6956 (mt-10) REVERT: H 27 ILE cc_start: 0.6487 (pt) cc_final: 0.6270 (pp) REVERT: H 54 ARG cc_start: 0.6351 (ttp80) cc_final: 0.6015 (ttp-110) REVERT: H 58 GLN cc_start: 0.6489 (pt0) cc_final: 0.6163 (pt0) REVERT: H 64 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7377 (mm-30) REVERT: H 69 ARG cc_start: 0.6655 (mtm-85) cc_final: 0.6301 (mpp80) REVERT: H 75 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6936 (ttp-110) REVERT: H 98 GLU cc_start: 0.6365 (mp0) cc_final: 0.5856 (mm-30) REVERT: H 104 GLU cc_start: 0.6857 (pp20) cc_final: 0.6291 (mp0) REVERT: H 109 MET cc_start: 0.7122 (mmm) cc_final: 0.6860 (mmp) REVERT: H 123 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: H 126 GLU cc_start: 0.6756 (pt0) cc_final: 0.6120 (pt0) REVERT: H 137 ASN cc_start: 0.6847 (OUTLIER) cc_final: 0.6033 (t0) REVERT: H 149 ASP cc_start: 0.6768 (m-30) cc_final: 0.5618 (t70) REVERT: H 189 ASP cc_start: 0.5523 (t70) cc_final: 0.5140 (m-30) REVERT: H 197 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7288 (mm-40) REVERT: H 199 LYS cc_start: 0.6612 (ttpp) cc_final: 0.6354 (ttmm) REVERT: H 200 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7271 (mtm-85) REVERT: H 226 LYS cc_start: 0.6631 (ttpt) cc_final: 0.6075 (tttp) REVERT: H 227 ARG cc_start: 0.6333 (mmm160) cc_final: 0.5938 (tpt-90) REVERT: H 234 LEU cc_start: 0.7276 (tp) cc_final: 0.7018 (tp) REVERT: H 247 LYS cc_start: 0.7147 (mttt) cc_final: 0.6924 (mttm) REVERT: H 272 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6702 (mt) REVERT: H 345 ASN cc_start: 0.7350 (m-40) cc_final: 0.7115 (m110) REVERT: H 367 MET cc_start: 0.7278 (ptm) cc_final: 0.7070 (ptm) REVERT: H 386 GLU cc_start: 0.5356 (tp30) cc_final: 0.5048 (tp30) REVERT: H 393 GLU cc_start: 0.6521 (tp30) cc_final: 0.6010 (tp30) REVERT: H 397 MET cc_start: 0.7017 (tmm) cc_final: 0.6597 (tmm) REVERT: H 402 LYS cc_start: 0.6629 (mmtp) cc_final: 0.6084 (mptp) REVERT: H 423 ASP cc_start: 0.5986 (m-30) cc_final: 0.4622 (t70) REVERT: H 427 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5542 (mp0) REVERT: H 452 ASN cc_start: 0.6675 (t0) cc_final: 0.6351 (t0) REVERT: H 457 ASP cc_start: 0.6724 (m-30) cc_final: 0.6249 (m-30) REVERT: H 460 LYS cc_start: 0.6526 (ptpp) cc_final: 0.5488 (pptt) REVERT: H 469 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6905 (mtp85) REVERT: H 490 LYS cc_start: 0.6267 (mmmt) cc_final: 0.5123 (mttm) REVERT: K 12 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6983 (mt-10) REVERT: K 27 ILE cc_start: 0.6448 (pt) cc_final: 0.6224 (pp) REVERT: K 54 ARG cc_start: 0.6737 (ttp80) cc_final: 0.6421 (ttp-110) REVERT: K 58 GLN cc_start: 0.6511 (pt0) cc_final: 0.6261 (pt0) REVERT: K 64 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7329 (mm-30) REVERT: K 69 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6451 (mpp80) REVERT: K 70 TYR cc_start: 0.6325 (p90) cc_final: 0.6044 (p90) REVERT: K 98 GLU cc_start: 0.6437 (mp0) cc_final: 0.5996 (mm-30) REVERT: K 104 GLU cc_start: 0.6867 (pp20) cc_final: 0.6088 (mp0) REVERT: K 109 MET cc_start: 0.6917 (mmm) cc_final: 0.6681 (mmp) REVERT: K 137 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6123 (t0) REVERT: K 149 ASP cc_start: 0.6887 (m-30) cc_final: 0.5717 (t70) REVERT: K 197 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7353 (mm-40) REVERT: K 199 LYS cc_start: 0.6616 (ttpp) cc_final: 0.6356 (ttmm) REVERT: K 226 LYS cc_start: 0.6362 (ttpt) cc_final: 0.5839 (tttp) REVERT: K 234 LEU cc_start: 0.7399 (tp) cc_final: 0.7142 (tp) REVERT: K 247 LYS cc_start: 0.7217 (mttt) cc_final: 0.6968 (mttm) REVERT: K 367 MET cc_start: 0.7280 (ptm) cc_final: 0.7060 (ptm) REVERT: K 393 GLU cc_start: 0.6402 (tp30) cc_final: 0.6049 (tp30) REVERT: K 397 MET cc_start: 0.6963 (tmm) cc_final: 0.6574 (tmm) REVERT: K 402 LYS cc_start: 0.6805 (mmtp) cc_final: 0.6286 (mptp) REVERT: K 423 ASP cc_start: 0.5863 (m-30) cc_final: 0.4388 (t70) REVERT: K 427 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: K 452 ASN cc_start: 0.6691 (t0) cc_final: 0.6346 (t0) REVERT: K 457 ASP cc_start: 0.6731 (m-30) cc_final: 0.6358 (m-30) REVERT: K 460 LYS cc_start: 0.6904 (ptpp) cc_final: 0.5890 (pptt) outliers start: 86 outliers final: 28 residues processed: 606 average time/residue: 0.6356 time to fit residues: 448.3952 Evaluate side-chains 469 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 420 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain H residue 11 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain K residue 11 TYR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 95 ASN A 201 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 95 ASN D 201 ASN F 58 GLN F 95 ASN F 201 ASN H 95 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 ASN K 295 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132377 restraints weight = 23080.376| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.16 r_work: 0.3392 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25536 Z= 0.184 Angle : 0.603 7.602 34668 Z= 0.333 Chirality : 0.048 0.382 3744 Planarity : 0.005 0.062 4350 Dihedral : 15.099 174.635 3679 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.14 % Rotamer: Outliers : 4.61 % Allowed : 16.89 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 2940 helix: 0.87 (0.12), residues: 1716 sheet: -0.22 (0.34), residues: 204 loop : -0.35 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 134 TYR 0.023 0.002 TYR K 475 PHE 0.014 0.002 PHE B 144 TRP 0.008 0.002 TRP F 363 HIS 0.006 0.001 HIS H 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (25536) covalent geometry : angle 0.60254 / 0.33 (34668) hydrogen bonds : bond 0.05337 / 3.61 ( 1261) hydrogen bonds : angle 4.94726 / 3.54 ( 3657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 445 time to evaluate : 1.054 Fit side-chains REVERT: A 54 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7296 (ttt-90) REVERT: A 135 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7696 (tt0) REVERT: A 137 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8202 (t0) REVERT: A 199 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8132 (ttmm) REVERT: A 227 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7586 (tpt-90) REVERT: A 301 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.5991 (mmm160) REVERT: A 385 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6964 (p0) REVERT: A 386 GLU cc_start: 0.6966 (tp30) cc_final: 0.6649 (tp30) REVERT: A 423 ASP cc_start: 0.7146 (m-30) cc_final: 0.6468 (t70) REVERT: A 427 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 436 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (mp) REVERT: A 457 ASP cc_start: 0.8144 (m-30) cc_final: 0.7944 (m-30) REVERT: A 460 LYS cc_start: 0.7619 (ptpp) cc_final: 0.6878 (pptt) REVERT: A 462 ASP cc_start: 0.7307 (t0) cc_final: 0.6884 (m-30) REVERT: A 490 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7696 (mmtm) REVERT: B 54 ARG cc_start: 0.7486 (ttp80) cc_final: 0.7217 (ttt-90) REVERT: B 66 TYR cc_start: 0.8846 (m-80) cc_final: 0.8640 (m-80) REVERT: B 69 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7768 (mtp85) REVERT: B 135 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7718 (tt0) REVERT: B 137 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8170 (t0) REVERT: B 199 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8048 (ttmm) REVERT: B 227 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7469 (tpt-90) REVERT: B 274 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7417 (mmtm) REVERT: B 301 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6124 (mmm160) REVERT: B 385 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6861 (p0) REVERT: B 386 GLU cc_start: 0.6752 (tp30) cc_final: 0.6451 (tp30) REVERT: B 423 ASP cc_start: 0.6879 (m-30) cc_final: 0.6226 (t70) REVERT: B 427 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 436 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 457 ASP cc_start: 0.8068 (m-30) cc_final: 0.7842 (m-30) REVERT: B 460 LYS cc_start: 0.7610 (ptpp) cc_final: 0.6889 (pptt) REVERT: B 462 ASP cc_start: 0.7408 (t0) cc_final: 0.7031 (m-30) REVERT: B 490 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7638 (mmtm) REVERT: D 10 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8050 (tp) REVERT: D 137 ASN cc_start: 0.8445 (m-40) cc_final: 0.8152 (t0) REVERT: D 199 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8117 (ttmm) REVERT: D 227 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7553 (tpt-90) REVERT: D 301 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5605 (mmm160) REVERT: D 349 TYR cc_start: 0.7203 (m-80) cc_final: 0.7000 (m-80) REVERT: D 385 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6872 (p0) REVERT: D 393 GLU cc_start: 0.8173 (tp30) cc_final: 0.7887 (tp30) REVERT: D 397 MET cc_start: 0.8731 (tmm) cc_final: 0.8423 (tmm) REVERT: D 402 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7720 (mptp) REVERT: D 407 MET cc_start: 0.8813 (tpp) cc_final: 0.8524 (tpp) REVERT: D 427 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: D 442 ASP cc_start: 0.8325 (t70) cc_final: 0.8114 (t70) REVERT: D 462 ASP cc_start: 0.7342 (t0) cc_final: 0.7130 (t70) REVERT: D 490 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7688 (mmtt) REVERT: F 54 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7316 (ttt-90) REVERT: F 125 TYR cc_start: 0.7634 (t80) cc_final: 0.7381 (t80) REVERT: F 135 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7774 (mt-10) REVERT: F 137 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8059 (t0) REVERT: F 199 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7957 (ttmm) REVERT: F 301 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6046 (mmm160) REVERT: F 348 GLU cc_start: 0.7522 (pt0) cc_final: 0.7136 (tm-30) REVERT: F 349 TYR cc_start: 0.6989 (m-80) cc_final: 0.6783 (m-10) REVERT: F 367 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8462 (ptm) REVERT: F 375 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7800 (mt) REVERT: F 397 MET cc_start: 0.8839 (tmm) cc_final: 0.8557 (tmm) REVERT: F 423 ASP cc_start: 0.6713 (m-30) cc_final: 0.6036 (t70) REVERT: F 427 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: F 457 ASP cc_start: 0.7875 (m-30) cc_final: 0.7665 (m-30) REVERT: F 460 LYS cc_start: 0.7623 (ptpp) cc_final: 0.6820 (pptt) REVERT: F 490 LYS cc_start: 0.7786 (mmmt) cc_final: 0.6981 (mttm) REVERT: H 54 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7158 (ttp-110) REVERT: H 58 GLN cc_start: 0.7857 (pt0) cc_final: 0.7615 (pt0) REVERT: H 109 MET cc_start: 0.8533 (mmm) cc_final: 0.8263 (mmp) REVERT: H 126 GLU cc_start: 0.7455 (pt0) cc_final: 0.7036 (pt0) REVERT: H 137 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8056 (t0) REVERT: H 149 ASP cc_start: 0.8037 (m-30) cc_final: 0.7560 (t70) REVERT: H 199 LYS cc_start: 0.8333 (ttpp) cc_final: 0.8119 (ttmm) REVERT: H 301 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5965 (mmm160) REVERT: H 304 ASP cc_start: 0.7070 (p0) cc_final: 0.6847 (p0) REVERT: H 348 GLU cc_start: 0.7632 (pt0) cc_final: 0.7285 (tm-30) REVERT: H 375 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8285 (mt) REVERT: H 385 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6986 (p0) REVERT: H 386 GLU cc_start: 0.7192 (tp30) cc_final: 0.6966 (tp30) REVERT: H 402 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7888 (mptp) REVERT: H 427 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: H 457 ASP cc_start: 0.8291 (m-30) cc_final: 0.8041 (m-30) REVERT: H 460 LYS cc_start: 0.7535 (ptpp) cc_final: 0.6827 (pptt) REVERT: H 490 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7343 (mttm) REVERT: K 54 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7380 (ttp-110) REVERT: K 58 GLN cc_start: 0.7820 (pt0) cc_final: 0.7576 (pt0) REVERT: K 149 ASP cc_start: 0.8071 (m-30) cc_final: 0.7692 (t70) REVERT: K 199 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8067 (ttmm) REVERT: K 301 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6090 (mmm160) REVERT: K 349 TYR cc_start: 0.7158 (m-80) cc_final: 0.6569 (m-80) REVERT: K 367 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8500 (ptm) REVERT: K 375 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8007 (mt) REVERT: K 423 ASP cc_start: 0.6923 (m-30) cc_final: 0.5909 (t70) REVERT: K 427 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: K 460 LYS cc_start: 0.7672 (ptpp) cc_final: 0.7071 (pptt) REVERT: K 490 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7804 (mmtt) outliers start: 125 outliers final: 42 residues processed: 534 average time/residue: 0.6836 time to fit residues: 421.4277 Evaluate side-chains 439 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 369 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 308 ASN Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 190 LYS Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 287 ASN Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 301 ARG Chi-restraints excluded: chain K residue 367 MET Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 444 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 184 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 401 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 401 ASN D 58 GLN F 58 GLN F 378 HIS ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 ASN H 295 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130648 restraints weight = 23221.844| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.15 r_work: 0.3374 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25536 Z= 0.148 Angle : 0.552 8.311 34668 Z= 0.304 Chirality : 0.045 0.354 3744 Planarity : 0.005 0.048 4350 Dihedral : 14.983 174.808 3644 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 3.91 % Allowed : 17.37 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 2940 helix: 1.25 (0.12), residues: 1740 sheet: -0.39 (0.36), residues: 192 loop : -0.29 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 227 TYR 0.020 0.002 TYR K 475 PHE 0.012 0.001 PHE K 144 TRP 0.009 0.001 TRP F 363 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (25536) covalent geometry : angle 0.55213 / 0.30 (34668) hydrogen bonds : bond 0.04903 / 3.30 ( 1261) hydrogen bonds : angle 4.69807 / 3.36 ( 3657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 390 time to evaluate : 1.066 Fit side-chains REVERT: A 54 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7303 (ttt-90) REVERT: A 135 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7768 (tt0) REVERT: A 137 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 199 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8058 (ttmm) REVERT: A 227 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7589 (tpt-90) REVERT: A 301 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5917 (mmm160) REVERT: A 377 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7431 (mp0) REVERT: A 386 GLU cc_start: 0.7009 (tp30) cc_final: 0.6707 (tp30) REVERT: A 424 ASP cc_start: 0.7602 (t70) cc_final: 0.7386 (p0) REVERT: A 436 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 452 ASN cc_start: 0.8568 (t0) cc_final: 0.8274 (t0) REVERT: A 457 ASP cc_start: 0.8159 (m-30) cc_final: 0.7948 (m-30) REVERT: A 460 LYS cc_start: 0.7584 (ptpp) cc_final: 0.6891 (pptt) REVERT: A 462 ASP cc_start: 0.7324 (t0) cc_final: 0.7075 (t70) REVERT: B 54 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7150 (ttt-90) REVERT: B 69 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7621 (mtt180) REVERT: B 135 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7796 (tt0) REVERT: B 137 ASN cc_start: 0.8342 (m-40) cc_final: 0.8125 (t0) REVERT: B 199 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8022 (ttmm) REVERT: B 227 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7547 (tpt-90) REVERT: B 301 ARG cc_start: 0.6711 (mpt180) cc_final: 0.6032 (mmm160) REVERT: B 349 TYR cc_start: 0.7184 (m-80) cc_final: 0.6759 (m-80) REVERT: B 377 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7409 (mp0) REVERT: B 385 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6951 (p0) REVERT: B 386 GLU cc_start: 0.6957 (tp30) cc_final: 0.6608 (tp30) REVERT: B 427 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: B 436 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 457 ASP cc_start: 0.8143 (m-30) cc_final: 0.7901 (m-30) REVERT: B 460 LYS cc_start: 0.7628 (ptpp) cc_final: 0.6894 (pptt) REVERT: B 462 ASP cc_start: 0.7340 (t0) cc_final: 0.6948 (m-30) REVERT: B 490 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7701 (mmtm) REVERT: D 10 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8128 (tp) REVERT: D 68 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8142 (p) REVERT: D 135 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7823 (mt-10) REVERT: D 137 ASN cc_start: 0.8477 (m-40) cc_final: 0.8172 (t0) REVERT: D 199 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8068 (ttmm) REVERT: D 227 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7615 (tpt-90) REVERT: D 349 TYR cc_start: 0.7256 (m-80) cc_final: 0.7014 (m-80) REVERT: D 385 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6677 (p0) REVERT: D 397 MET cc_start: 0.8815 (tmm) cc_final: 0.8486 (tmm) REVERT: D 402 LYS cc_start: 0.7990 (mmtp) cc_final: 0.7774 (mptp) REVERT: D 424 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7106 (p0) REVERT: D 427 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: D 462 ASP cc_start: 0.7328 (t0) cc_final: 0.7108 (t70) REVERT: D 490 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7785 (mmtm) REVERT: F 10 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8198 (tp) REVERT: F 54 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7336 (ttt-90) REVERT: F 125 TYR cc_start: 0.7663 (t80) cc_final: 0.7395 (t80) REVERT: F 135 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7773 (tt0) REVERT: F 137 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8084 (t0) REVERT: F 155 THR cc_start: 0.8184 (t) cc_final: 0.7880 (p) REVERT: F 199 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7868 (ttmm) REVERT: F 348 GLU cc_start: 0.7528 (pt0) cc_final: 0.7140 (tm-30) REVERT: F 349 TYR cc_start: 0.7121 (m-80) cc_final: 0.6904 (m-10) REVERT: F 367 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8443 (ptm) REVERT: F 385 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6835 (p0) REVERT: F 397 MET cc_start: 0.8877 (tmm) cc_final: 0.8569 (tmm) REVERT: F 423 ASP cc_start: 0.6910 (m-30) cc_final: 0.6357 (t70) REVERT: F 436 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8566 (mp) REVERT: F 460 LYS cc_start: 0.7587 (ptpp) cc_final: 0.6700 (pptt) REVERT: F 490 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7632 (mmtt) REVERT: H 10 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8549 (tp) REVERT: H 54 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7182 (ttp-110) REVERT: H 58 GLN cc_start: 0.7860 (pt0) cc_final: 0.7594 (pt0) REVERT: H 126 GLU cc_start: 0.7639 (pt0) cc_final: 0.7286 (pt0) REVERT: H 137 ASN cc_start: 0.8358 (m-40) cc_final: 0.8111 (t0) REVERT: H 199 LYS cc_start: 0.8313 (ttpp) cc_final: 0.8097 (ttmm) REVERT: H 301 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.5956 (mmm160) REVERT: H 348 GLU cc_start: 0.7702 (pt0) cc_final: 0.7350 (tm-30) REVERT: H 375 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8558 (mt) REVERT: H 385 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6887 (p0) REVERT: H 386 GLU cc_start: 0.7188 (tp30) cc_final: 0.6937 (tp30) REVERT: H 420 ASP cc_start: 0.8625 (m-30) cc_final: 0.8287 (m-30) REVERT: H 427 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: H 436 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8557 (mp) REVERT: H 460 LYS cc_start: 0.7484 (ptpp) cc_final: 0.6758 (pptt) REVERT: H 490 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7342 (mttm) REVERT: K 10 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8522 (tp) REVERT: K 54 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7427 (ttp-110) REVERT: K 58 GLN cc_start: 0.7847 (pt0) cc_final: 0.7561 (pt0) REVERT: K 69 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7993 (mtp85) REVERT: K 199 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8114 (ttmm) REVERT: K 301 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6007 (mmm160) REVERT: K 348 GLU cc_start: 0.7429 (pp20) cc_final: 0.6921 (tm-30) REVERT: K 367 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8526 (ptm) REVERT: K 375 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8330 (mt) REVERT: K 423 ASP cc_start: 0.7211 (m-30) cc_final: 0.6985 (m-30) REVERT: K 427 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: K 449 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: K 460 LYS cc_start: 0.7661 (ptpp) cc_final: 0.6954 (pptt) REVERT: K 490 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7824 (mmtt) outliers start: 106 outliers final: 42 residues processed: 457 average time/residue: 0.5803 time to fit residues: 307.5258 Evaluate side-chains 430 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 359 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 367 MET Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 287 ASN Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 301 ARG Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 367 MET Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 449 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 231 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 295 ASN B 58 GLN B 201 ASN B 378 HIS D 58 GLN F 58 GLN F 295 ASN F 378 HIS ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 ASN K 353 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128318 restraints weight = 22967.865| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.15 r_work: 0.3342 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25536 Z= 0.163 Angle : 0.558 8.209 34668 Z= 0.307 Chirality : 0.046 0.355 3744 Planarity : 0.005 0.047 4350 Dihedral : 14.950 176.332 3634 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.96 % Favored : 96.84 % Rotamer: Outliers : 4.65 % Allowed : 15.82 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 2940 helix: 1.43 (0.12), residues: 1740 sheet: -0.59 (0.36), residues: 192 loop : -0.29 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 TYR 0.021 0.002 TYR K 475 PHE 0.014 0.002 PHE K 144 TRP 0.009 0.001 TRP F 363 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (25536) covalent geometry : angle 0.55838 / 0.31 (34668) hydrogen bonds : bond 0.04877 / 3.30 ( 1261) hydrogen bonds : angle 4.61163 / 3.30 ( 3657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 376 time to evaluate : 1.021 Fit side-chains REVERT: A 54 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7286 (ttt-90) REVERT: A 123 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: A 135 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7804 (tt0) REVERT: A 137 ASN cc_start: 0.8496 (m-40) cc_final: 0.8260 (t0) REVERT: A 199 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8099 (ttmm) REVERT: A 227 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7570 (tpt-90) REVERT: A 301 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5921 (mmm160) REVERT: A 377 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7491 (mp0) REVERT: A 386 GLU cc_start: 0.7101 (tp30) cc_final: 0.6734 (tp30) REVERT: A 427 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: A 436 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8487 (mp) REVERT: A 452 ASN cc_start: 0.8623 (t0) cc_final: 0.8294 (t0) REVERT: A 457 ASP cc_start: 0.8225 (m-30) cc_final: 0.7995 (m-30) REVERT: A 460 LYS cc_start: 0.7591 (ptpp) cc_final: 0.6887 (pptt) REVERT: A 462 ASP cc_start: 0.7318 (t0) cc_final: 0.7051 (t70) REVERT: B 54 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7199 (ttt-90) REVERT: B 69 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7661 (mtp85) REVERT: B 123 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8357 (mtm) REVERT: B 135 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7812 (tt0) REVERT: B 137 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8216 (t0) REVERT: B 199 LYS cc_start: 0.8382 (ttpp) cc_final: 0.8074 (ttmm) REVERT: B 227 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7578 (tpt-90) REVERT: B 301 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6064 (mmm160) REVERT: B 349 TYR cc_start: 0.7270 (m-80) cc_final: 0.6872 (m-80) REVERT: B 377 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7504 (mp0) REVERT: B 386 GLU cc_start: 0.7072 (tp30) cc_final: 0.6717 (tp30) REVERT: B 427 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: B 436 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 457 ASP cc_start: 0.8219 (m-30) cc_final: 0.7972 (m-30) REVERT: B 460 LYS cc_start: 0.7570 (ptpp) cc_final: 0.6877 (pptt) REVERT: B 462 ASP cc_start: 0.7331 (t0) cc_final: 0.7111 (t70) REVERT: D 10 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8179 (tp) REVERT: D 68 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8081 (p) REVERT: D 135 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7701 (tt0) REVERT: D 137 ASN cc_start: 0.8555 (m-40) cc_final: 0.8179 (t0) REVERT: D 199 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8106 (ttmm) REVERT: D 227 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7612 (tpt-90) REVERT: D 301 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5767 (mmm160) REVERT: D 349 TYR cc_start: 0.7272 (m-80) cc_final: 0.7014 (m-80) REVERT: D 377 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7331 (mp0) REVERT: D 385 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: D 397 MET cc_start: 0.8845 (tmm) cc_final: 0.8579 (tmm) REVERT: D 402 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7892 (mptp) REVERT: D 424 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7063 (p0) REVERT: D 462 ASP cc_start: 0.7341 (t0) cc_final: 0.7137 (t70) REVERT: D 490 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7736 (mmtm) REVERT: F 10 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8216 (tp) REVERT: F 54 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7353 (ttt-90) REVERT: F 124 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7636 (m-40) REVERT: F 125 TYR cc_start: 0.7748 (t80) cc_final: 0.7452 (t80) REVERT: F 135 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7705 (tt0) REVERT: F 137 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8169 (t0) REVERT: F 155 THR cc_start: 0.8178 (t) cc_final: 0.7961 (p) REVERT: F 199 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8039 (ttmm) REVERT: F 301 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6013 (mmm160) REVERT: F 348 GLU cc_start: 0.7603 (pt0) cc_final: 0.7204 (tm-30) REVERT: F 349 TYR cc_start: 0.7212 (m-80) cc_final: 0.6971 (m-10) REVERT: F 375 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8540 (mt) REVERT: F 397 MET cc_start: 0.8870 (tmm) cc_final: 0.8558 (tmm) REVERT: F 460 LYS cc_start: 0.7539 (ptpp) cc_final: 0.6647 (pptt) REVERT: F 490 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7637 (mmtm) REVERT: H 10 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8573 (tp) REVERT: H 54 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7251 (ttp-110) REVERT: H 58 GLN cc_start: 0.7861 (pt0) cc_final: 0.7586 (pt0) REVERT: H 69 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7940 (mtp85) REVERT: H 126 GLU cc_start: 0.7636 (pt0) cc_final: 0.7215 (pt0) REVERT: H 137 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8202 (t0) REVERT: H 199 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8163 (ttmm) REVERT: H 301 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5940 (mmm160) REVERT: H 348 GLU cc_start: 0.7686 (pt0) cc_final: 0.7313 (tm-30) REVERT: H 349 TYR cc_start: 0.7403 (m-80) cc_final: 0.7077 (m-10) REVERT: H 385 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6843 (p0) REVERT: H 386 GLU cc_start: 0.7191 (tp30) cc_final: 0.6961 (tp30) REVERT: H 420 ASP cc_start: 0.8621 (m-30) cc_final: 0.8268 (m-30) REVERT: H 427 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: H 436 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8560 (mp) REVERT: H 460 LYS cc_start: 0.7510 (ptpp) cc_final: 0.6731 (pptt) REVERT: H 490 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7416 (mttm) REVERT: K 10 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8551 (tp) REVERT: K 54 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7406 (ttp-110) REVERT: K 58 GLN cc_start: 0.7884 (pt0) cc_final: 0.7583 (pt0) REVERT: K 69 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7983 (mtp85) REVERT: K 199 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8141 (ttmm) REVERT: K 301 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6074 (mmm160) REVERT: K 367 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8526 (ptm) REVERT: K 375 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8686 (mt) REVERT: K 385 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6844 (p0) REVERT: K 420 ASP cc_start: 0.8628 (m-30) cc_final: 0.8271 (m-30) REVERT: K 427 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: K 460 LYS cc_start: 0.7654 (ptpp) cc_final: 0.6933 (pptt) outliers start: 126 outliers final: 39 residues processed: 455 average time/residue: 0.5945 time to fit residues: 314.7877 Evaluate side-chains 436 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 363 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 308 ASN Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 367 MET Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 301 ARG Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 367 MET Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 68 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 58 GLN B 295 ASN D 58 GLN F 58 GLN F 378 HIS ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN H 186 HIS ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 453 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 201 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 = 0.3617 r_free = 0.3617 target = 0.141237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123367 restraints weight = 22784.447| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.13 r_work: 0.3276 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25536 Z= 0.264 Angle : 0.660 8.936 34668 Z= 0.361 Chirality : 0.051 0.355 3744 Planarity : 0.005 0.054 4350 Dihedral : 15.177 179.389 3624 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 4.90 % Allowed : 15.97 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 2940 helix: 1.21 (0.12), residues: 1752 sheet: -0.64 (0.36), residues: 192 loop : -0.20 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 142 TYR 0.026 0.003 TYR H 475 PHE 0.018 0.002 PHE K 144 TRP 0.012 0.002 TRP F 363 HIS 0.006 0.002 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (25536) covalent geometry : angle 0.65988 / 0.36 (34668) hydrogen bonds : bond 0.05735 / 3.93 ( 1261) hydrogen bonds : angle 4.77721 / 3.43 ( 3657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 378 time to evaluate : 1.060 Fit side-chains REVERT: A 54 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7431 (ttp-110) REVERT: A 58 GLN cc_start: 0.7932 (pt0) cc_final: 0.7608 (mm110) REVERT: A 97 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: A 123 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: A 135 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7872 (tt0) REVERT: A 137 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8255 (t0) REVERT: A 155 THR cc_start: 0.8387 (t) cc_final: 0.8120 (p) REVERT: A 199 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8208 (ttmm) REVERT: A 227 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7607 (tpt-90) REVERT: A 301 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.6124 (mmm160) REVERT: A 328 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: A 377 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 386 GLU cc_start: 0.7281 (tp30) cc_final: 0.6910 (tp30) REVERT: A 402 LYS cc_start: 0.8185 (mptp) cc_final: 0.7840 (mmtt) REVERT: A 416 LYS cc_start: 0.8390 (ttmp) cc_final: 0.8009 (tttm) REVERT: A 436 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 460 LYS cc_start: 0.7619 (ptpp) cc_final: 0.6927 (pptt) REVERT: A 462 ASP cc_start: 0.7311 (t0) cc_final: 0.7057 (t70) REVERT: A 490 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8032 (mmtm) REVERT: B 54 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7401 (ttp-110) REVERT: B 69 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7735 (mtp85) REVERT: B 97 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: B 123 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: B 135 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7820 (tt0) REVERT: B 137 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8269 (t0) REVERT: B 155 THR cc_start: 0.8367 (t) cc_final: 0.8121 (p) REVERT: B 192 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7946 (t0) REVERT: B 199 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8166 (ttmm) REVERT: B 227 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7626 (tpt-90) REVERT: B 301 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6268 (mmm160) REVERT: B 328 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: B 349 TYR cc_start: 0.7371 (m-80) cc_final: 0.6988 (m-80) REVERT: B 377 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: B 386 GLU cc_start: 0.7321 (tp30) cc_final: 0.6978 (tp30) REVERT: B 402 LYS cc_start: 0.8199 (mptp) cc_final: 0.7864 (mmtt) REVERT: B 427 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: B 436 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 460 LYS cc_start: 0.7696 (ptpp) cc_final: 0.6977 (pptt) REVERT: B 462 ASP cc_start: 0.7347 (t0) cc_final: 0.7117 (t70) REVERT: B 490 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7958 (mmtm) REVERT: D 10 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8257 (tp) REVERT: D 135 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7701 (tt0) REVERT: D 137 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8178 (t0) REVERT: D 155 THR cc_start: 0.8269 (t) cc_final: 0.8063 (p) REVERT: D 199 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8206 (ttmm) REVERT: D 301 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6000 (mmm160) REVERT: D 377 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7422 (mp0) REVERT: D 385 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6488 (m-30) REVERT: D 393 GLU cc_start: 0.8381 (tp30) cc_final: 0.8153 (tp30) REVERT: D 424 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7200 (p0) REVERT: D 460 LYS cc_start: 0.7469 (ptpp) cc_final: 0.6730 (pptt) REVERT: D 490 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7842 (mmtt) REVERT: F 10 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8264 (tp) REVERT: F 54 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7475 (ttp-110) REVERT: F 97 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: F 135 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7805 (mt-10) REVERT: F 137 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8203 (t0) REVERT: F 199 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8186 (ttmm) REVERT: F 301 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6043 (mmm160) REVERT: F 397 MET cc_start: 0.8867 (tmm) cc_final: 0.8646 (tmm) REVERT: F 424 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7283 (p0) REVERT: F 460 LYS cc_start: 0.7619 (ptpp) cc_final: 0.6794 (pptt) REVERT: F 490 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7878 (mmtt) REVERT: H 10 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8655 (tp) REVERT: H 54 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7386 (ttp-110) REVERT: H 58 GLN cc_start: 0.7897 (pt0) cc_final: 0.7590 (pt0) REVERT: H 69 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: H 97 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: H 126 GLU cc_start: 0.7691 (pt0) cc_final: 0.7461 (pt0) REVERT: H 137 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8179 (t0) REVERT: H 159 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8280 (p) REVERT: H 199 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8236 (ttmm) REVERT: H 301 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6213 (mmm160) REVERT: H 328 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: H 348 GLU cc_start: 0.7685 (pt0) cc_final: 0.7267 (tm-30) REVERT: H 349 TYR cc_start: 0.7500 (m-80) cc_final: 0.7171 (m-10) REVERT: H 385 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7021 (p0) REVERT: H 420 ASP cc_start: 0.8651 (m-30) cc_final: 0.8361 (m-30) REVERT: H 427 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: H 436 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8614 (mp) REVERT: H 460 LYS cc_start: 0.7609 (ptpp) cc_final: 0.6840 (pptt) REVERT: K 10 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8649 (tp) REVERT: K 54 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7473 (ttp-110) REVERT: K 58 GLN cc_start: 0.7889 (pt0) cc_final: 0.7589 (pt0) REVERT: K 69 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8000 (mtp85) REVERT: K 70 TYR cc_start: 0.8552 (p90) cc_final: 0.8305 (p90) REVERT: K 143 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8270 (mtt90) REVERT: K 159 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8337 (p) REVERT: K 199 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8252 (ttmm) REVERT: K 301 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6275 (mmm160) REVERT: K 309 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8057 (mmtm) REVERT: K 328 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: K 385 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7048 (p0) REVERT: K 420 ASP cc_start: 0.8681 (m-30) cc_final: 0.8350 (m-30) REVERT: K 427 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: K 436 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8606 (mp) REVERT: K 449 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: K 460 LYS cc_start: 0.7647 (ptpp) cc_final: 0.6937 (pptt) outliers start: 133 outliers final: 43 residues processed: 455 average time/residue: 0.6547 time to fit residues: 345.3341 Evaluate side-chains 445 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 356 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 301 ARG Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 328 GLN Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 143 ARG Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 301 ARG Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 328 GLN Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 444 SER Chi-restraints excluded: chain K residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 51 optimal weight: 0.0020 chunk 27 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN D 58 GLN D 147 ASN D 401 ASN F 58 GLN F 378 HIS H 58 GLN H 170 ASN H 201 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 ASN ** K 201 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 = 0.3689 r_free = 0.3689 target = 0.147244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129775 restraints weight = 22963.800| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.14 r_work: 0.3362 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25536 Z= 0.122 Angle : 0.526 6.818 34668 Z= 0.289 Chirality : 0.044 0.346 3744 Planarity : 0.004 0.051 4350 Dihedral : 14.726 178.653 3624 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.14 % Rotamer: Outliers : 2.73 % Allowed : 17.88 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.16), residues: 2940 helix: 1.56 (0.12), residues: 1740 sheet: -0.70 (0.36), residues: 192 loop : -0.29 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 200 TYR 0.016 0.001 TYR K 475 PHE 0.009 0.001 PHE A 144 TRP 0.010 0.001 TRP D 363 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (25536) covalent geometry : angle 0.52567 / 0.29 (34668) hydrogen bonds : bond 0.04255 / 2.86 ( 1261) hydrogen bonds : angle 4.53302 / 3.24 ( 3657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 365 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7283 (ttt-90) REVERT: A 58 GLN cc_start: 0.7895 (pt0) cc_final: 0.7544 (mm110) REVERT: A 69 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7577 (mtp85) REVERT: A 135 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7783 (tt0) REVERT: A 137 ASN cc_start: 0.8444 (m-40) cc_final: 0.8214 (t0) REVERT: A 192 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7854 (t0) REVERT: A 199 LYS cc_start: 0.8287 (ttpp) cc_final: 0.8037 (ttmm) REVERT: A 227 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7568 (tpt-90) REVERT: A 301 ARG cc_start: 0.6305 (mpt180) cc_final: 0.5919 (mmm160) REVERT: A 377 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7661 (mp0) REVERT: A 385 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6305 (m-30) REVERT: A 386 GLU cc_start: 0.7226 (tp30) cc_final: 0.6873 (tp30) REVERT: A 402 LYS cc_start: 0.8090 (mptp) cc_final: 0.7787 (mmtt) REVERT: A 436 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 460 LYS cc_start: 0.7551 (ptpp) cc_final: 0.6800 (pptt) REVERT: A 462 ASP cc_start: 0.7250 (t0) cc_final: 0.7025 (t70) REVERT: A 490 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7884 (mmtm) REVERT: B 54 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7248 (ttt-90) REVERT: B 58 GLN cc_start: 0.7910 (pt0) cc_final: 0.7546 (mm110) REVERT: B 69 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7551 (mtp85) REVERT: B 135 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7785 (tt0) REVERT: B 137 ASN cc_start: 0.8453 (m-40) cc_final: 0.8205 (t0) REVERT: B 199 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7973 (ttmm) REVERT: B 227 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7568 (tpt-90) REVERT: B 301 ARG cc_start: 0.6394 (mpt180) cc_final: 0.5987 (mmm160) REVERT: B 349 TYR cc_start: 0.7246 (m-80) cc_final: 0.6941 (m-80) REVERT: B 377 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7643 (mp0) REVERT: B 386 GLU cc_start: 0.7214 (tp30) cc_final: 0.6892 (tp30) REVERT: B 402 LYS cc_start: 0.8099 (mptp) cc_final: 0.7795 (mmtt) REVERT: B 427 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: B 436 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 460 LYS cc_start: 0.7569 (ptpp) cc_final: 0.6826 (pptt) REVERT: B 490 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7838 (mmtm) REVERT: D 10 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8306 (tp) REVERT: D 135 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7659 (tt0) REVERT: D 137 ASN cc_start: 0.8602 (m-40) cc_final: 0.8241 (t0) REVERT: D 199 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7987 (ttmm) REVERT: D 301 ARG cc_start: 0.6162 (mpt180) cc_final: 0.5660 (mmm160) REVERT: D 377 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7379 (mp0) REVERT: D 385 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: D 424 ASP cc_start: 0.7600 (p0) cc_final: 0.7233 (p0) REVERT: D 490 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7754 (mmtm) REVERT: F 10 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8215 (tp) REVERT: F 54 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7415 (ttp-110) REVERT: F 135 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7738 (tt0) REVERT: F 137 ASN cc_start: 0.8548 (m-40) cc_final: 0.8162 (t0) REVERT: F 199 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7916 (ttmm) REVERT: F 301 ARG cc_start: 0.6342 (mpt180) cc_final: 0.5879 (mmm160) REVERT: F 397 MET cc_start: 0.8875 (tmm) cc_final: 0.8623 (tmm) REVERT: F 424 ASP cc_start: 0.7584 (p0) cc_final: 0.7197 (p0) REVERT: F 436 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8595 (mp) REVERT: F 460 LYS cc_start: 0.7502 (ptpp) cc_final: 0.6679 (pptt) REVERT: F 490 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7741 (mmtm) REVERT: H 10 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8513 (tp) REVERT: H 54 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7366 (ttp-110) REVERT: H 58 GLN cc_start: 0.7804 (pt0) cc_final: 0.7525 (pt0) REVERT: H 126 GLU cc_start: 0.7685 (pt0) cc_final: 0.7268 (pt0) REVERT: H 137 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8174 (t0) REVERT: H 199 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8067 (ttmm) REVERT: H 348 GLU cc_start: 0.7665 (pt0) cc_final: 0.7225 (tm-30) REVERT: H 349 TYR cc_start: 0.7445 (m-80) cc_final: 0.7097 (m-10) REVERT: H 385 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6724 (p0) REVERT: H 397 MET cc_start: 0.8859 (tmm) cc_final: 0.8594 (tmm) REVERT: H 420 ASP cc_start: 0.8649 (m-30) cc_final: 0.8316 (m-30) REVERT: H 436 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8540 (mp) REVERT: H 460 LYS cc_start: 0.7512 (ptpp) cc_final: 0.6731 (pptt) REVERT: K 10 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8511 (tp) REVERT: K 54 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7436 (ttp-110) REVERT: K 58 GLN cc_start: 0.7808 (pt0) cc_final: 0.7522 (pt0) REVERT: K 69 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7907 (mtp85) REVERT: K 70 TYR cc_start: 0.8443 (p90) cc_final: 0.8211 (p90) REVERT: K 199 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8037 (ttmm) REVERT: K 301 ARG cc_start: 0.6402 (mpt180) cc_final: 0.5989 (mmm160) REVERT: K 348 GLU cc_start: 0.7432 (pp20) cc_final: 0.6919 (tm-30) REVERT: K 385 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6780 (p0) REVERT: K 397 MET cc_start: 0.8853 (tmm) cc_final: 0.8617 (tmm) REVERT: K 420 ASP cc_start: 0.8627 (m-30) cc_final: 0.8283 (m-30) REVERT: K 436 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8541 (mp) REVERT: K 460 LYS cc_start: 0.7559 (ptpp) cc_final: 0.6838 (pptt) outliers start: 74 outliers final: 18 residues processed: 423 average time/residue: 0.6403 time to fit residues: 314.9387 Evaluate side-chains 385 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 350 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 132 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 GLN D 58 GLN F 58 GLN F 328 GLN F 378 HIS H 170 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122249 restraints weight = 22730.276| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.13 r_work: 0.3261 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 25536 Z= 0.329 Angle : 0.704 7.649 34668 Z= 0.384 Chirality : 0.055 0.352 3744 Planarity : 0.006 0.053 4350 Dihedral : 15.164 179.888 3617 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % Rotamer: Outliers : 3.69 % Allowed : 16.59 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 2940 helix: 1.18 (0.12), residues: 1746 sheet: -0.69 (0.35), residues: 192 loop : -0.23 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 142 TYR 0.026 0.003 TYR K 475 PHE 0.019 0.003 PHE H 233 TRP 0.012 0.003 TRP B 409 HIS 0.008 0.002 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.33 (25536) covalent geometry : angle 0.70440 / 0.38 (34668) hydrogen bonds : bond 0.06001 / 4.12 ( 1261) hydrogen bonds : angle 4.80130 / 3.45 ( 3657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 362 time to evaluate : 1.018 Fit side-chains REVERT: A 54 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7451 (ttp-110) REVERT: A 58 GLN cc_start: 0.7985 (pt0) cc_final: 0.7652 (mm110) REVERT: A 97 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: A 123 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8330 (mtm) REVERT: A 135 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7856 (tt0) REVERT: A 137 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (t0) REVERT: A 192 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 199 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8252 (ttmm) REVERT: A 227 ARG cc_start: 0.7868 (mmm160) cc_final: 0.7598 (tpt-90) REVERT: A 301 ARG cc_start: 0.6656 (mpt180) cc_final: 0.6185 (mmm160) REVERT: A 304 ASP cc_start: 0.7408 (p0) cc_final: 0.7035 (p0) REVERT: A 328 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: A 377 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7731 (mp0) REVERT: A 385 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: A 386 GLU cc_start: 0.7301 (tp30) cc_final: 0.6926 (tp30) REVERT: A 402 LYS cc_start: 0.8183 (mptp) cc_final: 0.7855 (mmtt) REVERT: A 436 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 460 LYS cc_start: 0.7650 (ptpp) cc_final: 0.6950 (pptt) REVERT: A 490 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8063 (mmtm) REVERT: B 54 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7451 (ttp-110) REVERT: B 58 GLN cc_start: 0.7983 (pt0) cc_final: 0.7642 (mm110) REVERT: B 69 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7754 (mtp85) REVERT: B 97 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: B 123 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: B 135 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7884 (tt0) REVERT: B 137 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8277 (t0) REVERT: B 192 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7938 (t0) REVERT: B 199 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8229 (ttmm) REVERT: B 227 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7598 (tpt-90) REVERT: B 301 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6292 (mmm160) REVERT: B 328 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: B 349 TYR cc_start: 0.7437 (m-80) cc_final: 0.7093 (m-80) REVERT: B 377 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: B 386 GLU cc_start: 0.7256 (tp30) cc_final: 0.6917 (tp30) REVERT: B 402 LYS cc_start: 0.8182 (mptp) cc_final: 0.7865 (mmtt) REVERT: B 424 ASP cc_start: 0.7582 (p0) cc_final: 0.7304 (p0) REVERT: B 427 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: B 436 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 460 LYS cc_start: 0.7722 (ptpp) cc_final: 0.7002 (pptt) REVERT: B 490 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8029 (mmtm) REVERT: D 10 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8333 (tp) REVERT: D 135 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7710 (tt0) REVERT: D 137 ASN cc_start: 0.8550 (m-40) cc_final: 0.8146 (t0) REVERT: D 192 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8113 (t0) REVERT: D 199 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8286 (ttmm) REVERT: D 301 ARG cc_start: 0.6646 (mpt180) cc_final: 0.6034 (mmm160) REVERT: D 377 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7447 (mp0) REVERT: D 385 ASP cc_start: 0.6825 (OUTLIER) cc_final: 0.6473 (m-30) REVERT: D 424 ASP cc_start: 0.7583 (p0) cc_final: 0.7212 (p0) REVERT: D 460 LYS cc_start: 0.7485 (ptpp) cc_final: 0.6738 (pptt) REVERT: D 490 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7859 (mmtt) REVERT: F 10 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8341 (tp) REVERT: F 54 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7546 (ttp-110) REVERT: F 135 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7708 (tt0) REVERT: F 137 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8145 (t0) REVERT: F 192 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8093 (t0) REVERT: F 199 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8232 (ttmm) REVERT: F 301 ARG cc_start: 0.6677 (mpt180) cc_final: 0.6171 (mmm160) REVERT: F 377 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7409 (mp0) REVERT: F 424 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7317 (p0) REVERT: F 460 LYS cc_start: 0.7678 (ptpp) cc_final: 0.6804 (pptt) REVERT: F 490 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7888 (mmtt) REVERT: H 10 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8667 (tp) REVERT: H 54 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7475 (ttp-110) REVERT: H 58 GLN cc_start: 0.7913 (pt0) cc_final: 0.7628 (pt0) REVERT: H 70 TYR cc_start: 0.8589 (p90) cc_final: 0.8300 (p90) REVERT: H 126 GLU cc_start: 0.7538 (pt0) cc_final: 0.7185 (pt0) REVERT: H 137 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8212 (t0) REVERT: H 143 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8358 (mtt90) REVERT: H 159 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8261 (p) REVERT: H 199 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8144 (ttmm) REVERT: H 301 ARG cc_start: 0.6839 (mpt180) cc_final: 0.6385 (mmm160) REVERT: H 348 GLU cc_start: 0.7653 (pt0) cc_final: 0.7204 (tm-30) REVERT: H 349 TYR cc_start: 0.7528 (m-80) cc_final: 0.7186 (m-10) REVERT: H 385 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6620 (m-30) REVERT: H 420 ASP cc_start: 0.8643 (m-30) cc_final: 0.8338 (m-30) REVERT: H 427 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: H 436 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8610 (mp) REVERT: H 460 LYS cc_start: 0.7583 (ptpp) cc_final: 0.6772 (pptt) REVERT: K 10 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8680 (tp) REVERT: K 54 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7549 (ttp-110) REVERT: K 58 GLN cc_start: 0.7905 (pt0) cc_final: 0.7598 (pt0) REVERT: K 69 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: K 70 TYR cc_start: 0.8619 (p90) cc_final: 0.8294 (p90) REVERT: K 159 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8328 (p) REVERT: K 199 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8153 (ttmm) REVERT: K 301 ARG cc_start: 0.6854 (mpt180) cc_final: 0.6389 (mmm160) REVERT: K 348 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: K 385 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6934 (p0) REVERT: K 420 ASP cc_start: 0.8674 (m-30) cc_final: 0.8393 (m-30) REVERT: K 427 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: K 436 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8626 (mp) REVERT: K 449 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: K 460 LYS cc_start: 0.7625 (ptpp) cc_final: 0.6902 (pptt) outliers start: 100 outliers final: 41 residues processed: 427 average time/residue: 0.6632 time to fit residues: 327.7245 Evaluate side-chains 427 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 348 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 308 ASN Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 190 LYS Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 215 optimal weight: 0.0980 chunk 282 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 290 optimal weight: 0.8980 chunk 60 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 150 optimal weight: 0.4980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN B 170 ASN B 324 GLN D 58 GLN D 147 ASN D 170 ASN D 328 GLN F 58 GLN F 170 ASN H 170 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 ASN ** K 201 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 = 0.3675 r_free = 0.3675 target = 0.146088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128651 restraints weight = 22792.959| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.13 r_work: 0.3349 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25536 Z= 0.126 Angle : 0.540 6.586 34668 Z= 0.296 Chirality : 0.044 0.347 3744 Planarity : 0.004 0.050 4350 Dihedral : 14.759 179.529 3617 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.62 % Favored : 97.18 % Rotamer: Outliers : 2.51 % Allowed : 18.10 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 2940 helix: 1.53 (0.12), residues: 1740 sheet: -0.79 (0.36), residues: 192 loop : -0.24 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 69 TYR 0.016 0.002 TYR K 475 PHE 0.011 0.001 PHE A 144 TRP 0.012 0.002 TRP D 363 HIS 0.004 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (25536) covalent geometry : angle 0.53974 / 0.30 (34668) hydrogen bonds : bond 0.04380 / 2.95 ( 1261) hydrogen bonds : angle 4.54661 / 3.26 ( 3657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 362 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7282 (ttt-90) REVERT: A 58 GLN cc_start: 0.7920 (pt0) cc_final: 0.7560 (mm110) REVERT: A 135 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7735 (tt0) REVERT: A 137 ASN cc_start: 0.8458 (m-40) cc_final: 0.8222 (t0) REVERT: A 192 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7884 (t0) REVERT: A 199 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8061 (ttmm) REVERT: A 227 ARG cc_start: 0.7850 (mmm160) cc_final: 0.7534 (tpt-90) REVERT: A 301 ARG cc_start: 0.6318 (mpt180) cc_final: 0.5944 (mmm160) REVERT: A 377 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7721 (mp0) REVERT: A 385 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6462 (m-30) REVERT: A 386 GLU cc_start: 0.7160 (tp30) cc_final: 0.6917 (tm-30) REVERT: A 402 LYS cc_start: 0.8106 (mptp) cc_final: 0.7803 (mmtt) REVERT: A 436 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8502 (mp) REVERT: A 460 LYS cc_start: 0.7583 (ptpp) cc_final: 0.6828 (pptt) REVERT: A 490 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7898 (mmtm) REVERT: B 54 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7296 (ttt-90) REVERT: B 58 GLN cc_start: 0.7915 (pt0) cc_final: 0.7568 (mm110) REVERT: B 69 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7599 (mtp85) REVERT: B 135 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7752 (tt0) REVERT: B 137 ASN cc_start: 0.8456 (m-40) cc_final: 0.8200 (t0) REVERT: B 199 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8045 (ttmm) REVERT: B 227 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7535 (tpt-90) REVERT: B 301 ARG cc_start: 0.6339 (mpt180) cc_final: 0.5738 (mmm160) REVERT: B 349 TYR cc_start: 0.7302 (m-80) cc_final: 0.7007 (m-80) REVERT: B 377 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7699 (mp0) REVERT: B 386 GLU cc_start: 0.7307 (tp30) cc_final: 0.7022 (tp30) REVERT: B 402 LYS cc_start: 0.8105 (mptp) cc_final: 0.7818 (mmtt) REVERT: B 424 ASP cc_start: 0.7590 (p0) cc_final: 0.7285 (p0) REVERT: B 436 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 460 LYS cc_start: 0.7608 (ptpp) cc_final: 0.6856 (pptt) REVERT: B 490 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7904 (mmtm) REVERT: D 10 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8306 (tp) REVERT: D 97 GLU cc_start: 0.7851 (mp0) cc_final: 0.7627 (pm20) REVERT: D 135 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7671 (tt0) REVERT: D 137 ASN cc_start: 0.8574 (m-40) cc_final: 0.8227 (t0) REVERT: D 199 LYS cc_start: 0.8239 (ttpp) cc_final: 0.8000 (ttmm) REVERT: D 301 ARG cc_start: 0.6305 (mpt180) cc_final: 0.5789 (mmm160) REVERT: D 377 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7425 (mp0) REVERT: D 385 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6374 (m-30) REVERT: D 424 ASP cc_start: 0.7698 (p0) cc_final: 0.7245 (p0) REVERT: D 490 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7690 (mmtm) REVERT: F 10 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8246 (tp) REVERT: F 54 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7443 (ttp-110) REVERT: F 135 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7716 (tt0) REVERT: F 137 ASN cc_start: 0.8514 (m-40) cc_final: 0.8198 (t0) REVERT: F 186 HIS cc_start: 0.8698 (t-90) cc_final: 0.8494 (t-90) REVERT: F 199 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7923 (ttmm) REVERT: F 301 ARG cc_start: 0.6419 (mpt180) cc_final: 0.5973 (mmm160) REVERT: F 304 ASP cc_start: 0.7366 (p0) cc_final: 0.7083 (p0) REVERT: F 424 ASP cc_start: 0.7591 (p0) cc_final: 0.7217 (p0) REVERT: F 436 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8587 (mp) REVERT: F 460 LYS cc_start: 0.7520 (ptpp) cc_final: 0.6664 (pptt) REVERT: F 490 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7659 (mmtt) REVERT: H 10 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8529 (tp) REVERT: H 54 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7412 (ttp-110) REVERT: H 58 GLN cc_start: 0.7796 (pt0) cc_final: 0.7516 (pt0) REVERT: H 70 TYR cc_start: 0.8501 (p90) cc_final: 0.8229 (p90) REVERT: H 126 GLU cc_start: 0.7528 (pt0) cc_final: 0.7146 (pt0) REVERT: H 137 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8173 (t0) REVERT: H 199 LYS cc_start: 0.8276 (ttpp) cc_final: 0.8056 (ttmm) REVERT: H 301 ARG cc_start: 0.6392 (mpt180) cc_final: 0.5964 (mmm160) REVERT: H 348 GLU cc_start: 0.7679 (pt0) cc_final: 0.7227 (tm-30) REVERT: H 349 TYR cc_start: 0.7494 (m-80) cc_final: 0.7121 (m-10) REVERT: H 385 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6360 (m-30) REVERT: H 420 ASP cc_start: 0.8644 (m-30) cc_final: 0.8324 (m-30) REVERT: H 436 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8591 (mp) REVERT: H 460 LYS cc_start: 0.7503 (ptpp) cc_final: 0.6719 (pptt) REVERT: K 10 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8541 (tp) REVERT: K 54 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7494 (ttp-110) REVERT: K 58 GLN cc_start: 0.7795 (pt0) cc_final: 0.7500 (pt0) REVERT: K 70 TYR cc_start: 0.8507 (p90) cc_final: 0.8212 (p90) REVERT: K 199 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8061 (ttmm) REVERT: K 301 ARG cc_start: 0.6511 (mpt180) cc_final: 0.6072 (mmm160) REVERT: K 348 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: K 385 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6824 (p0) REVERT: K 397 MET cc_start: 0.8845 (tmm) cc_final: 0.8588 (tmm) REVERT: K 420 ASP cc_start: 0.8670 (m-30) cc_final: 0.8345 (m-30) REVERT: K 436 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (mp) REVERT: K 460 LYS cc_start: 0.7546 (ptpp) cc_final: 0.6778 (pptt) outliers start: 68 outliers final: 27 residues processed: 412 average time/residue: 0.6119 time to fit residues: 292.3440 Evaluate side-chains 393 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 190 LYS Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 217 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 273 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 182 optimal weight: 0.0970 chunk 123 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 324 GLN D 58 GLN D 170 ASN F 58 GLN F 170 ASN F 401 ASN H 170 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 ASN ** K 201 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 = 0.3685 r_free = 0.3685 target = 0.146865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129439 restraints weight = 22871.047| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.13 r_work: 0.3359 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25536 Z= 0.128 Angle : 0.537 7.929 34668 Z= 0.294 Chirality : 0.044 0.343 3744 Planarity : 0.004 0.049 4350 Dihedral : 14.575 177.740 3614 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 2.10 % Allowed : 18.81 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.16), residues: 2940 helix: 1.67 (0.12), residues: 1740 sheet: -0.76 (0.36), residues: 192 loop : -0.28 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 75 TYR 0.021 0.001 TYR A 11 PHE 0.011 0.001 PHE A 144 TRP 0.012 0.001 TRP D 363 HIS 0.002 0.001 HIS K 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (25536) covalent geometry : angle 0.53743 / 0.29 (34668) hydrogen bonds : bond 0.04304 / 2.90 ( 1261) hydrogen bonds : angle 4.42799 / 3.17 ( 3657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 365 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7274 (ttt-90) REVERT: A 58 GLN cc_start: 0.7883 (pt0) cc_final: 0.7576 (mm110) REVERT: A 135 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7816 (tt0) REVERT: A 137 ASN cc_start: 0.8447 (m-40) cc_final: 0.8235 (t0) REVERT: A 192 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7901 (t0) REVERT: A 199 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8111 (ttmm) REVERT: A 227 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7524 (tpt-90) REVERT: A 301 ARG cc_start: 0.6246 (mpt180) cc_final: 0.5856 (mmm160) REVERT: A 377 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7636 (mp0) REVERT: A 385 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6598 (m-30) REVERT: A 402 LYS cc_start: 0.8107 (mptp) cc_final: 0.7815 (mmtt) REVERT: A 424 ASP cc_start: 0.7261 (p0) cc_final: 0.6835 (p0) REVERT: A 436 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 460 LYS cc_start: 0.7553 (ptpp) cc_final: 0.6808 (pptt) REVERT: A 490 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7922 (mmtm) REVERT: B 54 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7316 (ttt-90) REVERT: B 58 GLN cc_start: 0.7883 (pt0) cc_final: 0.7579 (mm110) REVERT: B 69 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7561 (mtp85) REVERT: B 135 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7837 (tt0) REVERT: B 137 ASN cc_start: 0.8455 (m-40) cc_final: 0.8220 (t0) REVERT: B 192 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7900 (t0) REVERT: B 199 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8141 (ttmm) REVERT: B 227 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7525 (tpt-90) REVERT: B 301 ARG cc_start: 0.6268 (mpt180) cc_final: 0.5828 (mmm160) REVERT: B 349 TYR cc_start: 0.7271 (m-80) cc_final: 0.6983 (m-80) REVERT: B 377 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7695 (mp0) REVERT: B 386 GLU cc_start: 0.7307 (tp30) cc_final: 0.7030 (tp30) REVERT: B 402 LYS cc_start: 0.8108 (mptp) cc_final: 0.7821 (mmtt) REVERT: B 424 ASP cc_start: 0.7683 (p0) cc_final: 0.7386 (p0) REVERT: B 436 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8470 (mp) REVERT: B 460 LYS cc_start: 0.7585 (ptpp) cc_final: 0.6846 (pptt) REVERT: B 490 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7915 (mmtm) REVERT: D 10 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8251 (tp) REVERT: D 97 GLU cc_start: 0.7850 (mp0) cc_final: 0.7627 (pm20) REVERT: D 135 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7662 (tt0) REVERT: D 137 ASN cc_start: 0.8569 (m-40) cc_final: 0.8223 (t0) REVERT: D 199 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8082 (ttmm) REVERT: D 301 ARG cc_start: 0.6265 (mpt180) cc_final: 0.5769 (mmm160) REVERT: D 377 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7456 (mp0) REVERT: D 385 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: D 393 GLU cc_start: 0.8301 (tp30) cc_final: 0.8020 (tp30) REVERT: D 424 ASP cc_start: 0.7618 (p0) cc_final: 0.7243 (p0) REVERT: D 490 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7713 (mmtm) REVERT: F 10 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8210 (tp) REVERT: F 54 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7434 (ttp-110) REVERT: F 135 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7718 (tt0) REVERT: F 137 ASN cc_start: 0.8518 (m-40) cc_final: 0.8218 (t0) REVERT: F 199 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8079 (ttmm) REVERT: F 301 ARG cc_start: 0.6372 (mpt180) cc_final: 0.5960 (mmm160) REVERT: F 304 ASP cc_start: 0.7368 (p0) cc_final: 0.7047 (p0) REVERT: F 424 ASP cc_start: 0.7576 (p0) cc_final: 0.7215 (p0) REVERT: F 460 LYS cc_start: 0.7451 (ptpp) cc_final: 0.6664 (pptt) REVERT: F 490 LYS cc_start: 0.7855 (mmmt) cc_final: 0.7644 (mmtt) REVERT: H 10 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8544 (tp) REVERT: H 54 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7429 (ttp-110) REVERT: H 58 GLN cc_start: 0.7759 (pt0) cc_final: 0.7491 (pt0) REVERT: H 70 TYR cc_start: 0.8498 (p90) cc_final: 0.8237 (p90) REVERT: H 126 GLU cc_start: 0.7508 (pt0) cc_final: 0.7125 (pt0) REVERT: H 137 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8172 (t0) REVERT: H 199 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8128 (ttmm) REVERT: H 301 ARG cc_start: 0.6319 (mpt180) cc_final: 0.5997 (mmm160) REVERT: H 348 GLU cc_start: 0.7655 (pt0) cc_final: 0.7213 (tm-30) REVERT: H 349 TYR cc_start: 0.7472 (m-80) cc_final: 0.7104 (m-10) REVERT: H 385 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6424 (m-30) REVERT: H 420 ASP cc_start: 0.8646 (m-30) cc_final: 0.8315 (m-30) REVERT: H 436 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8542 (mp) REVERT: H 460 LYS cc_start: 0.7480 (ptpp) cc_final: 0.6693 (pptt) REVERT: K 10 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8554 (tp) REVERT: K 54 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7495 (ttp-110) REVERT: K 58 GLN cc_start: 0.7775 (pt0) cc_final: 0.7491 (pt0) REVERT: K 70 TYR cc_start: 0.8500 (p90) cc_final: 0.8226 (p90) REVERT: K 199 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8136 (ttmm) REVERT: K 301 ARG cc_start: 0.6399 (mpt180) cc_final: 0.5982 (mmm160) REVERT: K 348 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: K 385 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6743 (p0) REVERT: K 397 MET cc_start: 0.8844 (tmm) cc_final: 0.8579 (tmm) REVERT: K 420 ASP cc_start: 0.8658 (m-30) cc_final: 0.8326 (m-30) REVERT: K 436 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8558 (mp) REVERT: K 460 LYS cc_start: 0.7545 (ptpp) cc_final: 0.6742 (pptt) outliers start: 57 outliers final: 25 residues processed: 407 average time/residue: 0.5952 time to fit residues: 279.4614 Evaluate side-chains 397 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 356 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 235 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 328 GLN D 58 GLN D 324 GLN D 401 ASN F 58 GLN H 170 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 ASN ** K 201 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 = 0.3631 r_free = 0.3631 target = 0.142348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124665 restraints weight = 22792.681| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.13 r_work: 0.3295 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25536 Z= 0.220 Angle : 0.632 9.737 34668 Z= 0.345 Chirality : 0.049 0.335 3744 Planarity : 0.005 0.050 4350 Dihedral : 14.851 178.690 3614 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.10 % Favored : 96.70 % Rotamer: Outliers : 2.21 % Allowed : 18.58 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 2940 helix: 1.43 (0.12), residues: 1752 sheet: -0.75 (0.36), residues: 192 loop : -0.20 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 142 TYR 0.023 0.002 TYR H 475 PHE 0.017 0.002 PHE K 144 TRP 0.012 0.002 TRP F 363 HIS 0.005 0.001 HIS K 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (25536) covalent geometry : angle 0.63158 / 0.34 (34668) hydrogen bonds : bond 0.05267 / 3.60 ( 1261) hydrogen bonds : angle 4.61535 / 3.31 ( 3657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 365 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7422 (ttp-110) REVERT: A 58 GLN cc_start: 0.7957 (pt0) cc_final: 0.7638 (mm110) REVERT: A 135 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7817 (tt0) REVERT: A 137 ASN cc_start: 0.8541 (m-40) cc_final: 0.8257 (t0) REVERT: A 192 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7897 (t0) REVERT: A 199 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8143 (ttmm) REVERT: A 227 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7542 (tpt-90) REVERT: A 301 ARG cc_start: 0.6461 (mpt180) cc_final: 0.6054 (mmm160) REVERT: A 304 ASP cc_start: 0.7345 (p0) cc_final: 0.6957 (p0) REVERT: A 377 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7729 (mp0) REVERT: A 385 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6714 (m-30) REVERT: A 402 LYS cc_start: 0.8148 (mptp) cc_final: 0.7827 (mmtt) REVERT: A 424 ASP cc_start: 0.7289 (p0) cc_final: 0.6859 (p0) REVERT: A 436 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 460 LYS cc_start: 0.7594 (ptpp) cc_final: 0.6855 (pptt) REVERT: A 490 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8001 (mmtm) REVERT: B 54 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7294 (ttt-90) REVERT: B 58 GLN cc_start: 0.7925 (pt0) cc_final: 0.7637 (mm110) REVERT: B 69 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7659 (mtp85) REVERT: B 135 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7838 (tt0) REVERT: B 137 ASN cc_start: 0.8519 (m-40) cc_final: 0.8234 (t0) REVERT: B 192 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7925 (t0) REVERT: B 199 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8193 (ttmm) REVERT: B 227 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7610 (tpt-90) REVERT: B 301 ARG cc_start: 0.6467 (mpt180) cc_final: 0.5894 (mmm160) REVERT: B 349 TYR cc_start: 0.7311 (m-80) cc_final: 0.7021 (m-80) REVERT: B 377 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7760 (mp0) REVERT: B 386 GLU cc_start: 0.7305 (tp30) cc_final: 0.6990 (tp30) REVERT: B 402 LYS cc_start: 0.8151 (mptp) cc_final: 0.7837 (mmtt) REVERT: B 424 ASP cc_start: 0.7621 (p0) cc_final: 0.7316 (p0) REVERT: B 436 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8517 (mp) REVERT: B 460 LYS cc_start: 0.7593 (ptpp) cc_final: 0.6853 (pptt) REVERT: B 490 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8004 (mmtm) REVERT: D 10 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8235 (tp) REVERT: D 135 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7689 (tt0) REVERT: D 137 ASN cc_start: 0.8541 (m-40) cc_final: 0.8141 (t0) REVERT: D 199 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8131 (ttmm) REVERT: D 301 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5956 (mmm160) REVERT: D 377 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7423 (mp0) REVERT: D 385 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6449 (m-30) REVERT: D 386 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: D 393 GLU cc_start: 0.8334 (tp30) cc_final: 0.8084 (tp30) REVERT: D 424 ASP cc_start: 0.7678 (p0) cc_final: 0.7302 (p0) REVERT: D 460 LYS cc_start: 0.7424 (ptpp) cc_final: 0.6680 (pptt) REVERT: D 490 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7715 (mmtt) REVERT: F 10 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8238 (tp) REVERT: F 54 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7490 (ttp-110) REVERT: F 135 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7705 (tt0) REVERT: F 137 ASN cc_start: 0.8560 (m-40) cc_final: 0.8170 (t0) REVERT: F 192 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8031 (t0) REVERT: F 199 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8150 (ttmm) REVERT: F 301 ARG cc_start: 0.6601 (mpt180) cc_final: 0.6157 (mmm160) REVERT: F 304 ASP cc_start: 0.7432 (p0) cc_final: 0.7110 (p0) REVERT: F 424 ASP cc_start: 0.7637 (p0) cc_final: 0.7263 (p0) REVERT: F 460 LYS cc_start: 0.7502 (ptpp) cc_final: 0.6699 (pptt) REVERT: F 490 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7737 (mmtt) REVERT: H 10 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8647 (tp) REVERT: H 54 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7476 (ttp-110) REVERT: H 58 GLN cc_start: 0.7863 (pt0) cc_final: 0.7587 (pt0) REVERT: H 70 TYR cc_start: 0.8605 (p90) cc_final: 0.8300 (p90) REVERT: H 126 GLU cc_start: 0.7559 (pt0) cc_final: 0.7182 (pt0) REVERT: H 137 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8194 (t0) REVERT: H 199 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8095 (ttmm) REVERT: H 301 ARG cc_start: 0.6630 (mpt180) cc_final: 0.6244 (mmm160) REVERT: H 348 GLU cc_start: 0.7697 (pt0) cc_final: 0.7255 (tm-30) REVERT: H 349 TYR cc_start: 0.7519 (m-80) cc_final: 0.7160 (m-10) REVERT: H 385 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: H 420 ASP cc_start: 0.8644 (m-30) cc_final: 0.8324 (m-30) REVERT: H 436 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8578 (mp) REVERT: H 460 LYS cc_start: 0.7512 (ptpp) cc_final: 0.6688 (pptt) REVERT: K 10 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8670 (tp) REVERT: K 54 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7505 (ttp-110) REVERT: K 58 GLN cc_start: 0.7840 (pt0) cc_final: 0.7557 (pt0) REVERT: K 70 TYR cc_start: 0.8583 (p90) cc_final: 0.8268 (p90) REVERT: K 199 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8238 (ttmm) REVERT: K 301 ARG cc_start: 0.6644 (mpt180) cc_final: 0.6222 (mmm160) REVERT: K 348 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: K 385 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: K 420 ASP cc_start: 0.8670 (m-30) cc_final: 0.8345 (m-30) REVERT: K 436 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8594 (mp) REVERT: K 460 LYS cc_start: 0.7531 (ptpp) cc_final: 0.6728 (pptt) outliers start: 60 outliers final: 29 residues processed: 404 average time/residue: 0.6404 time to fit residues: 297.9101 Evaluate side-chains 404 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 356 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 308 ASN Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 112 optimal weight: 7.9990 chunk 3 optimal weight: 0.3980 chunk 151 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 328 GLN B 170 ASN B 324 GLN B 328 GLN D 58 GLN D 147 ASN D 170 ASN F 58 GLN F 170 ASN H 170 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128693 restraints weight = 22794.103| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.13 r_work: 0.3351 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25536 Z= 0.133 Angle : 0.551 8.957 34668 Z= 0.301 Chirality : 0.044 0.337 3744 Planarity : 0.004 0.048 4350 Dihedral : 14.554 178.542 3611 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.10 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 18.88 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2940 helix: 1.63 (0.12), residues: 1740 sheet: -1.08 (0.35), residues: 204 loop : -0.24 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 69 TYR 0.021 0.001 TYR A 11 PHE 0.011 0.001 PHE A 144 TRP 0.012 0.001 TRP F 363 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (25536) covalent geometry : angle 0.55137 / 0.30 (34668) hydrogen bonds : bond 0.04334 / 2.92 ( 1261) hydrogen bonds : angle 4.49289 / 3.21 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9765.14 seconds wall clock time: 167 minutes 14.91 seconds (10034.91 seconds total)