Starting phenix.real_space_refine on Sun Jul 5 04:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdp_64991/07_2026/9vdp_64991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdp_64991/07_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_64991/07_2026/9vdp_64991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdp_64991/07_2026/9vdp_64991.map" model { file = "/net/cci-nas-00/data/ceres_data/9vdp_64991/07_2026/9vdp_64991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdp_64991/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.46, per 1000 atoms: 0.14 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: 1.72 Conformation dependent library (CDL) restraints added in 726.4 milliseconds 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: 2.26 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: 3.43 Time building geometry restraints manager: 2.37 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: 0.05 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: 2.170 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- 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 : 0.724 10.101 34668 Z= 0.423 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 0.72384 / 0.42 (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 : 0.884 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: 0.6918 (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: 0.5301 time to fit residues: 374.4475 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 : 0.754 ------------------------------------------------------------------------------- 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 H 295 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131000 restraints weight = 23116.553| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.15 r_work: 0.3376 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1802 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= 0.195 Angle : 0.622 8.239 34668 Z= 0.342 Chirality : 0.047 0.385 3744 Planarity : 0.005 0.068 4350 Dihedral : 15.247 174.900 3679 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Rotamer: Outliers : 4.98 % Allowed : 16.08 % Favored : 78.95 % 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: 0.52 (0.15), residues: 2940 helix: 0.91 (0.12), residues: 1716 sheet: -0.14 (0.36), residues: 192 loop : -0.37 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 142 TYR 0.027 0.002 TYR K 475 PHE 0.016 0.002 PHE D 318 TRP 0.008 0.002 TRP F 363 HIS 0.007 0.002 HIS H 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (25536) covalent geometry : angle 0.62196 / 0.34 (34668) hydrogen bonds : bond 0.05258 / 3.56 ( 1261) hydrogen bonds : angle 4.90788 / 3.50 ( 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 581 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 446 time to evaluate : 0.862 Fit side-chains REVERT: A 54 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7281 (ttt-90) REVERT: A 135 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7717 (tt0) REVERT: A 137 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8176 (t0) REVERT: A 199 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8142 (ttmm) REVERT: A 227 ARG cc_start: 0.7893 (mmm160) cc_final: 0.7599 (tpt-90) REVERT: A 301 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5971 (mmm160) REVERT: A 385 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6933 (p0) REVERT: A 386 GLU cc_start: 0.6997 (tp30) cc_final: 0.6681 (tp30) REVERT: A 423 ASP cc_start: 0.7206 (m-30) cc_final: 0.6522 (t70) REVERT: A 424 ASP cc_start: 0.7642 (t70) cc_final: 0.7426 (p0) REVERT: A 427 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: A 436 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 457 ASP cc_start: 0.8134 (m-30) cc_final: 0.7897 (m-30) REVERT: A 460 LYS cc_start: 0.7639 (ptpp) cc_final: 0.6911 (pptt) REVERT: A 462 ASP cc_start: 0.7286 (t0) cc_final: 0.7047 (t70) REVERT: A 490 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7700 (mmtm) REVERT: B 54 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7104 (ttt-90) REVERT: B 135 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7699 (tt0) REVERT: B 137 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 199 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8089 (ttmm) REVERT: B 227 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7507 (tpt-90) REVERT: B 301 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6163 (mmm160) REVERT: B 385 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 386 GLU cc_start: 0.6836 (tp30) cc_final: 0.6521 (tp30) REVERT: B 423 ASP cc_start: 0.6987 (m-30) cc_final: 0.6306 (t70) REVERT: B 427 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: B 436 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8484 (mp) REVERT: B 457 ASP cc_start: 0.8118 (m-30) cc_final: 0.7885 (m-30) REVERT: B 460 LYS cc_start: 0.7616 (ptpp) cc_final: 0.6892 (pptt) REVERT: B 462 ASP cc_start: 0.7378 (t0) cc_final: 0.7007 (m-30) REVERT: B 490 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7616 (mmtm) REVERT: D 10 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8065 (tp) REVERT: D 137 ASN cc_start: 0.8483 (m-40) cc_final: 0.8154 (t0) REVERT: D 199 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8132 (ttmm) REVERT: D 227 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7771 (tpt-90) REVERT: D 301 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5613 (mmm160) REVERT: D 348 GLU cc_start: 0.7654 (pt0) cc_final: 0.7420 (tm-30) REVERT: D 349 TYR cc_start: 0.7214 (m-80) cc_final: 0.6985 (m-80) REVERT: D 377 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7285 (mp0) REVERT: D 385 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6819 (p0) REVERT: D 397 MET cc_start: 0.8748 (tmm) cc_final: 0.8464 (tmm) REVERT: D 402 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7849 (mptp) REVERT: D 407 MET cc_start: 0.8829 (tpp) cc_final: 0.8532 (tpp) REVERT: D 427 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: D 442 ASP cc_start: 0.8332 (t70) cc_final: 0.8123 (t70) REVERT: D 462 ASP cc_start: 0.7322 (t0) cc_final: 0.7109 (t70) REVERT: D 490 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7703 (mmtt) REVERT: F 10 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8187 (tp) REVERT: F 54 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7323 (ttt-90) REVERT: F 125 TYR cc_start: 0.7652 (t80) cc_final: 0.7354 (t80) REVERT: F 135 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7748 (tt0) REVERT: F 137 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8056 (t0) REVERT: F 199 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8014 (ttmm) REVERT: F 227 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7559 (tpt-90) REVERT: F 301 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6090 (mmm160) REVERT: F 348 GLU cc_start: 0.7560 (pt0) cc_final: 0.7182 (tm-30) REVERT: F 349 TYR cc_start: 0.7054 (m-80) cc_final: 0.6837 (m-10) REVERT: F 375 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7934 (mt) REVERT: F 397 MET cc_start: 0.8848 (tmm) cc_final: 0.8558 (tmm) REVERT: F 423 ASP cc_start: 0.6751 (m-30) cc_final: 0.6048 (t70) REVERT: F 427 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: F 457 ASP cc_start: 0.7905 (m-30) cc_final: 0.7698 (m-30) REVERT: F 460 LYS cc_start: 0.7616 (ptpp) cc_final: 0.6821 (pptt) REVERT: F 490 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7009 (mttm) REVERT: H 58 GLN cc_start: 0.7874 (pt0) cc_final: 0.7601 (pt0) REVERT: H 109 MET cc_start: 0.8613 (mmm) cc_final: 0.8386 (mmp) REVERT: H 126 GLU cc_start: 0.7457 (pt0) cc_final: 0.7109 (pt0) REVERT: H 137 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8104 (t0) REVERT: H 149 ASP cc_start: 0.8060 (m-30) cc_final: 0.7625 (t0) REVERT: H 199 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8134 (ttmm) REVERT: H 301 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5984 (mmm160) REVERT: H 304 ASP cc_start: 0.7097 (p0) cc_final: 0.6872 (p0) REVERT: H 348 GLU cc_start: 0.7665 (pt0) cc_final: 0.7289 (tm-30) REVERT: H 375 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8389 (mt) REVERT: H 385 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7027 (p0) REVERT: H 386 GLU cc_start: 0.7276 (tp30) cc_final: 0.7043 (tp30) REVERT: H 427 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: H 460 LYS cc_start: 0.7551 (ptpp) cc_final: 0.6836 (pptt) REVERT: H 490 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7340 (mttm) REVERT: K 54 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7390 (ttp-110) REVERT: K 58 GLN cc_start: 0.7821 (pt0) cc_final: 0.7550 (pt0) REVERT: K 109 MET cc_start: 0.8569 (mmm) cc_final: 0.8307 (mmp) REVERT: K 126 GLU cc_start: 0.7530 (pt0) cc_final: 0.7238 (pt0) REVERT: K 199 LYS cc_start: 0.8357 (ttpp) cc_final: 0.8141 (ttmm) REVERT: K 301 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6106 (mmm160) REVERT: K 367 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8539 (ptm) REVERT: K 375 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8166 (mt) REVERT: K 397 MET cc_start: 0.8811 (tmm) cc_final: 0.8590 (tmm) REVERT: K 423 ASP cc_start: 0.7046 (m-30) cc_final: 0.6038 (t70) REVERT: K 427 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: K 460 LYS cc_start: 0.7649 (ptpp) cc_final: 0.6970 (pptt) REVERT: K 490 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7821 (mmtt) outliers start: 135 outliers final: 38 residues processed: 538 average time/residue: 0.5897 time to fit residues: 366.4221 Evaluate side-chains 436 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 369 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 137 ASN 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 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 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 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 402 LYS 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 174 ILE 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 301 ARG Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 375 LEU 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 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 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 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 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: 0.9990 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 295 ASN 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 147 ASN F 295 ASN F 378 HIS ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 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 = 0.3698 r_free = 0.3698 target = 0.148081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130063 restraints weight = 23087.268| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.15 r_work: 0.3364 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2271 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 8.533 34668 Z= 0.303 Chirality : 0.045 0.334 3744 Planarity : 0.005 0.049 4350 Dihedral : 15.042 175.844 3642 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.97 % Rotamer: Outliers : 3.69 % Allowed : 17.48 % Favored : 78.83 % 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: 0.89 (0.15), residues: 2940 helix: 1.28 (0.12), residues: 1740 sheet: -0.42 (0.36), residues: 192 loop : -0.30 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 142 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 F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (25536) covalent geometry : angle 0.55227 / 0.30 (34668) hydrogen bonds : bond 0.04821 / 3.26 ( 1261) hydrogen bonds : angle 4.68154 / 3.35 ( 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 490 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 390 time to evaluate : 0.933 Fit side-chains REVERT: A 54 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7287 (ttt-90) REVERT: A 135 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7738 (tt0) REVERT: A 137 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8191 (t0) REVERT: A 199 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8041 (ttmm) REVERT: A 227 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7570 (tpt-90) REVERT: A 301 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5927 (mmm160) REVERT: A 377 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7443 (mp0) REVERT: A 386 GLU cc_start: 0.7065 (tp30) cc_final: 0.6766 (tp30) REVERT: A 436 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 457 ASP cc_start: 0.8169 (m-30) cc_final: 0.7935 (m-30) REVERT: A 460 LYS cc_start: 0.7572 (ptpp) cc_final: 0.6882 (pptt) REVERT: A 462 ASP cc_start: 0.7299 (t0) cc_final: 0.7066 (t70) REVERT: B 54 ARG cc_start: 0.7496 (ttp80) cc_final: 0.7205 (ttt-90) REVERT: B 123 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: B 135 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7754 (tt0) REVERT: B 137 ASN cc_start: 0.8369 (m-40) cc_final: 0.8141 (t0) REVERT: B 199 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8026 (ttmm) REVERT: B 227 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7593 (tpt-90) REVERT: B 301 ARG cc_start: 0.6660 (mpt180) cc_final: 0.5978 (mmm160) REVERT: B 349 TYR cc_start: 0.7244 (m-80) cc_final: 0.6808 (m-80) REVERT: B 377 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7453 (mp0) REVERT: B 386 GLU cc_start: 0.6963 (tp30) cc_final: 0.6635 (tp30) REVERT: B 427 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: B 436 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 457 ASP cc_start: 0.8176 (m-30) cc_final: 0.7933 (m-30) REVERT: B 460 LYS cc_start: 0.7628 (ptpp) cc_final: 0.6887 (pptt) REVERT: B 462 ASP cc_start: 0.7355 (t0) cc_final: 0.7129 (t70) REVERT: B 490 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7774 (mmtm) REVERT: D 10 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8132 (tp) REVERT: D 68 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8080 (p) REVERT: D 135 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7668 (tt0) REVERT: D 137 ASN cc_start: 0.8520 (m-40) cc_final: 0.8206 (t0) REVERT: D 199 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8064 (ttmm) REVERT: D 227 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7630 (tpt-90) REVERT: D 349 TYR cc_start: 0.7263 (m-80) cc_final: 0.7027 (m-80) REVERT: D 377 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7478 (mp0) REVERT: D 385 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6633 (p0) REVERT: D 397 MET cc_start: 0.8812 (tmm) cc_final: 0.8506 (tmm) REVERT: D 402 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7790 (mptp) REVERT: D 424 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7067 (p0) REVERT: D 462 ASP cc_start: 0.7315 (t0) cc_final: 0.7070 (t70) REVERT: D 490 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7772 (mmtm) REVERT: F 10 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8213 (tp) REVERT: F 54 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7344 (ttt-90) REVERT: F 125 TYR cc_start: 0.7685 (t80) cc_final: 0.7384 (t80) REVERT: F 135 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7784 (tt0) REVERT: F 137 ASN cc_start: 0.8524 (m-40) cc_final: 0.8140 (t0) REVERT: F 155 THR cc_start: 0.8188 (t) cc_final: 0.7921 (p) REVERT: F 199 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7919 (ttmm) REVERT: F 227 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7630 (tpt-90) REVERT: F 348 GLU cc_start: 0.7542 (pt0) cc_final: 0.7137 (tm-30) REVERT: F 349 TYR cc_start: 0.7117 (m-80) cc_final: 0.6887 (m-10) REVERT: F 397 MET cc_start: 0.8871 (tmm) cc_final: 0.8558 (tmm) REVERT: F 427 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: F 460 LYS cc_start: 0.7586 (ptpp) cc_final: 0.6686 (pptt) REVERT: F 490 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7599 (mmtt) REVERT: H 10 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8536 (tp) REVERT: H 58 GLN cc_start: 0.7851 (pt0) cc_final: 0.7579 (pt0) REVERT: H 126 GLU cc_start: 0.7638 (pt0) cc_final: 0.7291 (pt0) REVERT: H 137 ASN cc_start: 0.8408 (m-40) cc_final: 0.8133 (t0) REVERT: H 199 LYS cc_start: 0.8314 (ttpp) cc_final: 0.8091 (ttmm) REVERT: H 301 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5938 (mmm160) REVERT: H 348 GLU cc_start: 0.7665 (pt0) cc_final: 0.7280 (tm-30) REVERT: H 375 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8654 (mt) REVERT: H 385 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6893 (p0) REVERT: H 386 GLU cc_start: 0.7181 (tp30) cc_final: 0.6919 (tp30) REVERT: H 420 ASP cc_start: 0.8624 (m-30) cc_final: 0.8251 (m-30) REVERT: H 427 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: H 436 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8543 (mp) REVERT: H 460 LYS cc_start: 0.7493 (ptpp) cc_final: 0.6711 (pptt) REVERT: H 490 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7358 (mttm) REVERT: K 10 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8550 (tp) REVERT: K 54 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7428 (ttp-110) REVERT: K 58 GLN cc_start: 0.7873 (pt0) cc_final: 0.7615 (pt0) REVERT: K 69 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7956 (mtp85) REVERT: K 126 GLU cc_start: 0.7543 (pt0) cc_final: 0.7174 (pt0) REVERT: K 199 LYS cc_start: 0.8302 (ttpp) cc_final: 0.8090 (ttmm) REVERT: K 301 ARG cc_start: 0.6610 (mpt180) cc_final: 0.6107 (mmm160) REVERT: K 348 GLU cc_start: 0.7376 (pp20) cc_final: 0.6960 (tm-30) REVERT: K 367 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8534 (ptm) REVERT: K 375 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8448 (mt) REVERT: K 427 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: K 460 LYS cc_start: 0.7661 (ptpp) cc_final: 0.6950 (pptt) REVERT: K 490 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7869 (mmtt) outliers start: 100 outliers final: 36 residues processed: 456 average time/residue: 0.5501 time to fit residues: 290.8299 Evaluate side-chains 421 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 123 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 294 VAL 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 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 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER 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 427 GLU 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 294 VAL Chi-restraints excluded: chain H residue 301 ARG 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 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 444 SER 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 294 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 231 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 58 GLN B 201 ASN B 295 ASN D 58 GLN F 58 GLN F 378 HIS ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 HIS ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127663 restraints weight = 22834.308| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.14 r_work: 0.3333 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25536 Z= 0.164 Angle : 0.564 8.124 34668 Z= 0.310 Chirality : 0.045 0.330 3744 Planarity : 0.005 0.052 4350 Dihedral : 14.983 177.922 3627 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 4.54 % Allowed : 15.78 % Favored : 79.68 % 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: 1.07 (0.15), residues: 2940 helix: 1.46 (0.12), residues: 1740 sheet: -0.62 (0.36), residues: 192 loop : -0.25 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 142 TYR 0.022 0.002 TYR K 475 PHE 0.015 0.002 PHE K 432 TRP 0.009 0.002 TRP D 363 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (25536) covalent geometry : angle 0.56384 / 0.31 (34668) hydrogen bonds : bond 0.04863 / 3.29 ( 1261) hydrogen bonds : angle 4.59159 / 3.29 ( 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 501 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 378 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7304 (ttt-90) REVERT: A 135 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7791 (tt0) REVERT: A 137 ASN cc_start: 0.8455 (m-40) cc_final: 0.8213 (t0) REVERT: A 199 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8117 (ttmm) REVERT: A 227 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7595 (tpt-90) REVERT: A 301 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5980 (mmm160) REVERT: A 328 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: A 377 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7587 (mp0) REVERT: A 386 GLU cc_start: 0.7174 (tp30) cc_final: 0.6812 (tp30) REVERT: A 427 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: A 436 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8487 (mp) REVERT: A 457 ASP cc_start: 0.8299 (m-30) cc_final: 0.8085 (m-30) REVERT: A 460 LYS cc_start: 0.7614 (ptpp) cc_final: 0.6923 (pptt) REVERT: A 462 ASP cc_start: 0.7328 (t0) cc_final: 0.7083 (t70) REVERT: A 490 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7882 (mmtm) REVERT: B 54 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7249 (ttt-90) REVERT: B 69 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7737 (mtp85) REVERT: B 135 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7787 (tt0) REVERT: B 137 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8215 (t0) REVERT: B 155 THR cc_start: 0.8242 (t) cc_final: 0.8006 (p) REVERT: B 199 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8078 (ttmm) REVERT: B 227 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7567 (tpt-90) REVERT: B 301 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6110 (mmm160) REVERT: B 328 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: B 349 TYR cc_start: 0.7286 (m-80) cc_final: 0.6952 (m-80) REVERT: B 377 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7577 (mp0) REVERT: B 386 GLU cc_start: 0.7235 (tp30) cc_final: 0.6915 (tp30) REVERT: B 427 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: B 436 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 457 ASP cc_start: 0.8296 (m-30) cc_final: 0.8063 (m-30) REVERT: B 460 LYS cc_start: 0.7609 (ptpp) cc_final: 0.6904 (pptt) REVERT: B 462 ASP cc_start: 0.7298 (t0) cc_final: 0.7064 (t70) REVERT: D 10 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8195 (tp) REVERT: D 135 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7721 (tt0) REVERT: D 137 ASN cc_start: 0.8599 (m-40) cc_final: 0.8250 (t0) REVERT: D 155 THR cc_start: 0.8092 (t) cc_final: 0.7832 (p) REVERT: D 199 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8170 (ttmm) REVERT: D 227 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7594 (tpt-90) REVERT: D 301 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5808 (mmm160) REVERT: D 349 TYR cc_start: 0.7359 (m-80) cc_final: 0.7097 (m-80) REVERT: D 377 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7532 (mp0) REVERT: D 385 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6463 (m-30) REVERT: D 397 MET cc_start: 0.8854 (tmm) cc_final: 0.8574 (tmm) REVERT: D 402 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7861 (mptp) REVERT: D 424 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7205 (p0) REVERT: D 490 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7761 (mmtm) REVERT: F 10 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8208 (tp) REVERT: F 54 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7451 (ttp-110) REVERT: F 125 TYR cc_start: 0.7765 (t80) cc_final: 0.7482 (t80) REVERT: F 135 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7737 (tt0) REVERT: F 137 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8174 (t0) REVERT: F 149 ASP cc_start: 0.8039 (m-30) cc_final: 0.7833 (m-30) REVERT: F 199 LYS cc_start: 0.8341 (ttpp) cc_final: 0.8081 (ttmm) REVERT: F 227 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7609 (tpt-90) REVERT: F 301 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5948 (mmm160) REVERT: F 348 GLU cc_start: 0.7563 (pt0) cc_final: 0.7182 (tm-30) REVERT: F 349 TYR cc_start: 0.7329 (m-80) cc_final: 0.7065 (m-10) REVERT: F 393 GLU cc_start: 0.8344 (tp30) cc_final: 0.8110 (tp30) REVERT: F 397 MET cc_start: 0.8880 (tmm) cc_final: 0.8494 (tmm) REVERT: F 427 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: F 460 LYS cc_start: 0.7583 (ptpp) cc_final: 0.6683 (pptt) REVERT: F 490 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7753 (mmtt) REVERT: H 10 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8561 (tp) REVERT: H 58 GLN cc_start: 0.7855 (pt0) cc_final: 0.7553 (pt0) REVERT: H 69 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7909 (mtp85) REVERT: H 126 GLU cc_start: 0.7637 (pt0) cc_final: 0.7251 (pt0) REVERT: H 137 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8190 (t0) REVERT: H 199 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8181 (ttmm) REVERT: H 301 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5929 (mmm160) REVERT: H 348 GLU cc_start: 0.7676 (pt0) cc_final: 0.7312 (tm-30) REVERT: H 385 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6859 (p0) REVERT: H 386 GLU cc_start: 0.7229 (tp30) cc_final: 0.6914 (tp30) REVERT: H 420 ASP cc_start: 0.8631 (m-30) cc_final: 0.8286 (m-30) REVERT: H 436 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8553 (mp) REVERT: H 460 LYS cc_start: 0.7516 (ptpp) cc_final: 0.6719 (pptt) REVERT: K 10 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8580 (tp) REVERT: K 54 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7427 (ttp-110) REVERT: K 58 GLN cc_start: 0.7902 (pt0) cc_final: 0.7605 (pt0) REVERT: K 69 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (mtp85) REVERT: K 126 GLU cc_start: 0.7608 (pt0) cc_final: 0.7186 (pt0) REVERT: K 199 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8157 (ttmm) REVERT: K 301 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6137 (mmm160) REVERT: K 309 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7951 (mmtm) REVERT: K 348 GLU cc_start: 0.7373 (pp20) cc_final: 0.6989 (tm-30) REVERT: K 367 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8532 (ptm) REVERT: K 385 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6911 (p0) REVERT: K 420 ASP cc_start: 0.8658 (m-30) cc_final: 0.8305 (m-30) REVERT: K 460 LYS cc_start: 0.7671 (ptpp) cc_final: 0.6933 (pptt) outliers start: 123 outliers final: 43 residues processed: 454 average time/residue: 0.5372 time to fit residues: 283.1908 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 : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER 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 328 GLN 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 137 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU 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 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 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 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 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 427 GLU Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 459 ILE 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 157 ILE 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 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 157 ILE 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 367 MET 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: 7.9990 chunk 282 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 58 GLN D 58 GLN F 58 GLN F 378 HIS ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126480 restraints weight = 22804.191| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.14 r_work: 0.3317 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25536 Z= 0.176 Angle : 0.569 7.889 34668 Z= 0.313 Chirality : 0.046 0.319 3744 Planarity : 0.005 0.052 4350 Dihedral : 14.972 178.290 3625 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.79 % Favored : 97.01 % Rotamer: Outliers : 4.28 % Allowed : 16.48 % 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: 1.07 (0.15), residues: 2940 helix: 1.46 (0.12), residues: 1746 sheet: -0.73 (0.36), residues: 192 loop : -0.20 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 142 TYR 0.022 0.002 TYR H 475 PHE 0.014 0.002 PHE K 144 TRP 0.010 0.002 TRP D 363 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (25536) covalent geometry : angle 0.56908 / 0.31 (34668) hydrogen bonds : bond 0.04924 / 3.34 ( 1261) hydrogen bonds : angle 4.59417 / 3.29 ( 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 490 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 374 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7296 (ttt-90) REVERT: A 58 GLN cc_start: 0.7922 (pt0) cc_final: 0.7579 (mm110) REVERT: A 97 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: A 135 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7826 (tt0) REVERT: A 137 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8260 (t0) REVERT: A 155 THR cc_start: 0.8301 (t) cc_final: 0.8070 (p) REVERT: A 199 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8119 (ttmm) REVERT: A 227 ARG cc_start: 0.7868 (mmm160) cc_final: 0.7577 (tpt-90) REVERT: A 301 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.5998 (mmm160) REVERT: A 377 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: A 386 GLU cc_start: 0.7254 (tp30) cc_final: 0.6913 (tp30) REVERT: A 436 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 457 ASP cc_start: 0.8324 (m-30) cc_final: 0.8111 (m-30) REVERT: A 460 LYS cc_start: 0.7579 (ptpp) cc_final: 0.6892 (pptt) REVERT: A 462 ASP cc_start: 0.7345 (t0) cc_final: 0.7092 (t70) REVERT: A 490 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7981 (mmtm) REVERT: B 54 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7270 (ttt-90) REVERT: B 69 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7758 (mtp85) REVERT: B 135 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7823 (tt0) REVERT: B 137 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8250 (t0) REVERT: B 155 THR cc_start: 0.8297 (t) cc_final: 0.8076 (p) REVERT: B 199 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8060 (ttmm) REVERT: B 227 ARG cc_start: 0.7866 (mmm160) cc_final: 0.7585 (tpt-90) REVERT: B 301 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6127 (mmm160) REVERT: B 328 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: B 349 TYR cc_start: 0.7307 (m-80) cc_final: 0.7008 (m-80) REVERT: B 377 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: B 386 GLU cc_start: 0.7274 (tp30) cc_final: 0.6948 (tp30) REVERT: B 427 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: B 436 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 457 ASP cc_start: 0.8345 (m-30) cc_final: 0.8131 (m-30) REVERT: B 460 LYS cc_start: 0.7614 (ptpp) cc_final: 0.6909 (pptt) REVERT: B 490 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7939 (mmtm) REVERT: D 10 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8219 (tp) REVERT: D 135 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7699 (tt0) REVERT: D 137 ASN cc_start: 0.8568 (m-40) cc_final: 0.8182 (t0) REVERT: D 155 THR cc_start: 0.8242 (t) cc_final: 0.8011 (p) REVERT: D 199 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8052 (ttmm) REVERT: D 227 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7585 (tpt-90) REVERT: D 301 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5831 (mmm160) REVERT: D 349 TYR cc_start: 0.7329 (m-80) cc_final: 0.7104 (m-80) REVERT: D 377 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7551 (mp0) REVERT: D 385 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6463 (m-30) REVERT: D 397 MET cc_start: 0.8885 (tmm) cc_final: 0.8612 (tmm) REVERT: D 402 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (mptp) REVERT: D 424 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7216 (p0) REVERT: D 490 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7774 (mmtm) REVERT: F 10 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8222 (tp) REVERT: F 54 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7451 (ttp-110) REVERT: F 97 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7962 (mp0) REVERT: F 125 TYR cc_start: 0.7798 (t80) cc_final: 0.7537 (t80) REVERT: F 135 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7711 (tt0) REVERT: F 137 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8190 (t0) REVERT: F 199 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8059 (ttmm) REVERT: F 227 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7544 (tpt-90) REVERT: F 301 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5962 (mmm160) REVERT: F 397 MET cc_start: 0.8889 (tmm) cc_final: 0.8636 (tmm) REVERT: F 424 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7250 (p0) REVERT: F 427 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: F 460 LYS cc_start: 0.7568 (ptpp) cc_final: 0.6729 (pptt) REVERT: F 490 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7772 (mmtt) REVERT: H 10 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8599 (tp) REVERT: H 58 GLN cc_start: 0.7855 (pt0) cc_final: 0.7554 (pt0) REVERT: H 69 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: H 126 GLU cc_start: 0.7717 (pt0) cc_final: 0.7475 (pt0) REVERT: H 137 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8187 (t0) REVERT: H 159 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8172 (p) REVERT: H 199 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8172 (ttmm) REVERT: H 301 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6010 (mmm160) REVERT: H 348 GLU cc_start: 0.7691 (pt0) cc_final: 0.7270 (tm-30) REVERT: H 385 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6932 (p0) REVERT: H 386 GLU cc_start: 0.7239 (tp30) cc_final: 0.6973 (tp30) REVERT: H 420 ASP cc_start: 0.8663 (m-30) cc_final: 0.8328 (m-30) REVERT: H 436 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8570 (mp) REVERT: H 460 LYS cc_start: 0.7540 (ptpp) cc_final: 0.6750 (pptt) REVERT: K 10 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8596 (tp) REVERT: K 54 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7419 (ttp-110) REVERT: K 58 GLN cc_start: 0.7870 (pt0) cc_final: 0.7569 (pt0) REVERT: K 69 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7980 (mtp85) REVERT: K 159 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (p) REVERT: K 199 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8133 (ttmm) REVERT: K 301 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6148 (mmm160) REVERT: K 309 LYS cc_start: 0.8250 (mmtm) cc_final: 0.8000 (mmtm) REVERT: K 328 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: K 348 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: K 367 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8514 (ptm) REVERT: K 385 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6952 (p0) REVERT: K 420 ASP cc_start: 0.8681 (m-30) cc_final: 0.8330 (m-30) REVERT: K 427 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: K 436 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8564 (mp) REVERT: K 460 LYS cc_start: 0.7659 (ptpp) cc_final: 0.6910 (pptt) outliers start: 116 outliers final: 41 residues processed: 442 average time/residue: 0.5563 time to fit residues: 284.3314 Evaluate side-chains 438 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 137 ASN 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 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 137 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU 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 56 SER 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 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 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 427 GLU 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 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 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 H residue 444 SER 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 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 328 GLN Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 367 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS B 58 GLN D 58 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129062 restraints weight = 22908.332| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.14 r_work: 0.3353 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2975 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= 0.130 Angle : 0.525 7.028 34668 Z= 0.289 Chirality : 0.044 0.316 3744 Planarity : 0.004 0.051 4350 Dihedral : 14.791 177.703 3625 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 2.80 % Allowed : 17.99 % 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: 1.19 (0.16), residues: 2940 helix: 1.62 (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 0.004 0.000 ARG K 142 TYR 0.017 0.001 TYR H 475 PHE 0.011 0.001 PHE H 432 TRP 0.010 0.001 TRP F 363 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (25536) covalent geometry : angle 0.52511 / 0.29 (34668) hydrogen bonds : bond 0.04375 / 2.95 ( 1261) hydrogen bonds : angle 4.48096 / 3.21 ( 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 445 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 369 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7282 (ttt-90) REVERT: A 58 GLN cc_start: 0.7919 (pt0) cc_final: 0.7569 (mm110) REVERT: A 135 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7832 (tt0) REVERT: A 137 ASN cc_start: 0.8427 (m-40) cc_final: 0.8196 (t0) REVERT: A 192 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 199 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8052 (ttmm) REVERT: A 227 ARG cc_start: 0.7865 (mmm160) cc_final: 0.7543 (tpt-90) REVERT: A 301 ARG cc_start: 0.6270 (mpt180) cc_final: 0.5892 (mmm160) REVERT: A 377 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7572 (mp0) REVERT: A 385 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6350 (m-30) REVERT: A 386 GLU cc_start: 0.7243 (tp30) cc_final: 0.6885 (tp30) REVERT: A 436 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 457 ASP cc_start: 0.8308 (m-30) cc_final: 0.8100 (m-30) REVERT: A 460 LYS cc_start: 0.7555 (ptpp) cc_final: 0.6801 (pptt) REVERT: A 462 ASP cc_start: 0.7311 (t0) cc_final: 0.7087 (t70) REVERT: A 490 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7902 (mmtm) REVERT: B 54 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7261 (ttt-90) REVERT: B 58 GLN cc_start: 0.7918 (pt0) cc_final: 0.7554 (mm110) REVERT: B 69 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7656 (mtp85) REVERT: B 135 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7828 (tt0) REVERT: B 137 ASN cc_start: 0.8460 (m-40) cc_final: 0.8191 (t0) REVERT: B 192 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 199 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7988 (ttmm) REVERT: B 227 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7549 (tpt-90) REVERT: B 301 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6008 (mmm160) REVERT: B 349 TYR cc_start: 0.7275 (m-80) cc_final: 0.6978 (m-80) REVERT: B 377 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7643 (mp0) REVERT: B 386 GLU cc_start: 0.7252 (tp30) cc_final: 0.6975 (tp30) REVERT: B 424 ASP cc_start: 0.7599 (p0) cc_final: 0.7308 (p0) REVERT: B 436 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 457 ASP cc_start: 0.8357 (m-30) cc_final: 0.8131 (m-30) REVERT: B 460 LYS cc_start: 0.7589 (ptpp) cc_final: 0.6832 (pptt) REVERT: B 490 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7862 (mmtm) REVERT: D 10 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8235 (tp) REVERT: D 135 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7695 (tt0) REVERT: D 137 ASN cc_start: 0.8590 (m-40) cc_final: 0.8257 (t0) REVERT: D 199 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8030 (ttmm) REVERT: D 227 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7600 (tpt-90) REVERT: D 301 ARG cc_start: 0.6211 (mpt180) cc_final: 0.5649 (mmm160) REVERT: D 377 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7549 (mp0) REVERT: D 385 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: D 397 MET cc_start: 0.8875 (tmm) cc_final: 0.8602 (tmm) REVERT: D 402 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7858 (mptp) REVERT: D 424 ASP cc_start: 0.7583 (p0) cc_final: 0.7218 (p0) REVERT: D 490 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7747 (mmtm) REVERT: F 10 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8236 (tp) REVERT: F 54 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7397 (ttp-110) REVERT: F 135 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7770 (tt0) REVERT: F 137 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8181 (t0) REVERT: F 149 ASP cc_start: 0.7936 (m-30) cc_final: 0.7732 (m-30) REVERT: F 199 LYS cc_start: 0.8291 (ttpp) cc_final: 0.8017 (ttmm) REVERT: F 227 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7587 (tpt-90) REVERT: F 301 ARG cc_start: 0.6320 (mpt180) cc_final: 0.5868 (mmm160) REVERT: F 393 GLU cc_start: 0.8380 (tp30) cc_final: 0.8115 (tp30) REVERT: F 397 MET cc_start: 0.8911 (tmm) cc_final: 0.8628 (tmm) REVERT: F 424 ASP cc_start: 0.7604 (p0) cc_final: 0.7220 (p0) REVERT: F 427 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: F 460 LYS cc_start: 0.7491 (ptpp) cc_final: 0.6676 (pptt) REVERT: F 490 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7670 (mmtt) REVERT: H 10 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8577 (tp) REVERT: H 58 GLN cc_start: 0.7803 (pt0) cc_final: 0.7520 (pt0) REVERT: H 69 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7878 (mtp85) REVERT: H 126 GLU cc_start: 0.7664 (pt0) cc_final: 0.7262 (pt0) REVERT: H 137 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8172 (t0) REVERT: H 199 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8111 (ttmm) REVERT: H 287 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7942 (p0) REVERT: H 301 ARG cc_start: 0.6432 (mpt180) cc_final: 0.5969 (mmm160) REVERT: H 328 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: H 348 GLU cc_start: 0.7685 (pt0) cc_final: 0.7242 (tm-30) REVERT: H 385 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: H 386 GLU cc_start: 0.7239 (tp30) cc_final: 0.6966 (tp30) REVERT: H 393 GLU cc_start: 0.8312 (tp30) cc_final: 0.8104 (tp30) REVERT: H 420 ASP cc_start: 0.8644 (m-30) cc_final: 0.8303 (m-30) REVERT: H 436 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8547 (mp) REVERT: H 460 LYS cc_start: 0.7479 (ptpp) cc_final: 0.6656 (pptt) REVERT: K 10 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8579 (tp) REVERT: K 54 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7418 (ttp-110) REVERT: K 58 GLN cc_start: 0.7814 (pt0) cc_final: 0.7524 (pt0) REVERT: K 69 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7905 (mtp85) REVERT: K 199 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8091 (ttmm) REVERT: K 301 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6026 (mmm160) REVERT: K 348 GLU cc_start: 0.7453 (pp20) cc_final: 0.6982 (tm-30) REVERT: K 367 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8509 (ptm) REVERT: K 385 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6795 (p0) REVERT: K 420 ASP cc_start: 0.8640 (m-30) cc_final: 0.8292 (m-30) REVERT: K 436 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8558 (mp) REVERT: K 449 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: K 460 LYS cc_start: 0.7574 (ptpp) cc_final: 0.6798 (pptt) outliers start: 76 outliers final: 29 residues processed: 421 average time/residue: 0.6026 time to fit residues: 293.7001 Evaluate side-chains 411 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 176 LEU 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 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 176 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 301 ARG Chi-restraints excluded: chain B residue 307 LEU 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 D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 427 GLU 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 157 ILE Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain H residue 294 VAL 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 56 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 157 ILE 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 367 MET 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=2.50 ------------------------------------------------------------------------------- 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: 3.9990 chunk 127 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN D 58 GLN D 401 ASN F 58 GLN F 378 HIS H 170 ASN 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 = 0.3623 r_free = 0.3623 target = 0.141774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124021 restraints weight = 22790.302| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.13 r_work: 0.3284 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25536 Z= 0.246 Angle : 0.634 7.519 34668 Z= 0.348 Chirality : 0.049 0.320 3744 Planarity : 0.005 0.053 4350 Dihedral : 15.094 179.683 3617 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.03 % Favored : 96.77 % Rotamer: Outliers : 3.87 % Allowed : 16.26 % Favored : 79.87 % 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: 0.95 (0.15), residues: 2940 helix: 1.32 (0.12), residues: 1752 sheet: -0.78 (0.36), residues: 192 loop : -0.19 (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 K 475 PHE 0.017 0.002 PHE H 432 TRP 0.010 0.002 TRP F 363 HIS 0.006 0.001 HIS F 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (25536) covalent geometry : angle 0.63427 / 0.35 (34668) hydrogen bonds : bond 0.05476 / 3.74 ( 1261) hydrogen bonds : angle 4.68290 / 3.36 ( 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 471 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 366 time to evaluate : 1.026 Fit side-chains REVERT: A 54 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7455 (ttp-110) REVERT: A 58 GLN cc_start: 0.7942 (pt0) cc_final: 0.7631 (mm110) REVERT: A 97 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: A 135 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7822 (tt0) REVERT: A 137 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 192 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7931 (t0) REVERT: A 199 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8181 (ttmm) REVERT: A 227 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7605 (tpt-90) REVERT: A 301 ARG cc_start: 0.6548 (mpt180) cc_final: 0.6087 (mmm160) REVERT: A 377 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 385 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: A 386 GLU cc_start: 0.7300 (tp30) cc_final: 0.6940 (tp30) REVERT: A 436 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 457 ASP cc_start: 0.8363 (m-30) cc_final: 0.8158 (m-30) REVERT: A 460 LYS cc_start: 0.7602 (ptpp) cc_final: 0.6856 (pptt) REVERT: A 490 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8042 (mmtm) REVERT: B 54 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7457 (ttp-110) REVERT: B 58 GLN cc_start: 0.7971 (pt0) cc_final: 0.7625 (mm110) REVERT: B 135 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7840 (tt0) REVERT: B 137 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8259 (t0) REVERT: B 192 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7913 (t0) REVERT: B 199 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8181 (ttmm) REVERT: B 227 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7606 (tpt-90) REVERT: B 301 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6160 (mmm160) REVERT: B 328 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: B 349 TYR cc_start: 0.7350 (m-80) cc_final: 0.7063 (m-80) REVERT: B 377 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: B 386 GLU cc_start: 0.7295 (tp30) cc_final: 0.6960 (tp30) REVERT: B 424 ASP cc_start: 0.7585 (p0) cc_final: 0.7288 (p0) REVERT: B 436 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 460 LYS cc_start: 0.7633 (ptpp) cc_final: 0.6868 (pptt) REVERT: B 490 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8025 (mmtm) REVERT: D 10 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8244 (tp) REVERT: D 97 GLU cc_start: 0.7902 (mp0) cc_final: 0.7656 (pm20) REVERT: D 135 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7694 (tt0) REVERT: D 137 ASN cc_start: 0.8562 (m-40) cc_final: 0.8168 (t0) REVERT: D 192 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8121 (t0) REVERT: D 199 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8195 (ttmm) REVERT: D 301 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.5936 (mmm160) REVERT: D 377 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7514 (mp0) REVERT: D 385 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6444 (m-30) REVERT: D 397 MET cc_start: 0.8855 (tmm) cc_final: 0.8629 (tmm) REVERT: D 424 ASP cc_start: 0.7591 (p0) cc_final: 0.7223 (p0) REVERT: D 460 LYS cc_start: 0.7446 (ptpp) cc_final: 0.6700 (pptt) REVERT: D 490 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7805 (mmtt) REVERT: F 10 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8248 (tp) REVERT: F 54 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7518 (ttp-110) REVERT: F 135 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7700 (tt0) REVERT: F 137 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8176 (t0) REVERT: F 192 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8088 (t0) REVERT: F 199 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8182 (ttmm) REVERT: F 301 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6040 (mmm160) REVERT: F 424 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7246 (p0) REVERT: F 427 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: F 460 LYS cc_start: 0.7587 (ptpp) cc_final: 0.6756 (pptt) REVERT: F 490 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7794 (mmtt) REVERT: H 10 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8650 (tp) REVERT: H 58 GLN cc_start: 0.7879 (pt0) cc_final: 0.7575 (pt0) REVERT: H 69 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7971 (mtp85) REVERT: H 70 TYR cc_start: 0.8565 (p90) cc_final: 0.8295 (p90) REVERT: H 126 GLU cc_start: 0.7519 (pt0) cc_final: 0.7160 (pt0) REVERT: H 137 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (t0) REVERT: H 159 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8321 (p) REVERT: H 199 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8224 (ttmm) REVERT: H 301 ARG cc_start: 0.6719 (mpt180) cc_final: 0.6258 (mmm160) REVERT: H 328 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: H 348 GLU cc_start: 0.7724 (pt0) cc_final: 0.7326 (tm-30) REVERT: H 385 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: H 386 GLU cc_start: 0.7345 (tp30) cc_final: 0.7050 (tp30) REVERT: H 420 ASP cc_start: 0.8651 (m-30) cc_final: 0.8337 (m-30) REVERT: H 427 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: H 436 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8610 (mp) REVERT: H 460 LYS cc_start: 0.7521 (ptpp) cc_final: 0.6696 (pptt) REVERT: K 10 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8636 (tp) REVERT: K 54 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7508 (ttp-110) REVERT: K 58 GLN cc_start: 0.7874 (pt0) cc_final: 0.7569 (pt0) REVERT: K 69 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.8007 (mtp85) REVERT: K 70 TYR cc_start: 0.8563 (p90) cc_final: 0.8307 (p90) REVERT: K 143 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8114 (ptp-170) REVERT: K 159 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8339 (p) REVERT: K 199 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8224 (ttmm) REVERT: K 301 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6243 (mmm160) REVERT: K 309 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8020 (mmtm) REVERT: K 328 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: K 348 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: K 367 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8431 (ptm) REVERT: K 385 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6959 (p0) REVERT: K 420 ASP cc_start: 0.8653 (m-30) cc_final: 0.8336 (m-30) REVERT: K 427 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: K 436 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8619 (mp) REVERT: K 449 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: K 460 LYS cc_start: 0.7567 (ptpp) cc_final: 0.6795 (pptt) outliers start: 105 outliers final: 41 residues processed: 433 average time/residue: 0.6078 time to fit residues: 304.1356 Evaluate side-chains 441 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 358 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 137 ASN 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 377 GLU 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 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 436 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 157 ILE 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 301 ARG 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 157 ILE 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 301 ARG Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 427 GLU 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 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 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 56 SER 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 348 GLU Chi-restraints excluded: chain K residue 367 MET 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: 5.9990 chunk 66 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 282 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 150 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN B 170 ASN D 58 GLN D 328 GLN F 58 GLN F 170 ASN F 378 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127488 restraints weight = 22766.204| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.13 r_work: 0.3332 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3208 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= 0.143 Angle : 0.548 6.803 34668 Z= 0.301 Chirality : 0.044 0.315 3744 Planarity : 0.004 0.051 4350 Dihedral : 14.856 179.028 3617 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 3.06 % Allowed : 17.33 % Favored : 79.61 % 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: 1.50 (0.12), residues: 1746 sheet: -0.87 (0.36), residues: 192 loop : -0.18 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 142 TYR 0.019 0.002 TYR H 475 PHE 0.012 0.001 PHE A 144 TRP 0.011 0.002 TRP F 363 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (25536) covalent geometry : angle 0.54787 / 0.30 (34668) hydrogen bonds : bond 0.04558 / 3.08 ( 1261) hydrogen bonds : angle 4.54982 / 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 447 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 364 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7288 (ttt-90) REVERT: A 58 GLN cc_start: 0.7902 (pt0) cc_final: 0.7575 (mm110) REVERT: A 97 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 135 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7750 (tt0) REVERT: A 137 ASN cc_start: 0.8488 (m-40) cc_final: 0.8239 (t0) REVERT: A 192 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7914 (t0) REVERT: A 199 LYS cc_start: 0.8339 (ttpp) cc_final: 0.8073 (ttmm) REVERT: A 227 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7582 (tpt-90) REVERT: A 301 ARG cc_start: 0.6316 (mpt180) cc_final: 0.5925 (mmm160) REVERT: A 377 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7676 (mp0) REVERT: A 385 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: A 386 GLU cc_start: 0.7209 (tp30) cc_final: 0.7008 (tm-30) REVERT: A 436 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 460 LYS cc_start: 0.7577 (ptpp) cc_final: 0.6831 (pptt) REVERT: A 490 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7958 (mmtm) REVERT: B 54 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7432 (ttp-110) REVERT: B 58 GLN cc_start: 0.7951 (pt0) cc_final: 0.7596 (mm110) REVERT: B 69 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7694 (mtp85) REVERT: B 135 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7759 (tt0) REVERT: B 137 ASN cc_start: 0.8478 (m-40) cc_final: 0.8226 (t0) REVERT: B 192 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7914 (t0) REVERT: B 199 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8033 (ttmm) REVERT: B 227 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7572 (tpt-90) REVERT: B 301 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5960 (mmm160) REVERT: B 349 TYR cc_start: 0.7325 (m-80) cc_final: 0.7036 (m-80) REVERT: B 377 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: B 386 GLU cc_start: 0.7289 (tp30) cc_final: 0.7024 (tp30) REVERT: B 424 ASP cc_start: 0.7602 (p0) cc_final: 0.7287 (p0) REVERT: B 436 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8493 (mp) REVERT: B 460 LYS cc_start: 0.7596 (ptpp) cc_final: 0.6848 (pptt) REVERT: B 490 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7960 (mmtm) REVERT: D 10 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 135 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7670 (tt0) REVERT: D 137 ASN cc_start: 0.8579 (m-40) cc_final: 0.8227 (t0) REVERT: D 199 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8047 (ttmm) REVERT: D 301 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5740 (mmm160) REVERT: D 377 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7440 (mp0) REVERT: D 385 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: D 397 MET cc_start: 0.8830 (tmm) cc_final: 0.8594 (tmm) REVERT: D 424 ASP cc_start: 0.7596 (p0) cc_final: 0.7213 (p0) REVERT: D 460 LYS cc_start: 0.7348 (ptpp) cc_final: 0.6619 (pptt) REVERT: D 490 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7695 (mmtm) REVERT: F 10 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8244 (tp) REVERT: F 54 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7455 (ttp-110) REVERT: F 135 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7723 (tt0) REVERT: F 137 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8193 (t0) REVERT: F 192 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (t0) REVERT: F 199 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8050 (ttmm) REVERT: F 301 ARG cc_start: 0.6431 (mpt180) cc_final: 0.5992 (mmm160) REVERT: F 304 ASP cc_start: 0.7406 (p0) cc_final: 0.7120 (p0) REVERT: F 424 ASP cc_start: 0.7560 (p0) cc_final: 0.7205 (p0) REVERT: F 427 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: F 460 LYS cc_start: 0.7539 (ptpp) cc_final: 0.6700 (pptt) REVERT: F 490 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7633 (mmtt) REVERT: H 10 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8566 (tp) REVERT: H 58 GLN cc_start: 0.7816 (pt0) cc_final: 0.7527 (pt0) REVERT: H 70 TYR cc_start: 0.8502 (p90) cc_final: 0.8251 (p90) REVERT: H 126 GLU cc_start: 0.7512 (pt0) cc_final: 0.7147 (pt0) REVERT: H 137 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8213 (t0) REVERT: H 159 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8116 (p) REVERT: H 199 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8116 (ttmm) REVERT: H 301 ARG cc_start: 0.6441 (mpt180) cc_final: 0.6056 (mmm160) REVERT: H 348 GLU cc_start: 0.7708 (pt0) cc_final: 0.7278 (tm-30) REVERT: H 385 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: H 386 GLU cc_start: 0.7308 (tp30) cc_final: 0.7037 (tp30) REVERT: H 420 ASP cc_start: 0.8653 (m-30) cc_final: 0.8333 (m-30) REVERT: H 436 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (mp) REVERT: H 460 LYS cc_start: 0.7443 (ptpp) cc_final: 0.6601 (pptt) REVERT: K 10 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8574 (tp) REVERT: K 54 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7499 (ttp-110) REVERT: K 58 GLN cc_start: 0.7826 (pt0) cc_final: 0.7526 (pt0) REVERT: K 69 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: K 70 TYR cc_start: 0.8501 (p90) cc_final: 0.8213 (p90) REVERT: K 159 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8165 (p) REVERT: K 199 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8120 (ttmm) REVERT: K 301 ARG cc_start: 0.6570 (mpt180) cc_final: 0.6099 (mmm160) REVERT: K 309 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7882 (mmtm) REVERT: K 348 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: K 367 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8488 (ptm) REVERT: K 385 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6807 (p0) REVERT: K 420 ASP cc_start: 0.8650 (m-30) cc_final: 0.8321 (m-30) REVERT: K 436 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8569 (mp) REVERT: K 460 LYS cc_start: 0.7550 (ptpp) cc_final: 0.6725 (pptt) outliers start: 83 outliers final: 37 residues processed: 419 average time/residue: 0.5643 time to fit residues: 273.7792 Evaluate side-chains 416 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 385 ASP Chi-restraints excluded: chain A residue 436 LEU 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 377 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 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 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 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 382 ASP Chi-restraints excluded: chain F residue 427 GLU 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 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 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 H residue 444 SER 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 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 367 MET 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: 4.9990 chunk 42 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 248 optimal weight: 0.4980 chunk 265 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN B 328 GLN D 58 GLN 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** K 401 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127191 restraints weight = 22819.440| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.13 r_work: 0.3327 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25536 Z= 0.156 Angle : 0.557 8.070 34668 Z= 0.306 Chirality : 0.045 0.311 3744 Planarity : 0.005 0.050 4350 Dihedral : 14.818 178.652 3617 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 2.99 % Allowed : 17.85 % Favored : 79.17 % 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: 1.16 (0.16), residues: 2940 helix: 1.57 (0.12), residues: 1740 sheet: -0.86 (0.36), residues: 192 loop : -0.21 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 142 TYR 0.020 0.002 TYR H 475 PHE 0.013 0.001 PHE K 144 TRP 0.011 0.002 TRP F 363 HIS 0.003 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (25536) covalent geometry : angle 0.55684 / 0.31 (34668) hydrogen bonds : bond 0.04654 / 3.15 ( 1261) hydrogen bonds : angle 4.52215 / 3.24 ( 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 439 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 358 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7289 (ttt-90) REVERT: A 58 GLN cc_start: 0.7918 (pt0) cc_final: 0.7588 (mm110) REVERT: A 97 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: A 135 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7755 (tt0) REVERT: A 137 ASN cc_start: 0.8499 (m-40) cc_final: 0.8252 (t0) REVERT: A 192 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7908 (t0) REVERT: A 199 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8135 (ttmm) REVERT: A 227 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7575 (tpt-90) REVERT: A 301 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5971 (mmm160) REVERT: A 377 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: A 385 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: A 386 GLU cc_start: 0.7178 (tp30) cc_final: 0.6945 (tm-30) REVERT: A 424 ASP cc_start: 0.7261 (p0) cc_final: 0.6821 (p0) REVERT: A 436 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 460 LYS cc_start: 0.7585 (ptpp) cc_final: 0.6834 (pptt) REVERT: A 490 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7973 (mmtm) REVERT: B 54 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7304 (ttt-90) REVERT: B 58 GLN cc_start: 0.7956 (pt0) cc_final: 0.7611 (mm110) REVERT: B 135 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7803 (tt0) REVERT: B 137 ASN cc_start: 0.8482 (m-40) cc_final: 0.8182 (t0) REVERT: B 192 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7915 (t0) REVERT: B 199 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8107 (ttmm) REVERT: B 227 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7553 (tpt-90) REVERT: B 301 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5941 (mmm160) REVERT: B 349 TYR cc_start: 0.7332 (m-80) cc_final: 0.7057 (m-80) REVERT: B 377 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 386 GLU cc_start: 0.7333 (tp30) cc_final: 0.7105 (tp30) REVERT: B 424 ASP cc_start: 0.7612 (p0) cc_final: 0.7284 (p0) REVERT: B 436 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8495 (mp) REVERT: B 460 LYS cc_start: 0.7606 (ptpp) cc_final: 0.6860 (pptt) REVERT: B 490 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7965 (mmtm) REVERT: D 10 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8230 (tp) REVERT: D 135 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7677 (tt0) REVERT: D 137 ASN cc_start: 0.8586 (m-40) cc_final: 0.8236 (t0) REVERT: D 199 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8077 (ttmm) REVERT: D 301 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5800 (mmm160) REVERT: D 377 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7557 (mp0) REVERT: D 385 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6436 (m-30) REVERT: D 393 GLU cc_start: 0.8317 (tp30) cc_final: 0.8035 (tp30) REVERT: D 397 MET cc_start: 0.8845 (tmm) cc_final: 0.8592 (tmm) REVERT: D 424 ASP cc_start: 0.7685 (p0) cc_final: 0.7307 (p0) REVERT: D 460 LYS cc_start: 0.7359 (ptpp) cc_final: 0.6618 (pptt) REVERT: D 490 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7707 (mmtm) REVERT: F 10 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8221 (tp) REVERT: F 54 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7450 (ttp-110) REVERT: F 135 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7688 (tt0) REVERT: F 137 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8195 (t0) REVERT: F 192 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7996 (t0) REVERT: F 199 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8096 (ttmm) REVERT: F 301 ARG cc_start: 0.6469 (mpt180) cc_final: 0.6050 (mmm160) REVERT: F 304 ASP cc_start: 0.7345 (p0) cc_final: 0.7066 (p0) REVERT: F 424 ASP cc_start: 0.7578 (p0) cc_final: 0.7226 (p0) REVERT: F 427 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: F 460 LYS cc_start: 0.7528 (ptpp) cc_final: 0.6690 (pptt) REVERT: F 490 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7698 (mmtt) REVERT: H 10 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8602 (tp) REVERT: H 58 GLN cc_start: 0.7817 (pt0) cc_final: 0.7533 (pt0) REVERT: H 69 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7871 (mtt180) REVERT: H 70 TYR cc_start: 0.8543 (p90) cc_final: 0.8251 (p90) REVERT: H 126 GLU cc_start: 0.7497 (pt0) cc_final: 0.7155 (pt0) REVERT: H 137 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8167 (t0) REVERT: H 159 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8143 (p) REVERT: H 199 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8171 (ttmm) REVERT: H 301 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6074 (mmm160) REVERT: H 348 GLU cc_start: 0.7675 (pt0) cc_final: 0.7243 (tm-30) REVERT: H 385 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: H 386 GLU cc_start: 0.7304 (tp30) cc_final: 0.7031 (tp30) REVERT: H 420 ASP cc_start: 0.8656 (m-30) cc_final: 0.8331 (m-30) REVERT: H 436 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8576 (mp) REVERT: H 460 LYS cc_start: 0.7452 (ptpp) cc_final: 0.6602 (pptt) REVERT: K 10 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8622 (tp) REVERT: K 54 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7519 (ttp-110) REVERT: K 58 GLN cc_start: 0.7813 (pt0) cc_final: 0.7505 (pt0) REVERT: K 69 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7955 (mtp85) REVERT: K 70 TYR cc_start: 0.8548 (p90) cc_final: 0.8246 (p90) REVERT: K 159 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8180 (p) REVERT: K 199 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8167 (ttmm) REVERT: K 301 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6098 (mmm160) REVERT: K 309 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7928 (mmtm) REVERT: K 348 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: K 367 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8415 (ptm) REVERT: K 385 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6464 (m-30) REVERT: K 420 ASP cc_start: 0.8657 (m-30) cc_final: 0.8328 (m-30) REVERT: K 436 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8590 (mp) REVERT: K 460 LYS cc_start: 0.7581 (ptpp) cc_final: 0.6750 (pptt) outliers start: 81 outliers final: 35 residues processed: 411 average time/residue: 0.5826 time to fit residues: 276.2885 Evaluate side-chains 421 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 301 ARG Chi-restraints excluded: chain A residue 307 LEU 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 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 377 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 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 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 157 ILE 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 427 GLU 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 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 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 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 301 ARG Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 367 MET 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: 4.9990 chunk 188 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 328 GLN D 58 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127099 restraints weight = 22822.839| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.13 r_work: 0.3326 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3266 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= 0.160 Angle : 0.568 9.174 34668 Z= 0.311 Chirality : 0.045 0.306 3744 Planarity : 0.005 0.050 4350 Dihedral : 14.806 178.516 3617 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 2.80 % Allowed : 18.03 % Favored : 79.17 % 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: 1.16 (0.16), residues: 2940 helix: 1.55 (0.12), residues: 1746 sheet: -0.86 (0.36), residues: 192 loop : -0.17 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 142 TYR 0.020 0.002 TYR K 475 PHE 0.013 0.002 PHE B 144 TRP 0.011 0.002 TRP F 363 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (25536) covalent geometry : angle 0.56755 / 0.31 (34668) hydrogen bonds : bond 0.04664 / 3.16 ( 1261) hydrogen bonds : angle 4.52628 / 3.24 ( 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 433 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 357 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7281 (ttt-90) REVERT: A 58 GLN cc_start: 0.7917 (pt0) cc_final: 0.7594 (mm110) REVERT: A 97 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 135 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7769 (tt0) REVERT: A 137 ASN cc_start: 0.8502 (m-40) cc_final: 0.8252 (t0) REVERT: A 192 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7902 (t0) REVERT: A 199 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8099 (ttmm) REVERT: A 227 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7574 (tpt-90) REVERT: A 301 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5888 (mmm160) REVERT: A 377 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7648 (mp0) REVERT: A 385 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: A 386 GLU cc_start: 0.7175 (tp30) cc_final: 0.6946 (tm-30) REVERT: A 424 ASP cc_start: 0.7257 (p0) cc_final: 0.6815 (p0) REVERT: A 436 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 460 LYS cc_start: 0.7574 (ptpp) cc_final: 0.6836 (pptt) REVERT: A 490 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7968 (mmtm) REVERT: B 54 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7286 (ttt-90) REVERT: B 58 GLN cc_start: 0.7959 (pt0) cc_final: 0.7613 (mm110) REVERT: B 135 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7789 (tt0) REVERT: B 137 ASN cc_start: 0.8468 (m-40) cc_final: 0.8204 (t0) REVERT: B 192 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7924 (t0) REVERT: B 199 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8085 (ttmm) REVERT: B 227 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7554 (tpt-90) REVERT: B 301 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5880 (mmm160) REVERT: B 349 TYR cc_start: 0.7316 (m-80) cc_final: 0.7054 (m-80) REVERT: B 377 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7711 (mp0) REVERT: B 386 GLU cc_start: 0.7337 (tp30) cc_final: 0.7061 (tp30) REVERT: B 424 ASP cc_start: 0.7587 (p0) cc_final: 0.7258 (p0) REVERT: B 436 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 460 LYS cc_start: 0.7597 (ptpp) cc_final: 0.6858 (pptt) REVERT: B 490 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7967 (mmtm) REVERT: D 10 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8231 (tp) REVERT: D 135 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7677 (tt0) REVERT: D 137 ASN cc_start: 0.8582 (m-40) cc_final: 0.8234 (t0) REVERT: D 192 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7987 (t0) REVERT: D 199 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8068 (ttmm) REVERT: D 301 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5844 (mmm160) REVERT: D 377 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7507 (mp0) REVERT: D 385 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: D 393 GLU cc_start: 0.8309 (tp30) cc_final: 0.8065 (tp30) REVERT: D 397 MET cc_start: 0.8840 (tmm) cc_final: 0.8584 (tmm) REVERT: D 424 ASP cc_start: 0.7675 (p0) cc_final: 0.7292 (p0) REVERT: D 490 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7704 (mmtm) REVERT: F 10 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8217 (tp) REVERT: F 54 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7442 (ttp-110) REVERT: F 135 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7688 (tt0) REVERT: F 137 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8199 (t0) REVERT: F 192 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7987 (t0) REVERT: F 199 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8096 (ttmm) REVERT: F 301 ARG cc_start: 0.6455 (mpt180) cc_final: 0.6025 (mmm160) REVERT: F 304 ASP cc_start: 0.7347 (p0) cc_final: 0.7075 (p0) REVERT: F 382 ASP cc_start: 0.6029 (OUTLIER) cc_final: 0.5790 (m-30) REVERT: F 424 ASP cc_start: 0.7651 (p0) cc_final: 0.7298 (p0) REVERT: F 427 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: F 460 LYS cc_start: 0.7514 (ptpp) cc_final: 0.6677 (pptt) REVERT: F 490 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7704 (mmtt) REVERT: H 10 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8592 (tp) REVERT: H 58 GLN cc_start: 0.7811 (pt0) cc_final: 0.7527 (pt0) REVERT: H 69 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7928 (mtt180) REVERT: H 70 TYR cc_start: 0.8554 (p90) cc_final: 0.8226 (p90) REVERT: H 126 GLU cc_start: 0.7531 (pt0) cc_final: 0.7163 (pt0) REVERT: H 137 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8200 (t0) REVERT: H 159 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8140 (p) REVERT: H 199 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8150 (ttmm) REVERT: H 301 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.6069 (mmm160) REVERT: H 348 GLU cc_start: 0.7684 (pt0) cc_final: 0.7241 (tm-30) REVERT: H 385 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: H 386 GLU cc_start: 0.7309 (tp30) cc_final: 0.7031 (tp30) REVERT: H 420 ASP cc_start: 0.8649 (m-30) cc_final: 0.8326 (m-30) REVERT: H 436 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8565 (mp) REVERT: H 460 LYS cc_start: 0.7454 (ptpp) cc_final: 0.6672 (pptt) REVERT: K 10 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8616 (tp) REVERT: K 54 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7497 (ttp-110) REVERT: K 58 GLN cc_start: 0.7807 (pt0) cc_final: 0.7525 (pt0) REVERT: K 69 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7959 (mtp85) REVERT: K 70 TYR cc_start: 0.8559 (p90) cc_final: 0.8271 (p90) REVERT: K 159 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8149 (p) REVERT: K 199 LYS cc_start: 0.8370 (ttpp) cc_final: 0.8155 (ttmm) REVERT: K 301 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6100 (mmm160) REVERT: K 309 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7933 (mmtm) REVERT: K 348 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: K 367 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8410 (ptm) REVERT: K 385 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6461 (m-30) REVERT: K 420 ASP cc_start: 0.8648 (m-30) cc_final: 0.8314 (m-30) REVERT: K 436 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8577 (mp) REVERT: K 460 LYS cc_start: 0.7545 (ptpp) cc_final: 0.6736 (pptt) outliers start: 76 outliers final: 36 residues processed: 405 average time/residue: 0.5919 time to fit residues: 277.0891 Evaluate side-chains 417 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 350 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 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 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 436 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 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 301 ARG 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 157 ILE 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 382 ASP Chi-restraints excluded: chain F residue 427 GLU 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 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 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 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 348 GLU Chi-restraints excluded: chain K residue 367 MET 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 112 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN D 58 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128877 restraints weight = 22872.290| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.14 r_work: 0.3350 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25536 Z= 0.133 Angle : 0.539 9.064 34668 Z= 0.295 Chirality : 0.044 0.308 3744 Planarity : 0.004 0.048 4350 Dihedral : 14.663 178.192 3617 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.03 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 18.25 % 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: 1.25 (0.16), residues: 2940 helix: 1.67 (0.12), residues: 1740 sheet: -0.86 (0.36), residues: 192 loop : -0.22 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 142 TYR 0.022 0.002 TYR B 11 PHE 0.010 0.001 PHE B 144 TRP 0.011 0.001 TRP F 363 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (25536) covalent geometry : angle 0.53915 / 0.29 (34668) hydrogen bonds : bond 0.04315 / 2.91 ( 1261) hydrogen bonds : angle 4.46049 / 3.19 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8385.30 seconds wall clock time: 143 minutes 50.46 seconds (8630.46 seconds total)