Starting phenix.real_space_refine on Fri Feb 6 12:33:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdp_64991/02_2026/9vdp_64991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdp_64991/02_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_64991/02_2026/9vdp_64991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdp_64991/02_2026/9vdp_64991.map" model { file = "/net/cci-nas-00/data/ceres_data/9vdp_64991/02_2026/9vdp_64991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdp_64991/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 3.39, 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: 2.09 Conformation dependent library (CDL) restraints added in 950.0 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: 3.04 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: 5.16 Time building geometry restraints manager: 2.73 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 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.53e+00 bond pdb=" C3' DC E 5 " pdb=" O3' DC E 5 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.53e+00 bond pdb=" C3' DC I 5 " pdb=" O3' DC I 5 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.43e+00 bond pdb=" C3' DC G 5 " pdb=" O3' DC G 5 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.43e+00 bond pdb=" C3' DC J 5 " pdb=" O3' DC J 5 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.42e+00 ... (remaining 25531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 33858 2.02 - 4.04: 678 4.04 - 6.06: 90 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 - 0.037: 2297 0.037 - 0.074: 1006 0.074 - 0.110: 331 0.110 - 0.147: 76 0.147 - 0.184: 34 Chirality restraints: 3744 Sorted by residual: chirality pdb=" CA ASP F 385 " pdb=" N ASP F 385 " pdb=" C ASP F 385 " pdb=" CB ASP F 385 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA ASP B 385 " pdb=" N ASP B 385 " pdb=" C ASP B 385 " pdb=" CB ASP B 385 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA ASP H 385 " pdb=" N ASP H 385 " pdb=" C ASP H 385 " pdb=" CB ASP H 385 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 ... (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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.710 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 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 0.064 25536 Z= 0.175 Angle : 0.714 10.101 34668 Z= 0.398 Chirality : 0.048 0.184 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 covalent geometry : bond 0.00391 (25536) covalent geometry : angle 0.71416 (34668) hydrogen bonds : bond 0.14232 ( 1261) hydrogen bonds : angle 6.68494 ( 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 : 0.954 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: 0.5629 time to fit residues: 396.4578 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 : 0.934 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 95 ASN A 201 ASN A 295 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN D 58 GLN D 95 ASN D 201 ASN D 295 ASN F 58 GLN F 95 ASN F 201 ASN F 295 ASN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 ASN H 295 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 ASN ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 ASN K 295 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130110 restraints weight = 22962.695| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.15 r_work: 0.3362 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25536 Z= 0.185 Angle : 0.596 7.861 34668 Z= 0.330 Chirality : 0.045 0.154 3744 Planarity : 0.005 0.063 4350 Dihedral : 15.219 179.242 3679 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 4.65 % Allowed : 16.59 % Favored : 78.76 % 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: 0.44 (0.15), residues: 2940 helix: 0.83 (0.12), residues: 1728 sheet: -0.14 (0.36), residues: 192 loop : -0.39 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 142 TYR 0.025 0.002 TYR K 475 PHE 0.014 0.002 PHE D 144 TRP 0.009 0.002 TRP F 363 HIS 0.006 0.001 HIS H 91 Details of bonding type rmsd covalent geometry : bond 0.00397 (25536) covalent geometry : angle 0.59608 (34668) hydrogen bonds : bond 0.05282 ( 1261) hydrogen bonds : angle 4.87079 ( 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 584 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 458 time to evaluate : 0.988 Fit side-chains REVERT: A 54 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7281 (ttt-90) REVERT: A 135 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7651 (tt0) REVERT: A 137 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8182 (t0) REVERT: A 199 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8094 (ttmm) REVERT: A 227 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7581 (tpt-90) REVERT: A 301 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5972 (mmm160) REVERT: A 377 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7394 (mp0) REVERT: A 385 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6917 (p0) REVERT: A 386 GLU cc_start: 0.7082 (tp30) cc_final: 0.6748 (tp30) REVERT: A 427 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: A 436 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 452 ASN cc_start: 0.8281 (t0) cc_final: 0.8058 (t0) REVERT: A 457 ASP cc_start: 0.8157 (m-30) cc_final: 0.7953 (m-30) REVERT: A 460 LYS cc_start: 0.7622 (ptpp) cc_final: 0.6897 (pptt) REVERT: A 462 ASP cc_start: 0.7263 (t0) cc_final: 0.7013 (t70) REVERT: A 490 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7820 (mmtm) REVERT: B 54 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7188 (ttt-90) REVERT: B 66 TYR cc_start: 0.8864 (m-80) cc_final: 0.8651 (m-80) REVERT: B 69 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: B 135 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7657 (tt0) REVERT: B 137 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8139 (t0) REVERT: B 199 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8094 (ttmm) REVERT: B 226 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8307 (tttp) REVERT: B 227 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7591 (tpt-90) REVERT: B 301 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6167 (mmm160) REVERT: B 377 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7386 (mp0) REVERT: B 385 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6947 (p0) REVERT: B 386 GLU cc_start: 0.6980 (tp30) cc_final: 0.6621 (tp30) REVERT: B 423 ASP cc_start: 0.7153 (m-30) cc_final: 0.6466 (t70) REVERT: B 427 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: B 436 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8477 (mp) REVERT: B 457 ASP cc_start: 0.8144 (m-30) cc_final: 0.7928 (m-30) REVERT: B 460 LYS cc_start: 0.7643 (ptpp) cc_final: 0.6926 (pptt) REVERT: B 462 ASP cc_start: 0.7364 (t0) cc_final: 0.6957 (m-30) REVERT: B 490 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7794 (mmtm) REVERT: D 10 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8126 (tp) REVERT: D 54 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7439 (ttp-110) REVERT: D 137 ASN cc_start: 0.8560 (m-40) cc_final: 0.8187 (t0) REVERT: D 149 ASP cc_start: 0.8004 (m-30) cc_final: 0.7758 (t70) REVERT: D 199 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8144 (ttmm) REVERT: D 227 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7627 (tpt-90) REVERT: D 301 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5585 (mmm160) REVERT: D 348 GLU cc_start: 0.7676 (pt0) cc_final: 0.7447 (tm-30) REVERT: D 349 TYR cc_start: 0.7255 (m-80) cc_final: 0.7007 (m-80) REVERT: D 367 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8514 (ptm) REVERT: D 377 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7335 (mp0) REVERT: D 385 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6688 (p0) REVERT: D 397 MET cc_start: 0.8761 (tmm) cc_final: 0.8517 (tmm) REVERT: D 402 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7838 (mptp) REVERT: D 407 MET cc_start: 0.8851 (tpp) cc_final: 0.8616 (tpp) REVERT: D 427 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: D 462 ASP cc_start: 0.7316 (t0) cc_final: 0.7100 (t70) REVERT: D 490 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7773 (mmtm) REVERT: F 10 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8188 (tp) REVERT: F 54 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7354 (ttt-90) REVERT: F 125 TYR cc_start: 0.7671 (t80) cc_final: 0.7387 (t80) REVERT: F 135 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7807 (mt-10) REVERT: F 137 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8142 (t0) REVERT: F 155 THR cc_start: 0.8200 (t) cc_final: 0.7906 (p) REVERT: F 199 LYS cc_start: 0.8340 (ttpp) cc_final: 0.8020 (ttmm) REVERT: F 227 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7596 (tpt-90) REVERT: F 301 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6076 (mmm160) REVERT: F 348 GLU cc_start: 0.7538 (pt0) cc_final: 0.7149 (tm-30) REVERT: F 349 TYR cc_start: 0.7065 (m-80) cc_final: 0.6838 (m-10) REVERT: F 367 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8471 (ptm) REVERT: F 375 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8181 (mt) REVERT: F 397 MET cc_start: 0.8859 (tmm) cc_final: 0.8653 (tmm) REVERT: F 402 LYS cc_start: 0.8117 (mmtp) cc_final: 0.7904 (mptp) REVERT: F 423 ASP cc_start: 0.7056 (m-30) cc_final: 0.6518 (t70) REVERT: F 427 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: F 449 GLU cc_start: 0.7392 (pp20) cc_final: 0.7149 (tm-30) REVERT: F 460 LYS cc_start: 0.7620 (ptpp) cc_final: 0.6773 (pptt) REVERT: F 490 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7598 (mmtt) REVERT: H 54 ARG cc_start: 0.7406 (ttp80) cc_final: 0.7205 (ttp-110) REVERT: H 58 GLN cc_start: 0.7909 (pt0) cc_final: 0.7643 (pt0) REVERT: H 126 GLU cc_start: 0.7462 (pt0) cc_final: 0.7241 (pt0) REVERT: H 137 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8103 (t0) REVERT: H 199 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8130 (ttmm) REVERT: H 301 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6054 (mmm160) REVERT: H 304 ASP cc_start: 0.7117 (p0) cc_final: 0.6901 (p0) REVERT: H 348 GLU cc_start: 0.7666 (pt0) cc_final: 0.7340 (tm-30) REVERT: H 367 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8569 (ptm) REVERT: H 375 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8623 (mt) REVERT: H 385 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6957 (p0) REVERT: H 402 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7909 (mptp) REVERT: H 420 ASP cc_start: 0.8690 (m-30) cc_final: 0.8363 (m-30) REVERT: H 427 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: H 460 LYS cc_start: 0.7536 (ptpp) cc_final: 0.6811 (pptt) REVERT: H 490 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7282 (mttm) REVERT: K 54 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7410 (ttp-110) REVERT: K 58 GLN cc_start: 0.7895 (pt0) cc_final: 0.7643 (pt0) REVERT: K 137 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8162 (t0) REVERT: K 199 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8149 (ttmm) REVERT: K 301 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6130 (mmm160) REVERT: K 348 GLU cc_start: 0.7518 (pt0) cc_final: 0.7082 (tm-30) REVERT: K 349 TYR cc_start: 0.7254 (m-80) cc_final: 0.7034 (m-80) REVERT: K 367 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8579 (ptm) REVERT: K 375 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8401 (mt) REVERT: K 420 ASP cc_start: 0.8689 (m-30) cc_final: 0.8354 (m-30) REVERT: K 423 ASP cc_start: 0.7127 (m-30) cc_final: 0.6864 (m-30) REVERT: K 427 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: K 460 LYS cc_start: 0.7674 (ptpp) cc_final: 0.6986 (pptt) REVERT: K 490 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7859 (mmtt) outliers start: 126 outliers final: 35 residues processed: 543 average time/residue: 0.6459 time to fit residues: 402.4708 Evaluate side-chains 444 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 377 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 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 174 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 367 MET 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 367 MET 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 137 ASN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 184 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 233 optimal weight: 0.6980 chunk 272 optimal weight: 0.5980 chunk 243 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 401 ASN B 58 GLN B 201 ASN B 378 HIS B 401 ASN D 58 GLN F 58 GLN F 378 HIS H 58 GLN H 201 ASN K 58 GLN K 201 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131380 restraints weight = 23149.646| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.16 r_work: 0.3383 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2365 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= 0.129 Angle : 0.514 7.777 34668 Z= 0.282 Chirality : 0.042 0.189 3744 Planarity : 0.004 0.048 4350 Dihedral : 15.036 179.396 3644 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.03 % Favored : 96.77 % Rotamer: Outliers : 3.36 % Allowed : 17.77 % Favored : 78.87 % 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: 0.96 (0.15), residues: 2940 helix: 1.34 (0.12), residues: 1740 sheet: -0.48 (0.35), residues: 192 loop : -0.27 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 69 TYR 0.017 0.002 TYR H 475 PHE 0.009 0.001 PHE B 144 TRP 0.008 0.001 TRP F 363 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00275 (25536) covalent geometry : angle 0.51425 (34668) hydrogen bonds : bond 0.04507 ( 1261) hydrogen bonds : angle 4.58164 ( 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 482 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 391 time to evaluate : 0.933 Fit side-chains REVERT: A 54 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7285 (ttt-90) REVERT: A 123 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: A 135 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7807 (tt0) REVERT: A 137 ASN cc_start: 0.8441 (m-40) cc_final: 0.8184 (t0) REVERT: A 199 LYS cc_start: 0.8310 (ttpp) cc_final: 0.8053 (ttmm) REVERT: A 227 ARG cc_start: 0.7868 (mmm160) cc_final: 0.7568 (tpt-90) REVERT: A 301 ARG cc_start: 0.6371 (mpt180) cc_final: 0.5902 (mmm160) REVERT: A 377 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7495 (mp0) REVERT: A 386 GLU cc_start: 0.7059 (tp30) cc_final: 0.6756 (tp30) REVERT: A 427 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: A 436 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 457 ASP cc_start: 0.8155 (m-30) cc_final: 0.7938 (m-30) REVERT: A 460 LYS cc_start: 0.7564 (ptpp) cc_final: 0.6880 (pptt) REVERT: A 462 ASP cc_start: 0.7290 (t0) cc_final: 0.7049 (t70) REVERT: B 54 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7155 (ttt-90) REVERT: B 123 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: B 135 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7739 (tt0) REVERT: B 137 ASN cc_start: 0.8377 (m-40) cc_final: 0.8137 (t0) REVERT: B 199 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8000 (ttmm) REVERT: B 227 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7613 (tpt-90) REVERT: B 301 ARG cc_start: 0.6569 (mpt180) cc_final: 0.5983 (mmm160) REVERT: B 349 TYR cc_start: 0.7241 (m-80) cc_final: 0.6837 (m-80) REVERT: B 377 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7497 (mp0) REVERT: B 386 GLU cc_start: 0.6986 (tp30) cc_final: 0.6653 (tp30) REVERT: B 427 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: B 436 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8495 (mp) REVERT: B 457 ASP cc_start: 0.8165 (m-30) cc_final: 0.7934 (m-30) REVERT: B 460 LYS cc_start: 0.7586 (ptpp) cc_final: 0.6875 (pptt) REVERT: B 462 ASP cc_start: 0.7278 (t0) cc_final: 0.7034 (t70) REVERT: B 490 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7763 (mmtm) REVERT: D 10 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8149 (tp) REVERT: D 68 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8004 (p) REVERT: D 135 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7741 (tt0) REVERT: D 137 ASN cc_start: 0.8528 (m-40) cc_final: 0.8211 (t0) REVERT: D 149 ASP cc_start: 0.7956 (m-30) cc_final: 0.7711 (t70) REVERT: D 199 LYS cc_start: 0.8268 (ttpp) cc_final: 0.8042 (ttmm) REVERT: D 227 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7613 (tpt-90) REVERT: D 349 TYR cc_start: 0.7241 (m-80) cc_final: 0.6995 (m-80) REVERT: D 367 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (ptm) REVERT: D 377 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7496 (mp0) REVERT: D 385 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6491 (m-30) REVERT: D 397 MET cc_start: 0.8827 (tmm) cc_final: 0.8544 (tmm) REVERT: D 402 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7767 (mptp) REVERT: D 424 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7125 (p0) REVERT: D 462 ASP cc_start: 0.7226 (t0) cc_final: 0.7016 (t70) REVERT: D 490 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7704 (mmtm) REVERT: F 10 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8165 (tp) REVERT: F 54 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7356 (ttt-90) REVERT: F 125 TYR cc_start: 0.7673 (t80) cc_final: 0.7357 (t80) REVERT: F 135 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7787 (tt0) REVERT: F 137 ASN cc_start: 0.8475 (m-40) cc_final: 0.8158 (t0) REVERT: F 149 ASP cc_start: 0.7967 (m-30) cc_final: 0.7764 (m-30) REVERT: F 155 THR cc_start: 0.8113 (t) cc_final: 0.7911 (p) REVERT: F 199 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7913 (ttmm) REVERT: F 227 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7602 (tpt-90) REVERT: F 348 GLU cc_start: 0.7541 (pt0) cc_final: 0.7213 (tm-30) REVERT: F 349 TYR cc_start: 0.7079 (m-80) cc_final: 0.6862 (m-10) REVERT: F 367 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8464 (ptm) REVERT: F 397 MET cc_start: 0.8849 (tmm) cc_final: 0.8639 (tmm) REVERT: F 402 LYS cc_start: 0.8036 (mmtp) cc_final: 0.7832 (mptp) REVERT: F 427 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: F 460 LYS cc_start: 0.7571 (ptpp) cc_final: 0.6679 (pptt) REVERT: F 490 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7576 (mmtm) REVERT: H 10 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8517 (tp) REVERT: H 54 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7263 (ttp-110) REVERT: H 58 GLN cc_start: 0.7856 (pt0) cc_final: 0.7588 (pt0) REVERT: H 126 GLU cc_start: 0.7477 (pt0) cc_final: 0.7067 (pt0) REVERT: H 137 ASN cc_start: 0.8417 (m-40) cc_final: 0.8168 (t0) REVERT: H 199 LYS cc_start: 0.8282 (ttpp) cc_final: 0.8062 (ttmm) REVERT: H 301 ARG cc_start: 0.6406 (mpt180) cc_final: 0.5874 (mmm160) REVERT: H 348 GLU cc_start: 0.7626 (pt0) cc_final: 0.7296 (tm-30) REVERT: H 367 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (ptm) REVERT: H 385 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6808 (p0) REVERT: H 420 ASP cc_start: 0.8646 (m-30) cc_final: 0.8280 (m-30) REVERT: H 427 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: H 436 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8534 (mp) REVERT: H 460 LYS cc_start: 0.7480 (ptpp) cc_final: 0.6684 (pptt) REVERT: H 490 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7304 (mttm) REVERT: K 10 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8516 (tp) REVERT: K 58 GLN cc_start: 0.7817 (pt0) cc_final: 0.7552 (pt0) REVERT: K 69 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7917 (mtp85) REVERT: K 199 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8077 (ttmm) REVERT: K 301 ARG cc_start: 0.6588 (mpt180) cc_final: 0.6066 (mmm160) REVERT: K 348 GLU cc_start: 0.7550 (pt0) cc_final: 0.7076 (tm-30) REVERT: K 367 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8575 (ptm) REVERT: K 375 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8604 (mt) REVERT: K 385 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6801 (p0) REVERT: K 420 ASP cc_start: 0.8673 (m-30) cc_final: 0.8318 (m-30) REVERT: K 427 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: K 460 LYS cc_start: 0.7629 (ptpp) cc_final: 0.7000 (pptt) REVERT: K 490 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7877 (mmtt) outliers start: 91 outliers final: 25 residues processed: 455 average time/residue: 0.6309 time to fit residues: 331.5178 Evaluate side-chains 410 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 176 LEU 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 427 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 367 MET 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 294 VAL Chi-restraints excluded: chain F residue 367 MET 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 157 ILE Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 367 MET 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 68 THR Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 294 VAL 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: 0.9990 chunk 178 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 58 GLN D 58 GLN F 58 GLN F 378 HIS H 186 HIS H 353 GLN K 137 ASN K 353 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125298 restraints weight = 22819.866| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.14 r_work: 0.3301 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25536 Z= 0.212 Angle : 0.595 7.758 34668 Z= 0.327 Chirality : 0.046 0.197 3744 Planarity : 0.005 0.048 4350 Dihedral : 15.087 179.704 3623 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 4.50 % Allowed : 16.08 % Favored : 79.42 % 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: 0.90 (0.15), residues: 2940 helix: 1.30 (0.12), residues: 1752 sheet: -0.63 (0.36), residues: 192 loop : -0.28 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 142 TYR 0.025 0.002 TYR H 475 PHE 0.016 0.002 PHE D 144 TRP 0.010 0.002 TRP D 363 HIS 0.005 0.001 HIS F 9 Details of bonding type rmsd covalent geometry : bond 0.00471 (25536) covalent geometry : angle 0.59519 (34668) hydrogen bonds : bond 0.05321 ( 1261) hydrogen bonds : angle 4.66996 ( 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 506 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 384 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7277 (ttt-90) REVERT: A 58 GLN cc_start: 0.7924 (pt0) cc_final: 0.7539 (mm110) REVERT: A 135 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7843 (tt0) REVERT: A 137 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (t0) REVERT: A 199 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8193 (ttmm) REVERT: A 227 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7610 (tpt-90) REVERT: A 301 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6169 (mmm160) REVERT: A 328 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: A 377 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7655 (mp0) REVERT: A 386 GLU cc_start: 0.7242 (tp30) cc_final: 0.6890 (tp30) REVERT: A 427 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: A 436 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 460 LYS cc_start: 0.7622 (ptpp) cc_final: 0.6925 (pptt) REVERT: A 462 ASP cc_start: 0.7298 (t0) cc_final: 0.7061 (t70) REVERT: A 490 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8000 (mmtm) REVERT: B 54 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7269 (ttt-90) REVERT: B 97 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: B 135 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7884 (tt0) REVERT: B 137 ASN cc_start: 0.8516 (m-40) cc_final: 0.8247 (t0) REVERT: B 199 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8079 (ttmm) REVERT: B 227 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7547 (tpt-90) REVERT: B 301 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6170 (mmm160) REVERT: B 328 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: B 349 TYR cc_start: 0.7354 (m-80) cc_final: 0.7018 (m-80) REVERT: B 377 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7632 (mp0) REVERT: B 386 GLU cc_start: 0.7218 (tp30) cc_final: 0.6921 (tp30) REVERT: B 427 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: B 436 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8500 (mp) REVERT: B 457 ASP cc_start: 0.8350 (m-30) cc_final: 0.8142 (m-30) REVERT: B 460 LYS cc_start: 0.7635 (ptpp) cc_final: 0.6922 (pptt) REVERT: B 462 ASP cc_start: 0.7318 (t0) cc_final: 0.7094 (t70) REVERT: D 10 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8235 (tp) REVERT: D 135 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7678 (tt0) REVERT: D 137 ASN cc_start: 0.8561 (m-40) cc_final: 0.8212 (t0) REVERT: D 155 THR cc_start: 0.8284 (t) cc_final: 0.8052 (p) REVERT: D 199 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8194 (ttmm) REVERT: D 301 ARG cc_start: 0.6412 (mpt180) cc_final: 0.5880 (mmm160) REVERT: D 367 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8504 (ptm) REVERT: D 377 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7501 (mp0) REVERT: D 385 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6440 (m-30) REVERT: D 397 MET cc_start: 0.8901 (tmm) cc_final: 0.8640 (tmm) REVERT: D 402 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7921 (mptp) REVERT: D 424 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7170 (p0) REVERT: D 490 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7779 (mmtm) REVERT: F 10 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8233 (tp) REVERT: F 54 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7470 (ttp-110) REVERT: F 135 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7761 (tt0) REVERT: F 137 ASN cc_start: 0.8550 (m-40) cc_final: 0.8202 (t0) REVERT: F 199 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8156 (ttmm) REVERT: F 301 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.5996 (mmm160) REVERT: F 349 TYR cc_start: 0.7448 (m-80) cc_final: 0.7238 (m-10) REVERT: F 367 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8469 (ptm) REVERT: F 377 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7384 (mp0) REVERT: F 382 ASP cc_start: 0.6110 (OUTLIER) cc_final: 0.5893 (m-30) REVERT: F 393 GLU cc_start: 0.8353 (tp30) cc_final: 0.8125 (tp30) REVERT: F 397 MET cc_start: 0.8907 (tmm) cc_final: 0.8659 (tmm) REVERT: F 424 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7254 (p0) REVERT: F 427 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8008 (mm-30) REVERT: F 460 LYS cc_start: 0.7584 (ptpp) cc_final: 0.6693 (pptt) REVERT: F 490 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7836 (mmtt) REVERT: H 10 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8627 (tp) REVERT: H 54 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7370 (ttp-110) REVERT: H 58 GLN cc_start: 0.7892 (pt0) cc_final: 0.7594 (pt0) REVERT: H 69 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7983 (mtp85) REVERT: H 97 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: H 126 GLU cc_start: 0.7773 (pt0) cc_final: 0.7533 (pt0) REVERT: H 137 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (t0) REVERT: H 199 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8212 (ttmm) REVERT: H 301 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6088 (mmm160) REVERT: H 348 GLU cc_start: 0.7680 (pt0) cc_final: 0.7273 (tm-30) REVERT: H 385 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6878 (p0) REVERT: H 420 ASP cc_start: 0.8665 (m-30) cc_final: 0.8340 (m-30) REVERT: H 436 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8574 (mp) REVERT: H 449 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: H 460 LYS cc_start: 0.7553 (ptpp) cc_final: 0.6773 (pptt) REVERT: K 10 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8625 (tp) REVERT: K 58 GLN cc_start: 0.7901 (pt0) cc_final: 0.7579 (pt0) REVERT: K 69 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7995 (mtp85) REVERT: K 199 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8202 (ttmm) REVERT: K 301 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6209 (mmm160) REVERT: K 309 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8048 (mmtm) REVERT: K 348 GLU cc_start: 0.7620 (pt0) cc_final: 0.7155 (tm-30) REVERT: K 349 TYR cc_start: 0.7474 (m-80) cc_final: 0.7027 (m-10) REVERT: K 385 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6912 (p0) REVERT: K 420 ASP cc_start: 0.8658 (m-30) cc_final: 0.8348 (m-30) REVERT: K 427 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: K 436 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8585 (mp) REVERT: K 449 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: K 460 LYS cc_start: 0.7661 (ptpp) cc_final: 0.6927 (pptt) outliers start: 122 outliers final: 38 residues processed: 462 average time/residue: 0.6007 time to fit residues: 320.6682 Evaluate side-chains 429 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 328 GLN 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 97 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 328 GLN 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 307 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 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 367 MET Chi-restraints excluded: chain F residue 382 ASP 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 F residue 444 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 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 H residue 444 SER Chi-restraints excluded: chain H residue 449 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 68 optimal weight: 0.0870 chunk 282 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 237 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN D 58 GLN D 401 ASN F 58 GLN F 147 ASN H 170 ASN K 170 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130172 restraints weight = 22929.096| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.14 r_work: 0.3367 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2969 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= 0.124 Angle : 0.507 7.145 34668 Z= 0.279 Chirality : 0.041 0.184 3744 Planarity : 0.004 0.045 4350 Dihedral : 14.758 179.998 3621 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.14 % Rotamer: Outliers : 2.91 % Allowed : 17.70 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2940 helix: 1.61 (0.12), residues: 1740 sheet: -0.70 (0.36), residues: 192 loop : -0.30 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 69 TYR 0.015 0.001 TYR K 475 PHE 0.009 0.001 PHE B 144 TRP 0.009 0.001 TRP F 363 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00265 (25536) covalent geometry : angle 0.50733 (34668) hydrogen bonds : bond 0.04246 ( 1261) hydrogen bonds : angle 4.46773 ( 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 448 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 369 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7250 (ttt-90) REVERT: A 58 GLN cc_start: 0.7893 (pt0) cc_final: 0.7507 (mm110) REVERT: A 135 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7813 (tt0) REVERT: A 137 ASN cc_start: 0.8475 (m-40) cc_final: 0.8234 (t0) REVERT: A 199 LYS cc_start: 0.8295 (ttpp) cc_final: 0.8029 (ttmm) REVERT: A 227 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7539 (tpt-90) REVERT: A 301 ARG cc_start: 0.6343 (mpt180) cc_final: 0.5867 (mmm160) REVERT: A 377 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7580 (mp0) REVERT: A 386 GLU cc_start: 0.7227 (tp30) cc_final: 0.6847 (tp30) REVERT: A 436 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 460 LYS cc_start: 0.7556 (ptpp) cc_final: 0.6808 (pptt) REVERT: A 462 ASP cc_start: 0.7234 (t0) cc_final: 0.7012 (t70) REVERT: A 490 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7867 (mmtm) REVERT: B 54 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7207 (ttt-90) REVERT: B 58 GLN cc_start: 0.7909 (pt0) cc_final: 0.7525 (mm110) REVERT: B 135 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7885 (tt0) REVERT: B 137 ASN cc_start: 0.8437 (m-40) cc_final: 0.8196 (t0) REVERT: B 199 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7947 (ttmm) REVERT: B 227 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7552 (tpt-90) REVERT: B 301 ARG cc_start: 0.6400 (mpt180) cc_final: 0.5958 (mmm160) REVERT: B 349 TYR cc_start: 0.7305 (m-80) cc_final: 0.7001 (m-80) REVERT: B 377 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 386 GLU cc_start: 0.7192 (tp30) cc_final: 0.6977 (tp30) REVERT: B 427 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: B 436 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8484 (mp) REVERT: B 457 ASP cc_start: 0.8321 (m-30) cc_final: 0.8106 (m-30) REVERT: B 460 LYS cc_start: 0.7579 (ptpp) cc_final: 0.6813 (pptt) REVERT: B 462 ASP cc_start: 0.7293 (t0) cc_final: 0.7074 (t70) REVERT: D 10 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8239 (tp) REVERT: D 135 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7698 (tt0) REVERT: D 137 ASN cc_start: 0.8566 (m-40) cc_final: 0.8258 (t0) REVERT: D 186 HIS cc_start: 0.8724 (t-90) cc_final: 0.8512 (t-90) REVERT: D 199 LYS cc_start: 0.8261 (ttpp) cc_final: 0.8024 (ttmm) REVERT: D 301 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5755 (mmm160) REVERT: D 377 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7522 (mp0) REVERT: D 385 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: D 397 MET cc_start: 0.8886 (tmm) cc_final: 0.8588 (tmm) REVERT: D 402 LYS cc_start: 0.8064 (mmtp) cc_final: 0.7821 (mptp) REVERT: D 424 ASP cc_start: 0.7511 (p0) cc_final: 0.7149 (p0) REVERT: D 490 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7741 (mmtm) REVERT: F 10 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8240 (tp) REVERT: F 54 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7435 (ttp-110) REVERT: F 125 TYR cc_start: 0.7750 (t80) cc_final: 0.7398 (t80) REVERT: F 135 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7806 (tt0) REVERT: F 137 ASN cc_start: 0.8561 (m-40) cc_final: 0.8252 (t0) REVERT: F 199 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7992 (ttmm) REVERT: F 301 ARG cc_start: 0.6281 (mpt180) cc_final: 0.5818 (mmm160) REVERT: F 349 TYR cc_start: 0.7299 (m-80) cc_final: 0.7089 (m-10) REVERT: F 367 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8414 (ptm) REVERT: F 393 GLU cc_start: 0.8340 (tp30) cc_final: 0.8113 (tp30) REVERT: F 397 MET cc_start: 0.8908 (tmm) cc_final: 0.8631 (tmm) REVERT: F 424 ASP cc_start: 0.7552 (p0) cc_final: 0.7186 (p0) REVERT: F 427 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: F 460 LYS cc_start: 0.7463 (ptpp) cc_final: 0.6648 (pptt) REVERT: F 490 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7687 (mmtt) REVERT: H 10 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8510 (tp) REVERT: H 54 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7421 (ttp-110) REVERT: H 58 GLN cc_start: 0.7833 (pt0) cc_final: 0.7564 (pt0) REVERT: H 69 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (mtp85) REVERT: H 126 GLU cc_start: 0.7562 (pt0) cc_final: 0.7155 (pt0) REVERT: H 137 ASN cc_start: 0.8470 (m-40) cc_final: 0.8211 (t0) REVERT: H 199 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8099 (ttmm) REVERT: H 348 GLU cc_start: 0.7695 (pt0) cc_final: 0.7237 (tm-30) REVERT: H 385 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6685 (p0) REVERT: H 420 ASP cc_start: 0.8662 (m-30) cc_final: 0.8329 (m-30) REVERT: H 436 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8569 (mp) REVERT: H 460 LYS cc_start: 0.7505 (ptpp) cc_final: 0.6768 (pptt) REVERT: K 10 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8531 (tp) REVERT: K 58 GLN cc_start: 0.7823 (pt0) cc_final: 0.7516 (pt0) REVERT: K 69 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7894 (mtp85) REVERT: K 199 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8053 (ttmm) REVERT: K 301 ARG cc_start: 0.6525 (mpt180) cc_final: 0.6031 (mmm160) REVERT: K 328 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: K 348 GLU cc_start: 0.7626 (pt0) cc_final: 0.7120 (tm-30) REVERT: K 349 TYR cc_start: 0.7481 (m-80) cc_final: 0.7078 (m-10) REVERT: K 385 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6803 (p0) REVERT: K 397 MET cc_start: 0.8867 (tmm) cc_final: 0.8636 (tmm) REVERT: K 420 ASP cc_start: 0.8683 (m-30) cc_final: 0.8347 (m-30) REVERT: K 436 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8554 (mp) REVERT: K 460 LYS cc_start: 0.7549 (ptpp) cc_final: 0.6827 (pptt) outliers start: 79 outliers final: 25 residues processed: 422 average time/residue: 0.5949 time to fit residues: 289.9994 Evaluate side-chains 396 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 353 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER 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 436 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 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 275 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 301 ARG 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 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 367 MET 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 69 ARG Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 328 GLN Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 385 ASP Chi-restraints excluded: chain K residue 427 GLU Chi-restraints excluded: chain K residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN D 401 ASN F 58 GLN H 170 ASN K 170 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130149 restraints weight = 22984.691| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.14 r_work: 0.3367 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25536 Z= 0.128 Angle : 0.508 6.587 34668 Z= 0.279 Chirality : 0.041 0.186 3744 Planarity : 0.004 0.043 4350 Dihedral : 14.631 179.599 3618 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.96 % Favored : 96.84 % Rotamer: Outliers : 2.80 % Allowed : 17.92 % Favored : 79.28 % 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: 1.70 (0.12), residues: 1740 sheet: -0.81 (0.36), residues: 192 loop : -0.31 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 227 TYR 0.017 0.001 TYR K 475 PHE 0.010 0.001 PHE H 144 TRP 0.008 0.001 TRP F 363 HIS 0.002 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00278 (25536) covalent geometry : angle 0.50782 (34668) hydrogen bonds : bond 0.04275 ( 1261) hydrogen bonds : angle 4.38704 ( 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 441 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 365 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7241 (ttt-90) REVERT: A 58 GLN cc_start: 0.7906 (pt0) cc_final: 0.7525 (mm110) REVERT: A 135 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7844 (tt0) REVERT: A 137 ASN cc_start: 0.8432 (m-40) cc_final: 0.8212 (t0) REVERT: A 192 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7873 (t0) REVERT: A 199 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8093 (ttmm) REVERT: A 227 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7588 (tpt-90) REVERT: A 301 ARG cc_start: 0.6235 (mpt180) cc_final: 0.5834 (mmm160) REVERT: A 377 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7614 (mp0) REVERT: A 386 GLU cc_start: 0.7184 (tp30) cc_final: 0.6829 (tp30) REVERT: A 436 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 460 LYS cc_start: 0.7550 (ptpp) cc_final: 0.6797 (pptt) REVERT: A 490 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7852 (mmtm) REVERT: B 49 SER cc_start: 0.8750 (m) cc_final: 0.8536 (p) REVERT: B 54 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7235 (ttt-90) REVERT: B 58 GLN cc_start: 0.7867 (pt0) cc_final: 0.7528 (mm110) REVERT: B 135 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7858 (tt0) REVERT: B 137 ASN cc_start: 0.8434 (m-40) cc_final: 0.8191 (t0) REVERT: B 192 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 199 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8029 (ttmm) REVERT: B 227 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7592 (tpt-90) REVERT: B 301 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5870 (mmm160) REVERT: B 349 TYR cc_start: 0.7263 (m-80) cc_final: 0.6998 (m-80) REVERT: B 377 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7648 (mp0) REVERT: B 386 GLU cc_start: 0.7222 (tp30) cc_final: 0.6881 (tp30) REVERT: B 424 ASP cc_start: 0.7632 (p0) cc_final: 0.7345 (p0) REVERT: B 436 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8494 (mp) REVERT: B 457 ASP cc_start: 0.8324 (m-30) cc_final: 0.8095 (m-30) REVERT: B 460 LYS cc_start: 0.7578 (ptpp) cc_final: 0.6820 (pptt) REVERT: D 10 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8217 (tp) REVERT: D 135 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7735 (tt0) REVERT: D 137 ASN cc_start: 0.8582 (m-40) cc_final: 0.8232 (t0) REVERT: D 199 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8079 (ttmm) REVERT: D 301 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5712 (mmm160) REVERT: D 377 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7492 (mp0) REVERT: D 385 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6449 (m-30) REVERT: D 393 GLU cc_start: 0.8320 (tp30) cc_final: 0.8091 (tp30) REVERT: D 397 MET cc_start: 0.8842 (tmm) cc_final: 0.8570 (tmm) REVERT: D 402 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7842 (mptp) REVERT: D 424 ASP cc_start: 0.7548 (p0) cc_final: 0.7177 (p0) REVERT: D 490 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7667 (mmtm) REVERT: F 10 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8228 (tp) REVERT: F 49 SER cc_start: 0.8883 (m) cc_final: 0.8531 (p) REVERT: F 54 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7413 (ttp-110) REVERT: F 124 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7481 (m-40) REVERT: F 125 TYR cc_start: 0.7774 (t80) cc_final: 0.7438 (t80) REVERT: F 135 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7781 (tt0) REVERT: F 137 ASN cc_start: 0.8574 (m-40) cc_final: 0.8259 (t0) REVERT: F 199 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8058 (ttmm) REVERT: F 301 ARG cc_start: 0.6274 (mpt180) cc_final: 0.5777 (mmm160) REVERT: F 367 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8451 (ptm) REVERT: F 382 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5780 (m-30) REVERT: F 397 MET cc_start: 0.8894 (tmm) cc_final: 0.8611 (tmm) REVERT: F 424 ASP cc_start: 0.7564 (p0) cc_final: 0.7207 (p0) REVERT: F 427 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: F 460 LYS cc_start: 0.7436 (ptpp) cc_final: 0.6634 (pptt) REVERT: F 490 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7667 (mmtt) REVERT: H 10 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8553 (tp) REVERT: H 54 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7433 (ttp-110) REVERT: H 58 GLN cc_start: 0.7792 (pt0) cc_final: 0.7511 (pt0) REVERT: H 69 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7844 (mtp85) REVERT: H 126 GLU cc_start: 0.7548 (pt0) cc_final: 0.7147 (pt0) REVERT: H 137 ASN cc_start: 0.8466 (m-40) cc_final: 0.8214 (t0) REVERT: H 199 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8138 (ttmm) REVERT: H 348 GLU cc_start: 0.7712 (pt0) cc_final: 0.7262 (tm-30) REVERT: H 385 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: H 420 ASP cc_start: 0.8651 (m-30) cc_final: 0.8309 (m-30) REVERT: H 436 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8538 (mp) REVERT: H 460 LYS cc_start: 0.7446 (ptpp) cc_final: 0.6644 (pptt) REVERT: K 10 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8577 (tp) REVERT: K 58 GLN cc_start: 0.7793 (pt0) cc_final: 0.7480 (pt0) REVERT: K 69 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: K 199 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8106 (ttmm) REVERT: K 301 ARG cc_start: 0.6507 (mpt180) cc_final: 0.6004 (mmm160) REVERT: K 328 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: K 348 GLU cc_start: 0.7631 (pt0) cc_final: 0.7183 (tm-30) REVERT: K 349 TYR cc_start: 0.7475 (m-80) cc_final: 0.7083 (m-10) REVERT: K 385 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6820 (p0) REVERT: K 420 ASP cc_start: 0.8688 (m-30) cc_final: 0.8381 (m-30) REVERT: K 436 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8552 (mp) REVERT: K 449 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: K 460 LYS cc_start: 0.7544 (ptpp) cc_final: 0.6779 (pptt) outliers start: 76 outliers final: 35 residues processed: 416 average time/residue: 0.5924 time to fit residues: 284.9843 Evaluate side-chains 418 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 360 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 436 LEU 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 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 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 375 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 124 ASN Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 367 MET 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 69 ARG 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 367 MET 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 222 SER Chi-restraints excluded: chain K residue 275 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 328 GLN 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: 7.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 85 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN D 58 GLN D 324 GLN F 58 GLN H 170 ASN K 170 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128356 restraints weight = 22927.573| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.14 r_work: 0.3343 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3139 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= 0.149 Angle : 0.533 6.663 34668 Z= 0.293 Chirality : 0.042 0.198 3744 Planarity : 0.004 0.044 4350 Dihedral : 14.656 179.703 3615 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.93 % Favored : 96.87 % Rotamer: Outliers : 3.17 % Allowed : 17.26 % Favored : 79.57 % 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: 1.23 (0.16), residues: 2940 helix: 1.67 (0.12), residues: 1740 sheet: -0.86 (0.36), residues: 192 loop : -0.25 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 227 TYR 0.020 0.002 TYR H 475 PHE 0.012 0.001 PHE K 144 TRP 0.009 0.001 TRP F 363 HIS 0.003 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00327 (25536) covalent geometry : angle 0.53284 (34668) hydrogen bonds : bond 0.04538 ( 1261) hydrogen bonds : angle 4.42909 ( 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 455 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 369 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7245 (ttt-90) REVERT: A 58 GLN cc_start: 0.7925 (pt0) cc_final: 0.7556 (mm110) REVERT: A 135 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7814 (tt0) REVERT: A 137 ASN cc_start: 0.8500 (m-40) cc_final: 0.8269 (t0) REVERT: A 192 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7909 (t0) REVERT: A 199 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8083 (ttmm) REVERT: A 227 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7575 (tpt-90) REVERT: A 301 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5911 (mmm160) REVERT: A 377 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7602 (mp0) REVERT: A 386 GLU cc_start: 0.7186 (tp30) cc_final: 0.6902 (tp30) REVERT: A 436 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 460 LYS cc_start: 0.7555 (ptpp) cc_final: 0.6802 (pptt) REVERT: A 490 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7890 (mmtm) REVERT: B 49 SER cc_start: 0.8764 (m) cc_final: 0.8549 (p) REVERT: B 54 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7309 (ttt-90) REVERT: B 58 GLN cc_start: 0.7932 (pt0) cc_final: 0.7568 (mm110) REVERT: B 135 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7856 (tt0) REVERT: B 137 ASN cc_start: 0.8499 (m-40) cc_final: 0.8243 (t0) REVERT: B 192 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7918 (t0) REVERT: B 199 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8052 (ttmm) REVERT: B 227 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7573 (tpt-90) REVERT: B 301 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.5913 (mmm160) REVERT: B 377 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7627 (mp0) REVERT: B 386 GLU cc_start: 0.7231 (tp30) cc_final: 0.6910 (tp30) REVERT: B 424 ASP cc_start: 0.7656 (p0) cc_final: 0.7363 (p0) REVERT: B 436 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 457 ASP cc_start: 0.8344 (m-30) cc_final: 0.8104 (m-30) REVERT: B 460 LYS cc_start: 0.7588 (ptpp) cc_final: 0.6830 (pptt) REVERT: D 10 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8202 (tp) REVERT: D 97 GLU cc_start: 0.7865 (mp0) cc_final: 0.7586 (pm20) REVERT: D 135 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7674 (tt0) REVERT: D 137 ASN cc_start: 0.8560 (m-40) cc_final: 0.8247 (t0) REVERT: D 199 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8086 (ttmm) REVERT: D 301 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5770 (mmm160) REVERT: D 377 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7479 (mp0) REVERT: D 385 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: D 388 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8664 (tmtm) REVERT: D 397 MET cc_start: 0.8846 (tmm) cc_final: 0.8600 (tmm) REVERT: D 424 ASP cc_start: 0.7594 (p0) cc_final: 0.7226 (p0) REVERT: D 460 LYS cc_start: 0.7290 (ptpp) cc_final: 0.6573 (pptt) REVERT: D 490 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7696 (mmtm) REVERT: F 10 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8200 (tp) REVERT: F 49 SER cc_start: 0.8897 (m) cc_final: 0.8549 (p) REVERT: F 54 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7476 (ttp-110) REVERT: F 135 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7714 (tt0) REVERT: F 137 ASN cc_start: 0.8546 (m-40) cc_final: 0.8232 (t0) REVERT: F 199 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8068 (ttmm) REVERT: F 301 ARG cc_start: 0.6312 (mpt180) cc_final: 0.5849 (mmm160) REVERT: F 367 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8465 (ptm) REVERT: F 382 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5724 (m-30) REVERT: F 397 MET cc_start: 0.8885 (tmm) cc_final: 0.8650 (tmm) REVERT: F 424 ASP cc_start: 0.7581 (p0) cc_final: 0.7207 (p0) REVERT: F 427 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: F 460 LYS cc_start: 0.7503 (ptpp) cc_final: 0.6666 (pptt) REVERT: F 490 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7678 (mmtt) REVERT: H 10 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8591 (tp) REVERT: H 54 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7452 (ttp-110) REVERT: H 58 GLN cc_start: 0.7820 (pt0) cc_final: 0.7548 (pt0) REVERT: H 69 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7928 (mtp85) REVERT: H 70 TYR cc_start: 0.8469 (p90) cc_final: 0.8219 (p90) REVERT: H 126 GLU cc_start: 0.7530 (pt0) cc_final: 0.7146 (pt0) REVERT: H 137 ASN cc_start: 0.8483 (m-40) cc_final: 0.8221 (t0) REVERT: H 199 LYS cc_start: 0.8348 (ttpp) cc_final: 0.8129 (ttmm) REVERT: H 301 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6039 (mmm160) REVERT: H 348 GLU cc_start: 0.7735 (pt0) cc_final: 0.7283 (tm-30) REVERT: H 385 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6386 (m-30) REVERT: H 420 ASP cc_start: 0.8655 (m-30) cc_final: 0.8316 (m-30) REVERT: H 436 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8536 (mp) REVERT: H 460 LYS cc_start: 0.7441 (ptpp) cc_final: 0.6630 (pptt) REVERT: K 10 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (tp) REVERT: K 58 GLN cc_start: 0.7806 (pt0) cc_final: 0.7513 (pt0) REVERT: K 69 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7921 (mtp85) REVERT: K 199 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8138 (ttmm) REVERT: K 301 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6038 (mmm160) REVERT: K 309 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7908 (mmtm) REVERT: K 328 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: K 348 GLU cc_start: 0.7672 (pt0) cc_final: 0.7192 (tm-30) REVERT: K 349 TYR cc_start: 0.7509 (m-80) cc_final: 0.7116 (m-10) REVERT: K 385 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6772 (p0) REVERT: K 420 ASP cc_start: 0.8655 (m-30) cc_final: 0.8352 (m-30) REVERT: K 449 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: K 460 LYS cc_start: 0.7539 (ptpp) cc_final: 0.6705 (pptt) outliers start: 86 outliers final: 42 residues processed: 425 average time/residue: 0.6338 time to fit residues: 310.5015 Evaluate side-chains 428 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 361 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 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 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 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 375 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 388 LYS 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 367 MET 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 69 ARG 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 367 MET 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 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 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: 7.9990 chunk 66 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 290 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 150 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 328 GLN D 58 GLN D 401 ASN F 58 GLN H 170 ASN H 401 ASN K 170 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126232 restraints weight = 22784.124| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.14 r_work: 0.3314 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.004 0.046 25536 Z= 0.185 Angle : 0.573 7.479 34668 Z= 0.314 Chirality : 0.044 0.192 3744 Planarity : 0.005 0.042 4350 Dihedral : 14.759 179.811 3615 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 3.13 % Allowed : 17.55 % Favored : 79.31 % 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: 1.52 (0.12), residues: 1746 sheet: -0.93 (0.35), residues: 192 loop : -0.21 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 142 TYR 0.023 0.002 TYR H 475 PHE 0.015 0.002 PHE K 144 TRP 0.009 0.002 TRP D 363 HIS 0.004 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00415 (25536) covalent geometry : angle 0.57312 (34668) hydrogen bonds : bond 0.04926 ( 1261) hydrogen bonds : angle 4.53227 ( 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 453 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 368 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7394 (ttp-110) REVERT: A 58 GLN cc_start: 0.7968 (pt0) cc_final: 0.7607 (mm110) REVERT: A 135 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7807 (tt0) REVERT: A 137 ASN cc_start: 0.8523 (m-40) cc_final: 0.8271 (t0) REVERT: A 192 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7921 (t0) REVERT: A 199 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8138 (ttmm) REVERT: A 227 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7548 (tpt-90) REVERT: A 301 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6025 (mmm160) REVERT: A 377 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: A 386 GLU cc_start: 0.7237 (tp30) cc_final: 0.6931 (tp30) REVERT: A 424 ASP cc_start: 0.7284 (p0) cc_final: 0.6841 (p0) REVERT: A 436 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 460 LYS cc_start: 0.7665 (ptpp) cc_final: 0.6904 (pptt) REVERT: A 490 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7980 (mmtm) REVERT: B 54 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7278 (ttt-90) REVERT: B 58 GLN cc_start: 0.7968 (pt0) cc_final: 0.7603 (mm110) REVERT: B 135 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7824 (tt0) REVERT: B 137 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8221 (t0) REVERT: B 192 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7933 (t0) REVERT: B 199 LYS cc_start: 0.8386 (ttpp) cc_final: 0.8102 (ttmm) REVERT: B 227 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7550 (tpt-90) REVERT: B 301 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5955 (mmm160) REVERT: B 377 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7724 (mp0) REVERT: B 386 GLU cc_start: 0.7258 (tp30) cc_final: 0.6975 (tp30) REVERT: B 424 ASP cc_start: 0.7652 (p0) cc_final: 0.7343 (p0) REVERT: B 436 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 457 ASP cc_start: 0.8376 (m-30) cc_final: 0.8145 (m-30) REVERT: B 460 LYS cc_start: 0.7590 (ptpp) cc_final: 0.6856 (pptt) REVERT: D 10 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8217 (tp) REVERT: D 97 GLU cc_start: 0.7906 (mp0) cc_final: 0.7628 (pm20) REVERT: D 135 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7720 (tt0) REVERT: D 137 ASN cc_start: 0.8585 (m-40) cc_final: 0.8218 (t0) REVERT: D 192 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8010 (t0) REVERT: D 199 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8150 (ttmm) REVERT: D 301 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5908 (mmm160) REVERT: D 377 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7537 (mp0) REVERT: D 385 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: D 397 MET cc_start: 0.8836 (tmm) cc_final: 0.8605 (tmm) REVERT: D 424 ASP cc_start: 0.7615 (p0) cc_final: 0.7237 (p0) REVERT: D 460 LYS cc_start: 0.7417 (ptpp) cc_final: 0.6683 (pptt) REVERT: D 490 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7722 (mmtm) REVERT: F 10 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8237 (tp) REVERT: F 54 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7471 (ttp-110) REVERT: F 135 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7682 (tt0) REVERT: F 137 ASN cc_start: 0.8637 (m-40) cc_final: 0.8307 (t0) REVERT: F 192 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (t0) REVERT: F 199 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8134 (ttmm) REVERT: F 301 ARG cc_start: 0.6432 (mpt180) cc_final: 0.5966 (mmm160) REVERT: F 304 ASP cc_start: 0.7360 (p0) cc_final: 0.7073 (p0) REVERT: F 367 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8437 (ptm) REVERT: F 382 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5746 (m-30) REVERT: F 393 GLU cc_start: 0.8393 (tp30) cc_final: 0.8151 (tp30) REVERT: F 397 MET cc_start: 0.8845 (tmm) cc_final: 0.8637 (tmm) REVERT: F 424 ASP cc_start: 0.7599 (p0) cc_final: 0.7222 (p0) REVERT: F 427 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: F 460 LYS cc_start: 0.7532 (ptpp) cc_final: 0.6703 (pptt) REVERT: F 490 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7741 (mmtt) REVERT: H 10 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8621 (tp) REVERT: H 54 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7458 (ttp-110) REVERT: H 58 GLN cc_start: 0.7830 (pt0) cc_final: 0.7563 (pt0) REVERT: H 69 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7949 (mtp85) REVERT: H 70 TYR cc_start: 0.8544 (p90) cc_final: 0.8254 (p90) REVERT: H 126 GLU cc_start: 0.7542 (pt0) cc_final: 0.7159 (pt0) REVERT: H 137 ASN cc_start: 0.8484 (m-40) cc_final: 0.8216 (t0) REVERT: H 199 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8183 (ttmm) REVERT: H 301 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6151 (mmm160) REVERT: H 328 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: H 348 GLU cc_start: 0.7749 (pt0) cc_final: 0.7301 (tm-30) REVERT: H 385 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: H 420 ASP cc_start: 0.8654 (m-30) cc_final: 0.8329 (m-30) REVERT: H 436 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8575 (mp) REVERT: H 460 LYS cc_start: 0.7467 (ptpp) cc_final: 0.6627 (pptt) REVERT: K 10 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8636 (tp) REVERT: K 58 GLN cc_start: 0.7814 (pt0) cc_final: 0.7511 (pt0) REVERT: K 69 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7938 (mtp85) REVERT: K 199 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8207 (ttmm) REVERT: K 301 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6127 (mmm160) REVERT: K 309 LYS cc_start: 0.8233 (mmtm) cc_final: 0.7973 (mmtm) REVERT: K 328 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: K 348 GLU cc_start: 0.7701 (pt0) cc_final: 0.7224 (tm-30) REVERT: K 349 TYR cc_start: 0.7537 (m-80) cc_final: 0.7128 (m-10) REVERT: K 385 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6510 (m-30) REVERT: K 420 ASP cc_start: 0.8653 (m-30) cc_final: 0.8358 (m-30) REVERT: K 436 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8547 (mp) REVERT: K 449 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: K 460 LYS cc_start: 0.7557 (ptpp) cc_final: 0.6743 (pptt) outliers start: 85 outliers final: 41 residues processed: 424 average time/residue: 0.6590 time to fit residues: 321.7211 Evaluate side-chains 428 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 357 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 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 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 56 SER Chi-restraints excluded: chain D residue 157 ILE 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 157 ILE 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 367 MET 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 69 ARG 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 328 GLN Chi-restraints excluded: chain H residue 367 MET 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 H residue 459 ILE Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 222 SER Chi-restraints excluded: chain K residue 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 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 Chi-restraints excluded: chain K residue 449 GLU Chi-restraints excluded: chain K residue 459 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 217 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 248 optimal weight: 0.1980 chunk 265 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN D 58 GLN F 58 GLN F 170 ASN H 170 ASN K 170 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128709 restraints weight = 22914.158| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.13 r_work: 0.3349 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25536 Z= 0.139 Angle : 0.534 7.956 34668 Z= 0.292 Chirality : 0.042 0.184 3744 Planarity : 0.004 0.042 4350 Dihedral : 14.654 179.783 3615 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 2.95 % Allowed : 17.85 % 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: 1.22 (0.16), residues: 2940 helix: 1.66 (0.12), residues: 1740 sheet: -0.97 (0.35), residues: 192 loop : -0.23 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 227 TYR 0.019 0.002 TYR B 11 PHE 0.011 0.001 PHE B 144 TRP 0.009 0.001 TRP D 363 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00305 (25536) covalent geometry : angle 0.53429 (34668) hydrogen bonds : bond 0.04386 ( 1261) hydrogen bonds : angle 4.44855 ( 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 437 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7440 (ttp-110) REVERT: A 58 GLN cc_start: 0.7939 (pt0) cc_final: 0.7583 (mm110) REVERT: A 135 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7812 (tt0) REVERT: A 137 ASN cc_start: 0.8494 (m-40) cc_final: 0.8253 (t0) REVERT: A 192 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7902 (t0) REVERT: A 199 LYS cc_start: 0.8326 (ttpp) cc_final: 0.8064 (ttmm) REVERT: A 227 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7575 (tpt-90) REVERT: A 301 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5891 (mmm160) REVERT: A 377 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7637 (mp0) REVERT: A 386 GLU cc_start: 0.7218 (tp30) cc_final: 0.6924 (tp30) REVERT: A 424 ASP cc_start: 0.7269 (p0) cc_final: 0.6827 (p0) REVERT: A 436 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 460 LYS cc_start: 0.7647 (ptpp) cc_final: 0.6872 (pptt) REVERT: A 490 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7935 (mmtm) REVERT: B 54 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7264 (ttt-90) REVERT: B 58 GLN cc_start: 0.7923 (pt0) cc_final: 0.7578 (mm110) REVERT: B 135 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7807 (tt0) REVERT: B 137 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 192 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7905 (t0) REVERT: B 199 LYS cc_start: 0.8312 (ttpp) cc_final: 0.8018 (ttmm) REVERT: B 227 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7575 (tpt-90) REVERT: B 301 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5865 (mmm160) REVERT: B 377 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7665 (mp0) REVERT: B 386 GLU cc_start: 0.7232 (tp30) cc_final: 0.6951 (tp30) REVERT: B 424 ASP cc_start: 0.7649 (p0) cc_final: 0.7330 (p0) REVERT: B 436 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8489 (mp) REVERT: B 457 ASP cc_start: 0.8367 (m-30) cc_final: 0.8139 (m-30) REVERT: B 460 LYS cc_start: 0.7642 (ptpp) cc_final: 0.6878 (pptt) REVERT: D 10 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8231 (tp) REVERT: D 97 GLU cc_start: 0.7879 (mp0) cc_final: 0.7644 (pm20) REVERT: D 135 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7714 (tt0) REVERT: D 137 ASN cc_start: 0.8557 (m-40) cc_final: 0.8250 (t0) REVERT: D 199 LYS cc_start: 0.8290 (ttpp) cc_final: 0.8058 (ttmm) REVERT: D 301 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5799 (mmm160) REVERT: D 377 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7475 (mp0) REVERT: D 385 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: D 397 MET cc_start: 0.8830 (tmm) cc_final: 0.8566 (tmm) REVERT: D 424 ASP cc_start: 0.7628 (p0) cc_final: 0.7252 (p0) REVERT: D 460 LYS cc_start: 0.7354 (ptpp) cc_final: 0.6630 (pptt) REVERT: D 490 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7706 (mmtm) REVERT: F 10 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8229 (tp) REVERT: F 49 SER cc_start: 0.8888 (m) cc_final: 0.8536 (p) REVERT: F 54 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7463 (ttp-110) REVERT: F 135 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7676 (tt0) REVERT: F 137 ASN cc_start: 0.8584 (m-40) cc_final: 0.8277 (t0) REVERT: F 192 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7998 (t0) REVERT: F 199 LYS cc_start: 0.8314 (ttpp) cc_final: 0.8059 (ttmm) REVERT: F 301 ARG cc_start: 0.6414 (mpt180) cc_final: 0.5985 (mmm160) REVERT: F 304 ASP cc_start: 0.7310 (p0) cc_final: 0.7033 (p0) REVERT: F 367 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (ptm) REVERT: F 382 ASP cc_start: 0.5943 (OUTLIER) cc_final: 0.5703 (m-30) REVERT: F 393 GLU cc_start: 0.8340 (tp30) cc_final: 0.8083 (tp30) REVERT: F 397 MET cc_start: 0.8853 (tmm) cc_final: 0.8628 (tmm) REVERT: F 424 ASP cc_start: 0.7629 (p0) cc_final: 0.7249 (p0) REVERT: F 427 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: F 460 LYS cc_start: 0.7482 (ptpp) cc_final: 0.6662 (pptt) REVERT: F 490 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7701 (mmtt) REVERT: H 10 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8572 (tp) REVERT: H 54 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7454 (ttp-110) REVERT: H 58 GLN cc_start: 0.7783 (pt0) cc_final: 0.7527 (pt0) REVERT: H 69 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7907 (mtp85) REVERT: H 70 TYR cc_start: 0.8514 (p90) cc_final: 0.8232 (p90) REVERT: H 126 GLU cc_start: 0.7551 (pt0) cc_final: 0.7139 (pt0) REVERT: H 137 ASN cc_start: 0.8478 (m-40) cc_final: 0.8222 (t0) REVERT: H 199 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8105 (ttmm) REVERT: H 301 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5985 (mmm160) REVERT: H 348 GLU cc_start: 0.7679 (pt0) cc_final: 0.7227 (tm-30) REVERT: H 385 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6452 (m-30) REVERT: H 420 ASP cc_start: 0.8661 (m-30) cc_final: 0.8325 (m-30) REVERT: H 436 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8559 (mp) REVERT: H 460 LYS cc_start: 0.7398 (ptpp) cc_final: 0.6588 (pptt) REVERT: K 10 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8599 (tp) REVERT: K 58 GLN cc_start: 0.7763 (pt0) cc_final: 0.7480 (pt0) REVERT: K 199 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8114 (ttmm) REVERT: K 301 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6036 (mmm160) REVERT: K 309 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7880 (mmtm) REVERT: K 348 GLU cc_start: 0.7676 (pt0) cc_final: 0.7193 (tm-30) REVERT: K 349 TYR cc_start: 0.7509 (m-80) cc_final: 0.7094 (m-10) REVERT: K 385 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: K 420 ASP cc_start: 0.8631 (m-30) cc_final: 0.8338 (m-30) REVERT: K 436 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8546 (mp) REVERT: K 449 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: K 460 LYS cc_start: 0.7490 (ptpp) cc_final: 0.6653 (pptt) outliers start: 80 outliers final: 35 residues processed: 407 average time/residue: 0.6646 time to fit residues: 311.0576 Evaluate side-chains 413 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 307 LEU 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 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 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 436 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 157 ILE 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 367 MET 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 69 ARG Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 367 MET Chi-restraints excluded: chain H residue 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 235 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN D 58 GLN ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN F 58 GLN H 170 ASN K 170 ASN K 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123772 restraints weight = 22817.327| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.13 r_work: 0.3281 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25536 Z= 0.266 Angle : 0.652 10.083 34668 Z= 0.356 Chirality : 0.049 0.192 3744 Planarity : 0.005 0.043 4350 Dihedral : 14.846 179.774 3615 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 2.69 % Allowed : 18.03 % Favored : 79.28 % 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: 0.92 (0.15), residues: 2940 helix: 1.31 (0.12), residues: 1752 sheet: -0.83 (0.36), residues: 192 loop : -0.22 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 142 TYR 0.028 0.003 TYR H 475 PHE 0.021 0.003 PHE K 144 TRP 0.009 0.002 TRP F 363 HIS 0.006 0.002 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00607 (25536) covalent geometry : angle 0.65153 (34668) hydrogen bonds : bond 0.05535 ( 1261) hydrogen bonds : angle 4.67618 ( 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 436 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 363 time to evaluate : 1.006 Fit side-chains REVERT: A 54 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7569 (ttp-110) REVERT: A 58 GLN cc_start: 0.7986 (pt0) cc_final: 0.7631 (mm110) REVERT: A 135 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7853 (tt0) REVERT: A 137 ASN cc_start: 0.8563 (m-40) cc_final: 0.8259 (t0) REVERT: A 192 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7924 (t0) REVERT: A 199 LYS cc_start: 0.8493 (ttpp) cc_final: 0.8213 (ttmm) REVERT: A 227 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7595 (tpt-90) REVERT: A 301 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6092 (mmm160) REVERT: A 304 ASP cc_start: 0.7379 (p0) cc_final: 0.6986 (p0) REVERT: A 377 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 386 GLU cc_start: 0.7233 (tp30) cc_final: 0.6904 (tp30) REVERT: A 424 ASP cc_start: 0.7313 (p0) cc_final: 0.6869 (p0) REVERT: A 436 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 460 LYS cc_start: 0.7569 (ptpp) cc_final: 0.6840 (pptt) REVERT: A 490 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8039 (mmtm) REVERT: B 58 GLN cc_start: 0.7999 (pt0) cc_final: 0.7658 (mm110) REVERT: B 135 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7850 (tt0) REVERT: B 137 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8224 (t0) REVERT: B 192 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7917 (t0) REVERT: B 199 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8182 (ttmm) REVERT: B 227 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7602 (tpt-90) REVERT: B 301 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6079 (mmm160) REVERT: B 377 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7756 (mp0) REVERT: B 386 GLU cc_start: 0.7326 (tp30) cc_final: 0.7033 (tp30) REVERT: B 424 ASP cc_start: 0.7566 (p0) cc_final: 0.7253 (p0) REVERT: B 436 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 457 ASP cc_start: 0.8387 (m-30) cc_final: 0.8185 (m-30) REVERT: B 460 LYS cc_start: 0.7602 (ptpp) cc_final: 0.6849 (pptt) REVERT: D 10 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8256 (tp) REVERT: D 97 GLU cc_start: 0.7903 (mp0) cc_final: 0.7629 (pm20) REVERT: D 135 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7726 (tt0) REVERT: D 137 ASN cc_start: 0.8586 (m-40) cc_final: 0.8206 (t0) REVERT: D 192 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8017 (t0) REVERT: D 199 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8211 (ttmm) REVERT: D 301 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5986 (mmm160) REVERT: D 377 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7581 (mp0) REVERT: D 385 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6501 (m-30) REVERT: D 386 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7122 (tm-30) REVERT: D 397 MET cc_start: 0.8857 (tmm) cc_final: 0.8628 (tmm) REVERT: D 424 ASP cc_start: 0.7606 (p0) cc_final: 0.7154 (p0) REVERT: D 460 LYS cc_start: 0.7542 (ptpp) cc_final: 0.6763 (pptt) REVERT: D 490 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7804 (mmtt) REVERT: F 10 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8262 (tp) REVERT: F 54 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7490 (ttp-110) REVERT: F 135 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7697 (tt0) REVERT: F 137 ASN cc_start: 0.8598 (m-40) cc_final: 0.8236 (t0) REVERT: F 192 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8002 (t0) REVERT: F 199 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8186 (ttmm) REVERT: F 301 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6214 (mmm160) REVERT: F 304 ASP cc_start: 0.7432 (p0) cc_final: 0.7157 (p0) REVERT: F 367 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8459 (ptm) REVERT: F 382 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5872 (m-30) REVERT: F 424 ASP cc_start: 0.7645 (p0) cc_final: 0.7262 (p0) REVERT: F 427 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: F 460 LYS cc_start: 0.7567 (ptpp) cc_final: 0.6750 (pptt) REVERT: F 490 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7798 (mmtt) REVERT: H 10 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8698 (tp) REVERT: H 54 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7480 (ttp-110) REVERT: H 58 GLN cc_start: 0.7901 (pt0) cc_final: 0.7608 (pt0) REVERT: H 69 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7971 (mtp85) REVERT: H 70 TYR cc_start: 0.8604 (p90) cc_final: 0.8284 (p90) REVERT: H 137 ASN cc_start: 0.8491 (m-40) cc_final: 0.8204 (t0) REVERT: H 199 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8244 (ttmm) REVERT: H 301 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6314 (mmm160) REVERT: H 328 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: H 348 GLU cc_start: 0.7752 (pt0) cc_final: 0.7313 (tm-30) REVERT: H 385 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6553 (m-30) REVERT: H 420 ASP cc_start: 0.8642 (m-30) cc_final: 0.8336 (m-30) REVERT: H 427 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: H 436 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8594 (mp) REVERT: H 460 LYS cc_start: 0.7511 (ptpp) cc_final: 0.6727 (pptt) REVERT: K 10 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8693 (tp) REVERT: K 58 GLN cc_start: 0.7838 (pt0) cc_final: 0.7537 (pt0) REVERT: K 69 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7940 (mtt180) REVERT: K 199 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8272 (ttmm) REVERT: K 301 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6300 (mmm160) REVERT: K 328 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: K 348 GLU cc_start: 0.7705 (pt0) cc_final: 0.7294 (tm-30) REVERT: K 349 TYR cc_start: 0.7537 (m-80) cc_final: 0.7154 (m-10) REVERT: K 385 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6509 (m-30) REVERT: K 420 ASP cc_start: 0.8640 (m-30) cc_final: 0.8352 (m-30) REVERT: K 427 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: K 436 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8583 (mp) REVERT: K 449 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: K 460 LYS cc_start: 0.7546 (ptpp) cc_final: 0.6736 (pptt) outliers start: 73 outliers final: 35 residues processed: 406 average time/residue: 0.6675 time to fit residues: 311.2539 Evaluate side-chains 422 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 355 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 377 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 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 56 SER Chi-restraints excluded: chain D residue 157 ILE 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 D residue 445 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 157 ILE 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 367 MET 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 69 ARG Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 294 VAL Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 328 GLN Chi-restraints excluded: chain H residue 367 MET 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 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 328 GLN 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 Chi-restraints excluded: chain K residue 449 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 112 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 277 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 324 GLN B 170 ASN B 324 GLN D 58 GLN ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 147 ASN F 170 ASN H 170 ASN K 170 ASN 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 = 0.145626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128218 restraints weight = 22880.687| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.13 r_work: 0.3343 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25536 Z= 0.140 Angle : 0.548 9.109 34668 Z= 0.299 Chirality : 0.042 0.180 3744 Planarity : 0.004 0.042 4350 Dihedral : 14.634 179.283 3615 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 2.65 % Allowed : 18.18 % 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: 1.17 (0.16), residues: 2940 helix: 1.58 (0.12), residues: 1740 sheet: -0.87 (0.36), residues: 192 loop : -0.20 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.019 0.002 TYR B 11 PHE 0.011 0.001 PHE B 144 TRP 0.009 0.001 TRP F 363 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00307 (25536) covalent geometry : angle 0.54837 (34668) hydrogen bonds : bond 0.04418 ( 1261) hydrogen bonds : angle 4.50666 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9102.87 seconds wall clock time: 156 minutes 0.52 seconds (9360.52 seconds total)