Starting phenix.real_space_refine on Fri Mar 6 05:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uc2_20725/03_2026/6uc2_20725.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uc2_20725/03_2026/6uc2_20725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uc2_20725/03_2026/6uc2_20725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uc2_20725/03_2026/6uc2_20725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uc2_20725/03_2026/6uc2_20725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uc2_20725/03_2026/6uc2_20725.map" } resolution = 4.48 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= 0.148 sd= 3.127 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 72 5.49 5 S 144 5.16 5 C 17688 2.51 5 N 4880 2.21 5 O 5624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28408 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.79, per 1000 atoms: 0.13 Number of scatterers: 28408 At special positions: 0 Unit cell: (152.25, 152.25, 116.55, 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 144 16.00 P 72 15.00 O 5624 8.00 N 4880 7.00 C 17688 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 64 sheets defined 42.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.658A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.951A pdb=" N GLU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 removed outlier: 4.411A pdb=" N PHE A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.708A pdb=" N ASP A 184 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.809A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.753A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.660A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.094A pdb=" N ALA A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.809A pdb=" N ALA A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.692A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 4.054A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.594A pdb=" N LEU A 390 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 455 removed outlier: 3.517A pdb=" N LYS A 455 " --> pdb=" O SER A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 455' Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 494 through 500 removed outlier: 4.328A pdb=" N ALA A 497 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 499 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 500 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.657A pdb=" N ASN B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.951A pdb=" N GLU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 removed outlier: 4.412A pdb=" N PHE B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.708A pdb=" N ASP B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.810A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.752A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.660A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.094A pdb=" N ALA B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 338' Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.691A pdb=" N ALA B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 4.054A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.593A pdb=" N LEU B 390 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 removed outlier: 3.517A pdb=" N LYS B 455 " --> pdb=" O SER B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 486 Processing helix chain 'B' and resid 494 through 500 removed outlier: 4.328A pdb=" N ALA B 497 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 499 " --> pdb=" O SER B 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.657A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.952A pdb=" N GLU C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 removed outlier: 4.411A pdb=" N PHE C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 181 through 185 removed outlier: 3.708A pdb=" N ASP C 184 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.810A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.752A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.659A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 removed outlier: 4.094A pdb=" N ALA C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 338' Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.691A pdb=" N ALA C 346 " --> pdb=" O PRO C 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 4.053A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.593A pdb=" N LEU C 390 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 455 removed outlier: 3.517A pdb=" N LYS C 455 " --> pdb=" O SER C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 452 through 455' Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 500 removed outlier: 4.328A pdb=" N ALA C 497 " --> pdb=" O THR C 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 499 " --> pdb=" O SER C 496 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 500 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.658A pdb=" N ASN D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.952A pdb=" N GLU D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 4.411A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.709A pdb=" N ASP D 184 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.809A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.753A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.660A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.094A pdb=" N ALA D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.692A pdb=" N ALA D 346 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 4.054A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.594A pdb=" N LEU D 390 " --> pdb=" O GLY D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 455 removed outlier: 3.518A pdb=" N LYS D 455 " --> pdb=" O SER D 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 452 through 455' Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 486 Processing helix chain 'D' and resid 494 through 500 removed outlier: 4.327A pdb=" N ALA D 497 " --> pdb=" O THR D 494 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL D 499 " --> pdb=" O SER D 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 500 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.658A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.539A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.952A pdb=" N GLU E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 138 removed outlier: 4.412A pdb=" N PHE E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 181 through 185 removed outlier: 3.708A pdb=" N ASP E 184 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.809A pdb=" N ALA E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.753A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.659A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.094A pdb=" N ALA E 310 " --> pdb=" O THR E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 334 through 338' Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.692A pdb=" N ALA E 346 " --> pdb=" O PRO E 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 4.053A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.594A pdb=" N LEU E 390 " --> pdb=" O GLY E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 removed outlier: 3.518A pdb=" N LYS E 455 " --> pdb=" O SER E 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 452 through 455' Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 500 removed outlier: 4.328A pdb=" N ALA E 497 " --> pdb=" O THR E 494 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL E 499 " --> pdb=" O SER E 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E 500 " --> pdb=" O ALA E 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.657A pdb=" N ASN F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.952A pdb=" N GLU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 138 removed outlier: 4.411A pdb=" N PHE F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.708A pdb=" N ASP F 184 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 removed outlier: 3.809A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.753A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.659A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 removed outlier: 4.093A pdb=" N ALA F 310 " --> pdb=" O THR F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA F 338 " --> pdb=" O GLN F 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 338' Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.691A pdb=" N ALA F 346 " --> pdb=" O PRO F 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 4.054A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.593A pdb=" N LEU F 390 " --> pdb=" O GLY F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 removed outlier: 3.518A pdb=" N LYS F 455 " --> pdb=" O SER F 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 452 through 455' Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 500 removed outlier: 4.327A pdb=" N ALA F 497 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL F 499 " --> pdb=" O SER F 496 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 500 " --> pdb=" O ALA F 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.657A pdb=" N ASN G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 3.951A pdb=" N GLU G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 138 removed outlier: 4.412A pdb=" N PHE G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 181 through 185 removed outlier: 3.709A pdb=" N ASP G 184 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.810A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.753A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.659A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.094A pdb=" N ALA G 310 " --> pdb=" O THR G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA G 338 " --> pdb=" O GLN G 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 334 through 338' Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.692A pdb=" N ALA G 346 " --> pdb=" O PRO G 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 4.054A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.594A pdb=" N LEU G 390 " --> pdb=" O GLY G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 455 removed outlier: 3.519A pdb=" N LYS G 455 " --> pdb=" O SER G 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 452 through 455' Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 500 removed outlier: 4.329A pdb=" N ALA G 497 " --> pdb=" O THR G 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL G 499 " --> pdb=" O SER G 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 500 " --> pdb=" O ALA G 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.657A pdb=" N ASN H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.538A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.951A pdb=" N GLU H 103 " --> pdb=" O PHE H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 removed outlier: 4.411A pdb=" N PHE H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 181 through 185 removed outlier: 3.708A pdb=" N ASP H 184 " --> pdb=" O LYS H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.810A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 removed outlier: 4.380A pdb=" N LYS H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.752A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.660A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 317 removed outlier: 4.093A pdb=" N ALA H 310 " --> pdb=" O THR H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 removed outlier: 3.808A pdb=" N ALA H 338 " --> pdb=" O GLN H 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 334 through 338' Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.692A pdb=" N ALA H 346 " --> pdb=" O PRO H 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 4.053A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 391 removed outlier: 3.594A pdb=" N LEU H 390 " --> pdb=" O GLY H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 455 removed outlier: 3.518A pdb=" N LYS H 455 " --> pdb=" O SER H 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 452 through 455' Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 500 removed outlier: 4.328A pdb=" N ALA H 497 " --> pdb=" O THR H 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL H 499 " --> pdb=" O SER H 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU H 500 " --> pdb=" O ALA H 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU A 36 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 491 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.600A pdb=" N VAL A 66 " --> pdb=" O VAL A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 4.023A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 323 removed outlier: 6.396A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.569A pdb=" N LEU A 408 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU B 36 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 491 " --> pdb=" O LEU B 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.600A pdb=" N VAL B 66 " --> pdb=" O VAL B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB4, first strand: chain 'B' and resid 188 through 189 removed outlier: 4.023A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 321 through 323 removed outlier: 6.397A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU B 408 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU C 36 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 491 " --> pdb=" O LEU C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.599A pdb=" N VAL C 66 " --> pdb=" O VAL C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 142 through 145 Processing sheet with id=AC3, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.023A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 321 through 323 removed outlier: 6.397A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU C 408 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU D 36 " --> pdb=" O GLU D 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 491 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.599A pdb=" N VAL D 66 " --> pdb=" O VAL D 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AD2, first strand: chain 'D' and resid 188 through 189 removed outlier: 4.023A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 321 through 323 removed outlier: 6.397A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU D 408 " --> pdb=" O PHE D 401 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU E 36 " --> pdb=" O GLU E 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 491 " --> pdb=" O LEU E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.599A pdb=" N VAL E 66 " --> pdb=" O VAL E 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AE1, first strand: chain 'E' and resid 188 through 189 removed outlier: 4.024A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 249 through 250 removed outlier: 6.321A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 321 through 323 removed outlier: 6.397A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU E 408 " --> pdb=" O PHE E 401 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU F 36 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 491 " --> pdb=" O LEU F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AE7, first strand: chain 'F' and resid 65 through 66 removed outlier: 3.599A pdb=" N VAL F 66 " --> pdb=" O VAL F 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AE9, first strand: chain 'F' and resid 188 through 189 removed outlier: 4.023A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 321 through 323 removed outlier: 6.397A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU F 408 " --> pdb=" O PHE F 401 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU G 36 " --> pdb=" O GLU G 491 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU G 491 " --> pdb=" O LEU G 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'G' and resid 65 through 66 removed outlier: 3.600A pdb=" N VAL G 66 " --> pdb=" O VAL G 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AF8, first strand: chain 'G' and resid 188 through 189 removed outlier: 4.023A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 321 through 323 removed outlier: 6.396A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'G' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU G 408 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU H 36 " --> pdb=" O GLU H 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU H 491 " --> pdb=" O LEU H 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AG5, first strand: chain 'H' and resid 65 through 66 removed outlier: 3.599A pdb=" N VAL H 66 " --> pdb=" O VAL H 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'H' and resid 142 through 145 Processing sheet with id=AG7, first strand: chain 'H' and resid 188 through 189 removed outlier: 4.022A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 249 through 250 removed outlier: 6.320A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 321 through 323 removed outlier: 6.398A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'H' and resid 400 through 401 removed outlier: 3.568A pdb=" N LEU H 408 " --> pdb=" O PHE H 401 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4872 1.31 - 1.44: 6832 1.44 - 1.56: 16697 1.56 - 1.69: 231 1.69 - 1.81: 232 Bond restraints: 28864 Sorted by residual: bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.34e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.32e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.32e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.31e+02 bond pdb=" C2' ATP C 603 " pdb=" C3' ATP C 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.31e+02 ... (remaining 28859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 38140 4.94 - 9.87: 788 9.87 - 14.81: 136 14.81 - 19.75: 48 19.75 - 24.69: 24 Bond angle restraints: 39136 Sorted by residual: angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 ... (remaining 39131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 16637 33.77 - 67.55: 875 67.55 - 101.32: 45 101.32 - 135.10: 19 135.10 - 168.87: 24 Dihedral angle restraints: 17600 sinusoidal: 7264 harmonic: 10336 Sorted by residual: dihedral pdb=" CA GLU B 111 " pdb=" C GLU B 111 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " ideal model delta harmonic sigma weight residual -180.00 -131.80 -48.20 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLU C 111 " pdb=" C GLU C 111 " pdb=" N GLN C 112 " pdb=" CA GLN C 112 " ideal model delta harmonic sigma weight residual -180.00 -131.81 -48.19 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLU D 111 " pdb=" C GLU D 111 " pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta harmonic sigma weight residual 180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 ... (remaining 17597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3536 0.087 - 0.174: 807 0.174 - 0.261: 89 0.261 - 0.348: 24 0.348 - 0.436: 16 Chirality restraints: 4472 Sorted by residual: chirality pdb=" CB VAL A 479 " pdb=" CA VAL A 479 " pdb=" CG1 VAL A 479 " pdb=" CG2 VAL A 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CB VAL H 479 " pdb=" CA VAL H 479 " pdb=" CG1 VAL H 479 " pdb=" CG2 VAL H 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB VAL B 479 " pdb=" CA VAL B 479 " pdb=" CG1 VAL B 479 " pdb=" CG2 VAL B 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 4469 not shown) Planarity restraints: 4928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 72 " 0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C THR C 72 " -0.063 2.00e-02 2.50e+03 pdb=" O THR C 72 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 73 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 72 " -0.019 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR D 72 " 0.063 2.00e-02 2.50e+03 pdb=" O THR D 72 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL D 73 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 72 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C THR G 72 " 0.063 2.00e-02 2.50e+03 pdb=" O THR G 72 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL G 73 " -0.020 2.00e-02 2.50e+03 ... (remaining 4925 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4098 2.75 - 3.29: 28467 3.29 - 3.82: 51510 3.82 - 4.36: 58082 4.36 - 4.90: 89259 Nonbonded interactions: 231416 Sorted by model distance: nonbonded pdb=" O PRO B 64 " pdb=" OG1 THR B 383 " model vdw 2.208 3.040 nonbonded pdb=" O PRO A 64 " pdb=" OG1 THR A 383 " model vdw 2.208 3.040 nonbonded pdb=" O PRO C 64 " pdb=" OG1 THR C 383 " model vdw 2.209 3.040 nonbonded pdb=" O PRO G 64 " pdb=" OG1 THR G 383 " model vdw 2.209 3.040 nonbonded pdb=" O PRO H 64 " pdb=" OG1 THR H 383 " model vdw 2.209 3.040 ... (remaining 231411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.280 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.016 0.289 28872 Z= 0.937 Angle : 1.928 24.685 39136 Z= 1.081 Chirality : 0.078 0.436 4472 Planarity : 0.008 0.059 4928 Dihedral : 20.466 168.874 10976 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 14.82 % Allowed : 15.90 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.92 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.11), residues: 3576 helix: -3.27 (0.10), residues: 1192 sheet: -3.01 (0.27), residues: 272 loop : -2.79 (0.11), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.003 ARG E 105 TYR 0.027 0.004 TYR E 411 PHE 0.024 0.004 PHE B 456 HIS 0.010 0.003 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.01634 (28864) covalent geometry : angle 1.92819 (39136) hydrogen bonds : bond 0.20498 ( 888) hydrogen bonds : angle 9.18466 ( 2448) Misc. bond : bond 0.09172 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1883 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 440 poor density : 1443 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8848 (tpp) cc_final: 0.8426 (tpp) REVERT: A 93 HIS cc_start: 0.9184 (p90) cc_final: 0.8812 (p90) REVERT: A 94 ASN cc_start: 0.8893 (t0) cc_final: 0.8655 (t0) REVERT: A 104 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.8886 (t) REVERT: A 108 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9201 (mtmt) REVERT: A 109 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8894 (tptp) REVERT: A 137 HIS cc_start: 0.9665 (m-70) cc_final: 0.9247 (m-70) REVERT: A 166 LEU cc_start: 0.9070 (pt) cc_final: 0.8338 (tp) REVERT: A 174 PHE cc_start: 0.9144 (m-80) cc_final: 0.8815 (m-80) REVERT: A 198 ASN cc_start: 0.9698 (m110) cc_final: 0.9320 (m110) REVERT: A 199 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9254 (mp0) REVERT: A 209 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (tm) REVERT: A 224 ARG cc_start: 0.8205 (tpt170) cc_final: 0.7522 (tpt-90) REVERT: A 229 LYS cc_start: 0.9411 (mttt) cc_final: 0.9157 (mmtt) REVERT: A 231 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8781 (ptm-80) REVERT: A 245 LEU cc_start: 0.9198 (mm) cc_final: 0.8771 (mm) REVERT: A 269 ASP cc_start: 0.9143 (t0) cc_final: 0.8335 (t0) REVERT: A 276 SER cc_start: 0.9205 (m) cc_final: 0.8969 (p) REVERT: A 283 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.9309 (mm-40) REVERT: A 296 ASN cc_start: 0.9208 (p0) cc_final: 0.8521 (p0) REVERT: A 297 LEU cc_start: 0.9300 (mm) cc_final: 0.8965 (mm) REVERT: A 298 GLN cc_start: 0.9199 (mm110) cc_final: 0.8716 (mm-40) REVERT: A 325 MET cc_start: 0.7464 (pmm) cc_final: 0.7088 (pmm) REVERT: A 351 SER cc_start: 0.8520 (p) cc_final: 0.8085 (p) REVERT: A 355 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8006 (ptt180) REVERT: A 372 HIS cc_start: 0.9572 (m170) cc_final: 0.9349 (m170) REVERT: A 402 PHE cc_start: 0.8531 (m-10) cc_final: 0.8259 (m-80) REVERT: A 450 LYS cc_start: 0.6934 (pttm) cc_final: 0.6188 (ptmm) REVERT: A 465 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: A 482 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8873 (tmm) REVERT: A 489 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8499 (ttpt) REVERT: B 82 MET cc_start: 0.8783 (tpp) cc_final: 0.8351 (tpp) REVERT: B 104 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8740 (t) REVERT: B 108 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9230 (mtmt) REVERT: B 109 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8793 (tptp) REVERT: B 137 HIS cc_start: 0.9680 (m-70) cc_final: 0.9278 (m-70) REVERT: B 154 LEU cc_start: 0.9764 (mm) cc_final: 0.9544 (mm) REVERT: B 166 LEU cc_start: 0.9021 (pt) cc_final: 0.8239 (tp) REVERT: B 174 PHE cc_start: 0.9064 (m-80) cc_final: 0.8714 (m-80) REVERT: B 198 ASN cc_start: 0.9634 (m110) cc_final: 0.9237 (m110) REVERT: B 199 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9225 (mp0) REVERT: B 231 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8839 (ptm-80) REVERT: B 245 LEU cc_start: 0.9221 (mm) cc_final: 0.8855 (mm) REVERT: B 269 ASP cc_start: 0.9204 (t0) cc_final: 0.8244 (t0) REVERT: B 277 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 281 ILE cc_start: 0.9421 (mm) cc_final: 0.9118 (mm) REVERT: B 283 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9253 (mm-40) REVERT: B 285 ASN cc_start: 0.9455 (m110) cc_final: 0.9195 (m110) REVERT: B 296 ASN cc_start: 0.9322 (p0) cc_final: 0.8550 (p0) REVERT: B 297 LEU cc_start: 0.9396 (mm) cc_final: 0.8917 (mm) REVERT: B 298 GLN cc_start: 0.9083 (mm110) cc_final: 0.8657 (mm-40) REVERT: B 321 LEU cc_start: 0.9795 (mm) cc_final: 0.9583 (mm) REVERT: B 325 MET cc_start: 0.7527 (pmm) cc_final: 0.7236 (pmm) REVERT: B 355 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8029 (ptt180) REVERT: B 372 HIS cc_start: 0.9539 (m170) cc_final: 0.9303 (m170) REVERT: B 402 PHE cc_start: 0.8351 (m-10) cc_final: 0.8094 (m-80) REVERT: B 450 LYS cc_start: 0.7039 (pttm) cc_final: 0.6254 (ptmm) REVERT: B 482 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8892 (tmm) REVERT: B 489 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8602 (ttpt) REVERT: C 14 PRO cc_start: 0.9109 (Cg_exo) cc_final: 0.8864 (Cg_endo) REVERT: C 82 MET cc_start: 0.8832 (tpp) cc_final: 0.8412 (tpp) REVERT: C 104 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8712 (p) REVERT: C 108 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9204 (mtmt) REVERT: C 109 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8872 (tptp) REVERT: C 137 HIS cc_start: 0.9678 (m-70) cc_final: 0.9218 (m-70) REVERT: C 155 VAL cc_start: 0.9359 (t) cc_final: 0.9127 (t) REVERT: C 174 PHE cc_start: 0.9197 (m-80) cc_final: 0.8888 (m-80) REVERT: C 199 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9107 (mp0) REVERT: C 209 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9029 (tm) REVERT: C 231 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8799 (ptm-80) REVERT: C 245 LEU cc_start: 0.9267 (mm) cc_final: 0.8924 (mm) REVERT: C 253 HIS cc_start: 0.9314 (m-70) cc_final: 0.9059 (m-70) REVERT: C 269 ASP cc_start: 0.9193 (t0) cc_final: 0.8403 (t0) REVERT: C 276 SER cc_start: 0.9215 (m) cc_final: 0.9011 (p) REVERT: C 283 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9267 (mm-40) REVERT: C 297 LEU cc_start: 0.9303 (mm) cc_final: 0.8949 (mm) REVERT: C 298 GLN cc_start: 0.9161 (mm110) cc_final: 0.8656 (mm-40) REVERT: C 349 LYS cc_start: 0.9479 (mtmt) cc_final: 0.9234 (mtpt) REVERT: C 355 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8521 (tmm-80) REVERT: C 402 PHE cc_start: 0.8337 (m-10) cc_final: 0.8131 (m-80) REVERT: C 450 LYS cc_start: 0.6895 (pttm) cc_final: 0.6187 (ptmm) REVERT: C 465 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: C 482 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8920 (tmm) REVERT: C 489 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8530 (ttpt) REVERT: D 82 MET cc_start: 0.8800 (tpp) cc_final: 0.8370 (tpp) REVERT: D 88 ILE cc_start: 0.7492 (mt) cc_final: 0.7289 (mp) REVERT: D 104 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8702 (t) REVERT: D 108 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9225 (mtmt) REVERT: D 109 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8842 (tptp) REVERT: D 137 HIS cc_start: 0.9664 (m-70) cc_final: 0.9259 (m-70) REVERT: D 154 LEU cc_start: 0.9778 (mm) cc_final: 0.9514 (mm) REVERT: D 166 LEU cc_start: 0.8953 (pt) cc_final: 0.8058 (tp) REVERT: D 198 ASN cc_start: 0.9634 (m110) cc_final: 0.9246 (m110) REVERT: D 199 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9219 (mp0) REVERT: D 231 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8818 (ptm-80) REVERT: D 245 LEU cc_start: 0.9242 (mm) cc_final: 0.8846 (mm) REVERT: D 265 GLN cc_start: 0.9500 (mt0) cc_final: 0.9249 (tp40) REVERT: D 269 ASP cc_start: 0.9181 (t0) cc_final: 0.8228 (t0) REVERT: D 281 ILE cc_start: 0.9407 (mm) cc_final: 0.9100 (mm) REVERT: D 285 ASN cc_start: 0.9475 (m110) cc_final: 0.9214 (m110) REVERT: D 296 ASN cc_start: 0.9327 (p0) cc_final: 0.8627 (p0) REVERT: D 297 LEU cc_start: 0.9416 (mm) cc_final: 0.8939 (mm) REVERT: D 298 GLN cc_start: 0.9110 (mm110) cc_final: 0.8678 (mm-40) REVERT: D 325 MET cc_start: 0.7236 (pmm) cc_final: 0.6890 (pmm) REVERT: D 355 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8117 (ptt180) REVERT: D 372 HIS cc_start: 0.9592 (m170) cc_final: 0.9366 (m170) REVERT: D 401 PHE cc_start: 0.9309 (p90) cc_final: 0.9100 (p90) REVERT: D 402 PHE cc_start: 0.8360 (m-10) cc_final: 0.8092 (m-80) REVERT: D 450 LYS cc_start: 0.7000 (pttm) cc_final: 0.6266 (ptmm) REVERT: D 465 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: D 482 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8943 (tmm) REVERT: E 12 TYR cc_start: 0.9275 (t80) cc_final: 0.8921 (t80) REVERT: E 82 MET cc_start: 0.8844 (tpp) cc_final: 0.8436 (tpp) REVERT: E 104 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8841 (t) REVERT: E 108 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9192 (mtmt) REVERT: E 109 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8837 (tptp) REVERT: E 137 HIS cc_start: 0.9692 (m-70) cc_final: 0.9268 (m-70) REVERT: E 154 LEU cc_start: 0.9763 (mm) cc_final: 0.9512 (mm) REVERT: E 166 LEU cc_start: 0.9027 (pt) cc_final: 0.8241 (tp) REVERT: E 174 PHE cc_start: 0.9092 (m-80) cc_final: 0.8778 (m-80) REVERT: E 198 ASN cc_start: 0.9673 (m110) cc_final: 0.9287 (m110) REVERT: E 199 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9244 (mp0) REVERT: E 209 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9152 (tm) REVERT: E 229 LYS cc_start: 0.9403 (mttt) cc_final: 0.9152 (mmtt) REVERT: E 231 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8814 (ptm-80) REVERT: E 245 LEU cc_start: 0.9201 (mm) cc_final: 0.8798 (mm) REVERT: E 269 ASP cc_start: 0.9158 (t0) cc_final: 0.8328 (t0) REVERT: E 281 ILE cc_start: 0.9356 (mm) cc_final: 0.9138 (mm) REVERT: E 282 PHE cc_start: 0.8853 (m-80) cc_final: 0.8623 (m-80) REVERT: E 285 ASN cc_start: 0.9501 (m110) cc_final: 0.9280 (m110) REVERT: E 296 ASN cc_start: 0.9257 (p0) cc_final: 0.8581 (p0) REVERT: E 297 LEU cc_start: 0.9373 (mm) cc_final: 0.8997 (mm) REVERT: E 298 GLN cc_start: 0.9148 (mm110) cc_final: 0.8649 (mm-40) REVERT: E 321 LEU cc_start: 0.9770 (mm) cc_final: 0.9560 (mm) REVERT: E 325 MET cc_start: 0.7445 (pmm) cc_final: 0.7106 (pmm) REVERT: E 351 SER cc_start: 0.8581 (p) cc_final: 0.8043 (p) REVERT: E 355 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8161 (ptt180) REVERT: E 372 HIS cc_start: 0.9571 (m170) cc_final: 0.9316 (m170) REVERT: E 402 PHE cc_start: 0.8460 (m-10) cc_final: 0.8253 (m-80) REVERT: E 450 LYS cc_start: 0.6995 (pttm) cc_final: 0.6263 (ptmm) REVERT: E 465 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: E 482 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8936 (tmm) REVERT: E 489 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8511 (ttpt) REVERT: F 82 MET cc_start: 0.8785 (tpp) cc_final: 0.8336 (tpp) REVERT: F 88 ILE cc_start: 0.7440 (mt) cc_final: 0.7154 (mp) REVERT: F 109 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8898 (tptp) REVERT: F 137 HIS cc_start: 0.9666 (m-70) cc_final: 0.9279 (m-70) REVERT: F 174 PHE cc_start: 0.9056 (m-80) cc_final: 0.8689 (m-80) REVERT: F 198 ASN cc_start: 0.9660 (m110) cc_final: 0.9273 (m110) REVERT: F 199 GLU cc_start: 0.9528 (OUTLIER) cc_final: 0.9245 (mp0) REVERT: F 209 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9106 (tm) REVERT: F 231 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8839 (ptm-80) REVERT: F 232 ASP cc_start: 0.9204 (t70) cc_final: 0.8996 (m-30) REVERT: F 269 ASP cc_start: 0.9188 (t0) cc_final: 0.8279 (t0) REVERT: F 277 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8220 (tm-30) REVERT: F 281 ILE cc_start: 0.9418 (mm) cc_final: 0.9106 (mm) REVERT: F 283 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9253 (mm-40) REVERT: F 285 ASN cc_start: 0.9436 (m110) cc_final: 0.9169 (m110) REVERT: F 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8572 (p0) REVERT: F 297 LEU cc_start: 0.9435 (mm) cc_final: 0.8999 (mm) REVERT: F 298 GLN cc_start: 0.9131 (mm110) cc_final: 0.8664 (mm-40) REVERT: F 321 LEU cc_start: 0.9802 (mm) cc_final: 0.9600 (mm) REVERT: F 325 MET cc_start: 0.7134 (pmm) cc_final: 0.6795 (pmm) REVERT: F 355 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8182 (ptt180) REVERT: F 372 HIS cc_start: 0.9599 (m170) cc_final: 0.9360 (m170) REVERT: F 402 PHE cc_start: 0.8361 (m-10) cc_final: 0.8091 (m-80) REVERT: F 482 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9000 (tmm) REVERT: G 22 GLN cc_start: 0.9262 (mt0) cc_final: 0.8633 (mp10) REVERT: G 65 LEU cc_start: 0.8977 (pt) cc_final: 0.8689 (pt) REVERT: G 82 MET cc_start: 0.8854 (tpp) cc_final: 0.8452 (tpp) REVERT: G 93 HIS cc_start: 0.9159 (p90) cc_final: 0.8746 (p90) REVERT: G 94 ASN cc_start: 0.8912 (t0) cc_final: 0.8662 (t0) REVERT: G 104 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8869 (m) REVERT: G 108 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9206 (mtmt) REVERT: G 109 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8822 (tptp) REVERT: G 137 HIS cc_start: 0.9671 (m-70) cc_final: 0.9246 (m-70) REVERT: G 166 LEU cc_start: 0.9061 (pt) cc_final: 0.8330 (tp) REVERT: G 199 GLU cc_start: 0.9573 (OUTLIER) cc_final: 0.9182 (mp0) REVERT: G 209 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8940 (tm) REVERT: G 224 ARG cc_start: 0.8206 (tpt170) cc_final: 0.7560 (tpt-90) REVERT: G 231 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8822 (ptm-80) REVERT: G 245 LEU cc_start: 0.9226 (mm) cc_final: 0.8872 (mm) REVERT: G 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8319 (t0) REVERT: G 276 SER cc_start: 0.9182 (m) cc_final: 0.8958 (p) REVERT: G 283 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9326 (mm-40) REVERT: G 296 ASN cc_start: 0.9233 (p0) cc_final: 0.8560 (p0) REVERT: G 297 LEU cc_start: 0.9329 (mm) cc_final: 0.8998 (mm) REVERT: G 298 GLN cc_start: 0.9198 (mm110) cc_final: 0.8679 (mm-40) REVERT: G 351 SER cc_start: 0.8542 (p) cc_final: 0.8047 (p) REVERT: G 355 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8155 (ptt180) REVERT: G 401 PHE cc_start: 0.9311 (p90) cc_final: 0.9094 (p90) REVERT: G 402 PHE cc_start: 0.8515 (m-10) cc_final: 0.8249 (m-80) REVERT: G 450 LYS cc_start: 0.6987 (pttm) cc_final: 0.6354 (ptmm) REVERT: G 465 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: G 482 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9028 (tmm) REVERT: H 44 PHE cc_start: 0.7863 (p90) cc_final: 0.7580 (p90) REVERT: H 65 LEU cc_start: 0.8911 (pt) cc_final: 0.8600 (pt) REVERT: H 82 MET cc_start: 0.8827 (tpp) cc_final: 0.8409 (tpp) REVERT: H 88 ILE cc_start: 0.7461 (mt) cc_final: 0.7195 (mp) REVERT: H 104 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8690 (t) REVERT: H 108 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9220 (mtmt) REVERT: H 109 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8843 (tptp) REVERT: H 137 HIS cc_start: 0.9688 (m-70) cc_final: 0.9276 (m-70) REVERT: H 154 LEU cc_start: 0.9751 (mm) cc_final: 0.9502 (mm) REVERT: H 161 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.9169 (mpp80) REVERT: H 166 LEU cc_start: 0.8992 (pt) cc_final: 0.8112 (tp) REVERT: H 174 PHE cc_start: 0.9059 (m-80) cc_final: 0.8752 (m-80) REVERT: H 198 ASN cc_start: 0.9651 (m110) cc_final: 0.9244 (m110) REVERT: H 199 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9262 (mp0) REVERT: H 209 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9053 (tm) REVERT: H 231 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8858 (ptm-80) REVERT: H 245 LEU cc_start: 0.9224 (mm) cc_final: 0.8914 (mm) REVERT: H 269 ASP cc_start: 0.9170 (t0) cc_final: 0.8242 (t0) REVERT: H 283 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9266 (mm-40) REVERT: H 285 ASN cc_start: 0.9486 (m110) cc_final: 0.9238 (m110) REVERT: H 296 ASN cc_start: 0.9335 (p0) cc_final: 0.8619 (p0) REVERT: H 297 LEU cc_start: 0.9419 (mm) cc_final: 0.8988 (mm) REVERT: H 298 GLN cc_start: 0.9122 (mm110) cc_final: 0.8613 (mm-40) REVERT: H 321 LEU cc_start: 0.9783 (mm) cc_final: 0.9568 (mm) REVERT: H 325 MET cc_start: 0.7257 (pmm) cc_final: 0.6929 (pmm) REVERT: H 351 SER cc_start: 0.8605 (p) cc_final: 0.8125 (p) REVERT: H 355 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8129 (ptt180) REVERT: H 357 PHE cc_start: 0.9148 (m-80) cc_final: 0.8858 (m-80) REVERT: H 372 HIS cc_start: 0.9555 (m170) cc_final: 0.9335 (m170) REVERT: H 401 PHE cc_start: 0.9272 (p90) cc_final: 0.9058 (p90) REVERT: H 402 PHE cc_start: 0.8378 (m-10) cc_final: 0.8104 (m-80) REVERT: H 465 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: H 482 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8925 (tmm) REVERT: H 489 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8552 (ttpt) outliers start: 440 outliers final: 183 residues processed: 1615 average time/residue: 0.1967 time to fit residues: 494.2425 Evaluate side-chains 1393 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 1137 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 4.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 298 GLN A 466 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 298 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 230 ASN C 298 GLN C 343 GLN C 466 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 283 GLN D 298 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 298 GLN E 466 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 298 GLN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN F 466 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 298 GLN G 466 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 298 GLN H 466 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091741 restraints weight = 53553.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095992 restraints weight = 33706.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099255 restraints weight = 24046.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101741 restraints weight = 18557.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103669 restraints weight = 15172.164| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28872 Z= 0.161 Angle : 0.932 10.361 39136 Z= 0.452 Chirality : 0.052 0.208 4472 Planarity : 0.005 0.046 4928 Dihedral : 19.249 171.432 4368 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.74 % Allowed : 6.17 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.12), residues: 3576 helix: -2.07 (0.12), residues: 1240 sheet: -2.65 (0.20), residues: 520 loop : -2.19 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 407 TYR 0.027 0.002 TYR F 233 PHE 0.035 0.002 PHE F 456 HIS 0.003 0.001 HIS F 454 Details of bonding type rmsd covalent geometry : bond 0.00339 (28864) covalent geometry : angle 0.93212 (39136) hydrogen bonds : bond 0.04341 ( 888) hydrogen bonds : angle 6.57390 ( 2448) Misc. bond : bond 0.00224 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1478 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 SER cc_start: 0.8768 (m) cc_final: 0.8351 (t) REVERT: A 78 MET cc_start: 0.7513 (mpp) cc_final: 0.6708 (mpp) REVERT: A 82 MET cc_start: 0.8883 (tpp) cc_final: 0.8507 (tpp) REVERT: A 93 HIS cc_start: 0.9254 (p90) cc_final: 0.8861 (p90) REVERT: A 94 ASN cc_start: 0.8859 (t0) cc_final: 0.8601 (t0) REVERT: A 103 GLU cc_start: 0.9225 (mp0) cc_final: 0.9020 (mp0) REVERT: A 166 LEU cc_start: 0.8861 (pt) cc_final: 0.8305 (tp) REVERT: A 174 PHE cc_start: 0.9036 (m-80) cc_final: 0.8730 (m-80) REVERT: A 230 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8731 (m-40) REVERT: A 232 ASP cc_start: 0.9017 (m-30) cc_final: 0.8797 (m-30) REVERT: A 269 ASP cc_start: 0.9237 (t0) cc_final: 0.8394 (t0) REVERT: A 276 SER cc_start: 0.9074 (m) cc_final: 0.8810 (p) REVERT: A 285 ASN cc_start: 0.9531 (m110) cc_final: 0.9293 (m110) REVERT: A 296 ASN cc_start: 0.9342 (p0) cc_final: 0.8676 (p0) REVERT: A 297 LEU cc_start: 0.9145 (mm) cc_final: 0.8656 (mm) REVERT: A 298 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8344 (mm-40) REVERT: A 321 LEU cc_start: 0.9730 (mm) cc_final: 0.9468 (mm) REVERT: A 364 ASP cc_start: 0.8950 (t0) cc_final: 0.8690 (t0) REVERT: A 489 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7968 (ttpt) REVERT: B 66 VAL cc_start: 0.9055 (m) cc_final: 0.8316 (m) REVERT: B 67 SER cc_start: 0.8814 (m) cc_final: 0.8004 (t) REVERT: B 78 MET cc_start: 0.7510 (mpp) cc_final: 0.6644 (mpp) REVERT: B 93 HIS cc_start: 0.9281 (p90) cc_final: 0.8888 (p90) REVERT: B 94 ASN cc_start: 0.8961 (t0) cc_final: 0.8758 (t0) REVERT: B 154 LEU cc_start: 0.9672 (mm) cc_final: 0.9458 (mm) REVERT: B 166 LEU cc_start: 0.8848 (pt) cc_final: 0.8230 (tp) REVERT: B 174 PHE cc_start: 0.8956 (m-80) cc_final: 0.8630 (m-80) REVERT: B 215 ASP cc_start: 0.9026 (m-30) cc_final: 0.8630 (t0) REVERT: B 216 ASP cc_start: 0.9060 (t0) cc_final: 0.8820 (t0) REVERT: B 232 ASP cc_start: 0.9046 (m-30) cc_final: 0.8839 (m-30) REVERT: B 253 HIS cc_start: 0.9027 (t-90) cc_final: 0.8812 (t-90) REVERT: B 262 LEU cc_start: 0.9735 (tt) cc_final: 0.9529 (tt) REVERT: B 269 ASP cc_start: 0.9254 (t0) cc_final: 0.8257 (t0) REVERT: B 277 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8539 (tm-30) REVERT: B 285 ASN cc_start: 0.9430 (m110) cc_final: 0.9179 (m110) REVERT: B 291 LYS cc_start: 0.9652 (pttp) cc_final: 0.9447 (pttm) REVERT: B 296 ASN cc_start: 0.9435 (p0) cc_final: 0.8682 (p0) REVERT: B 297 LEU cc_start: 0.9306 (mm) cc_final: 0.8739 (mm) REVERT: B 298 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8267 (mm-40) REVERT: B 321 LEU cc_start: 0.9750 (mm) cc_final: 0.9506 (mm) REVERT: B 489 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7969 (ttpt) REVERT: C 67 SER cc_start: 0.8725 (m) cc_final: 0.8280 (t) REVERT: C 78 MET cc_start: 0.7454 (mpp) cc_final: 0.6820 (mpp) REVERT: C 82 MET cc_start: 0.8848 (tpp) cc_final: 0.8489 (tpp) REVERT: C 93 HIS cc_start: 0.9252 (p90) cc_final: 0.8715 (p90) REVERT: C 94 ASN cc_start: 0.8947 (t0) cc_final: 0.8678 (t0) REVERT: C 103 GLU cc_start: 0.9221 (mp0) cc_final: 0.8974 (mp0) REVERT: C 166 LEU cc_start: 0.8854 (pt) cc_final: 0.8380 (tp) REVERT: C 178 ILE cc_start: 0.9327 (mp) cc_final: 0.8849 (mp) REVERT: C 232 ASP cc_start: 0.9013 (m-30) cc_final: 0.8806 (m-30) REVERT: C 262 LEU cc_start: 0.9754 (tt) cc_final: 0.9552 (tt) REVERT: C 269 ASP cc_start: 0.9212 (t0) cc_final: 0.8332 (t0) REVERT: C 276 SER cc_start: 0.9112 (m) cc_final: 0.8849 (p) REVERT: C 281 ILE cc_start: 0.9418 (mm) cc_final: 0.9211 (mm) REVERT: C 285 ASN cc_start: 0.9481 (m110) cc_final: 0.9234 (m110) REVERT: C 297 LEU cc_start: 0.9227 (mm) cc_final: 0.8692 (mm) REVERT: C 298 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8310 (mm-40) REVERT: C 321 LEU cc_start: 0.9741 (mm) cc_final: 0.9470 (mm) REVERT: C 489 LYS cc_start: 0.8290 (ttpt) cc_final: 0.8080 (ttpt) REVERT: D 28 ASP cc_start: 0.9264 (t0) cc_final: 0.8988 (t0) REVERT: D 66 VAL cc_start: 0.9033 (m) cc_final: 0.8431 (m) REVERT: D 67 SER cc_start: 0.8794 (m) cc_final: 0.7913 (t) REVERT: D 103 GLU cc_start: 0.9137 (mp0) cc_final: 0.8934 (mp0) REVERT: D 166 LEU cc_start: 0.8782 (pt) cc_final: 0.8227 (tp) REVERT: D 215 ASP cc_start: 0.9186 (m-30) cc_final: 0.8619 (t0) REVERT: D 217 GLU cc_start: 0.9009 (mp0) cc_final: 0.8527 (mp0) REVERT: D 232 ASP cc_start: 0.8993 (m-30) cc_final: 0.8793 (m-30) REVERT: D 258 TYR cc_start: 0.9596 (t80) cc_final: 0.9062 (t80) REVERT: D 261 ASP cc_start: 0.9107 (m-30) cc_final: 0.8491 (p0) REVERT: D 262 LEU cc_start: 0.9705 (tt) cc_final: 0.9490 (tt) REVERT: D 269 ASP cc_start: 0.9213 (t0) cc_final: 0.8191 (t0) REVERT: D 277 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8436 (tm-30) REVERT: D 281 ILE cc_start: 0.9408 (mm) cc_final: 0.9172 (mm) REVERT: D 285 ASN cc_start: 0.9429 (m110) cc_final: 0.9165 (m110) REVERT: D 296 ASN cc_start: 0.9436 (p0) cc_final: 0.8693 (p0) REVERT: D 297 LEU cc_start: 0.9324 (mm) cc_final: 0.8788 (mm) REVERT: D 298 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8204 (mm-40) REVERT: D 321 LEU cc_start: 0.9730 (mm) cc_final: 0.9480 (mm) REVERT: D 353 TYR cc_start: 0.9129 (t80) cc_final: 0.8601 (t80) REVERT: D 401 PHE cc_start: 0.9359 (p90) cc_final: 0.9084 (p90) REVERT: D 450 LYS cc_start: 0.7332 (pttm) cc_final: 0.6525 (ptmm) REVERT: E 12 TYR cc_start: 0.9221 (t80) cc_final: 0.8827 (t80) REVERT: E 66 VAL cc_start: 0.9179 (m) cc_final: 0.8823 (m) REVERT: E 67 SER cc_start: 0.8791 (m) cc_final: 0.8339 (t) REVERT: E 78 MET cc_start: 0.7366 (mpp) cc_final: 0.6492 (mpp) REVERT: E 82 MET cc_start: 0.8867 (tpp) cc_final: 0.8483 (tpp) REVERT: E 93 HIS cc_start: 0.9210 (p90) cc_final: 0.8854 (p90) REVERT: E 94 ASN cc_start: 0.8871 (t0) cc_final: 0.8666 (t0) REVERT: E 146 ASP cc_start: 0.9407 (p0) cc_final: 0.9172 (p0) REVERT: E 153 ARG cc_start: 0.9344 (ttp80) cc_final: 0.8960 (tmm-80) REVERT: E 154 LEU cc_start: 0.9400 (mm) cc_final: 0.9007 (mm) REVERT: E 155 VAL cc_start: 0.9001 (t) cc_final: 0.7756 (t) REVERT: E 166 LEU cc_start: 0.8807 (pt) cc_final: 0.8211 (tp) REVERT: E 215 ASP cc_start: 0.9289 (m-30) cc_final: 0.8550 (t0) REVERT: E 230 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8737 (m-40) REVERT: E 232 ASP cc_start: 0.9032 (m-30) cc_final: 0.8825 (m-30) REVERT: E 261 ASP cc_start: 0.9277 (m-30) cc_final: 0.8577 (p0) REVERT: E 262 LEU cc_start: 0.9740 (tt) cc_final: 0.9498 (tt) REVERT: E 269 ASP cc_start: 0.9233 (t0) cc_final: 0.8364 (t0) REVERT: E 276 SER cc_start: 0.9053 (m) cc_final: 0.8801 (p) REVERT: E 285 ASN cc_start: 0.9488 (m110) cc_final: 0.9253 (m110) REVERT: E 286 MET cc_start: 0.8783 (mtm) cc_final: 0.8582 (mtt) REVERT: E 296 ASN cc_start: 0.9389 (p0) cc_final: 0.8724 (p0) REVERT: E 297 LEU cc_start: 0.9295 (mm) cc_final: 0.8760 (mm) REVERT: E 298 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8210 (mm-40) REVERT: E 321 LEU cc_start: 0.9722 (mm) cc_final: 0.9469 (mm) REVERT: E 353 TYR cc_start: 0.9143 (t80) cc_final: 0.8871 (t80) REVERT: E 364 ASP cc_start: 0.8876 (t0) cc_final: 0.8647 (t0) REVERT: E 489 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7829 (ttpt) REVERT: F 66 VAL cc_start: 0.9062 (m) cc_final: 0.8359 (m) REVERT: F 67 SER cc_start: 0.8809 (m) cc_final: 0.7924 (t) REVERT: F 78 MET cc_start: 0.7485 (mpp) cc_final: 0.6609 (mpp) REVERT: F 92 HIS cc_start: 0.8348 (p90) cc_final: 0.8069 (p90) REVERT: F 93 HIS cc_start: 0.9283 (p90) cc_final: 0.8761 (p90) REVERT: F 94 ASN cc_start: 0.8944 (t0) cc_final: 0.8589 (t0) REVERT: F 166 LEU cc_start: 0.8728 (pt) cc_final: 0.8017 (tp) REVERT: F 181 LYS cc_start: 0.9300 (mmpt) cc_final: 0.9080 (mmpt) REVERT: F 215 ASP cc_start: 0.9224 (m-30) cc_final: 0.8634 (t0) REVERT: F 216 ASP cc_start: 0.9056 (t70) cc_final: 0.8769 (t0) REVERT: F 269 ASP cc_start: 0.9249 (t0) cc_final: 0.8271 (t0) REVERT: F 277 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8496 (tm-30) REVERT: F 285 ASN cc_start: 0.9409 (m110) cc_final: 0.9142 (m110) REVERT: F 296 ASN cc_start: 0.9430 (p0) cc_final: 0.8692 (p0) REVERT: F 297 LEU cc_start: 0.9339 (mm) cc_final: 0.8813 (mm) REVERT: F 298 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8255 (mm-40) REVERT: F 321 LEU cc_start: 0.9760 (mm) cc_final: 0.9532 (mm) REVERT: F 353 TYR cc_start: 0.9115 (t80) cc_final: 0.8671 (t80) REVERT: G 65 LEU cc_start: 0.8856 (pt) cc_final: 0.8651 (pt) REVERT: G 66 VAL cc_start: 0.9089 (m) cc_final: 0.8659 (m) REVERT: G 67 SER cc_start: 0.8777 (m) cc_final: 0.8296 (t) REVERT: G 78 MET cc_start: 0.7552 (mpp) cc_final: 0.6679 (mpp) REVERT: G 82 MET cc_start: 0.8874 (tpp) cc_final: 0.8507 (tpp) REVERT: G 93 HIS cc_start: 0.9243 (p90) cc_final: 0.8735 (p90) REVERT: G 94 ASN cc_start: 0.8888 (t0) cc_final: 0.8628 (t0) REVERT: G 103 GLU cc_start: 0.9230 (mp0) cc_final: 0.9013 (mp0) REVERT: G 132 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9189 (pp20) REVERT: G 166 LEU cc_start: 0.8847 (pt) cc_final: 0.8251 (tp) REVERT: G 232 ASP cc_start: 0.9064 (m-30) cc_final: 0.8821 (m-30) REVERT: G 269 ASP cc_start: 0.9214 (t0) cc_final: 0.8369 (t0) REVERT: G 276 SER cc_start: 0.9055 (m) cc_final: 0.8777 (p) REVERT: G 285 ASN cc_start: 0.9539 (m110) cc_final: 0.9296 (m110) REVERT: G 286 MET cc_start: 0.8937 (mtm) cc_final: 0.8676 (mtt) REVERT: G 296 ASN cc_start: 0.9348 (p0) cc_final: 0.8709 (p0) REVERT: G 297 LEU cc_start: 0.9187 (mm) cc_final: 0.8718 (mm) REVERT: G 298 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8318 (mm-40) REVERT: G 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9491 (mm) REVERT: G 349 LYS cc_start: 0.9452 (mtpt) cc_final: 0.9245 (mtpt) REVERT: G 395 GLU cc_start: 0.8846 (mp0) cc_final: 0.8617 (mp0) REVERT: G 401 PHE cc_start: 0.9357 (p90) cc_final: 0.9106 (p90) REVERT: H 66 VAL cc_start: 0.9049 (m) cc_final: 0.8462 (m) REVERT: H 67 SER cc_start: 0.8774 (m) cc_final: 0.7904 (t) REVERT: H 78 MET cc_start: 0.7509 (mpp) cc_final: 0.6964 (mpp) REVERT: H 88 ILE cc_start: 0.7867 (mt) cc_final: 0.7611 (mp) REVERT: H 93 HIS cc_start: 0.9261 (p90) cc_final: 0.8874 (p90) REVERT: H 94 ASN cc_start: 0.8964 (t0) cc_final: 0.8752 (t0) REVERT: H 103 GLU cc_start: 0.9223 (mp0) cc_final: 0.8930 (mp0) REVERT: H 166 LEU cc_start: 0.8879 (pt) cc_final: 0.8302 (tp) REVERT: H 174 PHE cc_start: 0.8950 (m-80) cc_final: 0.8599 (m-80) REVERT: H 178 ILE cc_start: 0.9214 (mp) cc_final: 0.8542 (mp) REVERT: H 181 LYS cc_start: 0.9293 (mmpt) cc_final: 0.9027 (mmpt) REVERT: H 215 ASP cc_start: 0.9143 (m-30) cc_final: 0.8633 (t0) REVERT: H 217 GLU cc_start: 0.8901 (mp0) cc_final: 0.8359 (mp0) REVERT: H 258 TYR cc_start: 0.9608 (t80) cc_final: 0.9085 (t80) REVERT: H 261 ASP cc_start: 0.9204 (m-30) cc_final: 0.8456 (p0) REVERT: H 262 LEU cc_start: 0.9726 (tt) cc_final: 0.9442 (tt) REVERT: H 269 ASP cc_start: 0.9187 (t0) cc_final: 0.8214 (t0) REVERT: H 277 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8381 (tm-30) REVERT: H 285 ASN cc_start: 0.9444 (m110) cc_final: 0.9170 (m110) REVERT: H 286 MET cc_start: 0.8743 (mtm) cc_final: 0.8446 (mtt) REVERT: H 296 ASN cc_start: 0.9425 (p0) cc_final: 0.8663 (p0) REVERT: H 297 LEU cc_start: 0.9316 (mm) cc_final: 0.8785 (mm) REVERT: H 298 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8274 (mm-40) REVERT: H 321 LEU cc_start: 0.9712 (mm) cc_final: 0.9444 (mm) REVERT: H 357 PHE cc_start: 0.9173 (m-80) cc_final: 0.8797 (m-10) REVERT: H 375 LYS cc_start: 0.9520 (ptpp) cc_final: 0.9276 (ptpp) REVERT: H 401 PHE cc_start: 0.9340 (p90) cc_final: 0.9067 (p90) REVERT: H 450 LYS cc_start: 0.7226 (pttp) cc_final: 0.6796 (ptmm) outliers start: 22 outliers final: 3 residues processed: 1482 average time/residue: 0.1725 time to fit residues: 416.3046 Evaluate side-chains 1159 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1154 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 341 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089272 restraints weight = 54808.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093172 restraints weight = 35547.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.096129 restraints weight = 25848.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098428 restraints weight = 20206.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100169 restraints weight = 16668.071| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28872 Z= 0.185 Angle : 0.889 9.916 39136 Z= 0.435 Chirality : 0.050 0.193 4472 Planarity : 0.005 0.047 4928 Dihedral : 18.644 167.192 4368 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.13), residues: 3576 helix: -1.56 (0.13), residues: 1240 sheet: -3.08 (0.20), residues: 424 loop : -2.04 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 105 TYR 0.026 0.002 TYR F 233 PHE 0.042 0.002 PHE C 456 HIS 0.007 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00426 (28864) covalent geometry : angle 0.88900 (39136) hydrogen bonds : bond 0.03992 ( 888) hydrogen bonds : angle 6.23481 ( 2448) Misc. bond : bond 0.00179 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1311 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.9200 (t0) cc_final: 0.8924 (t0) REVERT: A 49 VAL cc_start: 0.8227 (t) cc_final: 0.7804 (m) REVERT: A 67 SER cc_start: 0.8737 (m) cc_final: 0.8464 (t) REVERT: A 78 MET cc_start: 0.7707 (mpp) cc_final: 0.6873 (mpp) REVERT: A 82 MET cc_start: 0.8950 (tpp) cc_final: 0.8547 (tpp) REVERT: A 93 HIS cc_start: 0.9303 (p90) cc_final: 0.8745 (p90) REVERT: A 94 ASN cc_start: 0.8874 (t0) cc_final: 0.8610 (t0) REVERT: A 103 GLU cc_start: 0.9216 (mp0) cc_final: 0.8962 (mp0) REVERT: A 166 LEU cc_start: 0.8874 (pt) cc_final: 0.8226 (tp) REVERT: A 181 LYS cc_start: 0.9393 (mmpt) cc_final: 0.9170 (mmpt) REVERT: A 199 GLU cc_start: 0.9621 (mt-10) cc_final: 0.9368 (pt0) REVERT: A 241 LYS cc_start: 0.9388 (tptp) cc_final: 0.9070 (tptp) REVERT: A 269 ASP cc_start: 0.9226 (t0) cc_final: 0.8389 (t0) REVERT: A 276 SER cc_start: 0.9169 (m) cc_final: 0.8861 (p) REVERT: A 285 ASN cc_start: 0.9559 (m110) cc_final: 0.9335 (m110) REVERT: A 286 MET cc_start: 0.8885 (mtm) cc_final: 0.8582 (mtt) REVERT: A 296 ASN cc_start: 0.9325 (p0) cc_final: 0.8644 (p0) REVERT: A 297 LEU cc_start: 0.9177 (mm) cc_final: 0.8681 (mm) REVERT: A 298 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8320 (mm-40) REVERT: A 321 LEU cc_start: 0.9721 (mm) cc_final: 0.9419 (mm) REVERT: A 369 ASN cc_start: 0.9320 (p0) cc_final: 0.9112 (p0) REVERT: A 492 LYS cc_start: 0.8366 (tptp) cc_final: 0.8037 (tptp) REVERT: A 493 ARG cc_start: 0.9317 (ttt90) cc_final: 0.9055 (ttm-80) REVERT: B 66 VAL cc_start: 0.9267 (m) cc_final: 0.8989 (m) REVERT: B 78 MET cc_start: 0.7736 (mpp) cc_final: 0.7262 (mpp) REVERT: B 166 LEU cc_start: 0.8886 (pt) cc_final: 0.8195 (tp) REVERT: B 199 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9368 (pt0) REVERT: B 229 LYS cc_start: 0.9450 (mttt) cc_final: 0.9025 (mttt) REVERT: B 261 ASP cc_start: 0.9271 (m-30) cc_final: 0.8596 (p0) REVERT: B 262 LEU cc_start: 0.9771 (tt) cc_final: 0.9541 (tt) REVERT: B 269 ASP cc_start: 0.9208 (t0) cc_final: 0.8375 (t0) REVERT: B 281 ILE cc_start: 0.9413 (mm) cc_final: 0.9179 (mm) REVERT: B 285 ASN cc_start: 0.9491 (m110) cc_final: 0.9205 (m110) REVERT: B 291 LYS cc_start: 0.9654 (pttp) cc_final: 0.9423 (pttt) REVERT: B 296 ASN cc_start: 0.9409 (p0) cc_final: 0.8556 (p0) REVERT: B 298 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8234 (mm-40) REVERT: B 321 LEU cc_start: 0.9746 (mm) cc_final: 0.9447 (mm) REVERT: B 375 LYS cc_start: 0.9512 (ptpp) cc_final: 0.9226 (ptpp) REVERT: B 450 LYS cc_start: 0.7188 (pttm) cc_final: 0.6140 (tmtt) REVERT: B 492 LYS cc_start: 0.8501 (tptp) cc_final: 0.8228 (tptp) REVERT: B 493 ARG cc_start: 0.9327 (ttt90) cc_final: 0.9107 (ttm-80) REVERT: C 28 ASP cc_start: 0.9054 (t0) cc_final: 0.8704 (t0) REVERT: C 67 SER cc_start: 0.8704 (m) cc_final: 0.8378 (t) REVERT: C 78 MET cc_start: 0.7479 (mpp) cc_final: 0.6727 (mpp) REVERT: C 82 MET cc_start: 0.8872 (tpp) cc_final: 0.8482 (tpp) REVERT: C 94 ASN cc_start: 0.8910 (t0) cc_final: 0.8697 (t0) REVERT: C 103 GLU cc_start: 0.9111 (mp0) cc_final: 0.8786 (mp0) REVERT: C 105 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8351 (ttp80) REVERT: C 109 LYS cc_start: 0.9233 (tptp) cc_final: 0.8992 (tptt) REVERT: C 166 LEU cc_start: 0.8777 (pt) cc_final: 0.8225 (tp) REVERT: C 178 ILE cc_start: 0.9282 (mp) cc_final: 0.9032 (mp) REVERT: C 261 ASP cc_start: 0.9357 (m-30) cc_final: 0.8666 (p0) REVERT: C 262 LEU cc_start: 0.9784 (tt) cc_final: 0.9572 (tt) REVERT: C 269 ASP cc_start: 0.9132 (t0) cc_final: 0.8280 (t0) REVERT: C 276 SER cc_start: 0.9205 (m) cc_final: 0.8898 (p) REVERT: C 281 ILE cc_start: 0.9416 (mm) cc_final: 0.9216 (mm) REVERT: C 285 ASN cc_start: 0.9503 (m110) cc_final: 0.9252 (m110) REVERT: C 286 MET cc_start: 0.8901 (mtm) cc_final: 0.8685 (mtt) REVERT: C 297 LEU cc_start: 0.9234 (mm) cc_final: 0.8671 (mm) REVERT: C 298 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8302 (mm-40) REVERT: C 321 LEU cc_start: 0.9752 (mm) cc_final: 0.9472 (mm) REVERT: C 372 HIS cc_start: 0.9539 (m90) cc_final: 0.9003 (m90) REVERT: C 395 GLU cc_start: 0.8853 (pm20) cc_final: 0.8464 (mp0) REVERT: C 489 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7944 (ttpt) REVERT: D 28 ASP cc_start: 0.9266 (t0) cc_final: 0.9045 (t0) REVERT: D 59 ILE cc_start: 0.9386 (pt) cc_final: 0.9160 (mp) REVERT: D 66 VAL cc_start: 0.9257 (m) cc_final: 0.8778 (m) REVERT: D 78 MET cc_start: 0.7320 (mpp) cc_final: 0.6577 (mpp) REVERT: D 109 LYS cc_start: 0.8950 (tptp) cc_final: 0.8566 (tptp) REVERT: D 119 VAL cc_start: 0.9270 (m) cc_final: 0.9061 (m) REVERT: D 134 LYS cc_start: 0.9374 (mmmt) cc_final: 0.9120 (mmmt) REVERT: D 163 ILE cc_start: 0.9404 (pt) cc_final: 0.8992 (pt) REVERT: D 166 LEU cc_start: 0.8924 (pt) cc_final: 0.8275 (tp) REVERT: D 261 ASP cc_start: 0.9255 (m-30) cc_final: 0.8511 (p0) REVERT: D 262 LEU cc_start: 0.9773 (tt) cc_final: 0.9283 (mt) REVERT: D 269 ASP cc_start: 0.9210 (t0) cc_final: 0.8272 (t0) REVERT: D 281 ILE cc_start: 0.9410 (mm) cc_final: 0.9168 (mm) REVERT: D 285 ASN cc_start: 0.9505 (m110) cc_final: 0.9213 (m110) REVERT: D 286 MET cc_start: 0.8696 (mtm) cc_final: 0.8479 (mtt) REVERT: D 296 ASN cc_start: 0.9439 (p0) cc_final: 0.8648 (p0) REVERT: D 298 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8143 (mm-40) REVERT: D 305 VAL cc_start: 0.8652 (m) cc_final: 0.7874 (p) REVERT: D 321 LEU cc_start: 0.9745 (mm) cc_final: 0.9445 (mm) REVERT: D 375 LYS cc_start: 0.9574 (ptpp) cc_final: 0.9316 (ptpp) REVERT: D 395 GLU cc_start: 0.8834 (pm20) cc_final: 0.8500 (mp0) REVERT: D 401 PHE cc_start: 0.9298 (p90) cc_final: 0.9067 (p90) REVERT: D 492 LYS cc_start: 0.8536 (tptp) cc_final: 0.8275 (tptp) REVERT: D 493 ARG cc_start: 0.9313 (ttt90) cc_final: 0.9039 (ttm-80) REVERT: E 12 TYR cc_start: 0.9194 (t80) cc_final: 0.8529 (t80) REVERT: E 49 VAL cc_start: 0.8280 (t) cc_final: 0.7819 (m) REVERT: E 66 VAL cc_start: 0.9193 (m) cc_final: 0.8705 (m) REVERT: E 67 SER cc_start: 0.8785 (m) cc_final: 0.8414 (t) REVERT: E 78 MET cc_start: 0.7629 (mpp) cc_final: 0.6764 (mpp) REVERT: E 82 MET cc_start: 0.8892 (tpp) cc_final: 0.8490 (tpp) REVERT: E 93 HIS cc_start: 0.9284 (p90) cc_final: 0.8772 (p90) REVERT: E 103 GLU cc_start: 0.9268 (mp0) cc_final: 0.9067 (mp0) REVERT: E 105 ARG cc_start: 0.8775 (mtt90) cc_final: 0.8236 (ttp80) REVERT: E 106 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8859 (mtpt) REVERT: E 109 LYS cc_start: 0.8949 (tptp) cc_final: 0.8471 (tptp) REVERT: E 166 LEU cc_start: 0.8791 (pt) cc_final: 0.8099 (tp) REVERT: E 261 ASP cc_start: 0.9331 (m-30) cc_final: 0.8622 (p0) REVERT: E 262 LEU cc_start: 0.9771 (tt) cc_final: 0.9477 (tt) REVERT: E 269 ASP cc_start: 0.9159 (t0) cc_final: 0.8330 (t0) REVERT: E 276 SER cc_start: 0.9089 (m) cc_final: 0.8767 (p) REVERT: E 285 ASN cc_start: 0.9467 (m110) cc_final: 0.9259 (m110) REVERT: E 286 MET cc_start: 0.8769 (mtm) cc_final: 0.8500 (mtt) REVERT: E 296 ASN cc_start: 0.9362 (p0) cc_final: 0.8708 (p0) REVERT: E 297 LEU cc_start: 0.9265 (mm) cc_final: 0.8741 (mm) REVERT: E 298 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8174 (mm-40) REVERT: E 305 VAL cc_start: 0.8668 (m) cc_final: 0.7871 (p) REVERT: E 321 LEU cc_start: 0.9711 (mm) cc_final: 0.9408 (mm) REVERT: E 492 LYS cc_start: 0.8469 (tptp) cc_final: 0.8087 (tptp) REVERT: E 493 ARG cc_start: 0.9277 (ttt90) cc_final: 0.8934 (ttm-80) REVERT: F 16 ASP cc_start: 0.8350 (m-30) cc_final: 0.8123 (m-30) REVERT: F 66 VAL cc_start: 0.9263 (m) cc_final: 0.8761 (m) REVERT: F 67 SER cc_start: 0.9067 (m) cc_final: 0.8850 (t) REVERT: F 78 MET cc_start: 0.7693 (mpp) cc_final: 0.6857 (mpp) REVERT: F 94 ASN cc_start: 0.9052 (t0) cc_final: 0.8753 (t0) REVERT: F 103 GLU cc_start: 0.9243 (mp0) cc_final: 0.8804 (mp0) REVERT: F 109 LYS cc_start: 0.8932 (tptp) cc_final: 0.8374 (tptp) REVERT: F 134 LYS cc_start: 0.9351 (mmmt) cc_final: 0.9101 (mmmt) REVERT: F 166 LEU cc_start: 0.8868 (pt) cc_final: 0.8111 (tp) REVERT: F 179 MET cc_start: 0.7854 (tpt) cc_final: 0.7609 (tpp) REVERT: F 181 LYS cc_start: 0.9336 (mmpt) cc_final: 0.9100 (mmpt) REVERT: F 216 ASP cc_start: 0.9059 (t70) cc_final: 0.8767 (t0) REVERT: F 229 LYS cc_start: 0.9574 (mttm) cc_final: 0.9343 (mmtm) REVERT: F 232 ASP cc_start: 0.9011 (t70) cc_final: 0.8643 (t0) REVERT: F 269 ASP cc_start: 0.9220 (t0) cc_final: 0.8406 (t0) REVERT: F 285 ASN cc_start: 0.9468 (m110) cc_final: 0.9222 (m110) REVERT: F 296 ASN cc_start: 0.9425 (p0) cc_final: 0.8639 (p0) REVERT: F 298 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8216 (mm-40) REVERT: F 321 LEU cc_start: 0.9766 (mm) cc_final: 0.9522 (mm) REVERT: F 351 SER cc_start: 0.9248 (m) cc_final: 0.9033 (p) REVERT: F 375 LYS cc_start: 0.9556 (ptpp) cc_final: 0.9331 (ptpp) REVERT: F 492 LYS cc_start: 0.8536 (tptp) cc_final: 0.8260 (tptp) REVERT: F 493 ARG cc_start: 0.9316 (ttt90) cc_final: 0.9033 (ttm-80) REVERT: G 28 ASP cc_start: 0.9188 (t0) cc_final: 0.8903 (t0) REVERT: G 66 VAL cc_start: 0.9132 (m) cc_final: 0.8541 (m) REVERT: G 67 SER cc_start: 0.8773 (m) cc_final: 0.8408 (t) REVERT: G 78 MET cc_start: 0.7728 (mpp) cc_final: 0.7214 (mpp) REVERT: G 82 MET cc_start: 0.8881 (tpp) cc_final: 0.8517 (tpp) REVERT: G 93 HIS cc_start: 0.9288 (p90) cc_final: 0.8727 (p90) REVERT: G 94 ASN cc_start: 0.8869 (t0) cc_final: 0.8589 (t0) REVERT: G 103 GLU cc_start: 0.9208 (mp0) cc_final: 0.8914 (mp0) REVERT: G 109 LYS cc_start: 0.8985 (tptp) cc_final: 0.8614 (tptp) REVERT: G 132 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9186 (pp20) REVERT: G 166 LEU cc_start: 0.8819 (pt) cc_final: 0.8177 (tp) REVERT: G 181 LYS cc_start: 0.9442 (mmpt) cc_final: 0.9237 (mmpt) REVERT: G 241 LYS cc_start: 0.9380 (tptp) cc_final: 0.9064 (tptp) REVERT: G 269 ASP cc_start: 0.9185 (t0) cc_final: 0.8328 (t0) REVERT: G 276 SER cc_start: 0.9121 (m) cc_final: 0.8818 (p) REVERT: G 285 ASN cc_start: 0.9507 (m110) cc_final: 0.9268 (m110) REVERT: G 296 ASN cc_start: 0.9338 (p0) cc_final: 0.8689 (p0) REVERT: G 297 LEU cc_start: 0.9221 (mm) cc_final: 0.8717 (mm) REVERT: G 298 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8267 (mm-40) REVERT: G 321 LEU cc_start: 0.9732 (mm) cc_final: 0.9445 (mm) REVERT: G 349 LYS cc_start: 0.9439 (mtpt) cc_final: 0.9229 (mtpt) REVERT: G 479 VAL cc_start: 0.9475 (p) cc_final: 0.9218 (t) REVERT: G 493 ARG cc_start: 0.9298 (ttt90) cc_final: 0.8937 (ttm-80) REVERT: H 66 VAL cc_start: 0.9243 (m) cc_final: 0.8480 (m) REVERT: H 67 SER cc_start: 0.9035 (m) cc_final: 0.8285 (t) REVERT: H 78 MET cc_start: 0.7386 (mpp) cc_final: 0.6741 (mpp) REVERT: H 109 LYS cc_start: 0.8968 (tptp) cc_final: 0.8544 (tptp) REVERT: H 134 LYS cc_start: 0.9333 (mmmt) cc_final: 0.9057 (mmmt) REVERT: H 166 LEU cc_start: 0.8930 (pt) cc_final: 0.8245 (tp) REVERT: H 181 LYS cc_start: 0.9277 (mmpt) cc_final: 0.8973 (mmpt) REVERT: H 199 GLU cc_start: 0.9639 (mt-10) cc_final: 0.9435 (pt0) REVERT: H 261 ASP cc_start: 0.9224 (m-30) cc_final: 0.8482 (p0) REVERT: H 262 LEU cc_start: 0.9741 (tt) cc_final: 0.9212 (mt) REVERT: H 269 ASP cc_start: 0.9192 (t0) cc_final: 0.8343 (t0) REVERT: H 285 ASN cc_start: 0.9487 (m110) cc_final: 0.9244 (m110) REVERT: H 286 MET cc_start: 0.8749 (mtm) cc_final: 0.8529 (mtt) REVERT: H 296 ASN cc_start: 0.9427 (p0) cc_final: 0.8690 (p0) REVERT: H 298 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8239 (mm-40) REVERT: H 321 LEU cc_start: 0.9739 (mm) cc_final: 0.9491 (mm) REVERT: H 364 ASP cc_start: 0.8708 (t0) cc_final: 0.8250 (t0) REVERT: H 375 LYS cc_start: 0.9542 (ptpp) cc_final: 0.9313 (ptpp) REVERT: H 395 GLU cc_start: 0.8848 (pm20) cc_final: 0.8503 (mp0) REVERT: H 401 PHE cc_start: 0.9261 (p90) cc_final: 0.9050 (p90) REVERT: H 493 ARG cc_start: 0.9337 (ttt90) cc_final: 0.9020 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 1311 average time/residue: 0.1840 time to fit residues: 385.6956 Evaluate side-chains 1057 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1057 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 322 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 232 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 343 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 465 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 230 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089265 restraints weight = 54758.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093223 restraints weight = 35156.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096235 restraints weight = 25362.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098559 restraints weight = 19735.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100390 restraints weight = 16197.275| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28872 Z= 0.161 Angle : 0.873 11.582 39136 Z= 0.424 Chirality : 0.051 0.210 4472 Planarity : 0.005 0.067 4928 Dihedral : 18.315 167.751 4368 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3576 helix: -1.28 (0.14), residues: 1224 sheet: -3.23 (0.19), residues: 424 loop : -1.93 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 480 TYR 0.027 0.002 TYR B 233 PHE 0.048 0.002 PHE F 456 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00378 (28864) covalent geometry : angle 0.87251 (39136) hydrogen bonds : bond 0.03855 ( 888) hydrogen bonds : angle 5.92496 ( 2448) Misc. bond : bond 0.00203 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1321 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.9243 (t0) cc_final: 0.8935 (t0) REVERT: A 49 VAL cc_start: 0.8218 (t) cc_final: 0.7604 (m) REVERT: A 67 SER cc_start: 0.8721 (m) cc_final: 0.8337 (t) REVERT: A 78 MET cc_start: 0.7602 (mpp) cc_final: 0.7182 (mpp) REVERT: A 82 MET cc_start: 0.8975 (tpp) cc_final: 0.8590 (tpp) REVERT: A 93 HIS cc_start: 0.9307 (p90) cc_final: 0.8719 (p90) REVERT: A 94 ASN cc_start: 0.8859 (t0) cc_final: 0.8528 (t0) REVERT: A 139 PHE cc_start: 0.8697 (p90) cc_final: 0.8059 (p90) REVERT: A 166 LEU cc_start: 0.8882 (pt) cc_final: 0.8169 (tp) REVERT: A 174 PHE cc_start: 0.8894 (m-80) cc_final: 0.8628 (m-80) REVERT: A 179 MET cc_start: 0.7635 (tpt) cc_final: 0.7165 (tpt) REVERT: A 199 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9381 (mt-10) REVERT: A 230 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8773 (m-40) REVERT: A 241 LYS cc_start: 0.9434 (tptp) cc_final: 0.9131 (tptp) REVERT: A 262 LEU cc_start: 0.9780 (tt) cc_final: 0.9425 (mt) REVERT: A 269 ASP cc_start: 0.9170 (t0) cc_final: 0.8261 (t0) REVERT: A 276 SER cc_start: 0.9182 (m) cc_final: 0.8870 (p) REVERT: A 285 ASN cc_start: 0.9568 (m110) cc_final: 0.9321 (m110) REVERT: A 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8576 (p0) REVERT: A 297 LEU cc_start: 0.9180 (mm) cc_final: 0.8736 (mm) REVERT: A 298 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8271 (mm110) REVERT: A 321 LEU cc_start: 0.9729 (mm) cc_final: 0.9441 (mm) REVERT: A 368 GLN cc_start: 0.9118 (mp10) cc_final: 0.8881 (mp-120) REVERT: A 489 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7055 (ttpt) REVERT: A 490 PHE cc_start: 0.8784 (m-80) cc_final: 0.8421 (m-80) REVERT: A 492 LYS cc_start: 0.8455 (tptp) cc_final: 0.8148 (tptp) REVERT: B 66 VAL cc_start: 0.9234 (m) cc_final: 0.8789 (m) REVERT: B 67 SER cc_start: 0.9269 (t) cc_final: 0.8243 (t) REVERT: B 78 MET cc_start: 0.7541 (mpp) cc_final: 0.6728 (mpp) REVERT: B 82 MET cc_start: 0.8916 (ttt) cc_final: 0.8576 (ttt) REVERT: B 93 HIS cc_start: 0.9329 (p90) cc_final: 0.8750 (p90) REVERT: B 94 ASN cc_start: 0.8937 (t0) cc_final: 0.8713 (t0) REVERT: B 109 LYS cc_start: 0.8793 (tptp) cc_final: 0.8274 (tptp) REVERT: B 127 VAL cc_start: 0.9097 (t) cc_final: 0.8591 (t) REVERT: B 166 LEU cc_start: 0.8930 (pt) cc_final: 0.8233 (tp) REVERT: B 181 LYS cc_start: 0.9215 (mmpt) cc_final: 0.8956 (mmpt) REVERT: B 229 LYS cc_start: 0.9433 (mttt) cc_final: 0.9037 (mttt) REVERT: B 261 ASP cc_start: 0.9261 (m-30) cc_final: 0.8694 (p0) REVERT: B 262 LEU cc_start: 0.9758 (tt) cc_final: 0.9540 (tt) REVERT: B 269 ASP cc_start: 0.9247 (t0) cc_final: 0.8267 (t0) REVERT: B 281 ILE cc_start: 0.9391 (mm) cc_final: 0.9168 (mm) REVERT: B 285 ASN cc_start: 0.9483 (m110) cc_final: 0.9192 (m110) REVERT: B 286 MET cc_start: 0.8680 (mtm) cc_final: 0.8403 (mtt) REVERT: B 296 ASN cc_start: 0.9415 (p0) cc_final: 0.8691 (p0) REVERT: B 297 LEU cc_start: 0.9238 (mm) cc_final: 0.8697 (mm) REVERT: B 298 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8223 (mm110) REVERT: B 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9495 (mm) REVERT: B 364 ASP cc_start: 0.8411 (t0) cc_final: 0.8128 (t0) REVERT: B 372 HIS cc_start: 0.9461 (m90) cc_final: 0.9057 (m170) REVERT: C 28 ASP cc_start: 0.9139 (t0) cc_final: 0.8818 (t0) REVERT: C 78 MET cc_start: 0.7913 (mpp) cc_final: 0.6970 (mpp) REVERT: C 82 MET cc_start: 0.9001 (tpp) cc_final: 0.8617 (tpp) REVERT: C 94 ASN cc_start: 0.8880 (t0) cc_final: 0.8654 (t0) REVERT: C 162 ASP cc_start: 0.9188 (m-30) cc_final: 0.8973 (m-30) REVERT: C 166 LEU cc_start: 0.8782 (pt) cc_final: 0.8095 (tp) REVERT: C 181 LYS cc_start: 0.9447 (mmpt) cc_final: 0.9198 (mmpt) REVERT: C 216 ASP cc_start: 0.8994 (t70) cc_final: 0.8697 (t70) REVERT: C 261 ASP cc_start: 0.9333 (m-30) cc_final: 0.8703 (p0) REVERT: C 262 LEU cc_start: 0.9766 (tt) cc_final: 0.9510 (tt) REVERT: C 265 GLN cc_start: 0.9556 (tm-30) cc_final: 0.9317 (tm-30) REVERT: C 281 ILE cc_start: 0.9415 (mm) cc_final: 0.9193 (mm) REVERT: C 285 ASN cc_start: 0.9510 (m110) cc_final: 0.9251 (m110) REVERT: C 297 LEU cc_start: 0.9166 (mm) cc_final: 0.8803 (mm) REVERT: C 321 LEU cc_start: 0.9732 (mm) cc_final: 0.9439 (mm) REVERT: C 364 ASP cc_start: 0.8750 (t0) cc_final: 0.8302 (t0) REVERT: C 372 HIS cc_start: 0.9493 (m90) cc_final: 0.8934 (m90) REVERT: C 450 LYS cc_start: 0.6917 (pttm) cc_final: 0.6344 (ptmm) REVERT: C 483 MET cc_start: 0.9443 (ptm) cc_final: 0.9237 (ppp) REVERT: C 489 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7539 (mtpt) REVERT: C 490 PHE cc_start: 0.8894 (m-80) cc_final: 0.8661 (m-80) REVERT: D 28 ASP cc_start: 0.9304 (t0) cc_final: 0.9024 (t0) REVERT: D 67 SER cc_start: 0.9305 (t) cc_final: 0.9083 (t) REVERT: D 78 MET cc_start: 0.7308 (mpp) cc_final: 0.6325 (mpp) REVERT: D 94 ASN cc_start: 0.8947 (t0) cc_final: 0.8735 (t0) REVERT: D 130 VAL cc_start: 0.9573 (m) cc_final: 0.9218 (m) REVERT: D 134 LYS cc_start: 0.9430 (mmmt) cc_final: 0.9058 (mmmt) REVERT: D 163 ILE cc_start: 0.9390 (pt) cc_final: 0.8940 (pt) REVERT: D 166 LEU cc_start: 0.8951 (pt) cc_final: 0.8216 (tp) REVERT: D 181 LYS cc_start: 0.9316 (mmpt) cc_final: 0.9058 (mmmt) REVERT: D 261 ASP cc_start: 0.9250 (m-30) cc_final: 0.8494 (p0) REVERT: D 262 LEU cc_start: 0.9753 (tt) cc_final: 0.9158 (mt) REVERT: D 269 ASP cc_start: 0.9161 (t0) cc_final: 0.8304 (t0) REVERT: D 276 SER cc_start: 0.9115 (m) cc_final: 0.8815 (p) REVERT: D 281 ILE cc_start: 0.9424 (mm) cc_final: 0.9207 (mm) REVERT: D 285 ASN cc_start: 0.9531 (m110) cc_final: 0.9233 (m110) REVERT: D 286 MET cc_start: 0.8768 (mtm) cc_final: 0.8455 (mtt) REVERT: D 296 ASN cc_start: 0.9418 (p0) cc_final: 0.8572 (p0) REVERT: D 298 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8234 (mm110) REVERT: D 321 LEU cc_start: 0.9740 (mm) cc_final: 0.9435 (mm) REVERT: D 353 TYR cc_start: 0.9250 (t80) cc_final: 0.8895 (t80) REVERT: D 364 ASP cc_start: 0.8468 (t0) cc_final: 0.8153 (t0) REVERT: D 372 HIS cc_start: 0.9507 (m90) cc_final: 0.8913 (m90) REVERT: D 395 GLU cc_start: 0.8859 (pm20) cc_final: 0.8577 (pm20) REVERT: D 492 LYS cc_start: 0.8635 (tptp) cc_final: 0.8401 (tptp) REVERT: E 12 TYR cc_start: 0.9227 (t80) cc_final: 0.8559 (t80) REVERT: E 49 VAL cc_start: 0.8109 (t) cc_final: 0.7569 (m) REVERT: E 66 VAL cc_start: 0.9188 (m) cc_final: 0.8704 (m) REVERT: E 78 MET cc_start: 0.7525 (mpp) cc_final: 0.7036 (mpp) REVERT: E 82 MET cc_start: 0.8962 (tpp) cc_final: 0.8578 (tpp) REVERT: E 93 HIS cc_start: 0.9252 (p90) cc_final: 0.8705 (p90) REVERT: E 94 ASN cc_start: 0.8880 (t0) cc_final: 0.8644 (t0) REVERT: E 103 GLU cc_start: 0.9160 (mp0) cc_final: 0.8909 (mp0) REVERT: E 105 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8339 (ttp80) REVERT: E 109 LYS cc_start: 0.9108 (tptp) cc_final: 0.8660 (tptp) REVERT: E 166 LEU cc_start: 0.8853 (pt) cc_final: 0.8122 (tp) REVERT: E 230 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8744 (m-40) REVERT: E 261 ASP cc_start: 0.9322 (m-30) cc_final: 0.8588 (p0) REVERT: E 262 LEU cc_start: 0.9774 (tt) cc_final: 0.9196 (mt) REVERT: E 269 ASP cc_start: 0.9161 (t0) cc_final: 0.8302 (t0) REVERT: E 296 ASN cc_start: 0.9373 (p0) cc_final: 0.8542 (p0) REVERT: E 298 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8173 (mm110) REVERT: E 368 GLN cc_start: 0.9125 (mp10) cc_final: 0.8914 (mp-120) REVERT: E 489 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7330 (ttpt) REVERT: E 490 PHE cc_start: 0.8953 (m-80) cc_final: 0.8515 (m-80) REVERT: E 492 LYS cc_start: 0.8607 (tptp) cc_final: 0.8372 (tptp) REVERT: F 28 ASP cc_start: 0.9247 (t0) cc_final: 0.8828 (t0) REVERT: F 66 VAL cc_start: 0.9261 (m) cc_final: 0.8977 (p) REVERT: F 67 SER cc_start: 0.9149 (m) cc_final: 0.8541 (t) REVERT: F 78 MET cc_start: 0.7976 (mpp) cc_final: 0.7367 (mpp) REVERT: F 82 MET cc_start: 0.8811 (ttt) cc_final: 0.8547 (ttt) REVERT: F 134 LYS cc_start: 0.9381 (mmmt) cc_final: 0.9105 (mmmt) REVERT: F 154 LEU cc_start: 0.9580 (mm) cc_final: 0.9357 (mm) REVERT: F 166 LEU cc_start: 0.8894 (pt) cc_final: 0.8125 (tp) REVERT: F 179 MET cc_start: 0.7766 (tpt) cc_final: 0.7566 (tpt) REVERT: F 261 ASP cc_start: 0.9301 (m-30) cc_final: 0.8727 (p0) REVERT: F 262 LEU cc_start: 0.9744 (tt) cc_final: 0.9484 (tt) REVERT: F 269 ASP cc_start: 0.9144 (t0) cc_final: 0.8318 (t0) REVERT: F 296 ASN cc_start: 0.9424 (p0) cc_final: 0.8610 (p0) REVERT: F 298 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8210 (mm-40) REVERT: F 321 LEU cc_start: 0.9752 (mm) cc_final: 0.9493 (mm) REVERT: F 353 TYR cc_start: 0.9211 (t80) cc_final: 0.8792 (t80) REVERT: F 364 ASP cc_start: 0.8452 (t0) cc_final: 0.8122 (t0) REVERT: F 372 HIS cc_start: 0.9507 (m90) cc_final: 0.8909 (m90) REVERT: F 401 PHE cc_start: 0.9301 (p90) cc_final: 0.9062 (p90) REVERT: F 492 LYS cc_start: 0.8577 (tptp) cc_final: 0.8327 (tptp) REVERT: G 28 ASP cc_start: 0.9218 (t0) cc_final: 0.8893 (t0) REVERT: G 65 LEU cc_start: 0.8893 (pt) cc_final: 0.8692 (pt) REVERT: G 66 VAL cc_start: 0.9148 (m) cc_final: 0.8547 (m) REVERT: G 78 MET cc_start: 0.7620 (mpp) cc_final: 0.6745 (mpp) REVERT: G 82 MET cc_start: 0.8923 (tpp) cc_final: 0.8579 (tpp) REVERT: G 94 ASN cc_start: 0.8871 (t0) cc_final: 0.8589 (t0) REVERT: G 166 LEU cc_start: 0.8859 (pt) cc_final: 0.8193 (tp) REVERT: G 174 PHE cc_start: 0.8934 (m-80) cc_final: 0.8617 (m-80) REVERT: G 179 MET cc_start: 0.7428 (tpt) cc_final: 0.7065 (tpt) REVERT: G 181 LYS cc_start: 0.9417 (mmpt) cc_final: 0.9186 (mmpt) REVERT: G 241 LYS cc_start: 0.9389 (tptp) cc_final: 0.9098 (tptp) REVERT: G 262 LEU cc_start: 0.9779 (tt) cc_final: 0.9413 (mt) REVERT: G 269 ASP cc_start: 0.9178 (t0) cc_final: 0.8301 (t0) REVERT: G 276 SER cc_start: 0.9113 (m) cc_final: 0.8825 (p) REVERT: G 285 ASN cc_start: 0.9556 (m110) cc_final: 0.9335 (m110) REVERT: G 296 ASN cc_start: 0.9341 (p0) cc_final: 0.8651 (p0) REVERT: G 297 LEU cc_start: 0.9205 (mm) cc_final: 0.8743 (mm) REVERT: G 298 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8325 (mm110) REVERT: G 321 LEU cc_start: 0.9738 (mm) cc_final: 0.9460 (mm) REVERT: G 372 HIS cc_start: 0.9517 (m170) cc_final: 0.9133 (m170) REVERT: G 401 PHE cc_start: 0.9362 (p90) cc_final: 0.9124 (p90) REVERT: G 490 PHE cc_start: 0.8868 (m-80) cc_final: 0.8196 (m-80) REVERT: H 28 ASP cc_start: 0.9330 (t0) cc_final: 0.8976 (t0) REVERT: H 66 VAL cc_start: 0.9383 (m) cc_final: 0.8957 (p) REVERT: H 67 SER cc_start: 0.9341 (m) cc_final: 0.8503 (t) REVERT: H 78 MET cc_start: 0.7400 (mpp) cc_final: 0.6381 (mpp) REVERT: H 130 VAL cc_start: 0.9591 (m) cc_final: 0.9160 (m) REVERT: H 134 LYS cc_start: 0.9432 (mmmt) cc_final: 0.9047 (mmmt) REVERT: H 161 ARG cc_start: 0.9473 (mtm180) cc_final: 0.9247 (mtm-85) REVERT: H 163 ILE cc_start: 0.9430 (pt) cc_final: 0.9001 (pt) REVERT: H 166 LEU cc_start: 0.8970 (pt) cc_final: 0.8025 (tp) REVERT: H 181 LYS cc_start: 0.9258 (mmpt) cc_final: 0.8906 (mmpt) REVERT: H 261 ASP cc_start: 0.9201 (m-30) cc_final: 0.8548 (p0) REVERT: H 262 LEU cc_start: 0.9738 (tt) cc_final: 0.9233 (mt) REVERT: H 269 ASP cc_start: 0.9146 (t0) cc_final: 0.8293 (t0) REVERT: H 285 ASN cc_start: 0.9491 (m110) cc_final: 0.9252 (m110) REVERT: H 286 MET cc_start: 0.8768 (mtm) cc_final: 0.8405 (mtt) REVERT: H 296 ASN cc_start: 0.9417 (p0) cc_final: 0.8574 (p0) REVERT: H 298 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8260 (mm110) REVERT: H 321 LEU cc_start: 0.9752 (mm) cc_final: 0.9472 (mm) REVERT: H 385 MET cc_start: 0.9108 (ttm) cc_final: 0.8732 (ttm) REVERT: H 395 GLU cc_start: 0.8906 (pm20) cc_final: 0.8464 (pm20) REVERT: H 493 ARG cc_start: 0.9326 (ttt90) cc_final: 0.9104 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 1321 average time/residue: 0.1764 time to fit residues: 374.2854 Evaluate side-chains 1030 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1028 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 250 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 299 optimal weight: 0.0070 chunk 279 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN F 230 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090953 restraints weight = 53984.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094972 restraints weight = 34854.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098035 restraints weight = 25265.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100373 restraints weight = 19704.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102180 restraints weight = 16243.939| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28872 Z= 0.144 Angle : 0.869 11.808 39136 Z= 0.414 Chirality : 0.050 0.206 4472 Planarity : 0.004 0.066 4928 Dihedral : 17.968 170.239 4368 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.13), residues: 3576 helix: -1.15 (0.14), residues: 1232 sheet: -3.22 (0.21), residues: 344 loop : -1.99 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 480 TYR 0.031 0.002 TYR D 233 PHE 0.038 0.002 PHE F 456 HIS 0.010 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00329 (28864) covalent geometry : angle 0.86909 (39136) hydrogen bonds : bond 0.03569 ( 888) hydrogen bonds : angle 5.65545 ( 2448) Misc. bond : bond 0.00214 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1346 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.9251 (t0) cc_final: 0.8956 (t0) REVERT: A 65 LEU cc_start: 0.8859 (pt) cc_final: 0.8624 (pt) REVERT: A 66 VAL cc_start: 0.8949 (m) cc_final: 0.8163 (m) REVERT: A 78 MET cc_start: 0.7454 (mpp) cc_final: 0.6747 (mpp) REVERT: A 82 MET cc_start: 0.8906 (tpp) cc_final: 0.8686 (tpp) REVERT: A 94 ASN cc_start: 0.8895 (t0) cc_final: 0.8650 (t0) REVERT: A 102 ASN cc_start: 0.9406 (t0) cc_final: 0.9187 (m-40) REVERT: A 105 ARG cc_start: 0.9000 (mmt-90) cc_final: 0.8783 (mmt90) REVERT: A 166 LEU cc_start: 0.8960 (pt) cc_final: 0.8262 (tp) REVERT: A 179 MET cc_start: 0.7453 (tpt) cc_final: 0.7047 (tpt) REVERT: A 241 LYS cc_start: 0.9415 (tptp) cc_final: 0.9122 (tptp) REVERT: A 261 ASP cc_start: 0.9384 (m-30) cc_final: 0.8708 (p0) REVERT: A 262 LEU cc_start: 0.9785 (tt) cc_final: 0.9239 (mt) REVERT: A 269 ASP cc_start: 0.9185 (t0) cc_final: 0.8245 (t0) REVERT: A 276 SER cc_start: 0.9194 (m) cc_final: 0.8868 (p) REVERT: A 285 ASN cc_start: 0.9566 (m110) cc_final: 0.9332 (m110) REVERT: A 296 ASN cc_start: 0.9369 (p0) cc_final: 0.8655 (p0) REVERT: A 297 LEU cc_start: 0.9004 (mm) cc_final: 0.8540 (mm) REVERT: A 298 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8277 (mm110) REVERT: A 372 HIS cc_start: 0.9437 (m90) cc_final: 0.9095 (m90) REVERT: A 456 PHE cc_start: 0.9618 (t80) cc_final: 0.9382 (t80) REVERT: A 489 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7964 (ttmt) REVERT: A 490 PHE cc_start: 0.8836 (m-80) cc_final: 0.8436 (m-80) REVERT: B 61 LEU cc_start: 0.8665 (mt) cc_final: 0.8437 (mp) REVERT: B 67 SER cc_start: 0.9561 (t) cc_final: 0.9303 (t) REVERT: B 78 MET cc_start: 0.7312 (mpp) cc_final: 0.6529 (mpp) REVERT: B 93 HIS cc_start: 0.9361 (p90) cc_final: 0.8743 (p90) REVERT: B 94 ASN cc_start: 0.8910 (t0) cc_final: 0.8677 (t0) REVERT: B 109 LYS cc_start: 0.8855 (tptp) cc_final: 0.8316 (tptp) REVERT: B 132 GLU cc_start: 0.9424 (pp20) cc_final: 0.9217 (pp20) REVERT: B 166 LEU cc_start: 0.8985 (pt) cc_final: 0.8286 (tp) REVERT: B 174 PHE cc_start: 0.8661 (m-80) cc_final: 0.8451 (m-80) REVERT: B 199 GLU cc_start: 0.9582 (mt-10) cc_final: 0.9366 (mt-10) REVERT: B 229 LYS cc_start: 0.9452 (mttt) cc_final: 0.8848 (mttt) REVERT: B 242 LYS cc_start: 0.8841 (tptm) cc_final: 0.8516 (tptp) REVERT: B 261 ASP cc_start: 0.9228 (m-30) cc_final: 0.8701 (p0) REVERT: B 262 LEU cc_start: 0.9754 (tt) cc_final: 0.9520 (tt) REVERT: B 269 ASP cc_start: 0.9247 (t0) cc_final: 0.8632 (t70) REVERT: B 296 ASN cc_start: 0.9503 (p0) cc_final: 0.8758 (p0) REVERT: B 297 LEU cc_start: 0.8993 (mm) cc_final: 0.8548 (mm) REVERT: B 298 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8344 (mm110) REVERT: B 372 HIS cc_start: 0.9490 (m90) cc_final: 0.8859 (m90) REVERT: B 450 LYS cc_start: 0.7052 (pttm) cc_final: 0.6209 (ptmm) REVERT: B 465 GLN cc_start: 0.9196 (mt0) cc_final: 0.8844 (pt0) REVERT: B 489 LYS cc_start: 0.7733 (ttpt) cc_final: 0.7250 (ttpt) REVERT: B 490 PHE cc_start: 0.8974 (m-80) cc_final: 0.8580 (m-80) REVERT: C 24 PHE cc_start: 0.8239 (m-80) cc_final: 0.7884 (m-80) REVERT: C 65 LEU cc_start: 0.8982 (pt) cc_final: 0.8731 (pt) REVERT: C 75 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C 78 MET cc_start: 0.7819 (mpp) cc_final: 0.6687 (mpp) REVERT: C 82 MET cc_start: 0.8926 (tpp) cc_final: 0.8517 (tpp) REVERT: C 94 ASN cc_start: 0.8805 (t0) cc_final: 0.8557 (t0) REVERT: C 109 LYS cc_start: 0.9205 (tptp) cc_final: 0.8992 (tptt) REVERT: C 166 LEU cc_start: 0.8770 (pt) cc_final: 0.8080 (tp) REVERT: C 216 ASP cc_start: 0.8972 (t70) cc_final: 0.8696 (t70) REVERT: C 269 ASP cc_start: 0.9251 (t70) cc_final: 0.8445 (t70) REVERT: C 286 MET cc_start: 0.8849 (mtm) cc_final: 0.8541 (mtt) REVERT: C 298 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8347 (mm110) REVERT: C 321 LEU cc_start: 0.9746 (mm) cc_final: 0.9496 (mm) REVERT: C 364 ASP cc_start: 0.8836 (t0) cc_final: 0.8534 (t0) REVERT: C 372 HIS cc_start: 0.9480 (m90) cc_final: 0.8922 (m90) REVERT: C 395 GLU cc_start: 0.9223 (pm20) cc_final: 0.8952 (pm20) REVERT: C 450 LYS cc_start: 0.6889 (pttm) cc_final: 0.6482 (ptmm) REVERT: C 489 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7490 (mtpt) REVERT: C 490 PHE cc_start: 0.8973 (m-80) cc_final: 0.8630 (m-80) REVERT: D 28 ASP cc_start: 0.9301 (t0) cc_final: 0.9043 (t0) REVERT: D 66 VAL cc_start: 0.9260 (p) cc_final: 0.8320 (p) REVERT: D 67 SER cc_start: 0.9573 (t) cc_final: 0.8419 (t) REVERT: D 75 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7973 (tm-30) REVERT: D 78 MET cc_start: 0.7267 (mpp) cc_final: 0.6439 (mpp) REVERT: D 82 MET cc_start: 0.9070 (ttt) cc_final: 0.8765 (ttt) REVERT: D 94 ASN cc_start: 0.8923 (t0) cc_final: 0.8717 (t0) REVERT: D 130 VAL cc_start: 0.9590 (m) cc_final: 0.9309 (m) REVERT: D 134 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9030 (mmmt) REVERT: D 166 LEU cc_start: 0.8996 (pt) cc_final: 0.8296 (tp) REVERT: D 174 PHE cc_start: 0.9004 (m-80) cc_final: 0.8742 (m-80) REVERT: D 261 ASP cc_start: 0.9258 (m-30) cc_final: 0.8615 (p0) REVERT: D 269 ASP cc_start: 0.9189 (t0) cc_final: 0.8255 (t0) REVERT: D 276 SER cc_start: 0.9135 (m) cc_final: 0.8845 (p) REVERT: D 281 ILE cc_start: 0.9423 (mm) cc_final: 0.9211 (mm) REVERT: D 285 ASN cc_start: 0.9529 (m110) cc_final: 0.9266 (m110) REVERT: D 286 MET cc_start: 0.8745 (mtm) cc_final: 0.8462 (mtt) REVERT: D 296 ASN cc_start: 0.9431 (p0) cc_final: 0.8745 (p0) REVERT: D 297 LEU cc_start: 0.9174 (mm) cc_final: 0.8626 (mm) REVERT: D 298 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8154 (mm110) REVERT: D 353 TYR cc_start: 0.9237 (t80) cc_final: 0.8972 (t80) REVERT: D 372 HIS cc_start: 0.9414 (m90) cc_final: 0.8853 (m90) REVERT: D 385 MET cc_start: 0.9292 (ttm) cc_final: 0.9082 (ttm) REVERT: D 401 PHE cc_start: 0.9318 (p90) cc_final: 0.9103 (p90) REVERT: D 490 PHE cc_start: 0.8929 (m-80) cc_final: 0.8133 (m-80) REVERT: E 12 TYR cc_start: 0.9261 (t80) cc_final: 0.8605 (t80) REVERT: E 65 LEU cc_start: 0.8972 (pt) cc_final: 0.8760 (pt) REVERT: E 66 VAL cc_start: 0.9129 (m) cc_final: 0.8399 (m) REVERT: E 67 SER cc_start: 0.9367 (t) cc_final: 0.8928 (t) REVERT: E 78 MET cc_start: 0.7342 (mpp) cc_final: 0.6552 (mpp) REVERT: E 82 MET cc_start: 0.8921 (tpp) cc_final: 0.8536 (tpp) REVERT: E 93 HIS cc_start: 0.9267 (p90) cc_final: 0.8698 (p90) REVERT: E 94 ASN cc_start: 0.8890 (t0) cc_final: 0.8632 (t0) REVERT: E 166 LEU cc_start: 0.8918 (pt) cc_final: 0.8198 (tp) REVERT: E 174 PHE cc_start: 0.8980 (m-80) cc_final: 0.8761 (m-80) REVERT: E 229 LYS cc_start: 0.9430 (mttt) cc_final: 0.9137 (mttt) REVERT: E 261 ASP cc_start: 0.9258 (m-30) cc_final: 0.8608 (p0) REVERT: E 262 LEU cc_start: 0.9763 (tt) cc_final: 0.9502 (tt) REVERT: E 269 ASP cc_start: 0.9178 (t0) cc_final: 0.8216 (t70) REVERT: E 286 MET cc_start: 0.8880 (mtm) cc_final: 0.8649 (mtt) REVERT: E 296 ASN cc_start: 0.9373 (p0) cc_final: 0.8685 (p0) REVERT: E 297 LEU cc_start: 0.9113 (mm) cc_final: 0.8642 (mm) REVERT: E 298 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8196 (mm110) REVERT: E 372 HIS cc_start: 0.9460 (m90) cc_final: 0.8833 (m90) REVERT: E 456 PHE cc_start: 0.9626 (t80) cc_final: 0.9366 (t80) REVERT: E 489 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8037 (ttmt) REVERT: E 490 PHE cc_start: 0.8940 (m-80) cc_final: 0.8584 (m-80) REVERT: F 28 ASP cc_start: 0.9272 (t0) cc_final: 0.8919 (t0) REVERT: F 66 VAL cc_start: 0.9437 (m) cc_final: 0.8939 (p) REVERT: F 67 SER cc_start: 0.9539 (m) cc_final: 0.8663 (t) REVERT: F 75 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 78 MET cc_start: 0.7633 (mpp) cc_final: 0.6902 (mpp) REVERT: F 94 ASN cc_start: 0.8846 (t0) cc_final: 0.8626 (t0) REVERT: F 130 VAL cc_start: 0.9579 (m) cc_final: 0.9208 (m) REVERT: F 134 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9009 (mmmt) REVERT: F 166 LEU cc_start: 0.8951 (pt) cc_final: 0.8136 (tp) REVERT: F 261 ASP cc_start: 0.9263 (m-30) cc_final: 0.8681 (p0) REVERT: F 262 LEU cc_start: 0.9739 (tt) cc_final: 0.9471 (tt) REVERT: F 269 ASP cc_start: 0.9147 (t0) cc_final: 0.8145 (t0) REVERT: F 296 ASN cc_start: 0.9425 (p0) cc_final: 0.8744 (p0) REVERT: F 297 LEU cc_start: 0.9175 (mm) cc_final: 0.8651 (mm) REVERT: F 298 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8267 (mm110) REVERT: F 353 TYR cc_start: 0.9191 (t80) cc_final: 0.8942 (t80) REVERT: F 372 HIS cc_start: 0.9434 (m90) cc_final: 0.8889 (m90) REVERT: F 385 MET cc_start: 0.9240 (ttm) cc_final: 0.8990 (ttm) REVERT: F 401 PHE cc_start: 0.9297 (p90) cc_final: 0.9087 (p90) REVERT: F 489 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7153 (ttpt) REVERT: F 490 PHE cc_start: 0.8958 (m-80) cc_final: 0.8072 (m-80) REVERT: F 492 LYS cc_start: 0.8633 (tptp) cc_final: 0.8364 (tptp) REVERT: F 493 ARG cc_start: 0.9171 (ttm-80) cc_final: 0.8905 (ttm-80) REVERT: G 67 SER cc_start: 0.9418 (t) cc_final: 0.8825 (t) REVERT: G 78 MET cc_start: 0.7471 (mpp) cc_final: 0.6678 (mpp) REVERT: G 82 MET cc_start: 0.8950 (tpp) cc_final: 0.8629 (tpp) REVERT: G 94 ASN cc_start: 0.8882 (t0) cc_final: 0.8643 (t0) REVERT: G 105 ARG cc_start: 0.9082 (mmt-90) cc_final: 0.8832 (mmt90) REVERT: G 166 LEU cc_start: 0.8873 (pt) cc_final: 0.8143 (tp) REVERT: G 179 MET cc_start: 0.7125 (tpt) cc_final: 0.6843 (tpt) REVERT: G 241 LYS cc_start: 0.9312 (tptp) cc_final: 0.9005 (tptp) REVERT: G 262 LEU cc_start: 0.9783 (tt) cc_final: 0.9424 (mt) REVERT: G 269 ASP cc_start: 0.9170 (t0) cc_final: 0.8221 (t0) REVERT: G 276 SER cc_start: 0.9130 (m) cc_final: 0.8806 (p) REVERT: G 285 ASN cc_start: 0.9577 (m110) cc_final: 0.9369 (m110) REVERT: G 296 ASN cc_start: 0.9358 (p0) cc_final: 0.8683 (p0) REVERT: G 297 LEU cc_start: 0.9102 (mm) cc_final: 0.8706 (mm) REVERT: G 298 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8226 (mm110) REVERT: G 369 ASN cc_start: 0.9185 (p0) cc_final: 0.8646 (p0) REVERT: G 372 HIS cc_start: 0.9436 (m170) cc_final: 0.9143 (m170) REVERT: G 456 PHE cc_start: 0.9637 (t80) cc_final: 0.9384 (t80) REVERT: G 489 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7101 (ttpt) REVERT: G 490 PHE cc_start: 0.8915 (m-80) cc_final: 0.8253 (m-80) REVERT: G 492 LYS cc_start: 0.8472 (tmtt) cc_final: 0.8260 (tmtt) REVERT: H 28 ASP cc_start: 0.9275 (t0) cc_final: 0.8816 (t0) REVERT: H 66 VAL cc_start: 0.9285 (m) cc_final: 0.8807 (p) REVERT: H 67 SER cc_start: 0.9454 (m) cc_final: 0.8495 (t) REVERT: H 75 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7986 (tm-30) REVERT: H 78 MET cc_start: 0.7333 (mpp) cc_final: 0.6374 (mpp) REVERT: H 82 MET cc_start: 0.8857 (ttt) cc_final: 0.8544 (ttt) REVERT: H 105 ARG cc_start: 0.9075 (mmt90) cc_final: 0.8801 (tpp-160) REVERT: H 161 ARG cc_start: 0.9449 (mtm180) cc_final: 0.9217 (mtm-85) REVERT: H 163 ILE cc_start: 0.9391 (pt) cc_final: 0.9020 (pt) REVERT: H 166 LEU cc_start: 0.8891 (pt) cc_final: 0.7928 (tp) REVERT: H 181 LYS cc_start: 0.9241 (mmpt) cc_final: 0.8995 (mmpt) REVERT: H 261 ASP cc_start: 0.9225 (m-30) cc_final: 0.8601 (p0) REVERT: H 262 LEU cc_start: 0.9739 (tt) cc_final: 0.9430 (tt) REVERT: H 269 ASP cc_start: 0.9149 (t0) cc_final: 0.8290 (t0) REVERT: H 285 ASN cc_start: 0.9479 (m110) cc_final: 0.9264 (m110) REVERT: H 286 MET cc_start: 0.8742 (mtm) cc_final: 0.8272 (mtt) REVERT: H 296 ASN cc_start: 0.9442 (p0) cc_final: 0.8805 (p0) REVERT: H 297 LEU cc_start: 0.9209 (mm) cc_final: 0.8669 (mm) REVERT: H 298 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8234 (mm-40) REVERT: H 372 HIS cc_start: 0.9545 (m170) cc_final: 0.9222 (m170) REVERT: H 456 PHE cc_start: 0.9633 (t80) cc_final: 0.9357 (t80) REVERT: H 489 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7393 (ttpt) REVERT: H 490 PHE cc_start: 0.9104 (m-80) cc_final: 0.8721 (m-80) outliers start: 2 outliers final: 2 residues processed: 1346 average time/residue: 0.1660 time to fit residues: 362.4190 Evaluate side-chains 1084 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1082 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 14 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 448 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 GLN F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084546 restraints weight = 58472.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088143 restraints weight = 38698.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090842 restraints weight = 28472.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092902 restraints weight = 22552.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094299 restraints weight = 18804.066| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 28872 Z= 0.261 Angle : 0.903 10.880 39136 Z= 0.452 Chirality : 0.052 0.228 4472 Planarity : 0.005 0.057 4928 Dihedral : 17.966 170.388 4368 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.13), residues: 3576 helix: -1.35 (0.13), residues: 1232 sheet: -3.02 (0.23), residues: 344 loop : -1.94 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 480 TYR 0.036 0.003 TYR H 233 PHE 0.040 0.002 PHE F 456 HIS 0.004 0.002 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00582 (28864) covalent geometry : angle 0.90339 (39136) hydrogen bonds : bond 0.03909 ( 888) hydrogen bonds : angle 5.85531 ( 2448) Misc. bond : bond 0.00176 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1259 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.9026 (mp) cc_final: 0.8822 (mp) REVERT: A 75 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 78 MET cc_start: 0.8079 (mpp) cc_final: 0.7363 (mpp) REVERT: A 82 MET cc_start: 0.9003 (tpp) cc_final: 0.8738 (tpp) REVERT: A 88 ILE cc_start: 0.7745 (pt) cc_final: 0.7216 (pt) REVERT: A 94 ASN cc_start: 0.8887 (t0) cc_final: 0.8612 (t0) REVERT: A 102 ASN cc_start: 0.9463 (t0) cc_final: 0.9206 (m-40) REVERT: A 109 LYS cc_start: 0.8819 (tptp) cc_final: 0.8201 (tptp) REVERT: A 166 LEU cc_start: 0.9096 (pt) cc_final: 0.8444 (tp) REVERT: A 178 ILE cc_start: 0.9370 (mp) cc_final: 0.8817 (mp) REVERT: A 261 ASP cc_start: 0.9365 (m-30) cc_final: 0.8821 (p0) REVERT: A 262 LEU cc_start: 0.9777 (tt) cc_final: 0.9188 (mt) REVERT: A 269 ASP cc_start: 0.9097 (t0) cc_final: 0.8287 (t0) REVERT: A 285 ASN cc_start: 0.9577 (m110) cc_final: 0.9345 (m110) REVERT: A 296 ASN cc_start: 0.9354 (p0) cc_final: 0.8571 (p0) REVERT: A 298 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8340 (mm-40) REVERT: A 479 VAL cc_start: 0.9425 (p) cc_final: 0.9156 (t) REVERT: B 67 SER cc_start: 0.9664 (t) cc_final: 0.9423 (t) REVERT: B 78 MET cc_start: 0.8262 (mpp) cc_final: 0.8011 (mpp) REVERT: B 163 ILE cc_start: 0.9520 (pt) cc_final: 0.9182 (pt) REVERT: B 166 LEU cc_start: 0.9147 (pt) cc_final: 0.8425 (tp) REVERT: B 184 ASP cc_start: 0.9367 (p0) cc_final: 0.9089 (p0) REVERT: B 229 LYS cc_start: 0.9489 (mttt) cc_final: 0.9186 (mttt) REVERT: B 261 ASP cc_start: 0.9252 (m-30) cc_final: 0.8767 (p0) REVERT: B 269 ASP cc_start: 0.9261 (t0) cc_final: 0.8682 (t70) REVERT: B 281 ILE cc_start: 0.9561 (mp) cc_final: 0.9268 (mp) REVERT: B 285 ASN cc_start: 0.9495 (m110) cc_final: 0.9256 (m110) REVERT: B 296 ASN cc_start: 0.9489 (p0) cc_final: 0.8614 (p0) REVERT: B 298 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8421 (mm-40) REVERT: B 321 LEU cc_start: 0.9748 (mm) cc_final: 0.9451 (mm) REVERT: B 375 LYS cc_start: 0.9516 (ptpp) cc_final: 0.9286 (ptpp) REVERT: B 401 PHE cc_start: 0.9290 (p90) cc_final: 0.9084 (p90) REVERT: B 465 GLN cc_start: 0.9316 (mt0) cc_final: 0.9016 (pt0) REVERT: B 493 ARG cc_start: 0.9296 (ttm-80) cc_final: 0.9033 (ttm-80) REVERT: C 42 ILE cc_start: 0.9094 (mp) cc_final: 0.8865 (mp) REVERT: C 66 VAL cc_start: 0.9257 (m) cc_final: 0.8694 (m) REVERT: C 75 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 78 MET cc_start: 0.8218 (mpp) cc_final: 0.7135 (mpp) REVERT: C 82 MET cc_start: 0.9073 (tpp) cc_final: 0.8461 (tpp) REVERT: C 94 ASN cc_start: 0.8837 (t0) cc_final: 0.8593 (t0) REVERT: C 109 LYS cc_start: 0.9284 (tptp) cc_final: 0.9069 (tptp) REVERT: C 163 ILE cc_start: 0.9467 (pt) cc_final: 0.9131 (pt) REVERT: C 166 LEU cc_start: 0.8961 (pt) cc_final: 0.8275 (tp) REVERT: C 175 LEU cc_start: 0.9221 (mt) cc_final: 0.8733 (mt) REVERT: C 181 LYS cc_start: 0.9478 (mmpt) cc_final: 0.9214 (mmpt) REVERT: C 202 GLN cc_start: 0.9346 (mp10) cc_final: 0.8744 (mp10) REVERT: C 216 ASP cc_start: 0.9033 (t70) cc_final: 0.8791 (t70) REVERT: C 261 ASP cc_start: 0.9312 (m-30) cc_final: 0.8755 (p0) REVERT: C 262 LEU cc_start: 0.9753 (tt) cc_final: 0.9471 (tt) REVERT: C 269 ASP cc_start: 0.9139 (t70) cc_final: 0.8427 (t70) REVERT: C 281 ILE cc_start: 0.9439 (mm) cc_final: 0.9193 (mm) REVERT: C 285 ASN cc_start: 0.9541 (m110) cc_final: 0.9264 (m110) REVERT: C 286 MET cc_start: 0.8986 (mtm) cc_final: 0.8025 (mtt) REVERT: C 298 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8346 (mm-40) REVERT: C 321 LEU cc_start: 0.9731 (mm) cc_final: 0.9420 (mm) REVERT: C 364 ASP cc_start: 0.8861 (t0) cc_final: 0.8504 (t0) REVERT: C 479 VAL cc_start: 0.9376 (p) cc_final: 0.9080 (t) REVERT: C 489 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7718 (ttmt) REVERT: C 493 ARG cc_start: 0.9176 (ttt90) cc_final: 0.8736 (ttm-80) REVERT: D 28 ASP cc_start: 0.9382 (t0) cc_final: 0.9135 (t0) REVERT: D 78 MET cc_start: 0.7719 (mpp) cc_final: 0.6899 (mpp) REVERT: D 88 ILE cc_start: 0.7269 (pt) cc_final: 0.6894 (pt) REVERT: D 94 ASN cc_start: 0.8972 (t0) cc_final: 0.8766 (t0) REVERT: D 130 VAL cc_start: 0.9670 (m) cc_final: 0.9329 (m) REVERT: D 134 LYS cc_start: 0.9464 (mmmt) cc_final: 0.9047 (mmmm) REVERT: D 163 ILE cc_start: 0.9410 (pt) cc_final: 0.9000 (pt) REVERT: D 166 LEU cc_start: 0.9035 (pt) cc_final: 0.8350 (tp) REVERT: D 261 ASP cc_start: 0.9281 (m-30) cc_final: 0.8706 (p0) REVERT: D 262 LEU cc_start: 0.9744 (tt) cc_final: 0.9295 (mt) REVERT: D 265 GLN cc_start: 0.9668 (tt0) cc_final: 0.9062 (tm-30) REVERT: D 269 ASP cc_start: 0.9082 (t0) cc_final: 0.8056 (t0) REVERT: D 281 ILE cc_start: 0.9470 (mm) cc_final: 0.9255 (mm) REVERT: D 285 ASN cc_start: 0.9558 (m110) cc_final: 0.9271 (m110) REVERT: D 286 MET cc_start: 0.8853 (mtm) cc_final: 0.8317 (mtt) REVERT: D 296 ASN cc_start: 0.9392 (p0) cc_final: 0.8560 (p0) REVERT: D 298 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8214 (mm-40) REVERT: D 321 LEU cc_start: 0.9783 (mm) cc_final: 0.9515 (mm) REVERT: D 353 TYR cc_start: 0.9300 (t80) cc_final: 0.9025 (t80) REVERT: E 12 TYR cc_start: 0.9273 (t80) cc_final: 0.8954 (t80) REVERT: E 42 ILE cc_start: 0.9120 (mp) cc_final: 0.8917 (mp) REVERT: E 67 SER cc_start: 0.9649 (t) cc_final: 0.9107 (t) REVERT: E 78 MET cc_start: 0.7962 (mpp) cc_final: 0.7117 (mpp) REVERT: E 82 MET cc_start: 0.9072 (tpp) cc_final: 0.8522 (tpp) REVERT: E 88 ILE cc_start: 0.7747 (pt) cc_final: 0.7203 (pt) REVERT: E 166 LEU cc_start: 0.9071 (pt) cc_final: 0.8356 (tp) REVERT: E 174 PHE cc_start: 0.9091 (m-80) cc_final: 0.8833 (m-80) REVERT: E 261 ASP cc_start: 0.9321 (m-30) cc_final: 0.8677 (p0) REVERT: E 262 LEU cc_start: 0.9758 (tt) cc_final: 0.9495 (tt) REVERT: E 269 ASP cc_start: 0.9046 (t0) cc_final: 0.8800 (t70) REVERT: E 286 MET cc_start: 0.8886 (mtm) cc_final: 0.8612 (mtt) REVERT: E 297 LEU cc_start: 0.9151 (mm) cc_final: 0.8719 (mm) REVERT: E 479 VAL cc_start: 0.9384 (p) cc_final: 0.9085 (t) REVERT: E 483 MET cc_start: 0.9458 (ptm) cc_final: 0.9235 (tmm) REVERT: E 489 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7879 (ttmt) REVERT: E 490 PHE cc_start: 0.8856 (m-80) cc_final: 0.8524 (m-80) REVERT: F 42 ILE cc_start: 0.9020 (mp) cc_final: 0.8799 (mp) REVERT: F 66 VAL cc_start: 0.9408 (m) cc_final: 0.9181 (m) REVERT: F 67 SER cc_start: 0.9534 (m) cc_final: 0.9130 (t) REVERT: F 75 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8378 (tm-30) REVERT: F 78 MET cc_start: 0.8149 (mpp) cc_final: 0.7513 (mpp) REVERT: F 94 ASN cc_start: 0.8863 (t0) cc_final: 0.8659 (t0) REVERT: F 109 LYS cc_start: 0.8843 (tptp) cc_final: 0.8250 (tptp) REVERT: F 130 VAL cc_start: 0.9679 (m) cc_final: 0.9326 (m) REVERT: F 134 LYS cc_start: 0.9439 (mmmt) cc_final: 0.8998 (mmmm) REVERT: F 163 ILE cc_start: 0.9403 (pt) cc_final: 0.8999 (pt) REVERT: F 166 LEU cc_start: 0.9096 (pt) cc_final: 0.8266 (tp) REVERT: F 261 ASP cc_start: 0.9298 (m-30) cc_final: 0.8718 (p0) REVERT: F 269 ASP cc_start: 0.9078 (t0) cc_final: 0.8244 (t0) REVERT: F 296 ASN cc_start: 0.9411 (p0) cc_final: 0.8605 (p0) REVERT: F 298 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8306 (mm-40) REVERT: F 321 LEU cc_start: 0.9784 (mm) cc_final: 0.9499 (mm) REVERT: F 401 PHE cc_start: 0.9292 (p90) cc_final: 0.9056 (p90) REVERT: F 479 VAL cc_start: 0.9410 (p) cc_final: 0.9112 (t) REVERT: G 12 TYR cc_start: 0.9369 (t80) cc_final: 0.8813 (t80) REVERT: G 28 ASP cc_start: 0.9310 (t0) cc_final: 0.9062 (t0) REVERT: G 78 MET cc_start: 0.7914 (mpp) cc_final: 0.7261 (mpp) REVERT: G 82 MET cc_start: 0.9050 (tpp) cc_final: 0.8526 (tpp) REVERT: G 94 ASN cc_start: 0.8868 (t0) cc_final: 0.8587 (t0) REVERT: G 166 LEU cc_start: 0.9032 (pt) cc_final: 0.8301 (tp) REVERT: G 261 ASP cc_start: 0.9353 (m-30) cc_final: 0.8802 (p0) REVERT: G 262 LEU cc_start: 0.9780 (tt) cc_final: 0.9177 (mt) REVERT: G 269 ASP cc_start: 0.9085 (t0) cc_final: 0.8229 (t0) REVERT: G 276 SER cc_start: 0.9260 (m) cc_final: 0.8953 (p) REVERT: G 285 ASN cc_start: 0.9585 (m110) cc_final: 0.9358 (m110) REVERT: G 286 MET cc_start: 0.8995 (mtm) cc_final: 0.8609 (mtt) REVERT: G 296 ASN cc_start: 0.9351 (p0) cc_final: 0.8561 (p0) REVERT: G 298 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8248 (mm110) REVERT: G 369 ASN cc_start: 0.9280 (p0) cc_final: 0.8728 (p0) REVERT: G 372 HIS cc_start: 0.9469 (m170) cc_final: 0.9198 (m170) REVERT: H 67 SER cc_start: 0.9373 (m) cc_final: 0.9170 (m) REVERT: H 75 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8126 (tm-30) REVERT: H 78 MET cc_start: 0.7713 (mpp) cc_final: 0.6775 (mpp) REVERT: H 82 MET cc_start: 0.8792 (ttt) cc_final: 0.8501 (ttm) REVERT: H 94 ASN cc_start: 0.8906 (t0) cc_final: 0.8692 (t0) REVERT: H 109 LYS cc_start: 0.8925 (tptp) cc_final: 0.8324 (tptp) REVERT: H 134 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9035 (mmmm) REVERT: H 163 ILE cc_start: 0.9460 (pt) cc_final: 0.9092 (pt) REVERT: H 166 LEU cc_start: 0.9000 (pt) cc_final: 0.8119 (tp) REVERT: H 261 ASP cc_start: 0.9244 (m-30) cc_final: 0.8731 (p0) REVERT: H 262 LEU cc_start: 0.9753 (tt) cc_final: 0.9495 (tt) REVERT: H 269 ASP cc_start: 0.9072 (t0) cc_final: 0.8210 (t0) REVERT: H 281 ILE cc_start: 0.9503 (mm) cc_final: 0.9294 (mm) REVERT: H 285 ASN cc_start: 0.9519 (m110) cc_final: 0.9305 (m110) REVERT: H 286 MET cc_start: 0.8808 (mtm) cc_final: 0.8343 (mtt) REVERT: H 296 ASN cc_start: 0.9400 (p0) cc_final: 0.8609 (p0) REVERT: H 298 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8240 (mm110) REVERT: H 321 LEU cc_start: 0.9793 (mm) cc_final: 0.9519 (mm) REVERT: H 364 ASP cc_start: 0.8431 (t0) cc_final: 0.7775 (t0) REVERT: H 372 HIS cc_start: 0.9596 (m170) cc_final: 0.9227 (m170) REVERT: H 401 PHE cc_start: 0.9297 (p90) cc_final: 0.9082 (p90) REVERT: H 456 PHE cc_start: 0.9649 (t80) cc_final: 0.9365 (t80) REVERT: H 460 LEU cc_start: 0.9859 (mt) cc_final: 0.9650 (mt) outliers start: 3 outliers final: 2 residues processed: 1259 average time/residue: 0.1741 time to fit residues: 349.9694 Evaluate side-chains 1023 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1021 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 325 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 348 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 465 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.088995 restraints weight = 55155.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092919 restraints weight = 35660.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095883 restraints weight = 25941.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098129 restraints weight = 20282.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099861 restraints weight = 16783.631| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28872 Z= 0.149 Angle : 0.886 13.718 39136 Z= 0.422 Chirality : 0.050 0.214 4472 Planarity : 0.005 0.050 4928 Dihedral : 17.770 177.665 4368 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.13), residues: 3576 helix: -1.20 (0.13), residues: 1216 sheet: -2.86 (0.24), residues: 344 loop : -1.91 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 480 TYR 0.029 0.002 TYR H 233 PHE 0.030 0.002 PHE C 456 HIS 0.005 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00345 (28864) covalent geometry : angle 0.88564 (39136) hydrogen bonds : bond 0.03578 ( 888) hydrogen bonds : angle 5.63591 ( 2448) Misc. bond : bond 0.00211 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1329 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.9212 (m) cc_final: 0.8942 (m) REVERT: A 88 ILE cc_start: 0.7478 (pt) cc_final: 0.7128 (pt) REVERT: A 93 HIS cc_start: 0.9107 (p90) cc_final: 0.8649 (p90) REVERT: A 94 ASN cc_start: 0.8898 (t0) cc_final: 0.8557 (t0) REVERT: A 105 ARG cc_start: 0.9123 (mmt-90) cc_final: 0.8816 (mmt180) REVERT: A 166 LEU cc_start: 0.9072 (pt) cc_final: 0.8422 (tp) REVERT: A 179 MET cc_start: 0.7347 (tpt) cc_final: 0.7068 (tpt) REVERT: A 199 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9326 (mt-10) REVERT: A 229 LYS cc_start: 0.9440 (mttt) cc_final: 0.9087 (mttt) REVERT: A 261 ASP cc_start: 0.9339 (m-30) cc_final: 0.8741 (p0) REVERT: A 262 LEU cc_start: 0.9740 (tt) cc_final: 0.9537 (tt) REVERT: A 269 ASP cc_start: 0.9132 (t0) cc_final: 0.8248 (t70) REVERT: A 276 SER cc_start: 0.9190 (m) cc_final: 0.8870 (p) REVERT: A 296 ASN cc_start: 0.9352 (p0) cc_final: 0.8696 (p0) REVERT: A 297 LEU cc_start: 0.8946 (mm) cc_final: 0.8480 (mm) REVERT: A 298 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8290 (mm110) REVERT: A 450 LYS cc_start: 0.7598 (pttm) cc_final: 0.6292 (ptmm) REVERT: A 489 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7567 (ttmt) REVERT: A 490 PHE cc_start: 0.8837 (m-80) cc_final: 0.8424 (m-80) REVERT: B 15 ASP cc_start: 0.9628 (t0) cc_final: 0.9328 (t0) REVERT: B 67 SER cc_start: 0.9435 (t) cc_final: 0.8798 (t) REVERT: B 93 HIS cc_start: 0.9323 (p90) cc_final: 0.8638 (p90) REVERT: B 94 ASN cc_start: 0.8873 (t0) cc_final: 0.8540 (t0) REVERT: B 105 ARG cc_start: 0.9024 (mmt-90) cc_final: 0.8735 (mmt180) REVERT: B 158 ILE cc_start: 0.8899 (mm) cc_final: 0.8558 (mm) REVERT: B 162 ASP cc_start: 0.9325 (m-30) cc_final: 0.9120 (m-30) REVERT: B 166 LEU cc_start: 0.9058 (pt) cc_final: 0.8381 (tp) REVERT: B 199 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9311 (mt-10) REVERT: B 215 ASP cc_start: 0.9116 (m-30) cc_final: 0.8802 (t0) REVERT: B 229 LYS cc_start: 0.9469 (mttt) cc_final: 0.8851 (mttt) REVERT: B 261 ASP cc_start: 0.9173 (m-30) cc_final: 0.8651 (p0) REVERT: B 269 ASP cc_start: 0.9299 (t0) cc_final: 0.7970 (t70) REVERT: B 276 SER cc_start: 0.9195 (m) cc_final: 0.8896 (p) REVERT: B 281 ILE cc_start: 0.9542 (mp) cc_final: 0.9206 (mp) REVERT: B 285 ASN cc_start: 0.9491 (m110) cc_final: 0.9255 (m110) REVERT: B 292 ASP cc_start: 0.9700 (m-30) cc_final: 0.9497 (m-30) REVERT: B 296 ASN cc_start: 0.9498 (p0) cc_final: 0.8635 (p0) REVERT: B 298 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8559 (mp-120) REVERT: B 465 GLN cc_start: 0.9171 (mt0) cc_final: 0.8818 (pt0) REVERT: B 490 PHE cc_start: 0.9066 (m-80) cc_final: 0.8731 (m-80) REVERT: B 493 ARG cc_start: 0.9219 (ttm-80) cc_final: 0.8998 (ttm-80) REVERT: C 19 THR cc_start: 0.9236 (p) cc_final: 0.8935 (p) REVERT: C 24 PHE cc_start: 0.8388 (m-80) cc_final: 0.8048 (m-80) REVERT: C 58 LYS cc_start: 0.9698 (mmpt) cc_final: 0.9495 (mmmm) REVERT: C 65 LEU cc_start: 0.9067 (pt) cc_final: 0.8823 (pt) REVERT: C 66 VAL cc_start: 0.9202 (m) cc_final: 0.8786 (m) REVERT: C 75 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 78 MET cc_start: 0.8043 (mpp) cc_final: 0.6614 (mpp) REVERT: C 82 MET cc_start: 0.9132 (tpp) cc_final: 0.8590 (tpp) REVERT: C 94 ASN cc_start: 0.8781 (t0) cc_final: 0.8498 (t0) REVERT: C 109 LYS cc_start: 0.9188 (tptp) cc_final: 0.8967 (tptp) REVERT: C 166 LEU cc_start: 0.8974 (pt) cc_final: 0.8349 (tp) REVERT: C 262 LEU cc_start: 0.9721 (tt) cc_final: 0.9489 (pp) REVERT: C 265 GLN cc_start: 0.9585 (tm-30) cc_final: 0.9369 (tm-30) REVERT: C 269 ASP cc_start: 0.9222 (t70) cc_final: 0.8714 (t70) REVERT: C 283 GLN cc_start: 0.9550 (mm-40) cc_final: 0.9270 (mm-40) REVERT: C 286 MET cc_start: 0.8788 (mtm) cc_final: 0.8477 (mtt) REVERT: C 298 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8467 (mm-40) REVERT: C 321 LEU cc_start: 0.9728 (mm) cc_final: 0.9463 (mm) REVERT: C 399 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9189 (tm-30) REVERT: C 479 VAL cc_start: 0.9288 (p) cc_final: 0.9038 (t) REVERT: C 489 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7301 (mtpt) REVERT: C 490 PHE cc_start: 0.8940 (m-80) cc_final: 0.8636 (m-80) REVERT: C 493 ARG cc_start: 0.9049 (ttt90) cc_final: 0.8724 (ttm-80) REVERT: D 28 ASP cc_start: 0.9331 (t0) cc_final: 0.9079 (t0) REVERT: D 67 SER cc_start: 0.9557 (t) cc_final: 0.8606 (t) REVERT: D 82 MET cc_start: 0.8997 (ttt) cc_final: 0.8728 (ttt) REVERT: D 94 ASN cc_start: 0.8876 (t0) cc_final: 0.8560 (t0) REVERT: D 134 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9161 (mmmt) REVERT: D 163 ILE cc_start: 0.9390 (pt) cc_final: 0.8992 (pt) REVERT: D 166 LEU cc_start: 0.9039 (pt) cc_final: 0.8387 (tp) REVERT: D 174 PHE cc_start: 0.9060 (m-80) cc_final: 0.8808 (m-80) REVERT: D 261 ASP cc_start: 0.9244 (m-30) cc_final: 0.8698 (p0) REVERT: D 262 LEU cc_start: 0.9722 (tt) cc_final: 0.9508 (tt) REVERT: D 269 ASP cc_start: 0.9154 (t0) cc_final: 0.8192 (t70) REVERT: D 276 SER cc_start: 0.9180 (m) cc_final: 0.8929 (p) REVERT: D 281 ILE cc_start: 0.9445 (mm) cc_final: 0.9217 (mm) REVERT: D 285 ASN cc_start: 0.9537 (m110) cc_final: 0.9276 (m110) REVERT: D 286 MET cc_start: 0.8818 (mtm) cc_final: 0.8255 (mtt) REVERT: D 296 ASN cc_start: 0.9401 (p0) cc_final: 0.8771 (p0) REVERT: D 297 LEU cc_start: 0.9113 (mm) cc_final: 0.8518 (mm) REVERT: D 298 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8274 (mm-40) REVERT: D 321 LEU cc_start: 0.9757 (mm) cc_final: 0.9497 (mm) REVERT: D 353 TYR cc_start: 0.9297 (t80) cc_final: 0.9072 (t80) REVERT: D 385 MET cc_start: 0.9273 (ttm) cc_final: 0.9071 (ttm) REVERT: E 12 TYR cc_start: 0.9310 (t80) cc_final: 0.8936 (t80) REVERT: E 65 LEU cc_start: 0.9205 (pt) cc_final: 0.8926 (pt) REVERT: E 82 MET cc_start: 0.9025 (tpp) cc_final: 0.8551 (tpp) REVERT: E 88 ILE cc_start: 0.7555 (pt) cc_final: 0.6977 (pt) REVERT: E 93 HIS cc_start: 0.9260 (p90) cc_final: 0.8608 (p90) REVERT: E 94 ASN cc_start: 0.8824 (t0) cc_final: 0.8546 (t0) REVERT: E 166 LEU cc_start: 0.9054 (pt) cc_final: 0.8347 (tp) REVERT: E 174 PHE cc_start: 0.9061 (m-80) cc_final: 0.8826 (m-80) REVERT: E 202 GLN cc_start: 0.9383 (mp10) cc_final: 0.8758 (mp10) REVERT: E 261 ASP cc_start: 0.9308 (m-30) cc_final: 0.8686 (p0) REVERT: E 262 LEU cc_start: 0.9716 (tt) cc_final: 0.9499 (tt) REVERT: E 269 ASP cc_start: 0.9159 (t0) cc_final: 0.8209 (t70) REVERT: E 276 SER cc_start: 0.9195 (m) cc_final: 0.8881 (p) REVERT: E 286 MET cc_start: 0.8891 (mtm) cc_final: 0.8534 (mtt) REVERT: E 296 ASN cc_start: 0.9287 (p0) cc_final: 0.8190 (p0) REVERT: E 297 LEU cc_start: 0.9055 (mm) cc_final: 0.8644 (mm) REVERT: E 298 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8255 (mm110) REVERT: E 399 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9155 (tm-30) REVERT: E 482 MET cc_start: 0.8851 (tmm) cc_final: 0.8540 (tmm) REVERT: E 489 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7804 (ttmt) REVERT: E 490 PHE cc_start: 0.8875 (m-80) cc_final: 0.8276 (m-80) REVERT: F 66 VAL cc_start: 0.9398 (m) cc_final: 0.9069 (m) REVERT: F 67 SER cc_start: 0.9269 (m) cc_final: 0.8667 (t) REVERT: F 75 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8024 (tm-30) REVERT: F 78 MET cc_start: 0.7824 (mpp) cc_final: 0.7076 (mpp) REVERT: F 94 ASN cc_start: 0.8785 (t0) cc_final: 0.8546 (t0) REVERT: F 134 LYS cc_start: 0.9494 (mmmt) cc_final: 0.9164 (mmmm) REVERT: F 166 LEU cc_start: 0.9068 (pt) cc_final: 0.8263 (tp) REVERT: F 232 ASP cc_start: 0.8980 (t70) cc_final: 0.8763 (t0) REVERT: F 261 ASP cc_start: 0.9209 (m-30) cc_final: 0.8604 (p0) REVERT: F 262 LEU cc_start: 0.9714 (tt) cc_final: 0.9469 (tt) REVERT: F 269 ASP cc_start: 0.9103 (t0) cc_final: 0.8073 (t70) REVERT: F 286 MET cc_start: 0.8750 (mtm) cc_final: 0.8548 (mtt) REVERT: F 296 ASN cc_start: 0.9415 (p0) cc_final: 0.8499 (p0) REVERT: F 297 LEU cc_start: 0.9111 (mm) cc_final: 0.8686 (mm) REVERT: F 298 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8287 (mm110) REVERT: F 482 MET cc_start: 0.8773 (tmm) cc_final: 0.8405 (tmm) REVERT: F 490 PHE cc_start: 0.8968 (m-80) cc_final: 0.8165 (m-80) REVERT: G 28 ASP cc_start: 0.9219 (t0) cc_final: 0.8994 (t0) REVERT: G 82 MET cc_start: 0.8989 (tpp) cc_final: 0.8589 (tpp) REVERT: G 94 ASN cc_start: 0.8879 (t0) cc_final: 0.8563 (t0) REVERT: G 154 LEU cc_start: 0.9591 (mm) cc_final: 0.9371 (mm) REVERT: G 166 LEU cc_start: 0.8997 (pt) cc_final: 0.8286 (tp) REVERT: G 179 MET cc_start: 0.7062 (tpt) cc_final: 0.6752 (tpt) REVERT: G 261 ASP cc_start: 0.9348 (m-30) cc_final: 0.8721 (p0) REVERT: G 269 ASP cc_start: 0.9160 (t0) cc_final: 0.8231 (t70) REVERT: G 276 SER cc_start: 0.9208 (m) cc_final: 0.8872 (p) REVERT: G 296 ASN cc_start: 0.9343 (p0) cc_final: 0.8669 (p0) REVERT: G 297 LEU cc_start: 0.8961 (mm) cc_final: 0.8505 (mm) REVERT: G 298 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8295 (mm110) REVERT: G 369 ASN cc_start: 0.9193 (p0) cc_final: 0.8707 (p0) REVERT: G 372 HIS cc_start: 0.9459 (m170) cc_final: 0.9140 (m170) REVERT: G 450 LYS cc_start: 0.7531 (pttm) cc_final: 0.6300 (ptmm) REVERT: G 482 MET cc_start: 0.8813 (tmm) cc_final: 0.8499 (tmm) REVERT: G 489 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7275 (ttpt) REVERT: G 490 PHE cc_start: 0.8894 (m-80) cc_final: 0.8247 (m-80) REVERT: G 493 ARG cc_start: 0.9203 (ttm-80) cc_final: 0.8895 (ttm-80) REVERT: H 66 VAL cc_start: 0.8938 (p) cc_final: 0.8716 (p) REVERT: H 82 MET cc_start: 0.8871 (ttt) cc_final: 0.8661 (ttm) REVERT: H 94 ASN cc_start: 0.8841 (t0) cc_final: 0.8604 (t0) REVERT: H 161 ARG cc_start: 0.9484 (mtm180) cc_final: 0.9228 (mtm-85) REVERT: H 163 ILE cc_start: 0.9436 (pt) cc_final: 0.9120 (pt) REVERT: H 166 LEU cc_start: 0.9039 (pt) cc_final: 0.8168 (tp) REVERT: H 167 LYS cc_start: 0.9522 (tmtt) cc_final: 0.9212 (ptpp) REVERT: H 199 GLU cc_start: 0.9525 (pt0) cc_final: 0.9306 (pt0) REVERT: H 261 ASP cc_start: 0.9208 (m-30) cc_final: 0.8664 (p0) REVERT: H 262 LEU cc_start: 0.9721 (tt) cc_final: 0.9409 (tt) REVERT: H 269 ASP cc_start: 0.9166 (t0) cc_final: 0.8195 (t70) REVERT: H 286 MET cc_start: 0.8816 (mtm) cc_final: 0.8508 (mtt) REVERT: H 296 ASN cc_start: 0.9397 (p0) cc_final: 0.8717 (p0) REVERT: H 297 LEU cc_start: 0.9079 (mm) cc_final: 0.8564 (mm) REVERT: H 298 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8325 (mm110) REVERT: H 357 PHE cc_start: 0.9226 (m-80) cc_final: 0.8780 (m-10) REVERT: H 372 HIS cc_start: 0.9594 (m170) cc_final: 0.9137 (m170) REVERT: H 401 PHE cc_start: 0.9289 (p90) cc_final: 0.9065 (p90) REVERT: H 482 MET cc_start: 0.8858 (tmm) cc_final: 0.8540 (tmm) REVERT: H 490 PHE cc_start: 0.9127 (m-80) cc_final: 0.8773 (m-80) REVERT: H 493 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8928 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 1329 average time/residue: 0.1766 time to fit residues: 375.2753 Evaluate side-chains 1041 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1041 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 177 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089388 restraints weight = 55556.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093282 restraints weight = 36005.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096209 restraints weight = 26179.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098484 restraints weight = 20545.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100166 restraints weight = 16981.319| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28872 Z= 0.152 Angle : 0.889 13.332 39136 Z= 0.427 Chirality : 0.050 0.227 4472 Planarity : 0.005 0.073 4928 Dihedral : 17.655 178.003 4368 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.13), residues: 3576 helix: -1.22 (0.13), residues: 1216 sheet: -2.73 (0.25), residues: 344 loop : -1.94 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 480 TYR 0.028 0.002 TYR H 233 PHE 0.043 0.002 PHE F 456 HIS 0.005 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00357 (28864) covalent geometry : angle 0.88879 (39136) hydrogen bonds : bond 0.03480 ( 888) hydrogen bonds : angle 5.69934 ( 2448) Misc. bond : bond 0.00214 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1266 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8930 (t0) cc_final: 0.8622 (t0) REVERT: A 66 VAL cc_start: 0.9318 (m) cc_final: 0.9108 (m) REVERT: A 82 MET cc_start: 0.9079 (tpt) cc_final: 0.8769 (tpp) REVERT: A 88 ILE cc_start: 0.7547 (pt) cc_final: 0.7203 (pt) REVERT: A 93 HIS cc_start: 0.9168 (p90) cc_final: 0.8715 (p90) REVERT: A 94 ASN cc_start: 0.8869 (t0) cc_final: 0.8530 (t0) REVERT: A 166 LEU cc_start: 0.9123 (pt) cc_final: 0.8463 (tp) REVERT: A 199 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9331 (mt-10) REVERT: A 203 ARG cc_start: 0.9472 (mmp80) cc_final: 0.9219 (mmp80) REVERT: A 229 LYS cc_start: 0.9425 (mttt) cc_final: 0.8835 (mttt) REVERT: A 261 ASP cc_start: 0.9337 (m-30) cc_final: 0.8933 (m-30) REVERT: A 269 ASP cc_start: 0.9158 (t0) cc_final: 0.8390 (t70) REVERT: A 276 SER cc_start: 0.9246 (m) cc_final: 0.8950 (p) REVERT: A 296 ASN cc_start: 0.9380 (p0) cc_final: 0.8741 (p0) REVERT: A 298 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8270 (mm110) REVERT: A 399 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9207 (tm-30) REVERT: A 450 LYS cc_start: 0.7481 (pttm) cc_final: 0.6343 (ptmm) REVERT: A 456 PHE cc_start: 0.9646 (t80) cc_final: 0.9423 (t80) REVERT: A 460 LEU cc_start: 0.9833 (mt) cc_final: 0.9598 (mp) REVERT: A 489 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7470 (ttmt) REVERT: A 490 PHE cc_start: 0.8798 (m-80) cc_final: 0.8539 (m-80) REVERT: B 67 SER cc_start: 0.9413 (t) cc_final: 0.8803 (t) REVERT: B 93 HIS cc_start: 0.9347 (p90) cc_final: 0.8660 (p90) REVERT: B 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8592 (t0) REVERT: B 132 GLU cc_start: 0.9440 (pp20) cc_final: 0.9218 (pp20) REVERT: B 166 LEU cc_start: 0.9081 (pt) cc_final: 0.8381 (tp) REVERT: B 199 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9312 (mt-10) REVERT: B 202 GLN cc_start: 0.9284 (mp10) cc_final: 0.8621 (mp10) REVERT: B 203 ARG cc_start: 0.9440 (mmp80) cc_final: 0.9197 (mmp80) REVERT: B 216 ASP cc_start: 0.9075 (t70) cc_final: 0.8850 (t70) REVERT: B 229 LYS cc_start: 0.9455 (mttt) cc_final: 0.8793 (mttt) REVERT: B 261 ASP cc_start: 0.9186 (m-30) cc_final: 0.8679 (p0) REVERT: B 269 ASP cc_start: 0.9241 (t0) cc_final: 0.8561 (t70) REVERT: B 276 SER cc_start: 0.9226 (m) cc_final: 0.8918 (p) REVERT: B 285 ASN cc_start: 0.9404 (m110) cc_final: 0.9097 (m-40) REVERT: B 296 ASN cc_start: 0.9495 (p0) cc_final: 0.8631 (p0) REVERT: B 297 LEU cc_start: 0.8939 (mm) cc_final: 0.8480 (mm) REVERT: B 298 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8316 (mm110) REVERT: B 461 ILE cc_start: 0.9728 (pt) cc_final: 0.9519 (pt) REVERT: B 465 GLN cc_start: 0.9214 (mt0) cc_final: 0.8828 (pt0) REVERT: B 490 PHE cc_start: 0.9084 (m-80) cc_final: 0.8735 (m-80) REVERT: B 493 ARG cc_start: 0.9085 (ttt90) cc_final: 0.8795 (ttm-80) REVERT: C 28 ASP cc_start: 0.9143 (t0) cc_final: 0.8917 (t0) REVERT: C 65 LEU cc_start: 0.9088 (pt) cc_final: 0.8863 (pt) REVERT: C 66 VAL cc_start: 0.9169 (m) cc_final: 0.8679 (m) REVERT: C 67 SER cc_start: 0.9535 (t) cc_final: 0.9114 (t) REVERT: C 75 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 78 MET cc_start: 0.8078 (mpp) cc_final: 0.6786 (mpp) REVERT: C 82 MET cc_start: 0.9082 (tpp) cc_final: 0.8524 (tpp) REVERT: C 94 ASN cc_start: 0.8757 (t0) cc_final: 0.8504 (t0) REVERT: C 166 LEU cc_start: 0.9037 (pt) cc_final: 0.8401 (tp) REVERT: C 175 LEU cc_start: 0.9255 (mt) cc_final: 0.8854 (mt) REVERT: C 178 ILE cc_start: 0.9257 (mp) cc_final: 0.9047 (mp) REVERT: C 261 ASP cc_start: 0.9301 (m-30) cc_final: 0.9059 (m-30) REVERT: C 269 ASP cc_start: 0.9254 (t70) cc_final: 0.8451 (t70) REVERT: C 276 SER cc_start: 0.9331 (m) cc_final: 0.9021 (p) REVERT: C 283 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9237 (mm-40) REVERT: C 286 MET cc_start: 0.8880 (mtm) cc_final: 0.8429 (mtt) REVERT: C 298 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8305 (mm110) REVERT: C 321 LEU cc_start: 0.9750 (mm) cc_final: 0.9480 (mm) REVERT: C 479 VAL cc_start: 0.9304 (p) cc_final: 0.9057 (t) REVERT: C 489 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7226 (mtpt) REVERT: C 490 PHE cc_start: 0.8867 (m-80) cc_final: 0.8590 (m-80) REVERT: C 493 ARG cc_start: 0.9047 (ttt90) cc_final: 0.8645 (ttm-80) REVERT: D 28 ASP cc_start: 0.9317 (t0) cc_final: 0.9059 (t0) REVERT: D 67 SER cc_start: 0.9591 (t) cc_final: 0.9240 (t) REVERT: D 88 ILE cc_start: 0.6801 (pt) cc_final: 0.6575 (pt) REVERT: D 94 ASN cc_start: 0.8891 (t0) cc_final: 0.8650 (t0) REVERT: D 105 ARG cc_start: 0.8846 (mmt180) cc_final: 0.8251 (tpp-160) REVERT: D 163 ILE cc_start: 0.9376 (pt) cc_final: 0.8978 (pt) REVERT: D 166 LEU cc_start: 0.9084 (pt) cc_final: 0.8375 (tp) REVERT: D 269 ASP cc_start: 0.9093 (t0) cc_final: 0.8210 (t70) REVERT: D 276 SER cc_start: 0.9184 (m) cc_final: 0.8919 (p) REVERT: D 281 ILE cc_start: 0.9448 (mm) cc_final: 0.9201 (mm) REVERT: D 285 ASN cc_start: 0.9531 (m110) cc_final: 0.9262 (m110) REVERT: D 286 MET cc_start: 0.8807 (mtm) cc_final: 0.8446 (mtt) REVERT: D 296 ASN cc_start: 0.9394 (p0) cc_final: 0.8618 (p0) REVERT: D 298 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8229 (mm110) REVERT: D 385 MET cc_start: 0.9237 (ttm) cc_final: 0.9029 (ttm) REVERT: D 482 MET cc_start: 0.8746 (tmm) cc_final: 0.8458 (tmm) REVERT: E 12 TYR cc_start: 0.9316 (t80) cc_final: 0.8977 (t80) REVERT: E 67 SER cc_start: 0.9598 (t) cc_final: 0.9227 (t) REVERT: E 82 MET cc_start: 0.8964 (tpp) cc_final: 0.8490 (tpp) REVERT: E 88 ILE cc_start: 0.7601 (pt) cc_final: 0.6981 (pt) REVERT: E 93 HIS cc_start: 0.9283 (p90) cc_final: 0.8621 (p90) REVERT: E 94 ASN cc_start: 0.8814 (t0) cc_final: 0.8554 (t0) REVERT: E 166 LEU cc_start: 0.9092 (pt) cc_final: 0.8378 (tp) REVERT: E 174 PHE cc_start: 0.8999 (m-80) cc_final: 0.8753 (m-80) REVERT: E 261 ASP cc_start: 0.9311 (m-30) cc_final: 0.8652 (p0) REVERT: E 276 SER cc_start: 0.9237 (m) cc_final: 0.8902 (p) REVERT: E 286 MET cc_start: 0.8866 (mtm) cc_final: 0.8455 (mtt) REVERT: E 465 GLN cc_start: 0.9226 (mt0) cc_final: 0.8947 (pt0) REVERT: E 482 MET cc_start: 0.8839 (tmm) cc_final: 0.8502 (tmm) REVERT: E 489 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7858 (ttmt) REVERT: E 490 PHE cc_start: 0.8853 (m-80) cc_final: 0.8435 (m-80) REVERT: F 66 VAL cc_start: 0.9396 (m) cc_final: 0.9056 (p) REVERT: F 67 SER cc_start: 0.9376 (m) cc_final: 0.8378 (t) REVERT: F 75 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 78 MET cc_start: 0.7882 (mpp) cc_final: 0.7139 (mpp) REVERT: F 94 ASN cc_start: 0.8798 (t0) cc_final: 0.8585 (t0) REVERT: F 108 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7930 (ptpp) REVERT: F 166 LEU cc_start: 0.9055 (pt) cc_final: 0.8266 (tp) REVERT: F 232 ASP cc_start: 0.8946 (t70) cc_final: 0.8729 (t0) REVERT: F 261 ASP cc_start: 0.9227 (m-30) cc_final: 0.8625 (p0) REVERT: F 262 LEU cc_start: 0.9722 (tt) cc_final: 0.9474 (tt) REVERT: F 269 ASP cc_start: 0.9095 (t0) cc_final: 0.8076 (t70) REVERT: F 276 SER cc_start: 0.9216 (m) cc_final: 0.8900 (p) REVERT: F 296 ASN cc_start: 0.9407 (p0) cc_final: 0.8365 (p0) REVERT: F 297 LEU cc_start: 0.9134 (mm) cc_final: 0.8636 (mm) REVERT: F 298 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8259 (mm110) REVERT: F 401 PHE cc_start: 0.9214 (p90) cc_final: 0.8945 (p90) REVERT: F 459 TYR cc_start: 0.9254 (t80) cc_final: 0.9053 (t80) REVERT: F 479 VAL cc_start: 0.9270 (p) cc_final: 0.9062 (t) REVERT: F 490 PHE cc_start: 0.8928 (m-80) cc_final: 0.8182 (m-80) REVERT: G 12 TYR cc_start: 0.9412 (t80) cc_final: 0.8909 (t80) REVERT: G 28 ASP cc_start: 0.9191 (t0) cc_final: 0.8970 (t0) REVERT: G 58 LYS cc_start: 0.9671 (mmpt) cc_final: 0.9464 (mmmm) REVERT: G 82 MET cc_start: 0.9048 (tpp) cc_final: 0.8574 (tpp) REVERT: G 94 ASN cc_start: 0.8916 (t0) cc_final: 0.8649 (t0) REVERT: G 166 LEU cc_start: 0.9051 (pt) cc_final: 0.8313 (tp) REVERT: G 179 MET cc_start: 0.7070 (tpt) cc_final: 0.6836 (tpt) REVERT: G 261 ASP cc_start: 0.9340 (m-30) cc_final: 0.8940 (m-30) REVERT: G 269 ASP cc_start: 0.9091 (t0) cc_final: 0.8249 (t70) REVERT: G 276 SER cc_start: 0.9256 (m) cc_final: 0.8912 (p) REVERT: G 298 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8219 (mm110) REVERT: G 369 ASN cc_start: 0.9122 (p0) cc_final: 0.8659 (p0) REVERT: G 372 HIS cc_start: 0.9419 (m170) cc_final: 0.9102 (m170) REVERT: G 386 MET cc_start: 0.8555 (mmp) cc_final: 0.8314 (mmp) REVERT: G 489 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7129 (ttpt) REVERT: G 490 PHE cc_start: 0.8875 (m-80) cc_final: 0.8287 (m-80) REVERT: G 493 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8856 (ttm-80) REVERT: H 31 THR cc_start: 0.9482 (t) cc_final: 0.9272 (p) REVERT: H 94 ASN cc_start: 0.8865 (t0) cc_final: 0.8626 (t0) REVERT: H 161 ARG cc_start: 0.9415 (mtm180) cc_final: 0.9126 (mtm110) REVERT: H 163 ILE cc_start: 0.9474 (pt) cc_final: 0.9176 (pt) REVERT: H 164 ASP cc_start: 0.8343 (p0) cc_final: 0.8112 (p0) REVERT: H 166 LEU cc_start: 0.9056 (pt) cc_final: 0.8209 (tp) REVERT: H 167 LYS cc_start: 0.9506 (tmtt) cc_final: 0.9212 (ptpp) REVERT: H 199 GLU cc_start: 0.9484 (pt0) cc_final: 0.9283 (pt0) REVERT: H 269 ASP cc_start: 0.9103 (t0) cc_final: 0.8130 (t70) REVERT: H 286 MET cc_start: 0.8782 (mtm) cc_final: 0.8481 (mtt) REVERT: H 297 LEU cc_start: 0.9038 (mm) cc_final: 0.8484 (mm) REVERT: H 298 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8286 (mm110) REVERT: H 357 PHE cc_start: 0.9192 (m-80) cc_final: 0.8806 (m-10) REVERT: H 372 HIS cc_start: 0.9555 (m170) cc_final: 0.9131 (m170) REVERT: H 401 PHE cc_start: 0.9242 (p90) cc_final: 0.9028 (p90) REVERT: H 490 PHE cc_start: 0.9079 (m-80) cc_final: 0.8796 (m-80) outliers start: 1 outliers final: 0 residues processed: 1267 average time/residue: 0.1757 time to fit residues: 357.2897 Evaluate side-chains 1041 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1041 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 94 optimal weight: 0.0000 chunk 311 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 283 optimal weight: 30.0000 chunk 214 optimal weight: 10.0000 chunk 229 optimal weight: 0.0670 chunk 294 optimal weight: 6.9990 overall best weight: 1.1726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090140 restraints weight = 55080.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094060 restraints weight = 35791.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097042 restraints weight = 26079.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.099290 restraints weight = 20462.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101089 restraints weight = 16938.643| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28872 Z= 0.147 Angle : 0.888 18.878 39136 Z= 0.424 Chirality : 0.050 0.255 4472 Planarity : 0.005 0.072 4928 Dihedral : 17.558 177.720 4368 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.03 % Allowed : 0.74 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.13), residues: 3576 helix: -1.25 (0.14), residues: 1224 sheet: -2.55 (0.25), residues: 344 loop : -1.94 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 480 TYR 0.027 0.002 TYR H 233 PHE 0.029 0.002 PHE C 456 HIS 0.006 0.001 HIS H 454 Details of bonding type rmsd covalent geometry : bond 0.00344 (28864) covalent geometry : angle 0.88805 (39136) hydrogen bonds : bond 0.03536 ( 888) hydrogen bonds : angle 5.66360 ( 2448) Misc. bond : bond 0.00227 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1295 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8829 (t0) cc_final: 0.8628 (t0) REVERT: A 58 LYS cc_start: 0.9657 (mmpt) cc_final: 0.9444 (mmmm) REVERT: A 66 VAL cc_start: 0.9314 (m) cc_final: 0.9009 (m) REVERT: A 82 MET cc_start: 0.9093 (tpt) cc_final: 0.8653 (tpp) REVERT: A 88 ILE cc_start: 0.7373 (pt) cc_final: 0.7011 (pt) REVERT: A 93 HIS cc_start: 0.9211 (p90) cc_final: 0.8801 (p90) REVERT: A 94 ASN cc_start: 0.8882 (t0) cc_final: 0.8542 (t0) REVERT: A 134 LYS cc_start: 0.9420 (mmtt) cc_final: 0.9089 (mmmt) REVERT: A 166 LEU cc_start: 0.9145 (pt) cc_final: 0.8485 (tp) REVERT: A 229 LYS cc_start: 0.9395 (mttt) cc_final: 0.8790 (mttt) REVERT: A 269 ASP cc_start: 0.9125 (t0) cc_final: 0.8277 (t70) REVERT: A 276 SER cc_start: 0.9272 (m) cc_final: 0.8961 (p) REVERT: A 296 ASN cc_start: 0.9378 (p0) cc_final: 0.8789 (p0) REVERT: A 297 LEU cc_start: 0.8793 (mm) cc_final: 0.8413 (mm) REVERT: A 298 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8244 (mm110) REVERT: A 399 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9241 (tm-30) REVERT: A 450 LYS cc_start: 0.7567 (pttm) cc_final: 0.6168 (ptmm) REVERT: A 460 LEU cc_start: 0.9837 (mt) cc_final: 0.9542 (mt) REVERT: A 482 MET cc_start: 0.8783 (tmm) cc_final: 0.8494 (tmm) REVERT: A 489 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7499 (ttmt) REVERT: A 490 PHE cc_start: 0.8867 (m-80) cc_final: 0.8572 (m-80) REVERT: A 493 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8002 (ttm110) REVERT: B 67 SER cc_start: 0.9349 (t) cc_final: 0.8699 (t) REVERT: B 93 HIS cc_start: 0.9353 (p90) cc_final: 0.8710 (p90) REVERT: B 94 ASN cc_start: 0.8919 (t0) cc_final: 0.8641 (t0) REVERT: B 132 GLU cc_start: 0.9452 (pp20) cc_final: 0.9222 (pp20) REVERT: B 153 ARG cc_start: 0.9427 (tpt170) cc_final: 0.9194 (tpp80) REVERT: B 154 LEU cc_start: 0.9449 (mm) cc_final: 0.9239 (mm) REVERT: B 166 LEU cc_start: 0.9069 (pt) cc_final: 0.8345 (tp) REVERT: B 199 GLU cc_start: 0.9581 (mt-10) cc_final: 0.9356 (mt-10) REVERT: B 216 ASP cc_start: 0.9394 (t70) cc_final: 0.8625 (t70) REVERT: B 229 LYS cc_start: 0.9455 (mttt) cc_final: 0.8849 (mttt) REVERT: B 269 ASP cc_start: 0.9254 (t0) cc_final: 0.8566 (t70) REVERT: B 276 SER cc_start: 0.9287 (m) cc_final: 0.8990 (p) REVERT: B 285 ASN cc_start: 0.9420 (m110) cc_final: 0.9132 (m110) REVERT: B 296 ASN cc_start: 0.9502 (p0) cc_final: 0.8637 (p0) REVERT: B 297 LEU cc_start: 0.8865 (mm) cc_final: 0.8367 (mm) REVERT: B 298 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8326 (mm-40) REVERT: B 401 PHE cc_start: 0.9257 (p90) cc_final: 0.9041 (p90) REVERT: B 450 LYS cc_start: 0.7591 (pttm) cc_final: 0.6601 (ptmm) REVERT: B 465 GLN cc_start: 0.9202 (mt0) cc_final: 0.8799 (pt0) REVERT: B 490 PHE cc_start: 0.9064 (m-80) cc_final: 0.8806 (m-80) REVERT: C 28 ASP cc_start: 0.9213 (t0) cc_final: 0.8944 (t0) REVERT: C 58 LYS cc_start: 0.9641 (mmpt) cc_final: 0.9391 (mmmm) REVERT: C 65 LEU cc_start: 0.9067 (pt) cc_final: 0.8752 (pt) REVERT: C 66 VAL cc_start: 0.9163 (m) cc_final: 0.8756 (m) REVERT: C 75 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 78 MET cc_start: 0.8159 (mpp) cc_final: 0.6974 (mpp) REVERT: C 82 MET cc_start: 0.9040 (tpp) cc_final: 0.8469 (tpp) REVERT: C 94 ASN cc_start: 0.8750 (t0) cc_final: 0.8499 (t0) REVERT: C 120 VAL cc_start: 0.9121 (m) cc_final: 0.8896 (m) REVERT: C 166 LEU cc_start: 0.9045 (pt) cc_final: 0.8361 (tp) REVERT: C 261 ASP cc_start: 0.9306 (m-30) cc_final: 0.8905 (m-30) REVERT: C 262 LEU cc_start: 0.9679 (tt) cc_final: 0.9454 (pp) REVERT: C 269 ASP cc_start: 0.9168 (t70) cc_final: 0.8830 (t70) REVERT: C 286 MET cc_start: 0.8840 (mtm) cc_final: 0.8423 (mtt) REVERT: C 296 ASN cc_start: 0.9334 (p0) cc_final: 0.8471 (p0) REVERT: C 298 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8307 (mm-40) REVERT: C 385 MET cc_start: 0.9269 (ttm) cc_final: 0.8891 (tpp) REVERT: C 479 VAL cc_start: 0.9361 (p) cc_final: 0.9137 (t) REVERT: C 489 LYS cc_start: 0.7530 (mtpt) cc_final: 0.6910 (mtmt) REVERT: C 490 PHE cc_start: 0.8892 (m-80) cc_final: 0.8575 (m-80) REVERT: D 28 ASP cc_start: 0.9297 (t0) cc_final: 0.8963 (t0) REVERT: D 31 THR cc_start: 0.9413 (t) cc_final: 0.9156 (p) REVERT: D 58 LYS cc_start: 0.9640 (mmpt) cc_final: 0.9428 (mmmm) REVERT: D 66 VAL cc_start: 0.9267 (p) cc_final: 0.9053 (p) REVERT: D 67 SER cc_start: 0.9570 (t) cc_final: 0.9226 (t) REVERT: D 94 ASN cc_start: 0.8901 (t0) cc_final: 0.8622 (t0) REVERT: D 105 ARG cc_start: 0.8858 (mmt180) cc_final: 0.8248 (tpp-160) REVERT: D 163 ILE cc_start: 0.9390 (pt) cc_final: 0.9046 (pt) REVERT: D 166 LEU cc_start: 0.9093 (pt) cc_final: 0.8408 (tp) REVERT: D 269 ASP cc_start: 0.9090 (t0) cc_final: 0.8233 (t70) REVERT: D 276 SER cc_start: 0.9234 (m) cc_final: 0.8977 (p) REVERT: D 286 MET cc_start: 0.8808 (mtm) cc_final: 0.8467 (mtt) REVERT: D 296 ASN cc_start: 0.9400 (p0) cc_final: 0.8662 (p0) REVERT: D 298 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8275 (mm110) REVERT: D 375 LYS cc_start: 0.9506 (ptpp) cc_final: 0.9285 (ptpp) REVERT: D 493 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8429 (ptm160) REVERT: E 12 TYR cc_start: 0.9408 (t80) cc_final: 0.9067 (t80) REVERT: E 66 VAL cc_start: 0.9256 (m) cc_final: 0.8832 (m) REVERT: E 82 MET cc_start: 0.8944 (tpp) cc_final: 0.8503 (tpp) REVERT: E 88 ILE cc_start: 0.7423 (pt) cc_final: 0.6945 (pt) REVERT: E 93 HIS cc_start: 0.9302 (p90) cc_final: 0.8675 (p90) REVERT: E 94 ASN cc_start: 0.8845 (t0) cc_final: 0.8575 (t0) REVERT: E 134 LYS cc_start: 0.9440 (mmmt) cc_final: 0.8977 (mmmt) REVERT: E 166 LEU cc_start: 0.9093 (pt) cc_final: 0.8361 (tp) REVERT: E 178 ILE cc_start: 0.9173 (mp) cc_final: 0.8711 (mp) REVERT: E 261 ASP cc_start: 0.9301 (m-30) cc_final: 0.8938 (m-30) REVERT: E 269 ASP cc_start: 0.9179 (t70) cc_final: 0.8970 (t70) REVERT: E 276 SER cc_start: 0.9282 (m) cc_final: 0.8966 (p) REVERT: E 286 MET cc_start: 0.8842 (mtm) cc_final: 0.8501 (mtt) REVERT: E 399 GLU cc_start: 0.9372 (tm-30) cc_final: 0.9158 (tm-30) REVERT: E 450 LYS cc_start: 0.7633 (pttm) cc_final: 0.6207 (ptmm) REVERT: E 465 GLN cc_start: 0.9209 (mt0) cc_final: 0.8918 (pt0) REVERT: E 489 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7740 (ttmt) REVERT: E 490 PHE cc_start: 0.8896 (m-80) cc_final: 0.8472 (m-80) REVERT: F 66 VAL cc_start: 0.9339 (m) cc_final: 0.8908 (m) REVERT: F 67 SER cc_start: 0.9572 (m) cc_final: 0.8707 (t) REVERT: F 75 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7892 (tm-30) REVERT: F 78 MET cc_start: 0.7777 (mpp) cc_final: 0.7404 (mpp) REVERT: F 94 ASN cc_start: 0.8815 (t0) cc_final: 0.8584 (t0) REVERT: F 166 LEU cc_start: 0.9026 (pt) cc_final: 0.8207 (tp) REVERT: F 232 ASP cc_start: 0.8855 (t70) cc_final: 0.8612 (t0) REVERT: F 269 ASP cc_start: 0.9138 (t0) cc_final: 0.8248 (t70) REVERT: F 276 SER cc_start: 0.9229 (m) cc_final: 0.8905 (p) REVERT: F 296 ASN cc_start: 0.9393 (p0) cc_final: 0.8511 (p0) REVERT: F 297 LEU cc_start: 0.9044 (mm) cc_final: 0.8572 (mm) REVERT: F 298 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8214 (mm110) REVERT: F 401 PHE cc_start: 0.9154 (p90) cc_final: 0.8908 (p90) REVERT: F 479 VAL cc_start: 0.9267 (p) cc_final: 0.9040 (t) REVERT: F 482 MET cc_start: 0.8805 (tmm) cc_final: 0.8467 (tmm) REVERT: F 490 PHE cc_start: 0.8895 (m-80) cc_final: 0.8163 (m-80) REVERT: G 12 TYR cc_start: 0.9413 (t80) cc_final: 0.9146 (t80) REVERT: G 28 ASP cc_start: 0.9234 (t0) cc_final: 0.8792 (t0) REVERT: G 58 LYS cc_start: 0.9662 (mmpt) cc_final: 0.9438 (mmmm) REVERT: G 82 MET cc_start: 0.8982 (tpp) cc_final: 0.8573 (tpp) REVERT: G 93 HIS cc_start: 0.9172 (p90) cc_final: 0.8738 (p90) REVERT: G 94 ASN cc_start: 0.8913 (t0) cc_final: 0.8570 (t0) REVERT: G 105 ARG cc_start: 0.9129 (mmt-90) cc_final: 0.8897 (mmt180) REVERT: G 166 LEU cc_start: 0.9056 (pt) cc_final: 0.8379 (tp) REVERT: G 261 ASP cc_start: 0.9313 (m-30) cc_final: 0.8918 (m-30) REVERT: G 269 ASP cc_start: 0.9128 (t0) cc_final: 0.8301 (t70) REVERT: G 276 SER cc_start: 0.9269 (m) cc_final: 0.8921 (p) REVERT: G 296 ASN cc_start: 0.9240 (p0) cc_final: 0.8562 (p0) REVERT: G 297 LEU cc_start: 0.8841 (mm) cc_final: 0.8445 (mm) REVERT: G 298 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8200 (mm110) REVERT: G 369 ASN cc_start: 0.9121 (p0) cc_final: 0.8658 (p0) REVERT: G 372 HIS cc_start: 0.9401 (m170) cc_final: 0.9082 (m170) REVERT: G 450 LYS cc_start: 0.7502 (pttm) cc_final: 0.6337 (ptmm) REVERT: G 482 MET cc_start: 0.8730 (tmm) cc_final: 0.8425 (tmm) REVERT: G 489 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7205 (ttpt) REVERT: G 490 PHE cc_start: 0.8930 (m-80) cc_final: 0.8417 (m-80) REVERT: H 12 TYR cc_start: 0.9584 (t80) cc_final: 0.9132 (t80) REVERT: H 28 ASP cc_start: 0.9269 (t0) cc_final: 0.8641 (t0) REVERT: H 31 THR cc_start: 0.9466 (t) cc_final: 0.9221 (p) REVERT: H 66 VAL cc_start: 0.8889 (p) cc_final: 0.8610 (p) REVERT: H 67 SER cc_start: 0.9475 (m) cc_final: 0.9212 (m) REVERT: H 82 MET cc_start: 0.8880 (ttt) cc_final: 0.8643 (ttt) REVERT: H 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8663 (t0) REVERT: H 105 ARG cc_start: 0.9091 (mmt180) cc_final: 0.8652 (mmt180) REVERT: H 163 ILE cc_start: 0.9465 (pt) cc_final: 0.9180 (pt) REVERT: H 166 LEU cc_start: 0.9061 (pt) cc_final: 0.8307 (tp) REVERT: H 167 LYS cc_start: 0.9468 (tmtt) cc_final: 0.9182 (ptpp) REVERT: H 269 ASP cc_start: 0.9094 (t0) cc_final: 0.8239 (t70) REVERT: H 286 MET cc_start: 0.8782 (mtm) cc_final: 0.8464 (mtt) REVERT: H 296 ASN cc_start: 0.9317 (p0) cc_final: 0.8668 (p0) REVERT: H 297 LEU cc_start: 0.8901 (mm) cc_final: 0.8436 (mm) REVERT: H 298 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8239 (mm110) REVERT: H 372 HIS cc_start: 0.9540 (m170) cc_final: 0.9024 (m170) REVERT: H 482 MET cc_start: 0.8887 (tmm) cc_final: 0.8585 (tmm) REVERT: H 490 PHE cc_start: 0.9109 (m-80) cc_final: 0.8788 (m-80) outliers start: 1 outliers final: 0 residues processed: 1296 average time/residue: 0.1792 time to fit residues: 371.6426 Evaluate side-chains 1038 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1038 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 262 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 310 optimal weight: 0.0970 chunk 297 optimal weight: 0.9990 chunk 214 optimal weight: 0.5980 chunk 314 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092091 restraints weight = 53929.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096074 restraints weight = 34775.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099110 restraints weight = 25250.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101470 restraints weight = 19718.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103236 restraints weight = 16252.697| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28872 Z= 0.146 Angle : 0.899 13.888 39136 Z= 0.429 Chirality : 0.050 0.209 4472 Planarity : 0.005 0.081 4928 Dihedral : 17.599 179.963 4368 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.13), residues: 3576 helix: -1.31 (0.13), residues: 1224 sheet: -2.52 (0.25), residues: 344 loop : -2.00 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 480 TYR 0.025 0.002 TYR D 233 PHE 0.041 0.002 PHE F 456 HIS 0.006 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00340 (28864) covalent geometry : angle 0.89940 (39136) hydrogen bonds : bond 0.03537 ( 888) hydrogen bonds : angle 5.76593 ( 2448) Misc. bond : bond 0.00235 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1288 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.9279 (m) cc_final: 0.9021 (m) REVERT: A 67 SER cc_start: 0.9251 (m) cc_final: 0.8840 (m) REVERT: A 82 MET cc_start: 0.9023 (tpt) cc_final: 0.8579 (tpp) REVERT: A 88 ILE cc_start: 0.7330 (pt) cc_final: 0.7030 (pt) REVERT: A 93 HIS cc_start: 0.9240 (p90) cc_final: 0.8847 (p90) REVERT: A 94 ASN cc_start: 0.8908 (t0) cc_final: 0.8596 (t0) REVERT: A 105 ARG cc_start: 0.8991 (mmt180) cc_final: 0.8786 (mmt180) REVERT: A 166 LEU cc_start: 0.9131 (pt) cc_final: 0.8479 (tp) REVERT: A 199 GLU cc_start: 0.9465 (pt0) cc_final: 0.9234 (pt0) REVERT: A 202 GLN cc_start: 0.9301 (mp10) cc_final: 0.8384 (mp10) REVERT: A 203 ARG cc_start: 0.9487 (mmp80) cc_final: 0.9086 (mmp80) REVERT: A 229 LYS cc_start: 0.9388 (mttt) cc_final: 0.8816 (mttt) REVERT: A 261 ASP cc_start: 0.9113 (m-30) cc_final: 0.8757 (p0) REVERT: A 269 ASP cc_start: 0.9201 (t0) cc_final: 0.8468 (t70) REVERT: A 276 SER cc_start: 0.9293 (m) cc_final: 0.8977 (p) REVERT: A 296 ASN cc_start: 0.9379 (p0) cc_final: 0.8792 (p0) REVERT: A 297 LEU cc_start: 0.8750 (mm) cc_final: 0.8333 (mm) REVERT: A 298 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8284 (mm110) REVERT: A 450 LYS cc_start: 0.7742 (pttm) cc_final: 0.6679 (ptmm) REVERT: A 460 LEU cc_start: 0.9835 (mt) cc_final: 0.9543 (mt) REVERT: A 482 MET cc_start: 0.8763 (tmm) cc_final: 0.8465 (tmm) REVERT: A 489 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7586 (ttmt) REVERT: A 490 PHE cc_start: 0.8934 (m-80) cc_final: 0.8615 (m-80) REVERT: A 493 ARG cc_start: 0.9121 (ttm-80) cc_final: 0.8020 (ttm110) REVERT: B 67 SER cc_start: 0.8700 (t) cc_final: 0.8378 (t) REVERT: B 75 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 82 MET cc_start: 0.8999 (ttt) cc_final: 0.8765 (ttm) REVERT: B 93 HIS cc_start: 0.9350 (p90) cc_final: 0.8733 (p90) REVERT: B 94 ASN cc_start: 0.8913 (t0) cc_final: 0.8633 (t0) REVERT: B 132 GLU cc_start: 0.9450 (pp20) cc_final: 0.9219 (pp20) REVERT: B 153 ARG cc_start: 0.9416 (tpt170) cc_final: 0.9185 (tpp80) REVERT: B 154 LEU cc_start: 0.9441 (mm) cc_final: 0.9226 (mm) REVERT: B 166 LEU cc_start: 0.9073 (pt) cc_final: 0.8368 (tp) REVERT: B 216 ASP cc_start: 0.9393 (t70) cc_final: 0.8520 (t70) REVERT: B 229 LYS cc_start: 0.9445 (mttt) cc_final: 0.8918 (mttt) REVERT: B 276 SER cc_start: 0.9270 (m) cc_final: 0.8974 (p) REVERT: B 285 ASN cc_start: 0.9384 (m110) cc_final: 0.9094 (m110) REVERT: B 296 ASN cc_start: 0.9508 (p0) cc_final: 0.8528 (p0) REVERT: B 297 LEU cc_start: 0.8811 (mm) cc_final: 0.8392 (mm) REVERT: B 298 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8379 (mm-40) REVERT: B 450 LYS cc_start: 0.7524 (pttm) cc_final: 0.6452 (ptmm) REVERT: B 465 GLN cc_start: 0.9175 (mt0) cc_final: 0.8774 (pt0) REVERT: B 489 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7731 (ttmt) REVERT: B 490 PHE cc_start: 0.9006 (m-80) cc_final: 0.8727 (m-80) REVERT: B 493 ARG cc_start: 0.9033 (ttm-80) cc_final: 0.8729 (ttm-80) REVERT: C 24 PHE cc_start: 0.8341 (m-80) cc_final: 0.8096 (m-80) REVERT: C 65 LEU cc_start: 0.8921 (pt) cc_final: 0.8688 (pt) REVERT: C 66 VAL cc_start: 0.9147 (m) cc_final: 0.8732 (m) REVERT: C 67 SER cc_start: 0.9400 (t) cc_final: 0.9190 (t) REVERT: C 75 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 78 MET cc_start: 0.8125 (mpp) cc_final: 0.6903 (mpp) REVERT: C 82 MET cc_start: 0.9051 (tpp) cc_final: 0.8507 (tpp) REVERT: C 94 ASN cc_start: 0.8771 (t0) cc_final: 0.8497 (t0) REVERT: C 166 LEU cc_start: 0.9068 (pt) cc_final: 0.8410 (tp) REVERT: C 199 GLU cc_start: 0.9423 (pt0) cc_final: 0.9124 (pt0) REVERT: C 202 GLN cc_start: 0.9284 (mp10) cc_final: 0.8431 (mp10) REVERT: C 203 ARG cc_start: 0.9461 (mmp80) cc_final: 0.9133 (mmp80) REVERT: C 261 ASP cc_start: 0.9300 (m-30) cc_final: 0.8925 (m-30) REVERT: C 262 LEU cc_start: 0.9690 (tt) cc_final: 0.9466 (pp) REVERT: C 269 ASP cc_start: 0.9210 (t70) cc_final: 0.7936 (t70) REVERT: C 276 SER cc_start: 0.9302 (m) cc_final: 0.8976 (p) REVERT: C 283 GLN cc_start: 0.9132 (mp10) cc_final: 0.8858 (mp10) REVERT: C 296 ASN cc_start: 0.9317 (p0) cc_final: 0.8004 (p0) REVERT: C 298 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8453 (mp-120) REVERT: C 385 MET cc_start: 0.9336 (ttm) cc_final: 0.8894 (tpp) REVERT: C 479 VAL cc_start: 0.9341 (p) cc_final: 0.9119 (t) REVERT: C 489 LYS cc_start: 0.7402 (mtpt) cc_final: 0.6804 (mtmt) REVERT: C 490 PHE cc_start: 0.8880 (m-80) cc_final: 0.8663 (m-80) REVERT: C 493 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8618 (ttm-80) REVERT: D 28 ASP cc_start: 0.9226 (t0) cc_final: 0.8938 (t0) REVERT: D 31 THR cc_start: 0.9423 (t) cc_final: 0.9208 (p) REVERT: D 67 SER cc_start: 0.9615 (t) cc_final: 0.9179 (t) REVERT: D 94 ASN cc_start: 0.8906 (t0) cc_final: 0.8667 (t0) REVERT: D 105 ARG cc_start: 0.8850 (mmt180) cc_final: 0.7600 (tpp-160) REVERT: D 163 ILE cc_start: 0.9371 (pt) cc_final: 0.9015 (pt) REVERT: D 166 LEU cc_start: 0.9111 (pt) cc_final: 0.8441 (tp) REVERT: D 199 GLU cc_start: 0.9442 (pt0) cc_final: 0.9184 (pt0) REVERT: D 203 ARG cc_start: 0.9439 (mmp80) cc_final: 0.9177 (mmp80) REVERT: D 269 ASP cc_start: 0.9086 (t0) cc_final: 0.8106 (t70) REVERT: D 276 SER cc_start: 0.9239 (m) cc_final: 0.8985 (p) REVERT: D 286 MET cc_start: 0.8811 (mtm) cc_final: 0.8448 (mtt) REVERT: D 296 ASN cc_start: 0.9403 (p0) cc_final: 0.8858 (p0) REVERT: D 297 LEU cc_start: 0.8969 (mm) cc_final: 0.8433 (mm) REVERT: D 298 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8176 (mm110) REVERT: D 375 LYS cc_start: 0.9495 (ptpp) cc_final: 0.9267 (ptpp) REVERT: D 482 MET cc_start: 0.8740 (tmm) cc_final: 0.8499 (tmm) REVERT: E 12 TYR cc_start: 0.9476 (t80) cc_final: 0.8995 (t80) REVERT: E 58 LYS cc_start: 0.9636 (mmpt) cc_final: 0.9416 (mmmm) REVERT: E 66 VAL cc_start: 0.9260 (m) cc_final: 0.8871 (m) REVERT: E 82 MET cc_start: 0.8910 (tpp) cc_final: 0.8459 (tpp) REVERT: E 88 ILE cc_start: 0.7444 (pt) cc_final: 0.7026 (pt) REVERT: E 93 HIS cc_start: 0.9275 (p90) cc_final: 0.8674 (p90) REVERT: E 94 ASN cc_start: 0.8903 (t0) cc_final: 0.8574 (t0) REVERT: E 166 LEU cc_start: 0.9077 (pt) cc_final: 0.8359 (tp) REVERT: E 203 ARG cc_start: 0.9467 (mmp80) cc_final: 0.9184 (mmp80) REVERT: E 261 ASP cc_start: 0.9267 (m-30) cc_final: 0.8881 (m-30) REVERT: E 269 ASP cc_start: 0.9136 (t70) cc_final: 0.8507 (t70) REVERT: E 276 SER cc_start: 0.9269 (m) cc_final: 0.8933 (p) REVERT: E 296 ASN cc_start: 0.9442 (p0) cc_final: 0.8488 (p0) REVERT: E 298 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8255 (mm110) REVERT: E 465 GLN cc_start: 0.9175 (mt0) cc_final: 0.8904 (pt0) REVERT: E 482 MET cc_start: 0.8798 (tmm) cc_final: 0.8496 (tmm) REVERT: E 489 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7669 (ttmt) REVERT: E 490 PHE cc_start: 0.8966 (m-80) cc_final: 0.8557 (m-80) REVERT: F 28 ASP cc_start: 0.8899 (t0) cc_final: 0.8530 (t0) REVERT: F 66 VAL cc_start: 0.9264 (m) cc_final: 0.8997 (m) REVERT: F 67 SER cc_start: 0.9460 (m) cc_final: 0.8812 (t) REVERT: F 75 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 78 MET cc_start: 0.8428 (mpp) cc_final: 0.7341 (mpp) REVERT: F 82 MET cc_start: 0.9193 (ppp) cc_final: 0.8950 (ppp) REVERT: F 94 ASN cc_start: 0.8869 (t0) cc_final: 0.8641 (t0) REVERT: F 109 LYS cc_start: 0.8859 (tptp) cc_final: 0.8241 (tptp) REVERT: F 166 LEU cc_start: 0.9048 (pt) cc_final: 0.8247 (tp) REVERT: F 232 ASP cc_start: 0.8796 (t70) cc_final: 0.8537 (t0) REVERT: F 262 LEU cc_start: 0.9656 (tt) cc_final: 0.9397 (pp) REVERT: F 269 ASP cc_start: 0.9084 (t0) cc_final: 0.8161 (t70) REVERT: F 276 SER cc_start: 0.9227 (m) cc_final: 0.8900 (p) REVERT: F 296 ASN cc_start: 0.9409 (p0) cc_final: 0.8505 (p0) REVERT: F 297 LEU cc_start: 0.8999 (mm) cc_final: 0.8523 (mm) REVERT: F 298 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8237 (mm110) REVERT: F 465 GLN cc_start: 0.9081 (mt0) cc_final: 0.8700 (pt0) REVERT: F 482 MET cc_start: 0.8785 (tmm) cc_final: 0.8526 (tmm) REVERT: G 66 VAL cc_start: 0.8894 (m) cc_final: 0.8231 (m) REVERT: G 82 MET cc_start: 0.8941 (tpp) cc_final: 0.8547 (tpp) REVERT: G 93 HIS cc_start: 0.9182 (p90) cc_final: 0.8764 (p90) REVERT: G 94 ASN cc_start: 0.8902 (t0) cc_final: 0.8576 (t0) REVERT: G 105 ARG cc_start: 0.9117 (mmt-90) cc_final: 0.8885 (mmt180) REVERT: G 166 LEU cc_start: 0.9065 (pt) cc_final: 0.8378 (tp) REVERT: G 261 ASP cc_start: 0.9294 (m-30) cc_final: 0.8942 (m-30) REVERT: G 269 ASP cc_start: 0.9198 (t0) cc_final: 0.8388 (t70) REVERT: G 276 SER cc_start: 0.9239 (m) cc_final: 0.8895 (p) REVERT: G 296 ASN cc_start: 0.9266 (p0) cc_final: 0.8603 (p0) REVERT: G 297 LEU cc_start: 0.8747 (mm) cc_final: 0.8352 (mm) REVERT: G 298 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8115 (mm110) REVERT: G 369 ASN cc_start: 0.9106 (p0) cc_final: 0.8630 (p0) REVERT: G 372 HIS cc_start: 0.9394 (m170) cc_final: 0.9077 (m170) REVERT: G 450 LYS cc_start: 0.7620 (pttm) cc_final: 0.6505 (ptmm) REVERT: G 482 MET cc_start: 0.8686 (tmm) cc_final: 0.8371 (tmm) REVERT: G 489 LYS cc_start: 0.7564 (ttpt) cc_final: 0.7118 (ttpt) REVERT: G 490 PHE cc_start: 0.8927 (m-80) cc_final: 0.8394 (m-80) REVERT: H 12 TYR cc_start: 0.9558 (t80) cc_final: 0.9128 (t80) REVERT: H 31 THR cc_start: 0.9484 (t) cc_final: 0.9247 (p) REVERT: H 58 LYS cc_start: 0.9648 (mmpt) cc_final: 0.9431 (mmmm) REVERT: H 66 VAL cc_start: 0.8922 (p) cc_final: 0.8698 (p) REVERT: H 82 MET cc_start: 0.8889 (ttt) cc_final: 0.8614 (ttt) REVERT: H 94 ASN cc_start: 0.8866 (t0) cc_final: 0.8540 (t0) REVERT: H 105 ARG cc_start: 0.9075 (mmt180) cc_final: 0.8740 (mmt180) REVERT: H 163 ILE cc_start: 0.9471 (pt) cc_final: 0.9181 (pt) REVERT: H 166 LEU cc_start: 0.9051 (pt) cc_final: 0.8297 (tp) REVERT: H 167 LYS cc_start: 0.9453 (tmtt) cc_final: 0.9195 (ptpp) REVERT: H 261 ASP cc_start: 0.9132 (m-30) cc_final: 0.8904 (m-30) REVERT: H 269 ASP cc_start: 0.9119 (t0) cc_final: 0.8255 (t70) REVERT: H 286 MET cc_start: 0.8740 (mtm) cc_final: 0.8411 (mtt) REVERT: H 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8623 (p0) REVERT: H 297 LEU cc_start: 0.8839 (mm) cc_final: 0.8363 (mm) REVERT: H 298 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8242 (mm110) REVERT: H 357 PHE cc_start: 0.9130 (m-80) cc_final: 0.8909 (m-10) REVERT: H 372 HIS cc_start: 0.9530 (m170) cc_final: 0.8988 (m170) REVERT: H 482 MET cc_start: 0.8781 (tmm) cc_final: 0.8447 (tmm) REVERT: H 490 PHE cc_start: 0.9118 (m-80) cc_final: 0.8850 (m-80) outliers start: 0 outliers final: 0 residues processed: 1288 average time/residue: 0.1825 time to fit residues: 375.7170 Evaluate side-chains 1052 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1052 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 101 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086159 restraints weight = 58330.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089797 restraints weight = 38372.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092534 restraints weight = 28235.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094588 restraints weight = 22323.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096221 restraints weight = 18593.140| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28872 Z= 0.234 Angle : 0.911 13.703 39136 Z= 0.452 Chirality : 0.052 0.283 4472 Planarity : 0.006 0.072 4928 Dihedral : 17.465 178.399 4368 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.13), residues: 3576 helix: -1.31 (0.13), residues: 1216 sheet: -2.48 (0.26), residues: 344 loop : -2.06 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 407 TYR 0.035 0.003 TYR B 233 PHE 0.036 0.002 PHE C 456 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd covalent geometry : bond 0.00525 (28864) covalent geometry : angle 0.91108 (39136) hydrogen bonds : bond 0.03842 ( 888) hydrogen bonds : angle 5.96426 ( 2448) Misc. bond : bond 0.00206 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6807.47 seconds wall clock time: 118 minutes 4.23 seconds (7084.23 seconds total)