Starting phenix.real_space_refine on Wed Nov 19 23:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uc2_20725/11_2025/6uc2_20725.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uc2_20725/11_2025/6uc2_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_20725/11_2025/6uc2_20725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uc2_20725/11_2025/6uc2_20725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uc2_20725/11_2025/6uc2_20725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uc2_20725/11_2025/6uc2_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-2.0-5881/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: 4.02, per 1000 atoms: 0.14 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 1.4 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: 1.22 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: 5.20 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: 0.10 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- 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 : 1.099 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: 0.9235 (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: 0.8334 (t0) REVERT: A 276 SER cc_start: 0.9206 (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: 0.7463 (pmm) cc_final: 0.7087 (pmm) REVERT: A 351 SER cc_start: 0.8521 (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: 0.9573 (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: 0.8784 (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: 0.9203 (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: 0.9538 (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: 0.8865 (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: 0.9205 (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: 0.9198 (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: 0.8336 (m-10) cc_final: 0.8131 (m-80) REVERT: C 450 LYS cc_start: 0.6896 (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: 0.8859 (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: 0.8701 (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: 0.8845 (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: 0.7001 (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: 0.7107 (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: 0.8160 (ptt180) REVERT: E 372 HIS cc_start: 0.9571 (m170) cc_final: 0.9317 (m170) REVERT: E 402 PHE cc_start: 0.8460 (m-10) cc_final: 0.8253 (m-80) REVERT: E 450 LYS cc_start: 0.6996 (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: 0.8893 (ttpt) cc_final: 0.8512 (ttpt) REVERT: F 82 MET cc_start: 0.8784 (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: 0.9189 (t0) cc_final: 0.8279 (t0) REVERT: F 277 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8221 (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: 0.9435 (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: 0.8181 (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: 0.8999 (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: 0.9246 (OUTLIER) cc_final: 0.8822 (ptm-80) REVERT: G 245 LEU cc_start: 0.9226 (mm) cc_final: 0.8873 (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: 0.9650 (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: 0.9169 (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: 0.6930 (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: 0.9556 (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: 0.8379 (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: 0.2013 time to fit residues: 504.7068 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 : 1.216 ------------------------------------------------------------------------------- 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 : 1.190 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: 0.9075 (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: 0.9025 (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: 0.9045 (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: 0.9255 (t0) cc_final: 0.8257 (t0) REVERT: B 277 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8540 (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: 0.7968 (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: 0.8379 (tp) REVERT: C 178 ILE cc_start: 0.9327 (mp) cc_final: 0.8849 (mp) REVERT: C 232 ASP cc_start: 0.9014 (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: 0.9226 (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: 0.8430 (m) REVERT: D 67 SER cc_start: 0.8794 (m) cc_final: 0.7912 (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: 0.8736 (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: 0.7333 (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: 0.8855 (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: 0.8784 (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: 0.8761 (mm) REVERT: E 298 GLN cc_start: 0.8712 (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: 0.9142 (t80) cc_final: 0.8871 (t80) REVERT: E 364 ASP cc_start: 0.8876 (t0) cc_final: 0.8648 (t0) REVERT: E 489 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7828 (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: 0.8633 (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: 0.8693 (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: 0.8652 (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: 0.8875 (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: 0.9056 (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: 0.9186 (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: 0.8929 (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: 0.9215 (mp) cc_final: 0.8542 (mp) REVERT: H 181 LYS cc_start: 0.9293 (mmpt) cc_final: 0.9028 (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: 0.9203 (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: 0.8664 (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: 0.1795 time to fit residues: 432.6253 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 : 1.124 ------------------------------------------------------------------------------- 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 : 1.077 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: 0.9201 (t0) cc_final: 0.8925 (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: 0.8949 (tpp) cc_final: 0.8547 (tpp) REVERT: A 93 HIS cc_start: 0.9304 (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: 0.8367 (tptp) cc_final: 0.8038 (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: 0.7737 (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: 0.9207 (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: 0.8233 (mm-40) REVERT: B 321 LEU cc_start: 0.9746 (mm) cc_final: 0.9447 (mm) REVERT: B 375 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9225 (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: 0.6728 (mpp) REVERT: C 82 MET cc_start: 0.8873 (tpp) cc_final: 0.8483 (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: 0.8778 (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: 0.9131 (t0) cc_final: 0.8280 (t0) REVERT: C 276 SER cc_start: 0.9205 (m) cc_final: 0.8898 (p) 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: 0.8852 (pm20) cc_final: 0.8463 (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: 0.9044 (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: 0.8276 (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: 0.8142 (mm-40) REVERT: D 305 VAL cc_start: 0.8652 (m) cc_final: 0.7873 (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: 0.9297 (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: 0.8281 (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: 0.8784 (m) cc_final: 0.8414 (t) REVERT: E 78 MET cc_start: 0.7628 (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: 0.9285 (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: 0.9159 (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: 0.9260 (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: 0.8468 (tptp) cc_final: 0.8087 (tptp) REVERT: E 493 ARG cc_start: 0.9277 (ttt90) cc_final: 0.8933 (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: 0.8754 (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: 0.9058 (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: 0.8261 (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: 0.8726 (p90) REVERT: G 94 ASN cc_start: 0.8869 (t0) cc_final: 0.8588 (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: 0.8176 (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: 0.9444 (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: 0.8543 (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: 0.9243 (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: 0.9490 (mm) REVERT: H 364 ASP cc_start: 0.8707 (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: 0.8849 (pm20) cc_final: 0.8503 (mp0) REVERT: H 401 PHE cc_start: 0.9261 (p90) cc_final: 0.9049 (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: 0.1899 time to fit residues: 396.5595 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 : 1.112 ------------------------------------------------------------------------------- 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: 0.3980 chunk 198 optimal weight: 10.0000 overall best weight: 1.0400 ------------------------------------------------------------------------------- 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** ** 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 = 0.3743 r_free = 0.3743 target = 0.128681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090063 restraints weight = 54531.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094038 restraints weight = 35165.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097025 restraints weight = 25424.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099391 restraints weight = 19864.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101199 restraints weight = 16292.125| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28872 Z= 0.153 Angle : 0.879 12.038 39136 Z= 0.424 Chirality : 0.051 0.201 4472 Planarity : 0.005 0.067 4928 Dihedral : 18.271 168.046 4368 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % 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: -2.78 (0.13), residues: 3576 helix: -1.24 (0.14), residues: 1224 sheet: -2.88 (0.19), residues: 480 loop : -1.95 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 480 TYR 0.027 0.002 TYR B 233 PHE 0.047 0.002 PHE F 456 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00353 (28864) covalent geometry : angle 0.87891 (39136) hydrogen bonds : bond 0.03768 ( 888) hydrogen bonds : angle 5.85236 ( 2448) Misc. bond : bond 0.00210 ( 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 1344 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1340 time to evaluate : 1.124 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: 0.9229 (t0) cc_final: 0.8961 (t0) REVERT: A 67 SER cc_start: 0.8636 (m) cc_final: 0.8273 (t) REVERT: A 78 MET cc_start: 0.7521 (mpp) cc_final: 0.7117 (mpp) REVERT: A 82 MET cc_start: 0.8962 (tpp) cc_final: 0.8589 (tpp) REVERT: A 93 HIS cc_start: 0.9313 (p90) cc_final: 0.8728 (p90) REVERT: A 94 ASN cc_start: 0.8872 (t0) cc_final: 0.8540 (t0) REVERT: A 139 PHE cc_start: 0.8669 (p90) cc_final: 0.8034 (p90) REVERT: A 166 LEU cc_start: 0.8876 (pt) cc_final: 0.8161 (tp) REVERT: A 174 PHE cc_start: 0.8890 (m-80) cc_final: 0.8629 (m-80) REVERT: A 179 MET cc_start: 0.7617 (tpt) cc_final: 0.7197 (tpt) REVERT: A 199 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9397 (mt-10) REVERT: A 230 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8744 (m-40) REVERT: A 241 LYS cc_start: 0.9435 (tptp) cc_final: 0.9143 (tptp) REVERT: A 262 LEU cc_start: 0.9785 (tt) cc_final: 0.9436 (mt) REVERT: A 269 ASP cc_start: 0.9171 (t0) cc_final: 0.8264 (t0) REVERT: A 276 SER cc_start: 0.9165 (m) cc_final: 0.8861 (p) REVERT: A 285 ASN cc_start: 0.9556 (m110) cc_final: 0.9322 (m110) REVERT: A 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8579 (p0) REVERT: A 297 LEU cc_start: 0.9163 (mm) cc_final: 0.8741 (mm) REVERT: A 298 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8366 (mm110) REVERT: A 321 LEU cc_start: 0.9729 (mm) cc_final: 0.9465 (mm) REVERT: A 368 GLN cc_start: 0.9118 (mp10) cc_final: 0.8897 (mp-120) REVERT: A 479 VAL cc_start: 0.9460 (m) cc_final: 0.9204 (t) REVERT: A 489 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7034 (ttpt) REVERT: A 490 PHE cc_start: 0.8860 (m-80) cc_final: 0.8508 (m-80) REVERT: A 492 LYS cc_start: 0.8486 (tptp) cc_final: 0.8190 (tptp) REVERT: B 66 VAL cc_start: 0.9234 (m) cc_final: 0.8842 (m) REVERT: B 67 SER cc_start: 0.9249 (t) cc_final: 0.8198 (t) REVERT: B 78 MET cc_start: 0.7430 (mpp) cc_final: 0.6616 (mpp) REVERT: B 82 MET cc_start: 0.8937 (ttt) cc_final: 0.8603 (ttt) REVERT: B 93 HIS cc_start: 0.9333 (p90) cc_final: 0.8754 (p90) REVERT: B 94 ASN cc_start: 0.8931 (t0) cc_final: 0.8703 (t0) REVERT: B 109 LYS cc_start: 0.8799 (tptp) cc_final: 0.8303 (tptp) REVERT: B 115 ILE cc_start: 0.7743 (pt) cc_final: 0.7371 (pt) REVERT: B 116 THR cc_start: 0.8834 (p) cc_final: 0.8629 (p) REVERT: B 127 VAL cc_start: 0.9072 (t) cc_final: 0.8546 (t) REVERT: B 166 LEU cc_start: 0.8926 (pt) cc_final: 0.8229 (tp) REVERT: B 181 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8964 (mmpt) REVERT: B 229 LYS cc_start: 0.9427 (mttt) cc_final: 0.9049 (mttt) REVERT: B 261 ASP cc_start: 0.9256 (m-30) cc_final: 0.8697 (p0) REVERT: B 262 LEU cc_start: 0.9755 (tt) cc_final: 0.9536 (tt) REVERT: B 269 ASP cc_start: 0.9256 (t0) cc_final: 0.8264 (t0) REVERT: B 281 ILE cc_start: 0.9388 (mm) cc_final: 0.9164 (mm) REVERT: B 285 ASN cc_start: 0.9486 (m110) cc_final: 0.9194 (m110) REVERT: B 286 MET cc_start: 0.8642 (mtm) cc_final: 0.8391 (mtt) REVERT: B 296 ASN cc_start: 0.9420 (p0) cc_final: 0.8700 (p0) REVERT: B 297 LEU cc_start: 0.9226 (mm) cc_final: 0.8711 (mm) REVERT: B 298 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8202 (mm110) REVERT: B 321 LEU cc_start: 0.9730 (mm) cc_final: 0.9485 (mm) REVERT: B 364 ASP cc_start: 0.8433 (t0) cc_final: 0.8169 (t0) REVERT: B 372 HIS cc_start: 0.9450 (m90) cc_final: 0.8907 (m90) REVERT: B 450 LYS cc_start: 0.7062 (pttm) cc_final: 0.6474 (ptmm) REVERT: C 28 ASP cc_start: 0.9125 (t0) cc_final: 0.8803 (t0) REVERT: C 67 SER cc_start: 0.8632 (m) cc_final: 0.8340 (t) REVERT: C 78 MET cc_start: 0.7915 (mpp) cc_final: 0.7098 (mpp) REVERT: C 82 MET cc_start: 0.8992 (tpp) cc_final: 0.8617 (tpp) REVERT: C 94 ASN cc_start: 0.8881 (t0) cc_final: 0.8657 (t0) REVERT: C 109 LYS cc_start: 0.9254 (tptp) cc_final: 0.9028 (tptp) REVERT: C 115 ILE cc_start: 0.7074 (pt) cc_final: 0.6786 (pt) REVERT: C 134 LYS cc_start: 0.9499 (tppt) cc_final: 0.9271 (mmtt) REVERT: C 139 PHE cc_start: 0.8797 (p90) cc_final: 0.8151 (p90) REVERT: C 162 ASP cc_start: 0.9199 (m-30) cc_final: 0.8973 (m-30) REVERT: C 166 LEU cc_start: 0.8779 (pt) cc_final: 0.8077 (tp) REVERT: C 181 LYS cc_start: 0.9437 (mmpt) cc_final: 0.9173 (mmpt) REVERT: C 216 ASP cc_start: 0.8996 (t70) cc_final: 0.8688 (t70) REVERT: C 261 ASP cc_start: 0.9311 (m-30) cc_final: 0.8678 (p0) REVERT: C 262 LEU cc_start: 0.9763 (tt) cc_final: 0.9508 (tt) REVERT: C 265 GLN cc_start: 0.9557 (tm-30) cc_final: 0.9317 (tm-30) REVERT: C 281 ILE cc_start: 0.9409 (mm) cc_final: 0.9188 (mm) REVERT: C 285 ASN cc_start: 0.9515 (m110) cc_final: 0.9259 (m110) REVERT: C 297 LEU cc_start: 0.9132 (mm) cc_final: 0.8768 (mm) REVERT: C 321 LEU cc_start: 0.9731 (mm) cc_final: 0.9430 (mm) REVERT: C 364 ASP cc_start: 0.8843 (t0) cc_final: 0.8375 (t0) REVERT: C 372 HIS cc_start: 0.9491 (m90) cc_final: 0.8946 (m90) REVERT: C 483 MET cc_start: 0.9439 (ptm) cc_final: 0.9228 (ppp) REVERT: C 489 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7484 (mtpt) REVERT: C 490 PHE cc_start: 0.8855 (m-80) cc_final: 0.8619 (m-80) REVERT: D 28 ASP cc_start: 0.9295 (t0) cc_final: 0.9015 (t0) REVERT: D 67 SER cc_start: 0.9221 (t) cc_final: 0.8693 (t) REVERT: D 78 MET cc_start: 0.7284 (mpp) cc_final: 0.6322 (mpp) REVERT: D 82 MET cc_start: 0.8977 (ttt) cc_final: 0.8620 (ttt) REVERT: D 94 ASN cc_start: 0.8941 (t0) cc_final: 0.8728 (t0) REVERT: D 130 VAL cc_start: 0.9560 (m) cc_final: 0.9113 (m) REVERT: D 134 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9051 (mmmt) REVERT: D 163 ILE cc_start: 0.9379 (pt) cc_final: 0.8951 (pt) REVERT: D 166 LEU cc_start: 0.8949 (pt) cc_final: 0.8207 (tp) REVERT: D 181 LYS cc_start: 0.9304 (mmpt) cc_final: 0.9041 (mmmt) REVERT: D 258 TYR cc_start: 0.9650 (t80) cc_final: 0.9099 (t80) REVERT: D 261 ASP cc_start: 0.9252 (m-30) cc_final: 0.8487 (p0) REVERT: D 262 LEU cc_start: 0.9750 (tt) cc_final: 0.9442 (tt) REVERT: D 269 ASP cc_start: 0.9166 (t0) cc_final: 0.8306 (t0) REVERT: D 276 SER cc_start: 0.9135 (m) cc_final: 0.8839 (p) REVERT: D 281 ILE cc_start: 0.9416 (mm) cc_final: 0.9173 (mm) REVERT: D 285 ASN cc_start: 0.9526 (m110) cc_final: 0.9227 (m110) REVERT: D 286 MET cc_start: 0.8762 (mtm) cc_final: 0.7734 (mtt) REVERT: D 296 ASN cc_start: 0.9415 (p0) cc_final: 0.8592 (p0) REVERT: D 298 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8211 (mm110) REVERT: D 321 LEU cc_start: 0.9742 (mm) cc_final: 0.9434 (mm) REVERT: D 353 TYR cc_start: 0.9240 (t80) cc_final: 0.8921 (t80) REVERT: D 364 ASP cc_start: 0.8512 (t0) cc_final: 0.8224 (t0) REVERT: D 372 HIS cc_start: 0.9484 (m90) cc_final: 0.8893 (m90) REVERT: D 395 GLU cc_start: 0.8875 (pm20) cc_final: 0.8480 (pm20) REVERT: D 401 PHE cc_start: 0.9305 (p90) cc_final: 0.9081 (p90) REVERT: D 492 LYS cc_start: 0.8637 (tptp) cc_final: 0.8410 (tptp) REVERT: E 12 TYR cc_start: 0.9226 (t80) cc_final: 0.8537 (t80) REVERT: E 66 VAL cc_start: 0.9184 (m) cc_final: 0.8691 (m) REVERT: E 78 MET cc_start: 0.7450 (mpp) cc_final: 0.6972 (mpp) REVERT: E 82 MET cc_start: 0.8951 (tpp) cc_final: 0.8578 (tpp) REVERT: E 93 HIS cc_start: 0.9255 (p90) cc_final: 0.8707 (p90) REVERT: E 94 ASN cc_start: 0.8873 (t0) cc_final: 0.8613 (t0) REVERT: E 103 GLU cc_start: 0.9156 (mp0) cc_final: 0.8900 (mp0) REVERT: E 105 ARG cc_start: 0.8792 (mtt90) cc_final: 0.8337 (ttp80) REVERT: E 109 LYS cc_start: 0.9130 (tptp) cc_final: 0.8705 (tptp) REVERT: E 166 LEU cc_start: 0.8847 (pt) cc_final: 0.8107 (tp) REVERT: E 261 ASP cc_start: 0.9303 (m-30) cc_final: 0.8639 (p0) REVERT: E 262 LEU cc_start: 0.9770 (tt) cc_final: 0.9515 (tt) REVERT: E 269 ASP cc_start: 0.9165 (t0) cc_final: 0.8304 (t0) REVERT: E 296 ASN cc_start: 0.9368 (p0) cc_final: 0.8546 (p0) REVERT: E 298 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8203 (mm110) REVERT: E 368 GLN cc_start: 0.9125 (mp10) cc_final: 0.8911 (mp-120) REVERT: E 489 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7287 (ttpt) REVERT: E 490 PHE cc_start: 0.8987 (m-80) cc_final: 0.8547 (m-80) REVERT: E 492 LYS cc_start: 0.8626 (tptp) cc_final: 0.8296 (tptp) REVERT: F 78 MET cc_start: 0.7934 (mpp) cc_final: 0.7342 (mpp) REVERT: F 103 GLU cc_start: 0.9455 (mp0) cc_final: 0.9249 (mp0) REVERT: F 134 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9102 (mmmt) REVERT: F 166 LEU cc_start: 0.8884 (pt) cc_final: 0.8109 (tp) REVERT: F 216 ASP cc_start: 0.9091 (t70) cc_final: 0.8795 (t0) REVERT: F 232 ASP cc_start: 0.8957 (t70) cc_final: 0.8746 (t0) REVERT: F 261 ASP cc_start: 0.9298 (m-30) cc_final: 0.8740 (p0) REVERT: F 262 LEU cc_start: 0.9742 (tt) cc_final: 0.9515 (tt) REVERT: F 265 GLN cc_start: 0.9637 (tt0) cc_final: 0.9182 (tm-30) REVERT: F 269 ASP cc_start: 0.9149 (t0) cc_final: 0.8262 (t0) REVERT: F 296 ASN cc_start: 0.9416 (p0) cc_final: 0.8588 (p0) REVERT: F 298 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8207 (mm110) REVERT: F 321 LEU cc_start: 0.9751 (mm) cc_final: 0.9489 (mm) REVERT: F 353 TYR cc_start: 0.9209 (t80) cc_final: 0.8823 (t80) REVERT: F 372 HIS cc_start: 0.9490 (m90) cc_final: 0.8876 (m90) REVERT: F 401 PHE cc_start: 0.9310 (p90) cc_final: 0.9077 (p90) REVERT: F 492 LYS cc_start: 0.8622 (tptp) cc_final: 0.8294 (tptp) REVERT: G 65 LEU cc_start: 0.8889 (pt) cc_final: 0.8680 (pt) REVERT: G 66 VAL cc_start: 0.9138 (m) cc_final: 0.8526 (m) REVERT: G 67 SER cc_start: 0.8659 (m) cc_final: 0.8329 (t) REVERT: G 78 MET cc_start: 0.7512 (mpp) cc_final: 0.6739 (mpp) REVERT: G 82 MET cc_start: 0.8903 (tpp) cc_final: 0.8576 (tpp) REVERT: G 94 ASN cc_start: 0.8901 (t0) cc_final: 0.8607 (t0) REVERT: G 105 ARG cc_start: 0.9044 (mmt90) cc_final: 0.8807 (mmt180) REVERT: G 108 LYS cc_start: 0.9433 (tptp) cc_final: 0.9175 (ptpp) REVERT: G 109 LYS cc_start: 0.9182 (tptp) cc_final: 0.8762 (tptp) REVERT: G 166 LEU cc_start: 0.8855 (pt) cc_final: 0.8190 (tp) REVERT: G 174 PHE cc_start: 0.8913 (m-80) cc_final: 0.8569 (m-80) REVERT: G 178 ILE cc_start: 0.9345 (mp) cc_final: 0.8669 (mp) REVERT: G 179 MET cc_start: 0.7432 (tpt) cc_final: 0.7073 (tpt) REVERT: G 181 LYS cc_start: 0.9405 (mmpt) cc_final: 0.9175 (mmpt) REVERT: G 241 LYS cc_start: 0.9360 (tptp) cc_final: 0.9076 (tptp) REVERT: G 262 LEU cc_start: 0.9778 (tt) cc_final: 0.9410 (mt) REVERT: G 269 ASP cc_start: 0.9179 (t0) cc_final: 0.8302 (t0) REVERT: G 276 SER cc_start: 0.9115 (m) cc_final: 0.8803 (p) REVERT: G 285 ASN cc_start: 0.9551 (m110) cc_final: 0.9335 (m110) REVERT: G 296 ASN cc_start: 0.9352 (p0) cc_final: 0.8687 (p0) REVERT: G 297 LEU cc_start: 0.9181 (mm) cc_final: 0.8740 (mm) REVERT: G 298 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8298 (mm110) REVERT: G 372 HIS cc_start: 0.9512 (m170) cc_final: 0.9168 (m170) REVERT: G 401 PHE cc_start: 0.9354 (p90) cc_final: 0.9133 (p90) REVERT: G 490 PHE cc_start: 0.8829 (m-80) cc_final: 0.8138 (m-80) REVERT: H 28 ASP cc_start: 0.9327 (t0) cc_final: 0.8983 (t0) REVERT: H 66 VAL cc_start: 0.9382 (m) cc_final: 0.9115 (p) REVERT: H 67 SER cc_start: 0.9342 (m) cc_final: 0.8905 (t) REVERT: H 78 MET cc_start: 0.7412 (mpp) cc_final: 0.6373 (mpp) REVERT: H 130 VAL cc_start: 0.9582 (m) cc_final: 0.9156 (m) REVERT: H 134 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9054 (mmmt) REVERT: H 161 ARG cc_start: 0.9464 (mtm180) cc_final: 0.9255 (mtm110) REVERT: H 166 LEU cc_start: 0.8960 (pt) cc_final: 0.8043 (tp) REVERT: H 181 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8873 (mmpt) REVERT: H 261 ASP cc_start: 0.9192 (m-30) cc_final: 0.8578 (p0) REVERT: H 262 LEU cc_start: 0.9733 (tt) cc_final: 0.9458 (tt) REVERT: H 269 ASP cc_start: 0.9154 (t0) cc_final: 0.8294 (t0) REVERT: H 285 ASN cc_start: 0.9511 (m110) cc_final: 0.9283 (m110) REVERT: H 286 MET cc_start: 0.8759 (mtm) cc_final: 0.8378 (mtt) REVERT: H 296 ASN cc_start: 0.9431 (p0) cc_final: 0.8590 (p0) REVERT: H 298 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8215 (mm110) REVERT: H 321 LEU cc_start: 0.9758 (mm) cc_final: 0.9465 (mm) REVERT: H 385 MET cc_start: 0.9145 (ttm) cc_final: 0.8766 (ttm) REVERT: H 395 GLU cc_start: 0.8903 (pm20) cc_final: 0.8389 (pm20) REVERT: H 493 ARG cc_start: 0.9317 (ttt90) cc_final: 0.9115 (ttm-80) outliers start: 4 outliers final: 1 residues processed: 1341 average time/residue: 0.1832 time to fit residues: 394.1137 Evaluate side-chains 1060 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1058 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** C 343 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN 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 F 465 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089845 restraints weight = 54453.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093826 restraints weight = 35061.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096850 restraints weight = 25368.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099099 restraints weight = 19811.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.100918 restraints weight = 16343.911| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4227 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= 0.152 Angle : 0.860 11.487 39136 Z= 0.414 Chirality : 0.050 0.224 4472 Planarity : 0.005 0.068 4928 Dihedral : 17.998 169.523 4368 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.09 % 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: -2.69 (0.13), residues: 3576 helix: -1.14 (0.14), residues: 1224 sheet: -3.25 (0.21), residues: 344 loop : -1.93 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 480 TYR 0.034 0.002 TYR D 233 PHE 0.048 0.002 PHE C 456 HIS 0.007 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00360 (28864) covalent geometry : angle 0.86029 (39136) hydrogen bonds : bond 0.03627 ( 888) hydrogen bonds : angle 5.73748 ( 2448) Misc. bond : bond 0.00209 ( 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 1331 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1330 time to evaluate : 1.089 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: A 28 ASP cc_start: 0.9264 (t0) cc_final: 0.8986 (t0) REVERT: A 78 MET cc_start: 0.7645 (mpp) cc_final: 0.6942 (mpp) REVERT: A 82 MET cc_start: 0.8987 (tpp) cc_final: 0.8734 (tpp) REVERT: A 94 ASN cc_start: 0.8885 (t0) cc_final: 0.8633 (t0) REVERT: A 105 ARG cc_start: 0.8998 (mmt-90) cc_final: 0.8792 (mmt180) REVERT: A 166 LEU cc_start: 0.8968 (pt) cc_final: 0.8270 (tp) REVERT: A 179 MET cc_start: 0.7451 (tpt) cc_final: 0.7060 (tpt) REVERT: A 241 LYS cc_start: 0.9431 (tptp) cc_final: 0.9137 (tptp) REVERT: A 262 LEU cc_start: 0.9788 (tt) cc_final: 0.9429 (mt) REVERT: A 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8197 (t0) REVERT: A 276 SER cc_start: 0.9190 (m) cc_final: 0.8871 (p) REVERT: A 285 ASN cc_start: 0.9576 (m110) cc_final: 0.9346 (m110) REVERT: A 296 ASN cc_start: 0.9349 (p0) cc_final: 0.8621 (p0) REVERT: A 297 LEU cc_start: 0.9082 (mm) cc_final: 0.8625 (mm) REVERT: A 298 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8334 (mm110) REVERT: A 450 LYS cc_start: 0.7417 (pttm) cc_final: 0.6299 (ptmm) REVERT: A 490 PHE cc_start: 0.8886 (m-80) cc_final: 0.8504 (m-80) REVERT: B 67 SER cc_start: 0.9539 (t) cc_final: 0.9309 (t) REVERT: B 78 MET cc_start: 0.7712 (mpp) cc_final: 0.7465 (mpp) REVERT: B 93 HIS cc_start: 0.9354 (p90) cc_final: 0.8714 (p90) REVERT: B 94 ASN cc_start: 0.8940 (t0) cc_final: 0.8716 (t0) REVERT: B 105 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8738 (mmt90) REVERT: B 109 LYS cc_start: 0.8856 (tptp) cc_final: 0.8347 (tptp) REVERT: B 166 LEU cc_start: 0.8988 (pt) cc_final: 0.8290 (tp) REVERT: B 174 PHE cc_start: 0.8665 (m-80) cc_final: 0.8432 (m-80) REVERT: B 199 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9386 (mt-10) REVERT: B 229 LYS cc_start: 0.9444 (mttt) cc_final: 0.8778 (mttt) REVERT: B 261 ASP cc_start: 0.9249 (m-30) cc_final: 0.8727 (p0) REVERT: B 262 LEU cc_start: 0.9760 (tt) cc_final: 0.9538 (tt) REVERT: B 269 ASP cc_start: 0.9227 (t0) cc_final: 0.8499 (t70) REVERT: B 296 ASN cc_start: 0.9480 (p0) cc_final: 0.8712 (p0) REVERT: B 297 LEU cc_start: 0.9045 (mm) cc_final: 0.8608 (mm) REVERT: B 298 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8343 (mm110) REVERT: B 372 HIS cc_start: 0.9505 (m90) cc_final: 0.8896 (m90) REVERT: B 465 GLN cc_start: 0.9193 (mt0) cc_final: 0.8862 (pt0) REVERT: B 489 LYS cc_start: 0.7813 (ttpt) cc_final: 0.7322 (ttpt) REVERT: B 490 PHE cc_start: 0.9037 (m-80) cc_final: 0.8597 (m-80) REVERT: B 492 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8449 (tmtt) REVERT: C 65 LEU cc_start: 0.8864 (pt) cc_final: 0.8625 (pt) REVERT: C 75 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 78 MET cc_start: 0.8055 (mpp) cc_final: 0.7032 (mpp) REVERT: C 82 MET cc_start: 0.8974 (tpp) cc_final: 0.8683 (tpp) REVERT: C 94 ASN cc_start: 0.8814 (t0) cc_final: 0.8553 (t0) REVERT: C 166 LEU cc_start: 0.8710 (pt) cc_final: 0.7982 (tp) REVERT: C 216 ASP cc_start: 0.8986 (t70) cc_final: 0.8724 (t70) REVERT: C 261 ASP cc_start: 0.9309 (m-30) cc_final: 0.8571 (p0) REVERT: C 262 LEU cc_start: 0.9750 (tt) cc_final: 0.9454 (tt) REVERT: C 265 GLN cc_start: 0.9578 (tm-30) cc_final: 0.9366 (tm-30) REVERT: C 286 MET cc_start: 0.8875 (mtm) cc_final: 0.8525 (mtt) REVERT: C 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9449 (mm) REVERT: C 364 ASP cc_start: 0.8846 (t0) cc_final: 0.8636 (t0) REVERT: C 372 HIS cc_start: 0.9486 (m90) cc_final: 0.8924 (m90) REVERT: C 450 LYS cc_start: 0.6976 (pttm) cc_final: 0.6475 (ptmm) REVERT: C 489 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7549 (mtpt) REVERT: C 490 PHE cc_start: 0.8998 (m-80) cc_final: 0.8624 (m-80) REVERT: D 28 ASP cc_start: 0.9322 (t0) cc_final: 0.9083 (t0) REVERT: D 66 VAL cc_start: 0.9233 (p) cc_final: 0.8273 (p) REVERT: D 67 SER cc_start: 0.9525 (t) cc_final: 0.8368 (t) REVERT: D 78 MET cc_start: 0.7602 (mpp) cc_final: 0.7382 (mpp) REVERT: D 82 MET cc_start: 0.9015 (ttt) cc_final: 0.8659 (ttt) REVERT: D 94 ASN cc_start: 0.8933 (t0) cc_final: 0.8719 (t0) REVERT: D 130 VAL cc_start: 0.9550 (m) cc_final: 0.9321 (m) REVERT: D 134 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9062 (mmmt) REVERT: D 163 ILE cc_start: 0.9390 (pt) cc_final: 0.8951 (pt) REVERT: D 166 LEU cc_start: 0.8998 (pt) cc_final: 0.8274 (tp) REVERT: D 178 ILE cc_start: 0.8992 (mp) cc_final: 0.8787 (mp) REVERT: D 199 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9388 (pt0) REVERT: D 261 ASP cc_start: 0.9248 (m-30) cc_final: 0.8469 (p0) REVERT: D 262 LEU cc_start: 0.9762 (tt) cc_final: 0.9145 (mt) REVERT: D 269 ASP cc_start: 0.9178 (t0) cc_final: 0.8349 (t0) REVERT: D 276 SER cc_start: 0.9130 (m) cc_final: 0.8839 (p) REVERT: D 281 ILE cc_start: 0.9421 (mm) cc_final: 0.9165 (mm) REVERT: D 285 ASN cc_start: 0.9536 (m110) cc_final: 0.9254 (m110) REVERT: D 286 MET cc_start: 0.8772 (mtm) cc_final: 0.7622 (mtt) REVERT: D 296 ASN cc_start: 0.9414 (p0) cc_final: 0.8635 (p0) REVERT: D 298 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8203 (mm110) REVERT: D 321 LEU cc_start: 0.9753 (mm) cc_final: 0.9446 (mm) REVERT: D 353 TYR cc_start: 0.9261 (t80) cc_final: 0.8912 (t80) REVERT: D 372 HIS cc_start: 0.9435 (m90) cc_final: 0.8862 (m90) REVERT: D 395 GLU cc_start: 0.8778 (pm20) cc_final: 0.8543 (mp0) REVERT: D 493 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8877 (ttm-80) REVERT: E 12 TYR cc_start: 0.9286 (t80) cc_final: 0.8625 (t80) REVERT: E 67 SER cc_start: 0.9378 (t) cc_final: 0.8958 (t) REVERT: E 78 MET cc_start: 0.7532 (mpp) cc_final: 0.6734 (mpp) REVERT: E 82 MET cc_start: 0.8930 (tpp) cc_final: 0.8539 (tpp) REVERT: E 93 HIS cc_start: 0.9262 (p90) cc_final: 0.8698 (p90) REVERT: E 94 ASN cc_start: 0.8881 (t0) cc_final: 0.8618 (t0) REVERT: E 166 LEU cc_start: 0.8922 (pt) cc_final: 0.8193 (tp) REVERT: E 174 PHE cc_start: 0.8983 (m-80) cc_final: 0.8738 (m-80) REVERT: E 229 LYS cc_start: 0.9449 (mttt) cc_final: 0.9132 (mttt) REVERT: E 261 ASP cc_start: 0.9281 (m-30) cc_final: 0.8626 (p0) REVERT: E 262 LEU cc_start: 0.9768 (tt) cc_final: 0.9517 (tt) REVERT: E 269 ASP cc_start: 0.9183 (t0) cc_final: 0.8233 (t0) REVERT: E 286 MET cc_start: 0.8892 (mtm) cc_final: 0.8640 (mtt) REVERT: E 296 ASN cc_start: 0.9370 (p0) cc_final: 0.8674 (p0) REVERT: E 297 LEU cc_start: 0.9156 (mm) cc_final: 0.8685 (mm) REVERT: E 298 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8231 (mm110) REVERT: E 489 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7924 (ttmt) REVERT: E 490 PHE cc_start: 0.8956 (m-80) cc_final: 0.8507 (m-80) REVERT: F 28 ASP cc_start: 0.9279 (t0) cc_final: 0.8921 (t0) REVERT: F 66 VAL cc_start: 0.9223 (p) cc_final: 0.8294 (p) REVERT: F 67 SER cc_start: 0.9570 (t) cc_final: 0.8445 (t) REVERT: F 75 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7711 (tm-30) REVERT: F 78 MET cc_start: 0.7773 (mpp) cc_final: 0.7035 (mpp) REVERT: F 82 MET cc_start: 0.9012 (ttt) cc_final: 0.8654 (ttt) REVERT: F 94 ASN cc_start: 0.8884 (t0) cc_final: 0.8651 (t0) REVERT: F 134 LYS cc_start: 0.9454 (mmmt) cc_final: 0.9173 (mmmt) REVERT: F 166 LEU cc_start: 0.8969 (pt) cc_final: 0.8156 (tp) REVERT: F 181 LYS cc_start: 0.9305 (mmpt) cc_final: 0.9075 (mmmt) REVERT: F 232 ASP cc_start: 0.8960 (t70) cc_final: 0.8725 (t0) REVERT: F 261 ASP cc_start: 0.9270 (m-30) cc_final: 0.8716 (p0) REVERT: F 262 LEU cc_start: 0.9749 (tt) cc_final: 0.9480 (tt) REVERT: F 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8132 (t0) REVERT: F 296 ASN cc_start: 0.9428 (p0) cc_final: 0.8767 (p0) REVERT: F 297 LEU cc_start: 0.9199 (mm) cc_final: 0.8670 (mm) REVERT: F 298 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8239 (mm110) REVERT: F 321 LEU cc_start: 0.9753 (mm) cc_final: 0.9523 (mm) REVERT: F 353 TYR cc_start: 0.9209 (t80) cc_final: 0.8932 (t80) REVERT: F 372 HIS cc_start: 0.9452 (m90) cc_final: 0.8915 (m90) REVERT: F 401 PHE cc_start: 0.9299 (p90) cc_final: 0.9067 (p90) REVERT: F 490 PHE cc_start: 0.8987 (m-80) cc_final: 0.8102 (m-80) REVERT: F 492 LYS cc_start: 0.8646 (tptp) cc_final: 0.8439 (tptp) REVERT: F 493 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8859 (ttm-80) REVERT: G 28 ASP cc_start: 0.9246 (t0) cc_final: 0.8948 (t0) REVERT: G 75 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7804 (tm-30) REVERT: G 78 MET cc_start: 0.7608 (mpp) cc_final: 0.6843 (mpp) REVERT: G 82 MET cc_start: 0.8967 (tpp) cc_final: 0.8741 (tpp) REVERT: G 94 ASN cc_start: 0.8891 (t0) cc_final: 0.8646 (t0) REVERT: G 105 ARG cc_start: 0.9091 (mmt90) cc_final: 0.8686 (mmt90) REVERT: G 108 LYS cc_start: 0.9423 (tptp) cc_final: 0.9189 (ptpp) REVERT: G 166 LEU cc_start: 0.8890 (pt) cc_final: 0.8181 (tp) REVERT: G 179 MET cc_start: 0.7117 (tpt) cc_final: 0.6833 (tpt) REVERT: G 241 LYS cc_start: 0.9339 (tptp) cc_final: 0.9053 (tptp) REVERT: G 261 ASP cc_start: 0.9361 (m-30) cc_final: 0.8690 (p0) REVERT: G 262 LEU cc_start: 0.9784 (tt) cc_final: 0.9103 (mt) REVERT: G 269 ASP cc_start: 0.9145 (t0) cc_final: 0.8232 (t0) REVERT: G 276 SER cc_start: 0.9144 (m) cc_final: 0.8818 (p) REVERT: G 296 ASN cc_start: 0.9363 (p0) cc_final: 0.8653 (p0) REVERT: G 297 LEU cc_start: 0.9116 (mm) cc_final: 0.8670 (mm) REVERT: G 298 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8261 (mm110) REVERT: G 372 HIS cc_start: 0.9520 (m170) cc_final: 0.9168 (m170) REVERT: G 401 PHE cc_start: 0.9348 (p90) cc_final: 0.9139 (p90) REVERT: G 489 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7084 (ttpt) REVERT: G 490 PHE cc_start: 0.8885 (m-80) cc_final: 0.8211 (m-80) REVERT: G 492 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8238 (tmtt) REVERT: G 493 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8813 (ttm-80) REVERT: H 28 ASP cc_start: 0.9287 (t0) cc_final: 0.8843 (t0) REVERT: H 66 VAL cc_start: 0.9400 (m) cc_final: 0.8913 (p) REVERT: H 67 SER cc_start: 0.9460 (m) cc_final: 0.8504 (t) REVERT: H 78 MET cc_start: 0.7374 (mpp) cc_final: 0.6428 (mpp) REVERT: H 82 MET cc_start: 0.8876 (ttt) cc_final: 0.8603 (ttt) REVERT: H 130 VAL cc_start: 0.9575 (m) cc_final: 0.9106 (m) REVERT: H 134 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9081 (mmmt) REVERT: H 161 ARG cc_start: 0.9463 (mtm180) cc_final: 0.9233 (mtm-85) REVERT: H 163 ILE cc_start: 0.9406 (pt) cc_final: 0.8970 (pt) REVERT: H 166 LEU cc_start: 0.8921 (pt) cc_final: 0.7997 (tp) REVERT: H 181 LYS cc_start: 0.9235 (mmpt) cc_final: 0.9000 (mmpt) REVERT: H 261 ASP cc_start: 0.9204 (m-30) cc_final: 0.8560 (p0) REVERT: H 262 LEU cc_start: 0.9743 (tt) cc_final: 0.9438 (tt) REVERT: H 269 ASP cc_start: 0.9161 (t0) cc_final: 0.8252 (t0) REVERT: H 285 ASN cc_start: 0.9482 (m110) cc_final: 0.9271 (m110) REVERT: H 286 MET cc_start: 0.8764 (mtm) cc_final: 0.8298 (mtt) REVERT: H 296 ASN cc_start: 0.9434 (p0) cc_final: 0.8733 (p0) REVERT: H 297 LEU cc_start: 0.9196 (mm) cc_final: 0.8668 (mm) REVERT: H 298 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8183 (mm110) REVERT: H 372 HIS cc_start: 0.9571 (m170) cc_final: 0.9302 (m170) REVERT: H 385 MET cc_start: 0.9194 (ttm) cc_final: 0.8955 (ttm) REVERT: H 450 LYS cc_start: 0.7225 (pttm) cc_final: 0.6015 (ptmm) outliers start: 1 outliers final: 0 residues processed: 1331 average time/residue: 0.1848 time to fit residues: 395.7694 Evaluate side-chains 1067 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1067 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 200 optimal weight: 0.0570 chunk 191 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- 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** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 343 GLN 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 198 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090128 restraints weight = 55307.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094059 restraints weight = 35836.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097054 restraints weight = 26103.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099311 restraints weight = 20442.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101127 restraints weight = 16909.746| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28872 Z= 0.150 Angle : 0.863 11.935 39136 Z= 0.416 Chirality : 0.050 0.207 4472 Planarity : 0.005 0.082 4928 Dihedral : 17.830 171.572 4368 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.56 % 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: 1240 sheet: -3.11 (0.22), residues: 344 loop : -1.87 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 480 TYR 0.039 0.002 TYR B 484 PHE 0.039 0.002 PHE F 456 HIS 0.005 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00351 (28864) covalent geometry : angle 0.86293 (39136) hydrogen bonds : bond 0.03505 ( 888) hydrogen bonds : angle 5.62287 ( 2448) Misc. bond : bond 0.00209 ( 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 1316 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1312 time to evaluate : 1.100 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 75 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 78 MET cc_start: 0.7642 (mpp) cc_final: 0.6870 (mpp) REVERT: A 94 ASN cc_start: 0.8891 (t0) cc_final: 0.8646 (t0) REVERT: A 105 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.8437 (tpp-160) REVERT: A 115 ILE cc_start: 0.7475 (pt) cc_final: 0.7214 (pt) REVERT: A 166 LEU cc_start: 0.9023 (pt) cc_final: 0.8332 (tp) REVERT: A 174 PHE cc_start: 0.8831 (m-80) cc_final: 0.8573 (m-80) REVERT: A 178 ILE cc_start: 0.9337 (mp) cc_final: 0.9096 (mp) REVERT: A 179 MET cc_start: 0.7347 (tpt) cc_final: 0.7014 (tpt) REVERT: A 229 LYS cc_start: 0.9435 (mttt) cc_final: 0.9068 (mttt) REVERT: A 261 ASP cc_start: 0.9369 (m-30) cc_final: 0.8697 (p0) REVERT: A 262 LEU cc_start: 0.9777 (tt) cc_final: 0.9248 (mt) REVERT: A 269 ASP cc_start: 0.9130 (t0) cc_final: 0.8172 (t70) REVERT: A 276 SER cc_start: 0.9221 (m) cc_final: 0.8900 (p) REVERT: A 285 ASN cc_start: 0.9555 (m110) cc_final: 0.9321 (m110) REVERT: A 296 ASN cc_start: 0.9332 (p0) cc_final: 0.8622 (p0) REVERT: A 297 LEU cc_start: 0.9007 (mm) cc_final: 0.8546 (mm) REVERT: A 298 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8325 (mm110) REVERT: A 489 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7446 (ttpt) REVERT: A 490 PHE cc_start: 0.8853 (m-80) cc_final: 0.8553 (m-80) REVERT: B 66 VAL cc_start: 0.9507 (m) cc_final: 0.8946 (p) REVERT: B 67 SER cc_start: 0.9617 (t) cc_final: 0.8205 (t) REVERT: B 78 MET cc_start: 0.7494 (mpp) cc_final: 0.7071 (mpp) REVERT: B 166 LEU cc_start: 0.9051 (pt) cc_final: 0.8331 (tp) REVERT: B 199 GLU cc_start: 0.9577 (mt-10) cc_final: 0.9165 (mt-10) REVERT: B 202 GLN cc_start: 0.9352 (mp10) cc_final: 0.8830 (pp30) REVERT: B 229 LYS cc_start: 0.9440 (mttt) cc_final: 0.8880 (mttt) REVERT: B 261 ASP cc_start: 0.9210 (m-30) cc_final: 0.8646 (p0) REVERT: B 269 ASP cc_start: 0.9299 (t0) cc_final: 0.8099 (t70) REVERT: B 296 ASN cc_start: 0.9486 (p0) cc_final: 0.8555 (p0) REVERT: B 298 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8513 (mp-120) REVERT: B 372 HIS cc_start: 0.9413 (m90) cc_final: 0.8845 (m90) REVERT: B 450 LYS cc_start: 0.7262 (pttm) cc_final: 0.6193 (ptmm) REVERT: B 461 ILE cc_start: 0.9729 (pt) cc_final: 0.9521 (pt) REVERT: B 465 GLN cc_start: 0.9202 (mt0) cc_final: 0.8863 (pt0) REVERT: B 489 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8030 (ttmt) REVERT: B 490 PHE cc_start: 0.9004 (m-80) cc_final: 0.8655 (m-80) REVERT: B 493 ARG cc_start: 0.9243 (ttm-80) cc_final: 0.8798 (ttm-80) REVERT: C 19 THR cc_start: 0.9202 (p) cc_final: 0.8578 (p) REVERT: C 58 LYS cc_start: 0.9688 (mmpt) cc_final: 0.9484 (mmmm) REVERT: C 75 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 78 MET cc_start: 0.8017 (mpp) cc_final: 0.6972 (mpp) REVERT: C 82 MET cc_start: 0.9009 (tpp) cc_final: 0.8700 (tpp) REVERT: C 94 ASN cc_start: 0.8821 (t0) cc_final: 0.8560 (t0) REVERT: C 108 LYS cc_start: 0.9525 (tmtt) cc_final: 0.9306 (mtmt) REVERT: C 109 LYS cc_start: 0.9328 (tptp) cc_final: 0.8980 (tptp) REVERT: C 166 LEU cc_start: 0.8888 (pt) cc_final: 0.8178 (tp) REVERT: C 181 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9207 (mmpt) REVERT: C 202 GLN cc_start: 0.9356 (mp10) cc_final: 0.8775 (mp10) REVERT: C 216 ASP cc_start: 0.9008 (t70) cc_final: 0.8727 (t70) REVERT: C 265 GLN cc_start: 0.9598 (tm-30) cc_final: 0.9360 (tm-30) REVERT: C 269 ASP cc_start: 0.9238 (t70) cc_final: 0.8790 (t70) REVERT: C 286 MET cc_start: 0.8935 (mtm) cc_final: 0.7994 (mtt) REVERT: C 298 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8412 (mm-40) REVERT: C 321 LEU cc_start: 0.9749 (mm) cc_final: 0.9468 (mm) REVERT: C 372 HIS cc_start: 0.9490 (m90) cc_final: 0.8929 (m90) REVERT: C 450 LYS cc_start: 0.6897 (pttm) cc_final: 0.6436 (ptmm) REVERT: C 489 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7250 (ttmt) REVERT: C 490 PHE cc_start: 0.8944 (m-80) cc_final: 0.8566 (m-80) REVERT: C 493 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8651 (ttm-80) REVERT: D 28 ASP cc_start: 0.9330 (t0) cc_final: 0.9080 (t0) REVERT: D 67 SER cc_start: 0.9356 (t) cc_final: 0.8674 (t) REVERT: D 82 MET cc_start: 0.9022 (ttt) cc_final: 0.8791 (ttt) REVERT: D 94 ASN cc_start: 0.8908 (t0) cc_final: 0.8672 (t0) REVERT: D 109 LYS cc_start: 0.8919 (tptp) cc_final: 0.8339 (tptp) REVERT: D 134 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9151 (mmmt) REVERT: D 166 LEU cc_start: 0.9062 (pt) cc_final: 0.8333 (tp) REVERT: D 174 PHE cc_start: 0.8985 (m-80) cc_final: 0.8743 (m-80) REVERT: D 261 ASP cc_start: 0.9230 (m-30) cc_final: 0.8622 (p0) REVERT: D 262 LEU cc_start: 0.9726 (tt) cc_final: 0.9492 (tt) REVERT: D 269 ASP cc_start: 0.9157 (t0) cc_final: 0.8230 (t70) REVERT: D 276 SER cc_start: 0.9146 (m) cc_final: 0.8869 (p) REVERT: D 281 ILE cc_start: 0.9404 (mm) cc_final: 0.9132 (mm) REVERT: D 285 ASN cc_start: 0.9528 (m110) cc_final: 0.9267 (m110) REVERT: D 286 MET cc_start: 0.8674 (mtm) cc_final: 0.8426 (mtt) REVERT: D 296 ASN cc_start: 0.9399 (p0) cc_final: 0.8620 (p0) REVERT: D 298 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8208 (mm110) REVERT: D 372 HIS cc_start: 0.9397 (m90) cc_final: 0.8845 (m90) REVERT: D 490 PHE cc_start: 0.8891 (m-80) cc_final: 0.8138 (m-80) REVERT: D 493 ARG cc_start: 0.9225 (ttm-80) cc_final: 0.9019 (ttm-80) REVERT: E 12 TYR cc_start: 0.9262 (t80) cc_final: 0.8630 (t80) REVERT: E 67 SER cc_start: 0.9508 (t) cc_final: 0.8887 (t) REVERT: E 78 MET cc_start: 0.7564 (mpp) cc_final: 0.6872 (mpp) REVERT: E 82 MET cc_start: 0.8967 (tpp) cc_final: 0.8580 (tpp) REVERT: E 88 ILE cc_start: 0.7560 (pt) cc_final: 0.7117 (pt) REVERT: E 93 HIS cc_start: 0.9292 (p90) cc_final: 0.8664 (p90) REVERT: E 94 ASN cc_start: 0.8864 (t0) cc_final: 0.8606 (t0) REVERT: E 105 ARG cc_start: 0.9173 (mmt180) cc_final: 0.8817 (tpp-160) REVERT: E 166 LEU cc_start: 0.8972 (pt) cc_final: 0.8243 (tp) REVERT: E 229 LYS cc_start: 0.9433 (mttt) cc_final: 0.9126 (mttt) REVERT: E 261 ASP cc_start: 0.9313 (m-30) cc_final: 0.8603 (p0) REVERT: E 262 LEU cc_start: 0.9753 (tt) cc_final: 0.9529 (tt) REVERT: E 269 ASP cc_start: 0.9110 (t0) cc_final: 0.8145 (t70) REVERT: E 286 MET cc_start: 0.8857 (mtm) cc_final: 0.8556 (mtt) REVERT: E 296 ASN cc_start: 0.9374 (p0) cc_final: 0.8462 (p0) REVERT: E 297 LEU cc_start: 0.9094 (mm) cc_final: 0.8728 (mm) REVERT: E 298 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8161 (mm110) REVERT: E 489 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7756 (ttmt) REVERT: E 490 PHE cc_start: 0.8984 (m-80) cc_final: 0.8575 (m-80) REVERT: F 28 ASP cc_start: 0.9259 (t0) cc_final: 0.8758 (t0) REVERT: F 67 SER cc_start: 0.9323 (t) cc_final: 0.8785 (t) REVERT: F 78 MET cc_start: 0.7740 (mpp) cc_final: 0.7090 (mpp) REVERT: F 94 ASN cc_start: 0.8846 (t0) cc_final: 0.8622 (t0) REVERT: F 130 VAL cc_start: 0.9617 (m) cc_final: 0.9177 (m) REVERT: F 134 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9064 (mmmt) REVERT: F 166 LEU cc_start: 0.9026 (pt) cc_final: 0.8198 (tp) REVERT: F 199 GLU cc_start: 0.9487 (pt0) cc_final: 0.9243 (pt0) REVERT: F 232 ASP cc_start: 0.8955 (t70) cc_final: 0.8711 (t0) REVERT: F 261 ASP cc_start: 0.9241 (m-30) cc_final: 0.8666 (p0) REVERT: F 262 LEU cc_start: 0.9729 (tt) cc_final: 0.9476 (tt) REVERT: F 269 ASP cc_start: 0.9117 (t0) cc_final: 0.8084 (t0) REVERT: F 296 ASN cc_start: 0.9422 (p0) cc_final: 0.8764 (p0) REVERT: F 297 LEU cc_start: 0.9167 (mm) cc_final: 0.8608 (mm) REVERT: F 298 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8250 (mm110) REVERT: F 353 TYR cc_start: 0.9222 (t80) cc_final: 0.8990 (t80) REVERT: F 372 HIS cc_start: 0.9416 (m90) cc_final: 0.8853 (m90) REVERT: F 401 PHE cc_start: 0.9296 (p90) cc_final: 0.9073 (p90) REVERT: F 465 GLN cc_start: 0.9013 (mt0) cc_final: 0.8735 (pt0) REVERT: F 490 PHE cc_start: 0.8962 (m-80) cc_final: 0.8143 (m-80) REVERT: G 28 ASP cc_start: 0.9271 (t0) cc_final: 0.9032 (t0) REVERT: G 75 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7850 (tm-30) REVERT: G 78 MET cc_start: 0.7643 (mpp) cc_final: 0.6830 (mpp) REVERT: G 82 MET cc_start: 0.9009 (tpp) cc_final: 0.8740 (tpp) REVERT: G 94 ASN cc_start: 0.8911 (t0) cc_final: 0.8664 (t0) REVERT: G 105 ARG cc_start: 0.9104 (mmt90) cc_final: 0.8784 (mmt90) REVERT: G 108 LYS cc_start: 0.9448 (tptp) cc_final: 0.9238 (ptpp) REVERT: G 166 LEU cc_start: 0.8964 (pt) cc_final: 0.8240 (tp) REVERT: G 179 MET cc_start: 0.7008 (tpt) cc_final: 0.6728 (tpt) REVERT: G 241 LYS cc_start: 0.9436 (tptp) cc_final: 0.9111 (tptp) REVERT: G 261 ASP cc_start: 0.9396 (m-30) cc_final: 0.8669 (p0) REVERT: G 262 LEU cc_start: 0.9781 (tt) cc_final: 0.9117 (mt) REVERT: G 269 ASP cc_start: 0.9156 (t0) cc_final: 0.8234 (t0) REVERT: G 276 SER cc_start: 0.9183 (m) cc_final: 0.8855 (p) REVERT: G 296 ASN cc_start: 0.9371 (p0) cc_final: 0.8694 (p0) REVERT: G 297 LEU cc_start: 0.9032 (mm) cc_final: 0.8585 (mm) REVERT: G 298 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8230 (mm110) REVERT: G 372 HIS cc_start: 0.9549 (m170) cc_final: 0.9084 (m170) REVERT: G 489 LYS cc_start: 0.7607 (ttpt) cc_final: 0.6963 (ttpt) REVERT: G 490 PHE cc_start: 0.8864 (m-80) cc_final: 0.8237 (m-80) REVERT: G 493 ARG cc_start: 0.9045 (ttm-80) cc_final: 0.8643 (ttm-80) REVERT: H 28 ASP cc_start: 0.9262 (t0) cc_final: 0.8964 (t0) REVERT: H 66 VAL cc_start: 0.9433 (m) cc_final: 0.9068 (p) REVERT: H 67 SER cc_start: 0.9485 (m) cc_final: 0.8696 (t) REVERT: H 75 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8002 (tm-30) REVERT: H 78 MET cc_start: 0.7398 (mpp) cc_final: 0.6486 (mpp) REVERT: H 94 ASN cc_start: 0.8883 (t0) cc_final: 0.8673 (t0) REVERT: H 130 VAL cc_start: 0.9564 (m) cc_final: 0.9130 (m) REVERT: H 134 LYS cc_start: 0.9467 (mmmt) cc_final: 0.9079 (mmmm) REVERT: H 161 ARG cc_start: 0.9443 (mtm180) cc_final: 0.9197 (mtm-85) REVERT: H 163 ILE cc_start: 0.9389 (pt) cc_final: 0.8958 (pt) REVERT: H 166 LEU cc_start: 0.8994 (pt) cc_final: 0.8023 (tp) REVERT: H 167 LYS cc_start: 0.9483 (tmtt) cc_final: 0.9131 (ptpp) REVERT: H 178 ILE cc_start: 0.9179 (mp) cc_final: 0.8845 (mp) REVERT: H 261 ASP cc_start: 0.9213 (m-30) cc_final: 0.8613 (p0) REVERT: H 262 LEU cc_start: 0.9722 (tt) cc_final: 0.9402 (tt) REVERT: H 269 ASP cc_start: 0.9143 (t0) cc_final: 0.8126 (t70) REVERT: H 281 ILE cc_start: 0.9495 (mm) cc_final: 0.9280 (mm) REVERT: H 285 ASN cc_start: 0.9468 (m110) cc_final: 0.9256 (m110) REVERT: H 286 MET cc_start: 0.8763 (mtm) cc_final: 0.8224 (mtt) REVERT: H 296 ASN cc_start: 0.9413 (p0) cc_final: 0.8737 (p0) REVERT: H 297 LEU cc_start: 0.9124 (mm) cc_final: 0.8595 (mm) REVERT: H 298 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8310 (mm110) REVERT: H 357 PHE cc_start: 0.9194 (m-80) cc_final: 0.8777 (m-10) REVERT: H 372 HIS cc_start: 0.9558 (m170) cc_final: 0.9147 (m170) REVERT: H 401 PHE cc_start: 0.9283 (p90) cc_final: 0.9078 (p90) REVERT: H 456 PHE cc_start: 0.9619 (t80) cc_final: 0.9405 (t80) REVERT: H 460 LEU cc_start: 0.9848 (mt) cc_final: 0.9630 (mt) REVERT: H 490 PHE cc_start: 0.9043 (m-80) cc_final: 0.8738 (m-80) outliers start: 4 outliers final: 3 residues processed: 1312 average time/residue: 0.1893 time to fit residues: 396.7881 Evaluate side-chains 1060 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1057 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 20.0000 chunk 348 optimal weight: 0.9990 chunk 315 optimal weight: 0.0370 chunk 131 optimal weight: 1.9990 chunk 217 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 253 HIS ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 253 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092359 restraints weight = 54568.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096534 restraints weight = 34871.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099715 restraints weight = 25059.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102069 restraints weight = 19435.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103989 restraints weight = 16013.451| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28872 Z= 0.147 Angle : 0.883 12.634 39136 Z= 0.421 Chirality : 0.050 0.203 4472 Planarity : 0.005 0.053 4928 Dihedral : 17.616 174.623 4368 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.24 % 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: -2.53 (0.13), residues: 3576 helix: -1.12 (0.14), residues: 1224 sheet: -2.84 (0.24), residues: 344 loop : -1.82 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 480 TYR 0.028 0.002 TYR B 233 PHE 0.042 0.002 PHE F 456 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00335 (28864) covalent geometry : angle 0.88337 (39136) hydrogen bonds : bond 0.03521 ( 888) hydrogen bonds : angle 5.63525 ( 2448) Misc. bond : bond 0.00208 ( 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 1370 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1368 time to evaluate : 1.152 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: A 28 ASP cc_start: 0.9171 (t0) cc_final: 0.8890 (t0) REVERT: A 75 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 78 MET cc_start: 0.7506 (mpp) cc_final: 0.6721 (mpp) REVERT: A 82 MET cc_start: 0.9051 (tpt) cc_final: 0.8753 (tpp) REVERT: A 88 ILE cc_start: 0.7221 (pt) cc_final: 0.6871 (pt) REVERT: A 94 ASN cc_start: 0.8916 (t0) cc_final: 0.8653 (t0) REVERT: A 115 ILE cc_start: 0.7378 (pt) cc_final: 0.7110 (pt) REVERT: A 166 LEU cc_start: 0.9079 (pt) cc_final: 0.8392 (tp) REVERT: A 178 ILE cc_start: 0.9274 (mp) cc_final: 0.8584 (mp) REVERT: A 179 MET cc_start: 0.7153 (tpt) cc_final: 0.6938 (tpt) REVERT: A 199 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9284 (mt-10) REVERT: A 216 ASP cc_start: 0.9166 (t70) cc_final: 0.8702 (t70) REVERT: A 229 LYS cc_start: 0.9461 (mttt) cc_final: 0.8778 (mttt) REVERT: A 269 ASP cc_start: 0.9195 (t0) cc_final: 0.8358 (t70) REVERT: A 276 SER cc_start: 0.9227 (m) cc_final: 0.8887 (p) REVERT: A 296 ASN cc_start: 0.9352 (p0) cc_final: 0.8767 (p0) REVERT: A 297 LEU cc_start: 0.8897 (mm) cc_final: 0.8452 (mm) REVERT: A 298 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8261 (mm110) REVERT: A 450 LYS cc_start: 0.7308 (pttm) cc_final: 0.6144 (ptmm) REVERT: A 489 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7587 (ttmt) REVERT: A 490 PHE cc_start: 0.8987 (m-80) cc_final: 0.8546 (m-80) REVERT: B 15 ASP cc_start: 0.9556 (t0) cc_final: 0.9302 (t0) REVERT: B 66 VAL cc_start: 0.9318 (m) cc_final: 0.8616 (m) REVERT: B 94 ASN cc_start: 0.8960 (t0) cc_final: 0.8752 (t0) REVERT: B 166 LEU cc_start: 0.9069 (pt) cc_final: 0.8341 (tp) REVERT: B 199 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9034 (mt-10) REVERT: B 202 GLN cc_start: 0.9323 (mp10) cc_final: 0.8855 (pp30) REVERT: B 203 ARG cc_start: 0.9405 (mmp80) cc_final: 0.8982 (mmm-85) REVERT: B 215 ASP cc_start: 0.9089 (m-30) cc_final: 0.8831 (t0) REVERT: B 216 ASP cc_start: 0.9038 (t0) cc_final: 0.8813 (t0) REVERT: B 229 LYS cc_start: 0.9422 (mttt) cc_final: 0.8899 (mttt) REVERT: B 269 ASP cc_start: 0.9266 (t0) cc_final: 0.7999 (t70) REVERT: B 292 ASP cc_start: 0.9678 (m-30) cc_final: 0.9371 (m-30) REVERT: B 296 ASN cc_start: 0.9500 (p0) cc_final: 0.8664 (p0) REVERT: B 298 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8534 (mp-120) REVERT: B 372 HIS cc_start: 0.9374 (m90) cc_final: 0.8803 (m90) REVERT: B 450 LYS cc_start: 0.7211 (pttm) cc_final: 0.6334 (ptmm) REVERT: B 461 ILE cc_start: 0.9734 (pt) cc_final: 0.9509 (pt) REVERT: B 465 GLN cc_start: 0.9164 (mt0) cc_final: 0.8814 (pt0) REVERT: B 489 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7945 (ttmt) REVERT: B 490 PHE cc_start: 0.8974 (m-80) cc_final: 0.8682 (m-80) REVERT: B 493 ARG cc_start: 0.9121 (ttm-80) cc_final: 0.8699 (ttm-80) REVERT: C 24 PHE cc_start: 0.8168 (m-80) cc_final: 0.7940 (m-80) REVERT: C 58 LYS cc_start: 0.9617 (mmpt) cc_final: 0.9379 (mmmm) REVERT: C 65 LEU cc_start: 0.8829 (pt) cc_final: 0.8531 (pt) REVERT: C 75 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 78 MET cc_start: 0.7951 (mpp) cc_final: 0.6828 (mpp) REVERT: C 82 MET cc_start: 0.8961 (tpp) cc_final: 0.8711 (tpp) REVERT: C 94 ASN cc_start: 0.8819 (t0) cc_final: 0.8551 (t0) REVERT: C 108 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9328 (mtmt) REVERT: C 109 LYS cc_start: 0.9346 (tptp) cc_final: 0.9041 (tptp) REVERT: C 129 ASP cc_start: 0.9254 (p0) cc_final: 0.9043 (p0) REVERT: C 134 LYS cc_start: 0.9501 (tppt) cc_final: 0.9279 (mmtt) REVERT: C 139 PHE cc_start: 0.8686 (p90) cc_final: 0.8400 (p90) REVERT: C 166 LEU cc_start: 0.8972 (pt) cc_final: 0.8264 (tp) REVERT: C 174 PHE cc_start: 0.9343 (m-80) cc_final: 0.9081 (m-80) REVERT: C 178 ILE cc_start: 0.9223 (mp) cc_final: 0.8959 (mp) REVERT: C 202 GLN cc_start: 0.9291 (mp10) cc_final: 0.8697 (mp10) REVERT: C 203 ARG cc_start: 0.9406 (mmp80) cc_final: 0.9148 (mmp80) REVERT: C 215 ASP cc_start: 0.8997 (t0) cc_final: 0.8733 (t0) REVERT: C 216 ASP cc_start: 0.9093 (t70) cc_final: 0.8800 (t0) REVERT: C 261 ASP cc_start: 0.9317 (m-30) cc_final: 0.9087 (m-30) REVERT: C 262 LEU cc_start: 0.9731 (tt) cc_final: 0.9490 (pp) REVERT: C 265 GLN cc_start: 0.9597 (tm-30) cc_final: 0.9374 (tm-30) REVERT: C 276 SER cc_start: 0.9204 (m) cc_final: 0.8872 (p) REVERT: C 283 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9245 (mm-40) REVERT: C 286 MET cc_start: 0.8899 (mtm) cc_final: 0.8498 (mtt) REVERT: C 292 ASP cc_start: 0.9638 (m-30) cc_final: 0.9319 (m-30) REVERT: C 297 LEU cc_start: 0.8738 (mm) cc_final: 0.8380 (mm) REVERT: C 298 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8343 (mm-40) REVERT: C 372 HIS cc_start: 0.9479 (m90) cc_final: 0.8940 (m90) REVERT: C 399 GLU cc_start: 0.9307 (tm-30) cc_final: 0.9051 (tm-30) REVERT: C 489 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7256 (mtpt) REVERT: C 490 PHE cc_start: 0.8929 (m-80) cc_final: 0.8652 (m-80) REVERT: C 493 ARG cc_start: 0.8958 (ttm-80) cc_final: 0.8589 (ttm-80) REVERT: D 28 ASP cc_start: 0.9326 (t0) cc_final: 0.9066 (t0) REVERT: D 67 SER cc_start: 0.9472 (t) cc_final: 0.8994 (t) REVERT: D 94 ASN cc_start: 0.8929 (t0) cc_final: 0.8708 (t0) REVERT: D 105 ARG cc_start: 0.8827 (mmt90) cc_final: 0.8346 (mmt180) REVERT: D 166 LEU cc_start: 0.9084 (pt) cc_final: 0.8370 (tp) REVERT: D 198 ASN cc_start: 0.9680 (m110) cc_final: 0.9376 (m110) REVERT: D 199 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9070 (mm-30) REVERT: D 202 GLN cc_start: 0.9322 (mp10) cc_final: 0.8361 (mp10) REVERT: D 203 ARG cc_start: 0.9454 (mmp80) cc_final: 0.9240 (mmp80) REVERT: D 261 ASP cc_start: 0.9245 (m-30) cc_final: 0.8697 (p0) REVERT: D 269 ASP cc_start: 0.9181 (t0) cc_final: 0.8315 (t70) REVERT: D 276 SER cc_start: 0.9170 (m) cc_final: 0.8880 (p) REVERT: D 283 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9268 (mm-40) REVERT: D 286 MET cc_start: 0.8657 (mtm) cc_final: 0.8252 (mtt) REVERT: D 296 ASN cc_start: 0.9400 (p0) cc_final: 0.8630 (p0) REVERT: D 298 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8244 (mm110) REVERT: D 372 HIS cc_start: 0.9388 (m90) cc_final: 0.8839 (m90) REVERT: E 12 TYR cc_start: 0.9317 (t80) cc_final: 0.8623 (t80) REVERT: E 65 LEU cc_start: 0.9175 (pt) cc_final: 0.8890 (pt) REVERT: E 75 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7754 (tm-30) REVERT: E 78 MET cc_start: 0.7356 (mpp) cc_final: 0.6734 (mpp) REVERT: E 82 MET cc_start: 0.8964 (tpp) cc_final: 0.8565 (tpp) REVERT: E 88 ILE cc_start: 0.7423 (pt) cc_final: 0.6906 (pt) REVERT: E 94 ASN cc_start: 0.8885 (t0) cc_final: 0.8665 (t0) REVERT: E 105 ARG cc_start: 0.9183 (mmt180) cc_final: 0.8933 (mmt90) REVERT: E 166 LEU cc_start: 0.9030 (pt) cc_final: 0.8299 (tp) REVERT: E 202 GLN cc_start: 0.9389 (mp10) cc_final: 0.8758 (mp10) REVERT: E 229 LYS cc_start: 0.9441 (mttt) cc_final: 0.8749 (mttt) REVERT: E 269 ASP cc_start: 0.9156 (t0) cc_final: 0.8242 (t70) REVERT: E 286 MET cc_start: 0.8856 (mtm) cc_final: 0.8491 (mtt) REVERT: E 296 ASN cc_start: 0.9377 (p0) cc_final: 0.8433 (p0) REVERT: E 297 LEU cc_start: 0.9013 (mm) cc_final: 0.8739 (mm) REVERT: E 298 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8196 (mm110) REVERT: E 399 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9034 (tm-30) REVERT: E 450 LYS cc_start: 0.7382 (pttm) cc_final: 0.6068 (ptmm) REVERT: E 489 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7836 (ttmt) REVERT: E 490 PHE cc_start: 0.9015 (m-80) cc_final: 0.8527 (m-80) REVERT: E 493 ARG cc_start: 0.8877 (ttt90) cc_final: 0.8633 (ttm-80) REVERT: F 67 SER cc_start: 0.9247 (t) cc_final: 0.8741 (t) REVERT: F 75 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7318 (tm-30) REVERT: F 78 MET cc_start: 0.7740 (mpp) cc_final: 0.6937 (mpp) REVERT: F 82 MET cc_start: 0.8933 (ttt) cc_final: 0.8641 (ttt) REVERT: F 94 ASN cc_start: 0.8833 (t0) cc_final: 0.8619 (t0) REVERT: F 108 LYS cc_start: 0.8006 (pttm) cc_final: 0.7691 (pttm) REVERT: F 127 VAL cc_start: 0.9271 (t) cc_final: 0.9001 (t) REVERT: F 166 LEU cc_start: 0.9036 (pt) cc_final: 0.8227 (tp) REVERT: F 199 GLU cc_start: 0.9445 (pt0) cc_final: 0.9205 (pt0) REVERT: F 203 ARG cc_start: 0.9376 (mmp80) cc_final: 0.9173 (mmp80) REVERT: F 232 ASP cc_start: 0.8914 (t70) cc_final: 0.8647 (t0) REVERT: F 261 ASP cc_start: 0.9200 (m-30) cc_final: 0.8509 (p0) REVERT: F 262 LEU cc_start: 0.9710 (tt) cc_final: 0.9422 (tt) REVERT: F 269 ASP cc_start: 0.9125 (t0) cc_final: 0.8110 (t70) REVERT: F 296 ASN cc_start: 0.9420 (p0) cc_final: 0.8515 (p0) REVERT: F 297 LEU cc_start: 0.9075 (mm) cc_final: 0.8669 (mm) REVERT: F 298 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8261 (mm110) REVERT: F 372 HIS cc_start: 0.9407 (m90) cc_final: 0.8852 (m90) REVERT: F 465 GLN cc_start: 0.9061 (mt0) cc_final: 0.8708 (pt0) REVERT: F 490 PHE cc_start: 0.8915 (m-80) cc_final: 0.8119 (m-80) REVERT: G 12 TYR cc_start: 0.9427 (t80) cc_final: 0.8824 (t80) REVERT: G 28 ASP cc_start: 0.9197 (t0) cc_final: 0.8940 (t0) REVERT: G 51 LEU cc_start: 0.8026 (mm) cc_final: 0.7819 (mm) REVERT: G 75 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7615 (tm-30) REVERT: G 78 MET cc_start: 0.7486 (mpp) cc_final: 0.6668 (mpp) REVERT: G 94 ASN cc_start: 0.8923 (t0) cc_final: 0.8665 (t0) REVERT: G 105 ARG cc_start: 0.9118 (mmt90) cc_final: 0.8787 (mmt90) REVERT: G 108 LYS cc_start: 0.9422 (tptp) cc_final: 0.9218 (ptpp) REVERT: G 166 LEU cc_start: 0.9011 (pt) cc_final: 0.8331 (tp) REVERT: G 241 LYS cc_start: 0.9403 (tptp) cc_final: 0.9063 (tptp) REVERT: G 262 LEU cc_start: 0.9768 (tt) cc_final: 0.9409 (mt) REVERT: G 269 ASP cc_start: 0.9198 (t0) cc_final: 0.8302 (t0) REVERT: G 276 SER cc_start: 0.9179 (m) cc_final: 0.8839 (p) REVERT: G 296 ASN cc_start: 0.9361 (p0) cc_final: 0.8701 (p0) REVERT: G 297 LEU cc_start: 0.8988 (mm) cc_final: 0.8560 (mm) REVERT: G 298 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8280 (mm110) REVERT: G 364 ASP cc_start: 0.8745 (t0) cc_final: 0.8442 (t0) REVERT: G 372 HIS cc_start: 0.9309 (m170) cc_final: 0.8982 (m170) REVERT: G 450 LYS cc_start: 0.7591 (pttm) cc_final: 0.6469 (ptmm) REVERT: G 489 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7975 (ttpt) REVERT: G 490 PHE cc_start: 0.8903 (m-80) cc_final: 0.8097 (m-80) REVERT: G 493 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8552 (ttm-80) REVERT: H 28 ASP cc_start: 0.9331 (t0) cc_final: 0.9016 (t0) REVERT: H 66 VAL cc_start: 0.9275 (m) cc_final: 0.8770 (m) REVERT: H 94 ASN cc_start: 0.8874 (t0) cc_final: 0.8644 (t0) REVERT: H 130 VAL cc_start: 0.9591 (m) cc_final: 0.9113 (m) REVERT: H 134 LYS cc_start: 0.9530 (mmmt) cc_final: 0.9175 (mmmt) REVERT: H 161 ARG cc_start: 0.9461 (mtm180) cc_final: 0.9189 (mtm-85) REVERT: H 163 ILE cc_start: 0.9390 (pt) cc_final: 0.8992 (pt) REVERT: H 166 LEU cc_start: 0.9009 (pt) cc_final: 0.8237 (tp) REVERT: H 167 LYS cc_start: 0.9494 (tmtt) cc_final: 0.9165 (ptpp) REVERT: H 199 GLU cc_start: 0.9487 (pt0) cc_final: 0.9212 (pt0) REVERT: H 202 GLN cc_start: 0.9349 (mp10) cc_final: 0.8526 (mp10) REVERT: H 269 ASP cc_start: 0.9178 (t0) cc_final: 0.8307 (t70) REVERT: H 286 MET cc_start: 0.8760 (mtm) cc_final: 0.8474 (mtt) REVERT: H 297 LEU cc_start: 0.9069 (mm) cc_final: 0.8530 (mm) REVERT: H 298 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8254 (mm-40) REVERT: H 357 PHE cc_start: 0.9205 (m-80) cc_final: 0.8835 (m-10) REVERT: H 372 HIS cc_start: 0.9515 (m170) cc_final: 0.9102 (m170) REVERT: H 385 MET cc_start: 0.8913 (tpp) cc_final: 0.8634 (tpp) REVERT: H 460 LEU cc_start: 0.9826 (mt) cc_final: 0.9620 (mt) REVERT: H 490 PHE cc_start: 0.9081 (m-80) cc_final: 0.8766 (m-80) outliers start: 2 outliers final: 0 residues processed: 1368 average time/residue: 0.1869 time to fit residues: 408.3977 Evaluate side-chains 1077 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1077 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 326 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 454 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** 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 309 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** 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 = 0.3777 r_free = 0.3777 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091613 restraints weight = 55032.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095647 restraints weight = 35656.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098704 restraints weight = 25889.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101017 restraints weight = 20207.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102759 restraints weight = 16656.318| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28872 Z= 0.158 Angle : 0.875 11.744 39136 Z= 0.423 Chirality : 0.049 0.198 4472 Planarity : 0.005 0.072 4928 Dihedral : 17.528 177.986 4368 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -2.52 (0.13), residues: 3576 helix: -1.17 (0.13), residues: 1232 sheet: -2.60 (0.25), residues: 344 loop : -1.83 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 480 TYR 0.030 0.002 TYR B 233 PHE 0.042 0.002 PHE F 456 HIS 0.004 0.001 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00361 (28864) covalent geometry : angle 0.87478 (39136) hydrogen bonds : bond 0.03507 ( 888) hydrogen bonds : angle 5.67773 ( 2448) Misc. bond : bond 0.00216 ( 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 1299 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1299 time to evaluate : 1.084 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: A 24 PHE cc_start: 0.8146 (m-80) cc_final: 0.7900 (m-80) REVERT: A 28 ASP cc_start: 0.8901 (t0) cc_final: 0.8561 (t0) REVERT: A 58 LYS cc_start: 0.9635 (mmpt) cc_final: 0.9412 (mmmm) REVERT: A 82 MET cc_start: 0.9109 (tpt) cc_final: 0.8729 (tpp) REVERT: A 88 ILE cc_start: 0.7506 (pt) cc_final: 0.7039 (pt) REVERT: A 94 ASN cc_start: 0.8928 (t0) cc_final: 0.8650 (t0) REVERT: A 105 ARG cc_start: 0.9033 (mmt90) cc_final: 0.8794 (mmt180) REVERT: A 166 LEU cc_start: 0.9146 (pt) cc_final: 0.8452 (tp) REVERT: A 199 GLU cc_start: 0.9612 (mt-10) cc_final: 0.9328 (mt-10) REVERT: A 203 ARG cc_start: 0.9476 (mmp80) cc_final: 0.9217 (mmp80) REVERT: A 216 ASP cc_start: 0.9164 (t70) cc_final: 0.8747 (t70) REVERT: A 229 LYS cc_start: 0.9417 (mttt) cc_final: 0.9155 (mttt) REVERT: A 261 ASP cc_start: 0.9351 (m-30) cc_final: 0.8929 (m-30) REVERT: A 269 ASP cc_start: 0.9181 (t0) cc_final: 0.8341 (t70) REVERT: A 276 SER cc_start: 0.9263 (m) cc_final: 0.8937 (p) REVERT: A 297 LEU cc_start: 0.8851 (mm) cc_final: 0.8474 (mm) REVERT: A 298 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8251 (mm110) REVERT: A 450 LYS cc_start: 0.7404 (pttm) cc_final: 0.6271 (ptmm) REVERT: A 456 PHE cc_start: 0.9604 (t80) cc_final: 0.9380 (t80) REVERT: A 460 LEU cc_start: 0.9801 (mt) cc_final: 0.9582 (mt) REVERT: A 489 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7301 (ttmt) REVERT: A 490 PHE cc_start: 0.8893 (m-80) cc_final: 0.8622 (m-80) REVERT: B 66 VAL cc_start: 0.9228 (m) cc_final: 0.8906 (m) REVERT: B 88 ILE cc_start: 0.7380 (pt) cc_final: 0.7165 (pt) REVERT: B 90 PHE cc_start: 0.8734 (m-80) cc_final: 0.8457 (m-80) REVERT: B 94 ASN cc_start: 0.9000 (t0) cc_final: 0.8796 (t0) REVERT: B 132 GLU cc_start: 0.9495 (pp20) cc_final: 0.9293 (pp20) REVERT: B 166 LEU cc_start: 0.9123 (pt) cc_final: 0.8399 (tp) REVERT: B 199 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9197 (mt-10) REVERT: B 202 GLN cc_start: 0.9315 (mp10) cc_final: 0.8448 (mp10) REVERT: B 203 ARG cc_start: 0.9483 (mmp80) cc_final: 0.9249 (mmp80) REVERT: B 229 LYS cc_start: 0.9439 (mttt) cc_final: 0.8906 (mttt) REVERT: B 269 ASP cc_start: 0.9204 (t0) cc_final: 0.8005 (t70) REVERT: B 296 ASN cc_start: 0.9503 (p0) cc_final: 0.8653 (p0) REVERT: B 298 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8540 (mp-120) REVERT: B 372 HIS cc_start: 0.9367 (m90) cc_final: 0.8803 (m90) REVERT: B 450 LYS cc_start: 0.7510 (pttm) cc_final: 0.6602 (ptmm) REVERT: B 461 ILE cc_start: 0.9735 (pt) cc_final: 0.9508 (pt) REVERT: B 465 GLN cc_start: 0.9192 (mt0) cc_final: 0.8802 (pt0) REVERT: B 479 VAL cc_start: 0.9244 (p) cc_final: 0.9031 (t) REVERT: B 489 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7889 (ttmt) REVERT: B 490 PHE cc_start: 0.8970 (m-80) cc_final: 0.8647 (m-80) REVERT: B 493 ARG cc_start: 0.9118 (ttm-80) cc_final: 0.8779 (ttm-80) REVERT: C 24 PHE cc_start: 0.8317 (m-80) cc_final: 0.7992 (m-80) REVERT: C 28 ASP cc_start: 0.9206 (t0) cc_final: 0.8961 (t0) REVERT: C 58 LYS cc_start: 0.9633 (mmpt) cc_final: 0.9367 (mmmm) REVERT: C 65 LEU cc_start: 0.8831 (pt) cc_final: 0.8562 (pt) REVERT: C 75 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 78 MET cc_start: 0.8320 (mpp) cc_final: 0.7084 (mpp) REVERT: C 82 MET cc_start: 0.8881 (tpp) cc_final: 0.8626 (tpp) REVERT: C 94 ASN cc_start: 0.8833 (t0) cc_final: 0.8575 (t0) REVERT: C 166 LEU cc_start: 0.9021 (pt) cc_final: 0.8409 (tp) REVERT: C 174 PHE cc_start: 0.9381 (m-80) cc_final: 0.9082 (m-80) REVERT: C 261 ASP cc_start: 0.9315 (m-30) cc_final: 0.9031 (m-30) REVERT: C 262 LEU cc_start: 0.9731 (tt) cc_final: 0.9512 (tt) REVERT: C 265 GLN cc_start: 0.9610 (tm-30) cc_final: 0.9388 (tm-30) REVERT: C 283 GLN cc_start: 0.9479 (mm-40) cc_final: 0.9246 (mm-40) REVERT: C 286 MET cc_start: 0.8873 (mtm) cc_final: 0.8406 (mtt) REVERT: C 296 ASN cc_start: 0.9315 (p0) cc_final: 0.8531 (p0) REVERT: C 297 LEU cc_start: 0.8747 (mm) cc_final: 0.8507 (mm) REVERT: C 298 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8261 (mm-40) REVERT: C 355 ARG cc_start: 0.9180 (ptm160) cc_final: 0.8811 (ptm160) REVERT: C 372 HIS cc_start: 0.9496 (m90) cc_final: 0.9156 (m90) REVERT: C 479 VAL cc_start: 0.9251 (p) cc_final: 0.8978 (t) REVERT: C 484 TYR cc_start: 0.8247 (m-80) cc_final: 0.7873 (m-80) REVERT: C 489 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7179 (mtpt) REVERT: C 490 PHE cc_start: 0.8944 (m-80) cc_final: 0.8650 (m-80) REVERT: C 493 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8444 (ttm-80) REVERT: D 28 ASP cc_start: 0.9330 (t0) cc_final: 0.9049 (t0) REVERT: D 67 SER cc_start: 0.9370 (t) cc_final: 0.8963 (t) REVERT: D 75 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 94 ASN cc_start: 0.8950 (t0) cc_final: 0.8701 (t0) REVERT: D 166 LEU cc_start: 0.9068 (pt) cc_final: 0.8310 (tp) REVERT: D 202 GLN cc_start: 0.9363 (mp10) cc_final: 0.8656 (mp10) REVERT: D 269 ASP cc_start: 0.9130 (t0) cc_final: 0.8309 (t70) REVERT: D 283 GLN cc_start: 0.9481 (mm-40) cc_final: 0.9226 (mm-40) REVERT: D 286 MET cc_start: 0.8685 (mtm) cc_final: 0.8235 (mtt) REVERT: D 296 ASN cc_start: 0.9396 (p0) cc_final: 0.8511 (p0) REVERT: D 298 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8146 (mm110) REVERT: D 372 HIS cc_start: 0.9229 (m90) cc_final: 0.9002 (m90) REVERT: D 493 ARG cc_start: 0.9039 (ttm-80) cc_final: 0.8831 (ttm-80) REVERT: E 12 TYR cc_start: 0.9329 (t80) cc_final: 0.8699 (t80) REVERT: E 58 LYS cc_start: 0.9634 (mmpt) cc_final: 0.9414 (mmmm) REVERT: E 66 VAL cc_start: 0.9321 (m) cc_final: 0.8983 (m) REVERT: E 67 SER cc_start: 0.9472 (t) cc_final: 0.9056 (t) REVERT: E 82 MET cc_start: 0.8935 (tpp) cc_final: 0.8476 (tpp) REVERT: E 88 ILE cc_start: 0.7542 (pt) cc_final: 0.7049 (pt) REVERT: E 94 ASN cc_start: 0.8908 (t0) cc_final: 0.8703 (t0) REVERT: E 105 ARG cc_start: 0.9289 (mmt180) cc_final: 0.8959 (mmt90) REVERT: E 166 LEU cc_start: 0.9075 (pt) cc_final: 0.8332 (tp) REVERT: E 178 ILE cc_start: 0.9209 (mp) cc_final: 0.8825 (mp) REVERT: E 229 LYS cc_start: 0.9423 (mttt) cc_final: 0.8824 (mttt) REVERT: E 261 ASP cc_start: 0.9306 (m-30) cc_final: 0.8858 (m-30) REVERT: E 269 ASP cc_start: 0.9186 (t0) cc_final: 0.8393 (t70) REVERT: E 296 ASN cc_start: 0.9353 (p0) cc_final: 0.8596 (p0) REVERT: E 298 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8225 (mm110) REVERT: E 450 LYS cc_start: 0.7435 (pttm) cc_final: 0.5967 (ptmm) REVERT: E 482 MET cc_start: 0.8738 (tmm) cc_final: 0.8387 (tmm) REVERT: E 489 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7756 (ttmt) REVERT: E 490 PHE cc_start: 0.8884 (m-80) cc_final: 0.8520 (m-80) REVERT: E 493 ARG cc_start: 0.9158 (ttt90) cc_final: 0.8736 (mtp-110) REVERT: F 28 ASP cc_start: 0.8966 (t0) cc_final: 0.8512 (t0) REVERT: F 75 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7429 (tm-30) REVERT: F 78 MET cc_start: 0.7947 (mpp) cc_final: 0.7064 (mpp) REVERT: F 88 ILE cc_start: 0.6591 (pt) cc_final: 0.6213 (pt) REVERT: F 109 LYS cc_start: 0.8888 (tptp) cc_final: 0.8278 (tptp) REVERT: F 134 LYS cc_start: 0.9516 (mmmt) cc_final: 0.9282 (mmmt) REVERT: F 166 LEU cc_start: 0.9099 (pt) cc_final: 0.8312 (tp) REVERT: F 232 ASP cc_start: 0.8912 (t70) cc_final: 0.8618 (t0) REVERT: F 261 ASP cc_start: 0.9213 (m-30) cc_final: 0.8555 (p0) REVERT: F 269 ASP cc_start: 0.9114 (t0) cc_final: 0.8124 (t70) REVERT: F 296 ASN cc_start: 0.9413 (p0) cc_final: 0.8656 (p0) REVERT: F 297 LEU cc_start: 0.9179 (mm) cc_final: 0.8663 (mm) REVERT: F 298 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8275 (mm110) REVERT: F 372 HIS cc_start: 0.9405 (m90) cc_final: 0.8871 (m90) REVERT: F 465 GLN cc_start: 0.9136 (mt0) cc_final: 0.8716 (pt0) REVERT: F 479 VAL cc_start: 0.9252 (p) cc_final: 0.9037 (t) REVERT: F 490 PHE cc_start: 0.8950 (m-80) cc_final: 0.8194 (m-80) REVERT: G 12 TYR cc_start: 0.9431 (t80) cc_final: 0.9120 (t80) REVERT: G 28 ASP cc_start: 0.9199 (t0) cc_final: 0.8962 (t0) REVERT: G 82 MET cc_start: 0.9011 (tpt) cc_final: 0.8654 (tpp) REVERT: G 94 ASN cc_start: 0.8917 (t0) cc_final: 0.8664 (t0) REVERT: G 166 LEU cc_start: 0.9055 (pt) cc_final: 0.8349 (tp) REVERT: G 241 LYS cc_start: 0.9414 (tptp) cc_final: 0.9078 (tptp) REVERT: G 261 ASP cc_start: 0.9354 (m-30) cc_final: 0.8937 (m-30) REVERT: G 269 ASP cc_start: 0.9192 (t0) cc_final: 0.8373 (t70) REVERT: G 276 SER cc_start: 0.9226 (m) cc_final: 0.8877 (p) REVERT: G 298 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8127 (mm110) REVERT: G 372 HIS cc_start: 0.9395 (m170) cc_final: 0.8943 (m170) REVERT: G 450 LYS cc_start: 0.7755 (pttm) cc_final: 0.6775 (ptmm) REVERT: G 489 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7764 (ttmt) REVERT: G 490 PHE cc_start: 0.8934 (m-80) cc_final: 0.8362 (m-80) REVERT: G 493 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8553 (ttm-80) REVERT: H 28 ASP cc_start: 0.9297 (t0) cc_final: 0.9002 (t0) REVERT: H 66 VAL cc_start: 0.9237 (m) cc_final: 0.8518 (m) REVERT: H 67 SER cc_start: 0.9389 (m) cc_final: 0.8798 (t) REVERT: H 82 MET cc_start: 0.8818 (ttt) cc_final: 0.8588 (ttt) REVERT: H 109 LYS cc_start: 0.8923 (tptp) cc_final: 0.8335 (tptp) REVERT: H 130 VAL cc_start: 0.9615 (m) cc_final: 0.9163 (m) REVERT: H 134 LYS cc_start: 0.9530 (mmmt) cc_final: 0.9161 (mmmt) REVERT: H 161 ARG cc_start: 0.9417 (mtm180) cc_final: 0.9155 (mtm110) REVERT: H 163 ILE cc_start: 0.9414 (pt) cc_final: 0.9018 (pt) REVERT: H 166 LEU cc_start: 0.9032 (pt) cc_final: 0.8254 (tp) REVERT: H 167 LYS cc_start: 0.9498 (tmtt) cc_final: 0.9173 (ptpp) REVERT: H 199 GLU cc_start: 0.9473 (pt0) cc_final: 0.9269 (pt0) REVERT: H 203 ARG cc_start: 0.9413 (mmp80) cc_final: 0.9213 (mmp80) REVERT: H 265 GLN cc_start: 0.9498 (tm-30) cc_final: 0.9231 (tm-30) REVERT: H 269 ASP cc_start: 0.9108 (t0) cc_final: 0.8224 (t70) REVERT: H 286 MET cc_start: 0.8762 (mtm) cc_final: 0.8456 (mtt) REVERT: H 297 LEU cc_start: 0.9033 (mm) cc_final: 0.8456 (mm) REVERT: H 298 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8187 (mm-40) REVERT: H 357 PHE cc_start: 0.9110 (m-80) cc_final: 0.8664 (m-10) REVERT: H 372 HIS cc_start: 0.9409 (m170) cc_final: 0.9036 (m170) REVERT: H 385 MET cc_start: 0.8883 (tpp) cc_final: 0.8589 (tpp) REVERT: H 456 PHE cc_start: 0.9650 (t80) cc_final: 0.9443 (t80) REVERT: H 460 LEU cc_start: 0.9820 (mt) cc_final: 0.9565 (mt) REVERT: H 490 PHE cc_start: 0.8995 (m-80) cc_final: 0.8717 (m-80) outliers start: 0 outliers final: 0 residues processed: 1299 average time/residue: 0.1896 time to fit residues: 392.0108 Evaluate side-chains 1066 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1066 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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: 0.9990 chunk 311 optimal weight: 0.9980 chunk 304 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 283 optimal weight: 30.0000 chunk 214 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 294 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 454 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092527 restraints weight = 54389.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096692 restraints weight = 34873.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.099835 restraints weight = 25136.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102224 restraints weight = 19545.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104140 restraints weight = 16039.919| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28872 Z= 0.145 Angle : 0.886 15.095 39136 Z= 0.424 Chirality : 0.050 0.207 4472 Planarity : 0.005 0.077 4928 Dihedral : 17.462 177.076 4368 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.07 % Allowed : 0.84 % Favored : 99.09 % 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: -2.54 (0.13), residues: 3576 helix: -1.21 (0.13), residues: 1232 sheet: -2.55 (0.26), residues: 344 loop : -1.84 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 480 TYR 0.027 0.002 TYR H 233 PHE 0.019 0.001 PHE D 456 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00340 (28864) covalent geometry : angle 0.88598 (39136) hydrogen bonds : bond 0.03475 ( 888) hydrogen bonds : angle 5.69360 ( 2448) Misc. bond : bond 0.00223 ( 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 1288 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1286 time to evaluate : 1.165 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: A 28 ASP cc_start: 0.8916 (t0) cc_final: 0.8624 (t0) REVERT: A 58 LYS cc_start: 0.9629 (mmpt) cc_final: 0.9393 (mmmm) REVERT: A 78 MET cc_start: 0.8312 (mpp) cc_final: 0.7261 (mpp) REVERT: A 82 MET cc_start: 0.9101 (tpt) cc_final: 0.8697 (tpp) REVERT: A 88 ILE cc_start: 0.7390 (pt) cc_final: 0.6883 (pt) REVERT: A 93 HIS cc_start: 0.9183 (p90) cc_final: 0.8769 (p90) REVERT: A 94 ASN cc_start: 0.8931 (t0) cc_final: 0.8597 (t0) REVERT: A 105 ARG cc_start: 0.9038 (mmt90) cc_final: 0.8794 (mmt180) REVERT: A 166 LEU cc_start: 0.9133 (pt) cc_final: 0.8463 (tp) REVERT: A 199 GLU cc_start: 0.9596 (mt-10) cc_final: 0.9297 (mt-10) REVERT: A 203 ARG cc_start: 0.9466 (mmp80) cc_final: 0.9207 (mmp80) REVERT: A 216 ASP cc_start: 0.9166 (t70) cc_final: 0.8743 (t70) REVERT: A 229 LYS cc_start: 0.9429 (mttt) cc_final: 0.8917 (mttt) REVERT: A 241 LYS cc_start: 0.9449 (tptp) cc_final: 0.9172 (tptp) REVERT: A 261 ASP cc_start: 0.9349 (m-30) cc_final: 0.8996 (m-30) REVERT: A 269 ASP cc_start: 0.9186 (t0) cc_final: 0.8429 (t70) REVERT: A 276 SER cc_start: 0.9271 (m) cc_final: 0.8938 (p) REVERT: A 296 ASN cc_start: 0.9286 (p0) cc_final: 0.8569 (p0) REVERT: A 297 LEU cc_start: 0.8772 (mm) cc_final: 0.8384 (mm) REVERT: A 298 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8271 (mm110) REVERT: A 450 LYS cc_start: 0.7485 (pttm) cc_final: 0.6266 (ptmm) REVERT: A 460 LEU cc_start: 0.9839 (mt) cc_final: 0.9637 (mt) REVERT: A 489 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7358 (ttpt) REVERT: B 58 LYS cc_start: 0.9607 (mmpt) cc_final: 0.9383 (mmmm) REVERT: B 88 ILE cc_start: 0.7120 (pt) cc_final: 0.6768 (pt) REVERT: B 90 PHE cc_start: 0.8727 (m-80) cc_final: 0.8454 (m-80) REVERT: B 94 ASN cc_start: 0.9018 (t0) cc_final: 0.8798 (t0) REVERT: B 166 LEU cc_start: 0.9099 (pt) cc_final: 0.8393 (tp) REVERT: B 199 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9182 (mt-10) REVERT: B 202 GLN cc_start: 0.9347 (mp10) cc_final: 0.8476 (mp10) REVERT: B 203 ARG cc_start: 0.9475 (mmp80) cc_final: 0.9214 (mmp80) REVERT: B 229 LYS cc_start: 0.9414 (mttt) cc_final: 0.8955 (mttt) REVERT: B 269 ASP cc_start: 0.9203 (t0) cc_final: 0.8613 (t70) REVERT: B 276 SER cc_start: 0.9267 (m) cc_final: 0.8948 (p) REVERT: B 296 ASN cc_start: 0.9510 (p0) cc_final: 0.8638 (p0) REVERT: B 297 LEU cc_start: 0.8850 (mm) cc_final: 0.8348 (mm) REVERT: B 298 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8310 (mm-40) REVERT: B 372 HIS cc_start: 0.9340 (m90) cc_final: 0.8769 (m90) REVERT: B 450 LYS cc_start: 0.7514 (pttm) cc_final: 0.6654 (ptmm) REVERT: B 461 ILE cc_start: 0.9731 (pt) cc_final: 0.9491 (pt) REVERT: B 465 GLN cc_start: 0.9152 (mt0) cc_final: 0.8747 (pt0) REVERT: B 479 VAL cc_start: 0.9249 (p) cc_final: 0.9025 (t) REVERT: B 489 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7931 (ttmt) REVERT: B 490 PHE cc_start: 0.9050 (m-80) cc_final: 0.8621 (m-80) REVERT: C 24 PHE cc_start: 0.8229 (m-80) cc_final: 0.7958 (m-80) REVERT: C 28 ASP cc_start: 0.9199 (t0) cc_final: 0.8983 (t0) REVERT: C 58 LYS cc_start: 0.9621 (mmpt) cc_final: 0.9363 (mmmm) REVERT: C 65 LEU cc_start: 0.8800 (pt) cc_final: 0.8585 (pt) REVERT: C 75 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 78 MET cc_start: 0.8192 (mpp) cc_final: 0.6988 (mpp) REVERT: C 82 MET cc_start: 0.8844 (tpp) cc_final: 0.8630 (tpp) REVERT: C 94 ASN cc_start: 0.8821 (t0) cc_final: 0.8562 (t0) REVERT: C 166 LEU cc_start: 0.8973 (pt) cc_final: 0.8277 (tp) REVERT: C 174 PHE cc_start: 0.9355 (m-80) cc_final: 0.9094 (m-80) REVERT: C 261 ASP cc_start: 0.9295 (m-30) cc_final: 0.8885 (m-30) REVERT: C 283 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9240 (mm-40) REVERT: C 286 MET cc_start: 0.8923 (mtm) cc_final: 0.8470 (mtt) REVERT: C 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8623 (p0) REVERT: C 298 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8310 (mm-40) REVERT: C 479 VAL cc_start: 0.9223 (p) cc_final: 0.8957 (t) REVERT: C 489 LYS cc_start: 0.7509 (mtpt) cc_final: 0.7162 (mtpt) REVERT: D 28 ASP cc_start: 0.9321 (t0) cc_final: 0.8903 (t0) REVERT: D 58 LYS cc_start: 0.9633 (mmpt) cc_final: 0.9425 (mmmm) REVERT: D 66 VAL cc_start: 0.8945 (p) cc_final: 0.8707 (p) REVERT: D 67 SER cc_start: 0.9389 (t) cc_final: 0.8994 (t) REVERT: D 94 ASN cc_start: 0.8957 (t0) cc_final: 0.8732 (t0) REVERT: D 105 ARG cc_start: 0.8672 (mmt180) cc_final: 0.8333 (mmt180) REVERT: D 166 LEU cc_start: 0.9050 (pt) cc_final: 0.8315 (tp) REVERT: D 199 GLU cc_start: 0.9580 (mt-10) cc_final: 0.9283 (mt-10) REVERT: D 202 GLN cc_start: 0.9318 (mp10) cc_final: 0.8823 (mp10) REVERT: D 203 ARG cc_start: 0.9433 (mmp80) cc_final: 0.9196 (mmp80) REVERT: D 229 LYS cc_start: 0.9517 (mttm) cc_final: 0.8996 (mttm) REVERT: D 269 ASP cc_start: 0.9090 (t0) cc_final: 0.8284 (t70) REVERT: D 276 SER cc_start: 0.9212 (m) cc_final: 0.8939 (p) REVERT: D 283 GLN cc_start: 0.9458 (mm-40) cc_final: 0.9205 (mm-40) REVERT: D 286 MET cc_start: 0.8695 (mtm) cc_final: 0.8253 (mtt) REVERT: D 296 ASN cc_start: 0.9397 (p0) cc_final: 0.8488 (p0) REVERT: D 298 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8173 (mm110) REVERT: D 372 HIS cc_start: 0.9232 (m90) cc_final: 0.8893 (m90) REVERT: D 482 MET cc_start: 0.8700 (tmm) cc_final: 0.8442 (tmm) REVERT: E 12 TYR cc_start: 0.9392 (t80) cc_final: 0.8717 (t80) REVERT: E 58 LYS cc_start: 0.9627 (mmpt) cc_final: 0.9405 (mmmm) REVERT: E 65 LEU cc_start: 0.8985 (pt) cc_final: 0.8782 (pt) REVERT: E 66 VAL cc_start: 0.9305 (m) cc_final: 0.8939 (m) REVERT: E 67 SER cc_start: 0.9487 (t) cc_final: 0.9067 (t) REVERT: E 78 MET cc_start: 0.8118 (mpp) cc_final: 0.7111 (mpp) REVERT: E 82 MET cc_start: 0.8866 (tpp) cc_final: 0.8455 (tpp) REVERT: E 88 ILE cc_start: 0.7508 (pt) cc_final: 0.7048 (pt) REVERT: E 94 ASN cc_start: 0.8907 (t0) cc_final: 0.8696 (t0) REVERT: E 105 ARG cc_start: 0.9307 (mmt180) cc_final: 0.7668 (ttp80) REVERT: E 164 ASP cc_start: 0.8492 (p0) cc_final: 0.8276 (p0) REVERT: E 166 LEU cc_start: 0.9091 (pt) cc_final: 0.8387 (tp) REVERT: E 174 PHE cc_start: 0.9241 (m-10) cc_final: 0.8909 (m-80) REVERT: E 178 ILE cc_start: 0.9094 (mp) cc_final: 0.8718 (mp) REVERT: E 229 LYS cc_start: 0.9407 (mttt) cc_final: 0.8853 (mttt) REVERT: E 261 ASP cc_start: 0.9308 (m-30) cc_final: 0.8917 (m-30) REVERT: E 262 LEU cc_start: 0.9725 (tt) cc_final: 0.9513 (pp) REVERT: E 269 ASP cc_start: 0.9159 (t0) cc_final: 0.8416 (t70) REVERT: E 296 ASN cc_start: 0.9365 (p0) cc_final: 0.8346 (p0) REVERT: E 298 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8233 (mm110) REVERT: E 450 LYS cc_start: 0.7456 (pttm) cc_final: 0.6081 (ptmm) REVERT: E 482 MET cc_start: 0.8743 (tmm) cc_final: 0.8374 (tmm) REVERT: E 489 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7635 (ttmt) REVERT: E 490 PHE cc_start: 0.8902 (m-80) cc_final: 0.8539 (m-80) REVERT: E 493 ARG cc_start: 0.8887 (ttt90) cc_final: 0.8466 (mtp-110) REVERT: F 12 TYR cc_start: 0.9574 (t80) cc_final: 0.9116 (t80) REVERT: F 28 ASP cc_start: 0.8834 (t0) cc_final: 0.8355 (t0) REVERT: F 58 LYS cc_start: 0.9623 (mmpt) cc_final: 0.9415 (mmmm) REVERT: F 67 SER cc_start: 0.9367 (t) cc_final: 0.9144 (t) REVERT: F 75 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 78 MET cc_start: 0.7820 (mpp) cc_final: 0.6926 (mpp) REVERT: F 88 ILE cc_start: 0.6384 (pt) cc_final: 0.6066 (pt) REVERT: F 134 LYS cc_start: 0.9531 (mmmt) cc_final: 0.9166 (mmmt) REVERT: F 166 LEU cc_start: 0.9082 (pt) cc_final: 0.8276 (tp) REVERT: F 232 ASP cc_start: 0.8853 (t70) cc_final: 0.8551 (t0) REVERT: F 269 ASP cc_start: 0.9116 (t0) cc_final: 0.8262 (t70) REVERT: F 296 ASN cc_start: 0.9397 (p0) cc_final: 0.8517 (p0) REVERT: F 297 LEU cc_start: 0.9062 (mm) cc_final: 0.8612 (mm) REVERT: F 298 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8195 (mm110) REVERT: F 353 TYR cc_start: 0.9191 (t80) cc_final: 0.8955 (t80) REVERT: F 372 HIS cc_start: 0.9385 (m90) cc_final: 0.8847 (m90) REVERT: F 461 ILE cc_start: 0.9732 (pt) cc_final: 0.9510 (pt) REVERT: F 465 GLN cc_start: 0.9045 (mt0) cc_final: 0.8685 (pt0) REVERT: F 479 VAL cc_start: 0.9236 (p) cc_final: 0.8986 (t) REVERT: F 489 LYS cc_start: 0.7313 (ttpt) cc_final: 0.6761 (ttpt) REVERT: F 490 PHE cc_start: 0.8876 (m-80) cc_final: 0.8075 (m-80) REVERT: G 12 TYR cc_start: 0.9437 (t80) cc_final: 0.9160 (t80) REVERT: G 28 ASP cc_start: 0.9225 (t0) cc_final: 0.9016 (t0) REVERT: G 58 LYS cc_start: 0.9638 (mmpt) cc_final: 0.9415 (mmmm) REVERT: G 67 SER cc_start: 0.9236 (m) cc_final: 0.8913 (m) REVERT: G 82 MET cc_start: 0.9010 (tpt) cc_final: 0.8705 (tpp) REVERT: G 88 ILE cc_start: 0.7355 (pt) cc_final: 0.7125 (pt) REVERT: G 94 ASN cc_start: 0.8917 (t0) cc_final: 0.8650 (t0) REVERT: G 166 LEU cc_start: 0.9015 (pt) cc_final: 0.8288 (tp) REVERT: G 241 LYS cc_start: 0.9399 (tptp) cc_final: 0.9049 (tptp) REVERT: G 261 ASP cc_start: 0.9355 (m-30) cc_final: 0.9008 (m-30) REVERT: G 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8346 (t70) REVERT: G 276 SER cc_start: 0.9207 (m) cc_final: 0.8864 (p) REVERT: G 298 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8275 (mm110) REVERT: G 372 HIS cc_start: 0.9388 (m170) cc_final: 0.8905 (m170) REVERT: G 450 LYS cc_start: 0.7636 (pttm) cc_final: 0.6738 (ptmm) REVERT: G 460 LEU cc_start: 0.9810 (mt) cc_final: 0.9568 (mt) REVERT: G 489 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7723 (ttmt) REVERT: G 490 PHE cc_start: 0.8938 (m-80) cc_final: 0.8315 (m-80) REVERT: H 12 TYR cc_start: 0.9578 (t80) cc_final: 0.9162 (t80) REVERT: H 28 ASP cc_start: 0.9327 (t0) cc_final: 0.9009 (t0) REVERT: H 66 VAL cc_start: 0.9239 (m) cc_final: 0.8815 (m) REVERT: H 67 SER cc_start: 0.9363 (m) cc_final: 0.8654 (t) REVERT: H 75 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7401 (tm-30) REVERT: H 82 MET cc_start: 0.8823 (ttt) cc_final: 0.8623 (ttt) REVERT: H 94 ASN cc_start: 0.8882 (t0) cc_final: 0.8646 (t0) REVERT: H 103 GLU cc_start: 0.9385 (mp0) cc_final: 0.9159 (mp0) REVERT: H 130 VAL cc_start: 0.9621 (m) cc_final: 0.9145 (m) REVERT: H 134 LYS cc_start: 0.9523 (mmmt) cc_final: 0.9159 (mmmt) REVERT: H 161 ARG cc_start: 0.9403 (mtm180) cc_final: 0.9173 (mtm-85) REVERT: H 163 ILE cc_start: 0.9408 (pt) cc_final: 0.8993 (pt) REVERT: H 166 LEU cc_start: 0.9024 (pt) cc_final: 0.8292 (tp) REVERT: H 167 LYS cc_start: 0.9492 (tmtt) cc_final: 0.9198 (ptpp) REVERT: H 269 ASP cc_start: 0.9121 (t0) cc_final: 0.8223 (t70) REVERT: H 286 MET cc_start: 0.8754 (mtm) cc_final: 0.8450 (mtt) REVERT: H 297 LEU cc_start: 0.8962 (mm) cc_final: 0.8415 (mm) REVERT: H 298 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8178 (mm-40) REVERT: H 372 HIS cc_start: 0.9385 (m170) cc_final: 0.9009 (m170) REVERT: H 385 MET cc_start: 0.8946 (tpp) cc_final: 0.8722 (tpp) REVERT: H 460 LEU cc_start: 0.9813 (mt) cc_final: 0.9576 (mt) REVERT: H 465 GLN cc_start: 0.9032 (mp10) cc_final: 0.8810 (pt0) REVERT: H 489 LYS cc_start: 0.7548 (ttpt) cc_final: 0.7199 (ttpt) REVERT: H 490 PHE cc_start: 0.8965 (m-80) cc_final: 0.8613 (m-80) outliers start: 2 outliers final: 0 residues processed: 1287 average time/residue: 0.1879 time to fit residues: 384.9274 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 : 1.093 ------------------------------------------------------------------------------- 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: 0.8980 chunk 158 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 227 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 314 optimal weight: 0.1980 chunk 247 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 454 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** 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 309 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 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 = 0.3787 r_free = 0.3787 target = 0.131323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092385 restraints weight = 54313.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096353 restraints weight = 35122.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099402 restraints weight = 25529.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101705 restraints weight = 19856.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103548 restraints weight = 16321.116| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5262 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= 0.154 Angle : 0.881 13.098 39136 Z= 0.426 Chirality : 0.049 0.207 4472 Planarity : 0.005 0.065 4928 Dihedral : 17.499 177.344 4368 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.52 (0.13), residues: 3576 helix: -1.22 (0.13), residues: 1224 sheet: -2.51 (0.26), residues: 344 loop : -1.81 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 480 TYR 0.029 0.002 TYR B 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 0.00363 (28864) covalent geometry : angle 0.88147 (39136) hydrogen bonds : bond 0.03657 ( 888) hydrogen bonds : angle 5.75603 ( 2448) Misc. bond : bond 0.00223 ( 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 1277 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1277 time to evaluate : 1.192 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: A 28 ASP cc_start: 0.8884 (t0) cc_final: 0.8613 (t0) REVERT: A 82 MET cc_start: 0.9113 (tpt) cc_final: 0.8651 (tpp) REVERT: A 88 ILE cc_start: 0.7381 (pt) cc_final: 0.6885 (pt) REVERT: A 93 HIS cc_start: 0.9206 (p90) cc_final: 0.8778 (p90) REVERT: A 94 ASN cc_start: 0.8918 (t0) cc_final: 0.8526 (t0) REVERT: A 105 ARG cc_start: 0.9012 (mmt90) cc_final: 0.8720 (mmt180) REVERT: A 166 LEU cc_start: 0.9169 (pt) cc_final: 0.8509 (tp) REVERT: A 199 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9316 (mt-10) REVERT: A 202 GLN cc_start: 0.9317 (mp10) cc_final: 0.8620 (mp10) REVERT: A 203 ARG cc_start: 0.9476 (mmp80) cc_final: 0.9180 (mmp80) REVERT: A 216 ASP cc_start: 0.9127 (t70) cc_final: 0.8714 (t70) REVERT: A 229 LYS cc_start: 0.9447 (mttt) cc_final: 0.8814 (mttt) REVERT: A 241 LYS cc_start: 0.9425 (tptp) cc_final: 0.9154 (tptp) REVERT: A 261 ASP cc_start: 0.9335 (m-30) cc_final: 0.8953 (m-30) REVERT: A 269 ASP cc_start: 0.9189 (t0) cc_final: 0.8437 (t70) REVERT: A 276 SER cc_start: 0.9293 (m) cc_final: 0.8946 (p) REVERT: A 296 ASN cc_start: 0.9296 (p0) cc_final: 0.8596 (p0) REVERT: A 297 LEU cc_start: 0.8778 (mm) cc_final: 0.8350 (mm) REVERT: A 298 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8294 (mm110) REVERT: A 450 LYS cc_start: 0.7498 (pttm) cc_final: 0.6274 (ptmm) REVERT: A 460 LEU cc_start: 0.9834 (mt) cc_final: 0.9520 (mt) REVERT: A 489 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7642 (ttmt) REVERT: B 28 ASP cc_start: 0.8706 (t0) cc_final: 0.8318 (t0) REVERT: B 75 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 90 PHE cc_start: 0.8757 (m-80) cc_final: 0.8514 (m-80) REVERT: B 94 ASN cc_start: 0.9025 (t0) cc_final: 0.8798 (t0) REVERT: B 103 GLU cc_start: 0.9316 (mp0) cc_final: 0.9090 (mp0) REVERT: B 132 GLU cc_start: 0.9448 (pp20) cc_final: 0.9238 (pp20) REVERT: B 166 LEU cc_start: 0.9121 (pt) cc_final: 0.8415 (tp) REVERT: B 199 GLU cc_start: 0.9600 (mt-10) cc_final: 0.9195 (mt-10) REVERT: B 202 GLN cc_start: 0.9344 (mp10) cc_final: 0.8529 (mp10) REVERT: B 203 ARG cc_start: 0.9472 (mmp80) cc_final: 0.9217 (mmp80) REVERT: B 229 LYS cc_start: 0.9421 (mttt) cc_final: 0.8944 (mttt) REVERT: B 269 ASP cc_start: 0.9174 (t0) cc_final: 0.8670 (p0) REVERT: B 276 SER cc_start: 0.9304 (m) cc_final: 0.8985 (p) REVERT: B 296 ASN cc_start: 0.9531 (p0) cc_final: 0.9239 (p0) REVERT: B 372 HIS cc_start: 0.9345 (m90) cc_final: 0.8800 (m90) REVERT: B 461 ILE cc_start: 0.9714 (pt) cc_final: 0.9509 (pt) REVERT: B 465 GLN cc_start: 0.9174 (mt0) cc_final: 0.8767 (pt0) REVERT: B 489 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7853 (ttmt) REVERT: B 490 PHE cc_start: 0.9060 (m-80) cc_final: 0.8690 (m-80) REVERT: B 493 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8662 (ttm-80) REVERT: C 24 PHE cc_start: 0.8344 (m-80) cc_final: 0.8079 (m-80) REVERT: C 28 ASP cc_start: 0.9216 (t0) cc_final: 0.9012 (t0) REVERT: C 65 LEU cc_start: 0.8774 (pt) cc_final: 0.8539 (pt) REVERT: C 66 VAL cc_start: 0.9025 (m) cc_final: 0.8358 (m) REVERT: C 75 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 78 MET cc_start: 0.8274 (mpp) cc_final: 0.7063 (mpp) REVERT: C 82 MET cc_start: 0.8850 (tpp) cc_final: 0.8635 (tpp) REVERT: C 94 ASN cc_start: 0.8819 (t0) cc_final: 0.8573 (t0) REVERT: C 105 ARG cc_start: 0.8976 (mtt90) cc_final: 0.8427 (mmt90) REVERT: C 166 LEU cc_start: 0.8968 (pt) cc_final: 0.8247 (tp) REVERT: C 174 PHE cc_start: 0.9334 (m-80) cc_final: 0.9081 (m-80) REVERT: C 261 ASP cc_start: 0.9279 (m-30) cc_final: 0.8882 (m-30) REVERT: C 265 GLN cc_start: 0.9610 (tm-30) cc_final: 0.9386 (tm-30) REVERT: C 276 SER cc_start: 0.9342 (m) cc_final: 0.9033 (p) REVERT: C 286 MET cc_start: 0.8887 (mtm) cc_final: 0.8592 (mtt) REVERT: C 296 ASN cc_start: 0.9350 (p0) cc_final: 0.8532 (p0) REVERT: C 298 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8381 (mm-40) REVERT: C 450 LYS cc_start: 0.7119 (pttm) cc_final: 0.5537 (ptmm) REVERT: C 479 VAL cc_start: 0.9247 (p) cc_final: 0.8982 (t) REVERT: C 489 LYS cc_start: 0.7635 (mtpt) cc_final: 0.7179 (mtpt) REVERT: D 28 ASP cc_start: 0.9264 (t0) cc_final: 0.8833 (t0) REVERT: D 30 LEU cc_start: 0.8416 (mt) cc_final: 0.7886 (mp) REVERT: D 58 LYS cc_start: 0.9640 (mmpt) cc_final: 0.9413 (mmmm) REVERT: D 67 SER cc_start: 0.9420 (t) cc_final: 0.9131 (t) REVERT: D 94 ASN cc_start: 0.8997 (t0) cc_final: 0.8761 (t0) REVERT: D 166 LEU cc_start: 0.9060 (pt) cc_final: 0.8338 (tp) REVERT: D 199 GLU cc_start: 0.9597 (mt-10) cc_final: 0.9254 (mt-10) REVERT: D 202 GLN cc_start: 0.9307 (mp10) cc_final: 0.8598 (mp10) REVERT: D 203 ARG cc_start: 0.9438 (mmp80) cc_final: 0.9140 (mmp80) REVERT: D 269 ASP cc_start: 0.9081 (t0) cc_final: 0.8240 (t70) REVERT: D 276 SER cc_start: 0.9256 (m) cc_final: 0.8973 (p) REVERT: D 283 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9194 (mm-40) REVERT: D 286 MET cc_start: 0.8680 (mtm) cc_final: 0.8227 (mtt) REVERT: D 296 ASN cc_start: 0.9384 (p0) cc_final: 0.8719 (p0) REVERT: D 298 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8190 (mm110) REVERT: D 372 HIS cc_start: 0.9169 (m90) cc_final: 0.8824 (m90) REVERT: D 490 PHE cc_start: 0.8798 (m-80) cc_final: 0.8006 (m-80) REVERT: E 12 TYR cc_start: 0.9405 (t80) cc_final: 0.8784 (t80) REVERT: E 58 LYS cc_start: 0.9640 (mmpt) cc_final: 0.9395 (mmmm) REVERT: E 66 VAL cc_start: 0.9267 (m) cc_final: 0.8892 (m) REVERT: E 67 SER cc_start: 0.9538 (t) cc_final: 0.9120 (t) REVERT: E 75 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8045 (tm-30) REVERT: E 78 MET cc_start: 0.8086 (mpp) cc_final: 0.6640 (mpp) REVERT: E 82 MET cc_start: 0.8843 (tpp) cc_final: 0.8418 (tpp) REVERT: E 88 ILE cc_start: 0.7369 (pt) cc_final: 0.6916 (pt) REVERT: E 94 ASN cc_start: 0.8912 (t0) cc_final: 0.8682 (t0) REVERT: E 105 ARG cc_start: 0.9148 (mmt180) cc_final: 0.8483 (tpp-160) REVERT: E 164 ASP cc_start: 0.8511 (p0) cc_final: 0.8304 (p0) REVERT: E 166 LEU cc_start: 0.9126 (pt) cc_final: 0.8461 (tp) REVERT: E 178 ILE cc_start: 0.9145 (mp) cc_final: 0.8780 (mp) REVERT: E 229 LYS cc_start: 0.9427 (mttt) cc_final: 0.8768 (mttt) REVERT: E 261 ASP cc_start: 0.9311 (m-30) cc_final: 0.8916 (m-30) REVERT: E 269 ASP cc_start: 0.9153 (t0) cc_final: 0.8439 (t70) REVERT: E 276 SER cc_start: 0.9282 (m) cc_final: 0.8956 (p) REVERT: E 296 ASN cc_start: 0.9372 (p0) cc_final: 0.8343 (p0) REVERT: E 298 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8231 (mm110) REVERT: E 450 LYS cc_start: 0.7494 (pttm) cc_final: 0.6034 (ptmm) REVERT: E 479 VAL cc_start: 0.9175 (p) cc_final: 0.8933 (t) REVERT: E 482 MET cc_start: 0.8768 (tmm) cc_final: 0.8396 (tmm) REVERT: E 489 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7624 (ttmt) REVERT: E 490 PHE cc_start: 0.8854 (m-80) cc_final: 0.8479 (m-80) REVERT: E 493 ARG cc_start: 0.8907 (ttt90) cc_final: 0.8244 (mtp-110) REVERT: F 58 LYS cc_start: 0.9623 (mmpt) cc_final: 0.9396 (mmmm) REVERT: F 75 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7348 (tm-30) REVERT: F 78 MET cc_start: 0.7942 (mpp) cc_final: 0.7072 (mpp) REVERT: F 102 ASN cc_start: 0.9418 (t0) cc_final: 0.9206 (p0) REVERT: F 109 LYS cc_start: 0.8983 (tptp) cc_final: 0.8320 (tptp) REVERT: F 134 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9159 (mmmt) REVERT: F 166 LEU cc_start: 0.9046 (pt) cc_final: 0.8072 (tp) REVERT: F 168 GLU cc_start: 0.9285 (mp0) cc_final: 0.8901 (mp0) REVERT: F 232 ASP cc_start: 0.8858 (t70) cc_final: 0.8548 (t0) REVERT: F 254 GLU cc_start: 0.9480 (tp30) cc_final: 0.9079 (pm20) REVERT: F 269 ASP cc_start: 0.9147 (t0) cc_final: 0.8239 (t70) REVERT: F 296 ASN cc_start: 0.9393 (p0) cc_final: 0.8535 (p0) REVERT: F 297 LEU cc_start: 0.9023 (mm) cc_final: 0.8575 (mm) REVERT: F 298 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8231 (mm110) REVERT: F 385 MET cc_start: 0.8246 (tpt) cc_final: 0.7931 (tpt) REVERT: F 395 GLU cc_start: 0.9307 (mp0) cc_final: 0.8927 (mp0) REVERT: F 461 ILE cc_start: 0.9752 (pt) cc_final: 0.9538 (pt) REVERT: F 465 GLN cc_start: 0.9086 (mt0) cc_final: 0.8716 (pt0) REVERT: F 479 VAL cc_start: 0.9221 (p) cc_final: 0.9002 (t) REVERT: F 482 MET cc_start: 0.8619 (tmm) cc_final: 0.8260 (tmm) REVERT: F 489 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6711 (ttpt) REVERT: F 490 PHE cc_start: 0.8902 (m-80) cc_final: 0.8168 (m-80) REVERT: G 12 TYR cc_start: 0.9440 (t80) cc_final: 0.9229 (t80) REVERT: G 28 ASP cc_start: 0.9233 (t0) cc_final: 0.8984 (t0) REVERT: G 82 MET cc_start: 0.9007 (tpt) cc_final: 0.8695 (tpp) REVERT: G 88 ILE cc_start: 0.7696 (pt) cc_final: 0.7235 (pt) REVERT: G 94 ASN cc_start: 0.8918 (t0) cc_final: 0.8565 (t0) REVERT: G 105 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8800 (mmt180) REVERT: G 166 LEU cc_start: 0.9046 (pt) cc_final: 0.8314 (tp) REVERT: G 241 LYS cc_start: 0.9413 (tptp) cc_final: 0.9105 (tptp) REVERT: G 261 ASP cc_start: 0.9359 (m-30) cc_final: 0.8976 (m-30) REVERT: G 269 ASP cc_start: 0.9134 (t0) cc_final: 0.8351 (t70) REVERT: G 276 SER cc_start: 0.9226 (m) cc_final: 0.8885 (p) REVERT: G 298 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8212 (mm110) REVERT: G 372 HIS cc_start: 0.9394 (m170) cc_final: 0.8905 (m170) REVERT: G 450 LYS cc_start: 0.7665 (pttm) cc_final: 0.6760 (ptmm) REVERT: G 489 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7829 (ttmt) REVERT: G 490 PHE cc_start: 0.8948 (m-80) cc_final: 0.8455 (m-80) REVERT: G 493 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8510 (ttm-80) REVERT: H 12 TYR cc_start: 0.9502 (t80) cc_final: 0.9144 (t80) REVERT: H 28 ASP cc_start: 0.9315 (t0) cc_final: 0.9031 (t0) REVERT: H 66 VAL cc_start: 0.9215 (m) cc_final: 0.8785 (m) REVERT: H 67 SER cc_start: 0.9395 (m) cc_final: 0.8649 (t) REVERT: H 75 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7449 (tm-30) REVERT: H 82 MET cc_start: 0.8803 (ttt) cc_final: 0.8593 (ttt) REVERT: H 94 ASN cc_start: 0.8889 (t0) cc_final: 0.8673 (t0) REVERT: H 103 GLU cc_start: 0.9379 (mp0) cc_final: 0.9112 (mp0) REVERT: H 109 LYS cc_start: 0.8924 (tptp) cc_final: 0.8424 (tptp) REVERT: H 130 VAL cc_start: 0.9653 (m) cc_final: 0.9200 (m) REVERT: H 134 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9172 (mmmt) REVERT: H 163 ILE cc_start: 0.9417 (pt) cc_final: 0.9029 (pt) REVERT: H 166 LEU cc_start: 0.9059 (pt) cc_final: 0.8334 (tp) REVERT: H 167 LYS cc_start: 0.9485 (tmtt) cc_final: 0.9187 (ptpp) REVERT: H 269 ASP cc_start: 0.9072 (t0) cc_final: 0.8642 (t70) REVERT: H 286 MET cc_start: 0.8741 (mtm) cc_final: 0.8433 (mtt) REVERT: H 297 LEU cc_start: 0.8940 (mm) cc_final: 0.8576 (mm) REVERT: H 372 HIS cc_start: 0.9453 (m170) cc_final: 0.8966 (m170) REVERT: H 385 MET cc_start: 0.8913 (tpp) cc_final: 0.8678 (tpp) REVERT: H 456 PHE cc_start: 0.9653 (t80) cc_final: 0.9448 (t80) REVERT: H 460 LEU cc_start: 0.9810 (mt) cc_final: 0.9564 (mt) REVERT: H 465 GLN cc_start: 0.9031 (mp10) cc_final: 0.8810 (pt0) REVERT: H 489 LYS cc_start: 0.7520 (ttpt) cc_final: 0.7190 (ttpt) REVERT: H 490 PHE cc_start: 0.8998 (m-80) cc_final: 0.8695 (m-80) outliers start: 0 outliers final: 0 residues processed: 1277 average time/residue: 0.1877 time to fit residues: 382.5026 Evaluate side-chains 1035 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1035 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 5.9990 chunk 229 optimal weight: 0.9990 chunk 280 optimal weight: 0.4980 chunk 13 optimal weight: 20.0000 chunk 336 optimal weight: 0.0970 chunk 48 optimal weight: 0.2980 chunk 59 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 309 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095068 restraints weight = 53320.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099250 restraints weight = 34235.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.102434 restraints weight = 24599.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104857 restraints weight = 19077.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106697 restraints weight = 15616.503| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28872 Z= 0.142 Angle : 0.891 12.913 39136 Z= 0.423 Chirality : 0.050 0.202 4472 Planarity : 0.005 0.061 4928 Dihedral : 17.327 178.485 4368 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.49 (0.13), residues: 3576 helix: -1.22 (0.14), residues: 1224 sheet: -2.34 (0.28), residues: 296 loop : -1.84 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 480 TYR 0.026 0.002 TYR G 484 PHE 0.027 0.002 PHE E 456 HIS 0.005 0.001 HIS H 454 Details of bonding type rmsd covalent geometry : bond 0.00325 (28864) covalent geometry : angle 0.89085 (39136) hydrogen bonds : bond 0.03531 ( 888) hydrogen bonds : angle 5.66036 ( 2448) Misc. bond : bond 0.00234 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7261.61 seconds wall clock time: 125 minutes 39.39 seconds (7539.39 seconds total)