Starting phenix.real_space_refine on Mon Sep 14 06:01:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uc2_20725/09_2026/6uc2_20725.cif" } 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-2.2.1-6174/lib/python3.11/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: 4.00, 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: 1.96 Conformation dependent library (CDL) restraints added in 1.2 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: 0.67 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: 5.56 Time building geometry restraints manager: 2.79 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: 16509 33.77 - 67.55: 763 67.55 - 101.32: 37 101.32 - 135.10: 19 135.10 - 168.87: 24 Dihedral angle restraints: 17352 sinusoidal: 7016 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 17349 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.060 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 19.835 168.874 10728 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/Z covalent geometry : bond 0.01634 / 0.93 (28864) covalent geometry : angle 1.92819 / 1.08 (39136) hydrogen bonds : bond 0.20498 / 13.56 ( 888) hydrogen bonds : angle 9.18466 / 6.20 ( 2448) Misc. bond : bond 0.09172 / 5.63 ( 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 : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8848 (tpp) cc_final: 0.8426 (tpp) REVERT: A 93 HIS cc_start: 0.9184 (p90) cc_final: 0.8812 (p90) REVERT: A 94 ASN cc_start: 0.8893 (t0) cc_final: 0.8655 (t0) REVERT: A 104 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.8886 (t) REVERT: A 108 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9201 (mtmt) REVERT: A 109 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8894 (tptp) REVERT: A 137 HIS cc_start: 0.9665 (m-70) cc_final: 0.9247 (m-70) REVERT: A 166 LEU cc_start: 0.9070 (pt) cc_final: 0.8338 (tp) REVERT: A 174 PHE cc_start: 0.9144 (m-80) cc_final: 0.8815 (m-80) REVERT: A 198 ASN cc_start: 0.9698 (m110) cc_final: 0.9320 (m110) REVERT: A 199 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9254 (mp0) REVERT: A 209 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (tm) REVERT: A 224 ARG cc_start: 0.8205 (tpt170) cc_final: 0.7522 (tpt-90) REVERT: A 229 LYS cc_start: 0.9411 (mttt) cc_final: 0.9157 (mmtt) REVERT: A 231 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8781 (ptm-80) REVERT: A 245 LEU cc_start: 0.9198 (mm) cc_final: 0.8771 (mm) REVERT: A 269 ASP cc_start: 0.9143 (t0) cc_final: 0.8335 (t0) REVERT: A 276 SER cc_start: 0.9205 (m) cc_final: 0.8969 (p) REVERT: A 283 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.9309 (mm-40) REVERT: A 296 ASN cc_start: 0.9208 (p0) cc_final: 0.8521 (p0) REVERT: A 297 LEU cc_start: 0.9300 (mm) cc_final: 0.8965 (mm) REVERT: A 298 GLN cc_start: 0.9199 (mm110) cc_final: 0.8716 (mm-40) REVERT: A 325 MET cc_start: 0.7464 (pmm) cc_final: 0.7088 (pmm) REVERT: A 351 SER cc_start: 0.8520 (p) cc_final: 0.8085 (p) REVERT: A 355 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8006 (ptt180) REVERT: A 372 HIS cc_start: 0.9572 (m170) cc_final: 0.9349 (m170) REVERT: A 402 PHE cc_start: 0.8531 (m-10) cc_final: 0.8259 (m-80) REVERT: A 450 LYS cc_start: 0.6934 (pttm) cc_final: 0.6188 (ptmm) REVERT: A 465 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: A 482 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8873 (tmm) REVERT: A 489 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8499 (ttpt) REVERT: B 82 MET cc_start: 0.8783 (tpp) cc_final: 0.8351 (tpp) REVERT: B 104 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8740 (t) REVERT: B 108 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9230 (mtmt) REVERT: B 109 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8793 (tptp) REVERT: B 137 HIS cc_start: 0.9680 (m-70) cc_final: 0.9278 (m-70) REVERT: B 154 LEU cc_start: 0.9764 (mm) cc_final: 0.9544 (mm) REVERT: B 166 LEU cc_start: 0.9021 (pt) cc_final: 0.8239 (tp) REVERT: B 174 PHE cc_start: 0.9064 (m-80) cc_final: 0.8714 (m-80) REVERT: B 198 ASN cc_start: 0.9634 (m110) cc_final: 0.9237 (m110) REVERT: B 199 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9225 (mp0) REVERT: B 231 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8839 (ptm-80) REVERT: B 245 LEU cc_start: 0.9221 (mm) cc_final: 0.8855 (mm) REVERT: B 269 ASP cc_start: 0.9204 (t0) cc_final: 0.8244 (t0) REVERT: B 277 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 281 ILE cc_start: 0.9421 (mm) cc_final: 0.9118 (mm) REVERT: B 283 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9253 (mm-40) REVERT: B 285 ASN cc_start: 0.9455 (m110) cc_final: 0.9195 (m110) REVERT: B 296 ASN cc_start: 0.9322 (p0) cc_final: 0.8550 (p0) REVERT: B 297 LEU cc_start: 0.9396 (mm) cc_final: 0.8917 (mm) REVERT: B 298 GLN cc_start: 0.9083 (mm110) cc_final: 0.8657 (mm-40) REVERT: B 321 LEU cc_start: 0.9795 (mm) cc_final: 0.9583 (mm) REVERT: B 325 MET cc_start: 0.7527 (pmm) cc_final: 0.7236 (pmm) REVERT: B 355 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8029 (ptt180) REVERT: B 372 HIS cc_start: 0.9539 (m170) cc_final: 0.9303 (m170) REVERT: B 402 PHE cc_start: 0.8351 (m-10) cc_final: 0.8094 (m-80) REVERT: B 450 LYS cc_start: 0.7039 (pttm) cc_final: 0.6254 (ptmm) REVERT: B 482 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8892 (tmm) REVERT: B 489 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8602 (ttpt) REVERT: C 14 PRO cc_start: 0.9109 (Cg_exo) cc_final: 0.8864 (Cg_endo) REVERT: C 82 MET cc_start: 0.8832 (tpp) cc_final: 0.8412 (tpp) REVERT: C 104 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8712 (p) REVERT: C 108 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9204 (mtmt) REVERT: C 109 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8872 (tptp) REVERT: C 137 HIS cc_start: 0.9678 (m-70) cc_final: 0.9218 (m-70) REVERT: C 155 VAL cc_start: 0.9359 (t) cc_final: 0.9127 (t) REVERT: C 174 PHE cc_start: 0.9197 (m-80) cc_final: 0.8888 (m-80) REVERT: C 199 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9107 (mp0) REVERT: C 209 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9029 (tm) REVERT: C 231 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8799 (ptm-80) REVERT: C 245 LEU cc_start: 0.9267 (mm) cc_final: 0.8924 (mm) REVERT: C 253 HIS cc_start: 0.9314 (m-70) cc_final: 0.9059 (m-70) REVERT: C 269 ASP cc_start: 0.9193 (t0) cc_final: 0.8403 (t0) REVERT: C 276 SER cc_start: 0.9215 (m) cc_final: 0.9011 (p) REVERT: C 283 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9267 (mm-40) REVERT: C 297 LEU cc_start: 0.9303 (mm) cc_final: 0.8949 (mm) REVERT: C 298 GLN cc_start: 0.9161 (mm110) cc_final: 0.8656 (mm-40) REVERT: C 349 LYS cc_start: 0.9479 (mtmt) cc_final: 0.9234 (mtpt) REVERT: C 355 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8521 (tmm-80) REVERT: C 402 PHE cc_start: 0.8337 (m-10) cc_final: 0.8131 (m-80) REVERT: C 450 LYS cc_start: 0.6895 (pttm) cc_final: 0.6187 (ptmm) REVERT: C 465 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: C 482 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8920 (tmm) REVERT: C 489 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8530 (ttpt) REVERT: D 82 MET cc_start: 0.8800 (tpp) cc_final: 0.8370 (tpp) REVERT: D 88 ILE cc_start: 0.7492 (mt) cc_final: 0.7289 (mp) REVERT: D 104 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8702 (t) REVERT: D 108 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9225 (mtmt) REVERT: D 109 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8842 (tptp) REVERT: D 137 HIS cc_start: 0.9664 (m-70) cc_final: 0.9259 (m-70) REVERT: D 154 LEU cc_start: 0.9778 (mm) cc_final: 0.9514 (mm) REVERT: D 166 LEU cc_start: 0.8953 (pt) cc_final: 0.8058 (tp) REVERT: D 198 ASN cc_start: 0.9634 (m110) cc_final: 0.9246 (m110) REVERT: D 199 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9219 (mp0) REVERT: D 231 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8818 (ptm-80) REVERT: D 245 LEU cc_start: 0.9242 (mm) cc_final: 0.8846 (mm) REVERT: D 265 GLN cc_start: 0.9500 (mt0) cc_final: 0.9249 (tp40) REVERT: D 269 ASP cc_start: 0.9181 (t0) cc_final: 0.8228 (t0) REVERT: D 281 ILE cc_start: 0.9407 (mm) cc_final: 0.9100 (mm) REVERT: D 285 ASN cc_start: 0.9475 (m110) cc_final: 0.9214 (m110) REVERT: D 296 ASN cc_start: 0.9327 (p0) cc_final: 0.8627 (p0) REVERT: D 297 LEU cc_start: 0.9416 (mm) cc_final: 0.8939 (mm) REVERT: D 298 GLN cc_start: 0.9110 (mm110) cc_final: 0.8678 (mm-40) REVERT: D 325 MET cc_start: 0.7236 (pmm) cc_final: 0.6890 (pmm) REVERT: D 355 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8117 (ptt180) REVERT: D 372 HIS cc_start: 0.9592 (m170) cc_final: 0.9366 (m170) REVERT: D 401 PHE cc_start: 0.9309 (p90) cc_final: 0.9100 (p90) REVERT: D 402 PHE cc_start: 0.8360 (m-10) cc_final: 0.8092 (m-80) REVERT: D 450 LYS cc_start: 0.7000 (pttm) cc_final: 0.6266 (ptmm) REVERT: D 465 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: D 482 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8943 (tmm) REVERT: E 12 TYR cc_start: 0.9275 (t80) cc_final: 0.8921 (t80) REVERT: E 82 MET cc_start: 0.8844 (tpp) cc_final: 0.8436 (tpp) REVERT: E 104 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8841 (t) REVERT: E 108 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9192 (mtmt) REVERT: E 109 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8837 (tptp) REVERT: E 137 HIS cc_start: 0.9692 (m-70) cc_final: 0.9268 (m-70) REVERT: E 154 LEU cc_start: 0.9763 (mm) cc_final: 0.9512 (mm) REVERT: E 166 LEU cc_start: 0.9027 (pt) cc_final: 0.8241 (tp) REVERT: E 174 PHE cc_start: 0.9092 (m-80) cc_final: 0.8778 (m-80) REVERT: E 198 ASN cc_start: 0.9673 (m110) cc_final: 0.9287 (m110) REVERT: E 199 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9244 (mp0) REVERT: E 209 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9152 (tm) REVERT: E 229 LYS cc_start: 0.9403 (mttt) cc_final: 0.9152 (mmtt) REVERT: E 231 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8814 (ptm-80) REVERT: E 245 LEU cc_start: 0.9201 (mm) cc_final: 0.8798 (mm) REVERT: E 269 ASP cc_start: 0.9158 (t0) cc_final: 0.8328 (t0) REVERT: E 281 ILE cc_start: 0.9356 (mm) cc_final: 0.9138 (mm) REVERT: E 282 PHE cc_start: 0.8853 (m-80) cc_final: 0.8623 (m-80) REVERT: E 285 ASN cc_start: 0.9501 (m110) cc_final: 0.9280 (m110) REVERT: E 296 ASN cc_start: 0.9257 (p0) cc_final: 0.8581 (p0) REVERT: E 297 LEU cc_start: 0.9373 (mm) cc_final: 0.8997 (mm) REVERT: E 298 GLN cc_start: 0.9148 (mm110) cc_final: 0.8649 (mm-40) REVERT: E 321 LEU cc_start: 0.9770 (mm) cc_final: 0.9560 (mm) REVERT: E 325 MET cc_start: 0.7445 (pmm) cc_final: 0.7106 (pmm) REVERT: E 351 SER cc_start: 0.8581 (p) cc_final: 0.8043 (p) REVERT: E 355 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8161 (ptt180) REVERT: E 372 HIS cc_start: 0.9571 (m170) cc_final: 0.9316 (m170) REVERT: E 402 PHE cc_start: 0.8460 (m-10) cc_final: 0.8253 (m-80) REVERT: E 450 LYS cc_start: 0.6995 (pttm) cc_final: 0.6263 (ptmm) REVERT: E 465 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: E 482 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8936 (tmm) REVERT: E 489 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8511 (ttpt) REVERT: F 82 MET cc_start: 0.8785 (tpp) cc_final: 0.8336 (tpp) REVERT: F 88 ILE cc_start: 0.7440 (mt) cc_final: 0.7154 (mp) REVERT: F 109 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8898 (tptp) REVERT: F 137 HIS cc_start: 0.9666 (m-70) cc_final: 0.9279 (m-70) REVERT: F 174 PHE cc_start: 0.9056 (m-80) cc_final: 0.8689 (m-80) REVERT: F 198 ASN cc_start: 0.9660 (m110) cc_final: 0.9273 (m110) REVERT: F 199 GLU cc_start: 0.9528 (OUTLIER) cc_final: 0.9245 (mp0) REVERT: F 209 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9106 (tm) REVERT: F 231 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8839 (ptm-80) REVERT: F 232 ASP cc_start: 0.9204 (t70) cc_final: 0.8996 (m-30) REVERT: F 269 ASP cc_start: 0.9188 (t0) cc_final: 0.8279 (t0) REVERT: F 277 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8220 (tm-30) REVERT: F 281 ILE cc_start: 0.9418 (mm) cc_final: 0.9106 (mm) REVERT: F 283 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9253 (mm-40) REVERT: F 285 ASN cc_start: 0.9436 (m110) cc_final: 0.9169 (m110) REVERT: F 296 ASN cc_start: 0.9328 (p0) cc_final: 0.8572 (p0) REVERT: F 297 LEU cc_start: 0.9435 (mm) cc_final: 0.8999 (mm) REVERT: F 298 GLN cc_start: 0.9131 (mm110) cc_final: 0.8664 (mm-40) REVERT: F 321 LEU cc_start: 0.9802 (mm) cc_final: 0.9600 (mm) REVERT: F 325 MET cc_start: 0.7134 (pmm) cc_final: 0.6795 (pmm) REVERT: F 355 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8182 (ptt180) REVERT: F 372 HIS cc_start: 0.9599 (m170) cc_final: 0.9360 (m170) REVERT: F 402 PHE cc_start: 0.8361 (m-10) cc_final: 0.8091 (m-80) REVERT: F 482 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9000 (tmm) REVERT: G 22 GLN cc_start: 0.9262 (mt0) cc_final: 0.8633 (mp10) REVERT: G 65 LEU cc_start: 0.8977 (pt) cc_final: 0.8689 (pt) REVERT: G 82 MET cc_start: 0.8854 (tpp) cc_final: 0.8452 (tpp) REVERT: G 93 HIS cc_start: 0.9159 (p90) cc_final: 0.8746 (p90) REVERT: G 94 ASN cc_start: 0.8912 (t0) cc_final: 0.8662 (t0) REVERT: G 104 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8869 (m) REVERT: G 108 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9206 (mtmt) REVERT: G 109 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8822 (tptp) REVERT: G 137 HIS cc_start: 0.9671 (m-70) cc_final: 0.9246 (m-70) REVERT: G 166 LEU cc_start: 0.9061 (pt) cc_final: 0.8330 (tp) REVERT: G 199 GLU cc_start: 0.9573 (OUTLIER) cc_final: 0.9182 (mp0) REVERT: G 209 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8940 (tm) REVERT: G 224 ARG cc_start: 0.8206 (tpt170) cc_final: 0.7560 (tpt-90) REVERT: G 231 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8822 (ptm-80) REVERT: G 245 LEU cc_start: 0.9226 (mm) cc_final: 0.8872 (mm) REVERT: G 269 ASP cc_start: 0.9142 (t0) cc_final: 0.8319 (t0) REVERT: G 276 SER cc_start: 0.9182 (m) cc_final: 0.8958 (p) REVERT: G 283 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9326 (mm-40) REVERT: G 296 ASN cc_start: 0.9233 (p0) cc_final: 0.8560 (p0) REVERT: G 297 LEU cc_start: 0.9329 (mm) cc_final: 0.8998 (mm) REVERT: G 298 GLN cc_start: 0.9198 (mm110) cc_final: 0.8679 (mm-40) REVERT: G 351 SER cc_start: 0.8542 (p) cc_final: 0.8047 (p) REVERT: G 355 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8155 (ptt180) REVERT: G 401 PHE cc_start: 0.9311 (p90) cc_final: 0.9094 (p90) REVERT: G 402 PHE cc_start: 0.8515 (m-10) cc_final: 0.8249 (m-80) REVERT: G 450 LYS cc_start: 0.6987 (pttm) cc_final: 0.6354 (ptmm) REVERT: G 465 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: G 482 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9028 (tmm) REVERT: H 44 PHE cc_start: 0.7863 (p90) cc_final: 0.7580 (p90) REVERT: H 65 LEU cc_start: 0.8911 (pt) cc_final: 0.8600 (pt) REVERT: H 82 MET cc_start: 0.8827 (tpp) cc_final: 0.8409 (tpp) REVERT: H 88 ILE cc_start: 0.7461 (mt) cc_final: 0.7195 (mp) REVERT: H 104 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8690 (t) REVERT: H 108 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9220 (mtmt) REVERT: H 109 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8843 (tptp) REVERT: H 137 HIS cc_start: 0.9688 (m-70) cc_final: 0.9276 (m-70) REVERT: H 154 LEU cc_start: 0.9751 (mm) cc_final: 0.9502 (mm) REVERT: H 161 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.9169 (mpp80) REVERT: H 166 LEU cc_start: 0.8992 (pt) cc_final: 0.8112 (tp) REVERT: H 174 PHE cc_start: 0.9059 (m-80) cc_final: 0.8752 (m-80) REVERT: H 198 ASN cc_start: 0.9651 (m110) cc_final: 0.9244 (m110) REVERT: H 199 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9262 (mp0) REVERT: H 209 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9053 (tm) REVERT: H 231 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8858 (ptm-80) REVERT: H 245 LEU cc_start: 0.9224 (mm) cc_final: 0.8914 (mm) REVERT: H 269 ASP cc_start: 0.9170 (t0) cc_final: 0.8242 (t0) REVERT: H 283 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9266 (mm-40) REVERT: H 285 ASN cc_start: 0.9486 (m110) cc_final: 0.9238 (m110) REVERT: H 296 ASN cc_start: 0.9335 (p0) cc_final: 0.8619 (p0) REVERT: H 297 LEU cc_start: 0.9419 (mm) cc_final: 0.8988 (mm) REVERT: H 298 GLN cc_start: 0.9122 (mm110) cc_final: 0.8613 (mm-40) REVERT: H 321 LEU cc_start: 0.9783 (mm) cc_final: 0.9568 (mm) REVERT: H 325 MET cc_start: 0.7257 (pmm) cc_final: 0.6929 (pmm) REVERT: H 351 SER cc_start: 0.8605 (p) cc_final: 0.8125 (p) REVERT: H 355 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8129 (ptt180) REVERT: H 357 PHE cc_start: 0.9148 (m-80) cc_final: 0.8858 (m-80) REVERT: H 372 HIS cc_start: 0.9555 (m170) cc_final: 0.9335 (m170) REVERT: H 401 PHE cc_start: 0.9272 (p90) cc_final: 0.9058 (p90) REVERT: H 402 PHE cc_start: 0.8378 (m-10) cc_final: 0.8104 (m-80) REVERT: H 465 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: H 482 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8925 (tmm) REVERT: H 489 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8552 (ttpt) outliers start: 440 outliers final: 183 residues processed: 1615 average time/residue: 0.1780 time to fit residues: 451.8149 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 : 1.007 ------------------------------------------------------------------------------- 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... ** 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 = 0.131640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091972 restraints weight = 53431.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096209 restraints weight = 33549.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.099460 restraints weight = 23906.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101924 restraints weight = 18455.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103866 restraints weight = 15087.846| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28872 Z= 0.157 Angle : 0.934 10.404 39136 Z= 0.453 Chirality : 0.052 0.212 4472 Planarity : 0.005 0.045 4928 Dihedral : 17.605 171.998 4120 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.74 % Allowed : 5.93 % Favored : 93.33 % 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: -3.36 (0.12), residues: 3576 helix: -2.05 (0.13), residues: 1240 sheet: -2.65 (0.20), residues: 520 loop : -2.18 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 407 TYR 0.028 0.003 TYR F 233 PHE 0.036 0.002 PHE F 456 HIS 0.003 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (28864) covalent geometry : angle 0.93442 / 0.45 (39136) hydrogen bonds : bond 0.04342 / 2.89 ( 888) hydrogen bonds : angle 6.52964 / 4.40 ( 2448) Misc. bond : bond 0.00238 / 0.14 ( 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 1497 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1475 time to evaluate : 1.040 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: 0.8759 (m) cc_final: 0.8359 (t) REVERT: A 82 MET cc_start: 0.8871 (tpp) cc_final: 0.8514 (tpp) REVERT: A 93 HIS cc_start: 0.9279 (p90) cc_final: 0.8886 (p90) REVERT: A 94 ASN cc_start: 0.8842 (t0) cc_final: 0.8593 (t0) REVERT: A 103 GLU cc_start: 0.9230 (mp0) cc_final: 0.9017 (mp0) REVERT: A 166 LEU cc_start: 0.8859 (pt) cc_final: 0.8301 (tp) REVERT: A 230 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8731 (m-40) REVERT: A 269 ASP cc_start: 0.9229 (t0) cc_final: 0.8371 (t0) REVERT: A 276 SER cc_start: 0.9090 (m) cc_final: 0.8823 (p) REVERT: A 285 ASN cc_start: 0.9541 (m110) cc_final: 0.9298 (m110) REVERT: A 296 ASN cc_start: 0.9357 (p0) cc_final: 0.8683 (p0) REVERT: A 297 LEU cc_start: 0.9155 (mm) cc_final: 0.8653 (mm) REVERT: A 298 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8351 (mm-40) REVERT: A 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9471 (mm) REVERT: A 364 ASP cc_start: 0.8944 (t0) cc_final: 0.8688 (t0) REVERT: A 489 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7940 (ttpt) REVERT: B 66 VAL cc_start: 0.9068 (m) cc_final: 0.8358 (m) REVERT: B 67 SER cc_start: 0.8818 (m) cc_final: 0.8405 (t) REVERT: B 82 MET cc_start: 0.8792 (tpp) cc_final: 0.8398 (tpp) REVERT: B 93 HIS cc_start: 0.9299 (p90) cc_final: 0.8914 (p90) REVERT: B 129 ASP cc_start: 0.9405 (p0) cc_final: 0.9199 (p0) REVERT: B 154 LEU cc_start: 0.9671 (mm) cc_final: 0.9460 (mm) REVERT: B 166 LEU cc_start: 0.8840 (pt) cc_final: 0.8218 (tp) REVERT: B 174 PHE cc_start: 0.8916 (m-80) cc_final: 0.8567 (m-80) REVERT: B 215 ASP cc_start: 0.9014 (m-30) cc_final: 0.8613 (t0) REVERT: B 216 ASP cc_start: 0.9064 (t0) cc_final: 0.8823 (t0) REVERT: B 232 ASP cc_start: 0.9041 (m-30) cc_final: 0.8840 (m-30) REVERT: B 253 HIS cc_start: 0.8988 (t-90) cc_final: 0.8785 (t-90) REVERT: B 269 ASP cc_start: 0.9236 (t0) cc_final: 0.8263 (t0) REVERT: B 277 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8567 (tm-30) REVERT: B 285 ASN cc_start: 0.9426 (m110) cc_final: 0.9171 (m110) REVERT: B 291 LYS cc_start: 0.9654 (pttp) cc_final: 0.9445 (pttm) REVERT: B 296 ASN cc_start: 0.9439 (p0) cc_final: 0.8664 (p0) REVERT: B 297 LEU cc_start: 0.9306 (mm) cc_final: 0.8722 (mm) REVERT: B 298 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8245 (mm-40) REVERT: B 321 LEU cc_start: 0.9754 (mm) cc_final: 0.9505 (mm) REVERT: B 489 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7955 (ttpt) REVERT: C 67 SER cc_start: 0.8736 (m) cc_final: 0.8295 (t) REVERT: C 78 MET cc_start: 0.7477 (mpp) cc_final: 0.6775 (mpp) REVERT: C 82 MET cc_start: 0.8835 (tpp) cc_final: 0.8485 (tpp) REVERT: C 93 HIS cc_start: 0.9278 (p90) cc_final: 0.8740 (p90) REVERT: C 94 ASN cc_start: 0.8930 (t0) cc_final: 0.8669 (t0) REVERT: C 103 GLU cc_start: 0.9224 (mp0) cc_final: 0.8966 (mp0) REVERT: C 166 LEU cc_start: 0.8841 (pt) cc_final: 0.8353 (tp) REVERT: C 178 ILE cc_start: 0.9324 (mp) cc_final: 0.8838 (mp) REVERT: C 232 ASP cc_start: 0.9002 (m-30) cc_final: 0.8798 (m-30) REVERT: C 269 ASP cc_start: 0.9198 (t0) cc_final: 0.8311 (t0) REVERT: C 276 SER cc_start: 0.9123 (m) cc_final: 0.8857 (p) REVERT: C 281 ILE cc_start: 0.9418 (mm) cc_final: 0.9206 (mm) REVERT: C 285 ASN cc_start: 0.9492 (m110) cc_final: 0.9242 (m110) REVERT: C 297 LEU cc_start: 0.9228 (mm) cc_final: 0.8685 (mm) REVERT: C 298 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8299 (mm-40) REVERT: C 321 LEU cc_start: 0.9748 (mm) cc_final: 0.9471 (mm) REVERT: C 355 ARG cc_start: 0.8679 (ptt90) cc_final: 0.8053 (ptm160) REVERT: D 28 ASP cc_start: 0.9246 (t0) cc_final: 0.8966 (t0) REVERT: D 65 LEU cc_start: 0.8869 (pt) cc_final: 0.8652 (pt) REVERT: D 66 VAL cc_start: 0.9054 (m) cc_final: 0.8482 (m) REVERT: D 67 SER cc_start: 0.8814 (m) cc_final: 0.8407 (t) REVERT: D 78 MET cc_start: 0.7578 (mpp) cc_final: 0.6929 (mpp) REVERT: D 82 MET cc_start: 0.8783 (tpp) cc_final: 0.8420 (tpp) REVERT: D 93 HIS cc_start: 0.9302 (p90) cc_final: 0.8790 (p90) REVERT: D 94 ASN cc_start: 0.8956 (t0) cc_final: 0.8726 (t0) REVERT: D 103 GLU cc_start: 0.9138 (mp0) cc_final: 0.8938 (mp0) REVERT: D 129 ASP cc_start: 0.9443 (p0) cc_final: 0.9067 (p0) REVERT: D 166 LEU cc_start: 0.8777 (pt) cc_final: 0.8203 (tp) REVERT: D 215 ASP cc_start: 0.9183 (m-30) cc_final: 0.8606 (t0) REVERT: D 217 GLU cc_start: 0.8992 (mp0) cc_final: 0.8480 (mp0) REVERT: D 258 TYR cc_start: 0.9608 (t80) cc_final: 0.9067 (t80) REVERT: D 261 ASP cc_start: 0.9107 (m-30) cc_final: 0.8475 (p0) REVERT: D 262 LEU cc_start: 0.9705 (tt) cc_final: 0.9493 (tt) REVERT: D 269 ASP cc_start: 0.9215 (t0) cc_final: 0.8206 (t0) REVERT: D 277 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8474 (tm-30) REVERT: D 281 ILE cc_start: 0.9410 (mm) cc_final: 0.9164 (mm) REVERT: D 285 ASN cc_start: 0.9426 (m110) cc_final: 0.9155 (m110) REVERT: D 296 ASN cc_start: 0.9451 (p0) cc_final: 0.8700 (p0) REVERT: D 297 LEU cc_start: 0.9323 (mm) cc_final: 0.8769 (mm) REVERT: D 298 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8201 (mm-40) REVERT: D 321 LEU cc_start: 0.9740 (mm) cc_final: 0.9488 (mm) REVERT: D 353 TYR cc_start: 0.9112 (t80) cc_final: 0.8634 (t80) REVERT: D 401 PHE cc_start: 0.9350 (p90) cc_final: 0.9074 (p90) REVERT: D 450 LYS cc_start: 0.7371 (pttm) cc_final: 0.6537 (ptmm) REVERT: D 489 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7782 (ttpt) REVERT: E 12 TYR cc_start: 0.9202 (t80) cc_final: 0.8824 (t80) REVERT: E 66 VAL cc_start: 0.9190 (m) cc_final: 0.8851 (m) REVERT: E 67 SER cc_start: 0.8764 (m) cc_final: 0.8303 (t) REVERT: E 82 MET cc_start: 0.8854 (tpp) cc_final: 0.8481 (tpp) REVERT: E 93 HIS cc_start: 0.9235 (p90) cc_final: 0.8880 (p90) REVERT: E 166 LEU cc_start: 0.8807 (pt) cc_final: 0.8206 (tp) REVERT: E 215 ASP cc_start: 0.9289 (m-30) cc_final: 0.8537 (t0) REVERT: E 261 ASP cc_start: 0.9271 (m-30) cc_final: 0.8556 (p0) REVERT: E 262 LEU cc_start: 0.9742 (tt) cc_final: 0.9500 (tt) REVERT: E 269 ASP cc_start: 0.9219 (t0) cc_final: 0.8349 (t0) REVERT: E 276 SER cc_start: 0.9067 (m) cc_final: 0.8813 (p) REVERT: E 285 ASN cc_start: 0.9488 (m110) cc_final: 0.9248 (m110) REVERT: E 296 ASN cc_start: 0.9400 (p0) cc_final: 0.8729 (p0) REVERT: E 297 LEU cc_start: 0.9290 (mm) cc_final: 0.8744 (mm) REVERT: E 298 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8177 (mm-40) REVERT: E 321 LEU cc_start: 0.9730 (mm) cc_final: 0.9476 (mm) REVERT: E 353 TYR cc_start: 0.9104 (t80) cc_final: 0.8823 (t80) REVERT: E 489 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7776 (ttpt) REVERT: F 65 LEU cc_start: 0.8895 (pt) cc_final: 0.8635 (pt) REVERT: F 66 VAL cc_start: 0.9075 (m) cc_final: 0.8419 (m) REVERT: F 67 SER cc_start: 0.8830 (m) cc_final: 0.8417 (t) REVERT: F 82 MET cc_start: 0.8748 (tpp) cc_final: 0.8383 (tpp) REVERT: F 92 HIS cc_start: 0.8360 (p90) cc_final: 0.8062 (p90) REVERT: F 93 HIS cc_start: 0.9307 (p90) cc_final: 0.8785 (p90) REVERT: F 94 ASN cc_start: 0.8926 (t0) cc_final: 0.8581 (t0) REVERT: F 121 LEU cc_start: 0.9319 (mm) cc_final: 0.9113 (tp) REVERT: F 166 LEU cc_start: 0.8731 (pt) cc_final: 0.8013 (tp) REVERT: F 181 LYS cc_start: 0.9299 (mmpt) cc_final: 0.9074 (mmpt) REVERT: F 215 ASP cc_start: 0.9210 (m-30) cc_final: 0.8616 (t0) REVERT: F 216 ASP cc_start: 0.9049 (t70) cc_final: 0.8753 (t0) REVERT: F 253 HIS cc_start: 0.9034 (t-90) cc_final: 0.8818 (t-90) REVERT: F 269 ASP cc_start: 0.9236 (t0) cc_final: 0.8251 (t0) REVERT: F 277 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8527 (tm-30) REVERT: F 285 ASN cc_start: 0.9408 (m110) cc_final: 0.9138 (m110) REVERT: F 296 ASN cc_start: 0.9443 (p0) cc_final: 0.8710 (p0) REVERT: F 297 LEU cc_start: 0.9341 (mm) cc_final: 0.8799 (mm) REVERT: F 298 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8261 (mm-40) REVERT: F 321 LEU cc_start: 0.9766 (mm) cc_final: 0.9537 (mm) REVERT: F 353 TYR cc_start: 0.9086 (t80) cc_final: 0.8692 (t80) REVERT: G 65 LEU cc_start: 0.8875 (pt) cc_final: 0.8673 (pt) REVERT: G 66 VAL cc_start: 0.9100 (m) cc_final: 0.8669 (m) REVERT: G 67 SER cc_start: 0.8765 (m) cc_final: 0.8298 (t) REVERT: G 78 MET cc_start: 0.7550 (mpp) cc_final: 0.6629 (mpp) REVERT: G 82 MET cc_start: 0.8864 (tpp) cc_final: 0.8506 (tpp) REVERT: G 93 HIS cc_start: 0.9268 (p90) cc_final: 0.8781 (p90) REVERT: G 94 ASN cc_start: 0.8874 (t0) cc_final: 0.8613 (t0) REVERT: G 103 GLU cc_start: 0.9222 (mp0) cc_final: 0.8996 (mp0) REVERT: G 132 GLU cc_start: 0.9403 (tm-30) cc_final: 0.9180 (pp20) REVERT: G 166 LEU cc_start: 0.8816 (pt) cc_final: 0.8241 (tp) REVERT: G 232 ASP cc_start: 0.9064 (m-30) cc_final: 0.8816 (m-30) REVERT: G 269 ASP cc_start: 0.9204 (t0) cc_final: 0.8352 (t0) REVERT: G 276 SER cc_start: 0.9073 (m) cc_final: 0.8790 (p) REVERT: G 285 ASN cc_start: 0.9535 (m110) cc_final: 0.9287 (m110) REVERT: G 286 MET cc_start: 0.8915 (mtm) cc_final: 0.8659 (mtt) REVERT: G 296 ASN cc_start: 0.9362 (p0) cc_final: 0.8715 (p0) REVERT: G 297 LEU cc_start: 0.9190 (mm) cc_final: 0.8710 (mm) REVERT: G 298 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8307 (mm-40) REVERT: G 321 LEU cc_start: 0.9744 (mm) cc_final: 0.9499 (mm) REVERT: G 349 LYS cc_start: 0.9454 (mtpt) cc_final: 0.9245 (mtpt) REVERT: G 395 GLU cc_start: 0.8859 (mp0) cc_final: 0.8608 (mp0) REVERT: G 401 PHE cc_start: 0.9351 (p90) cc_final: 0.9095 (p90) REVERT: H 65 LEU cc_start: 0.8808 (pt) cc_final: 0.8570 (pt) REVERT: H 66 VAL cc_start: 0.9037 (m) cc_final: 0.8482 (m) REVERT: H 67 SER cc_start: 0.8793 (m) cc_final: 0.8354 (t) REVERT: H 78 MET cc_start: 0.7540 (mpp) cc_final: 0.6926 (mpp) REVERT: H 82 MET cc_start: 0.8803 (tpp) cc_final: 0.8430 (tpp) REVERT: H 93 HIS cc_start: 0.9282 (p90) cc_final: 0.8897 (p90) REVERT: H 94 ASN cc_start: 0.8944 (t0) cc_final: 0.8743 (t0) REVERT: H 103 GLU cc_start: 0.9226 (mp0) cc_final: 0.8929 (mp0) REVERT: H 129 ASP cc_start: 0.9419 (p0) cc_final: 0.9041 (p0) REVERT: H 166 LEU cc_start: 0.8871 (pt) cc_final: 0.8293 (tp) REVERT: H 174 PHE cc_start: 0.8929 (m-80) cc_final: 0.8607 (m-80) REVERT: H 181 LYS cc_start: 0.9289 (mmpt) cc_final: 0.9019 (mmpt) REVERT: H 215 ASP cc_start: 0.9141 (m-30) cc_final: 0.8615 (t0) REVERT: H 217 GLU cc_start: 0.8888 (mp0) cc_final: 0.8314 (mp0) REVERT: H 258 TYR cc_start: 0.9622 (t80) cc_final: 0.9095 (t80) REVERT: H 261 ASP cc_start: 0.9202 (m-30) cc_final: 0.8434 (p0) REVERT: H 262 LEU cc_start: 0.9729 (tt) cc_final: 0.9456 (tt) REVERT: H 269 ASP cc_start: 0.9169 (t0) cc_final: 0.8193 (t0) REVERT: H 277 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8410 (tm-30) REVERT: H 285 ASN cc_start: 0.9442 (m110) cc_final: 0.9161 (m110) REVERT: H 286 MET cc_start: 0.8719 (mtm) cc_final: 0.8432 (mtt) REVERT: H 296 ASN cc_start: 0.9437 (p0) cc_final: 0.8674 (p0) REVERT: H 297 LEU cc_start: 0.9316 (mm) cc_final: 0.8770 (mm) REVERT: H 298 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8254 (mm-40) REVERT: H 321 LEU cc_start: 0.9729 (mm) cc_final: 0.9468 (mm) REVERT: H 357 PHE cc_start: 0.9146 (m-80) cc_final: 0.8788 (m-10) REVERT: H 375 LYS cc_start: 0.9504 (ptpp) cc_final: 0.9258 (ptpp) REVERT: H 401 PHE cc_start: 0.9328 (p90) cc_final: 0.9055 (p90) REVERT: H 450 LYS cc_start: 0.7214 (pttp) cc_final: 0.6770 (ptmm) outliers start: 22 outliers final: 5 residues processed: 1478 average time/residue: 0.1566 time to fit residues: 380.2841 Evaluate side-chains 1149 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1143 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 350 optimal weight: 0.2980 chunk 188 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 0.0050 chunk 150 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090128 restraints weight = 54377.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094085 restraints weight = 35126.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097088 restraints weight = 25439.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099423 restraints weight = 19868.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101249 restraints weight = 16351.156| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28872 Z= 0.171 Angle : 0.887 9.867 39136 Z= 0.432 Chirality : 0.050 0.198 4472 Planarity : 0.005 0.045 4928 Dihedral : 17.320 168.495 4120 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -3.03 (0.13), residues: 3576 helix: -1.52 (0.13), residues: 1232 sheet: -3.07 (0.20), residues: 424 loop : -2.08 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 105 TYR 0.026 0.002 TYR C 233 PHE 0.044 0.002 PHE E 456 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (28864) covalent geometry : angle 0.88665 / 0.43 (39136) hydrogen bonds : bond 0.04004 / 2.66 ( 888) hydrogen bonds : angle 6.13748 / 4.12 ( 2448) Misc. bond : bond 0.00177 / 0.11 ( 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 1324 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1324 time to evaluate : 1.027 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: 0.9181 (t0) cc_final: 0.8907 (t0) REVERT: A 49 VAL cc_start: 0.8086 (t) cc_final: 0.7789 (m) REVERT: A 67 SER cc_start: 0.8707 (m) cc_final: 0.8411 (t) REVERT: A 78 MET cc_start: 0.7671 (mpp) cc_final: 0.6811 (mpp) REVERT: A 82 MET cc_start: 0.8948 (tpp) cc_final: 0.8551 (tpp) REVERT: A 93 HIS cc_start: 0.9296 (p90) cc_final: 0.8729 (p90) REVERT: A 94 ASN cc_start: 0.8864 (t0) cc_final: 0.8595 (t0) REVERT: A 103 GLU cc_start: 0.9212 (mp0) cc_final: 0.8964 (mp0) REVERT: A 166 LEU cc_start: 0.8868 (pt) cc_final: 0.8210 (tp) REVERT: A 181 LYS cc_start: 0.9383 (mmpt) cc_final: 0.9175 (mmpt) REVERT: A 199 GLU cc_start: 0.9648 (mt-10) cc_final: 0.9352 (pt0) REVERT: A 241 LYS cc_start: 0.9382 (tptp) cc_final: 0.9053 (tptp) REVERT: A 262 LEU cc_start: 0.9789 (tt) cc_final: 0.9433 (mt) REVERT: A 269 ASP cc_start: 0.9227 (t0) cc_final: 0.8394 (t0) REVERT: A 276 SER cc_start: 0.9164 (m) cc_final: 0.8854 (p) REVERT: A 285 ASN cc_start: 0.9553 (m110) cc_final: 0.9328 (m110) REVERT: A 286 MET cc_start: 0.8865 (mtm) cc_final: 0.8570 (mtt) REVERT: A 296 ASN cc_start: 0.9344 (p0) cc_final: 0.8678 (p0) REVERT: A 297 LEU cc_start: 0.9166 (mm) cc_final: 0.8676 (mm) REVERT: A 298 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8293 (mm-40) REVERT: A 321 LEU cc_start: 0.9726 (mm) cc_final: 0.9414 (mm) REVERT: A 369 ASN cc_start: 0.9309 (p0) cc_final: 0.9108 (p0) REVERT: A 401 PHE cc_start: 0.9288 (p90) cc_final: 0.9038 (p90) REVERT: A 492 LYS cc_start: 0.8352 (tptp) cc_final: 0.8065 (tptp) REVERT: A 493 ARG cc_start: 0.9317 (ttt90) cc_final: 0.8930 (ttm-80) REVERT: B 66 VAL cc_start: 0.9157 (m) cc_final: 0.8700 (m) REVERT: B 67 SER cc_start: 0.8700 (m) cc_final: 0.8373 (t) REVERT: B 78 MET cc_start: 0.7696 (mpp) cc_final: 0.7134 (mpp) REVERT: B 82 MET cc_start: 0.8890 (tpp) cc_final: 0.8492 (tpp) REVERT: B 93 HIS cc_start: 0.9314 (p90) cc_final: 0.8779 (p90) REVERT: B 94 ASN cc_start: 0.8933 (t0) cc_final: 0.8730 (t0) REVERT: B 103 GLU cc_start: 0.9229 (mp0) cc_final: 0.9027 (mp0) REVERT: B 105 ARG cc_start: 0.9012 (mtt90) cc_final: 0.8791 (mmt90) REVERT: B 134 LYS cc_start: 0.9423 (tppt) cc_final: 0.9154 (mmtt) REVERT: B 139 PHE cc_start: 0.8684 (p90) cc_final: 0.8147 (p90) REVERT: B 166 LEU cc_start: 0.8883 (pt) cc_final: 0.8192 (tp) REVERT: B 179 MET cc_start: 0.7812 (tpt) cc_final: 0.7604 (tpp) REVERT: B 199 GLU cc_start: 0.9589 (mt-10) cc_final: 0.9331 (pt0) REVERT: B 229 LYS cc_start: 0.9437 (mttt) cc_final: 0.9056 (mttt) REVERT: B 261 ASP cc_start: 0.9267 (m-30) cc_final: 0.8600 (p0) REVERT: B 262 LEU cc_start: 0.9771 (tt) cc_final: 0.9527 (tt) REVERT: B 265 GLN cc_start: 0.9496 (tm-30) cc_final: 0.9116 (tm-30) REVERT: B 269 ASP cc_start: 0.9220 (t0) cc_final: 0.8263 (t0) REVERT: B 277 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 281 ILE cc_start: 0.9410 (mm) cc_final: 0.9173 (mm) REVERT: B 285 ASN cc_start: 0.9493 (m110) cc_final: 0.9210 (m110) REVERT: B 291 LYS cc_start: 0.9652 (pttp) cc_final: 0.9424 (pttt) REVERT: B 296 ASN cc_start: 0.9413 (p0) cc_final: 0.8658 (p0) REVERT: B 297 LEU cc_start: 0.9276 (mm) cc_final: 0.8716 (mm) REVERT: B 298 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8222 (mm-40) REVERT: B 321 LEU cc_start: 0.9750 (mm) cc_final: 0.9450 (mm) REVERT: B 375 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9231 (ptpp) REVERT: B 493 ARG cc_start: 0.9346 (ttt90) cc_final: 0.9003 (ttm-80) REVERT: C 67 SER cc_start: 0.8665 (m) cc_final: 0.8334 (t) REVERT: C 78 MET cc_start: 0.7388 (mpp) cc_final: 0.6674 (mpp) REVERT: C 82 MET cc_start: 0.8868 (tpp) cc_final: 0.8484 (tpp) REVERT: C 94 ASN cc_start: 0.8907 (t0) cc_final: 0.8693 (t0) REVERT: C 103 GLU cc_start: 0.9115 (mp0) cc_final: 0.8770 (mp0) REVERT: C 108 LYS cc_start: 0.8717 (pttm) cc_final: 0.8413 (pttm) REVERT: C 109 LYS cc_start: 0.9253 (tptp) cc_final: 0.9015 (tptt) REVERT: C 166 LEU cc_start: 0.8769 (pt) cc_final: 0.8191 (tp) REVERT: C 178 ILE cc_start: 0.9310 (mp) cc_final: 0.9050 (mp) REVERT: C 199 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9404 (pt0) REVERT: C 261 ASP cc_start: 0.9356 (m-30) cc_final: 0.8674 (p0) REVERT: C 262 LEU cc_start: 0.9782 (tt) cc_final: 0.9567 (tt) REVERT: C 265 GLN cc_start: 0.9571 (tm-30) cc_final: 0.9327 (tm-30) REVERT: C 269 ASP cc_start: 0.9160 (t0) cc_final: 0.8380 (t0) REVERT: C 276 SER cc_start: 0.9195 (m) cc_final: 0.8886 (p) REVERT: C 285 ASN cc_start: 0.9523 (m110) cc_final: 0.9271 (m110) REVERT: C 286 MET cc_start: 0.8899 (mtm) cc_final: 0.8684 (mtt) REVERT: C 297 LEU cc_start: 0.9219 (mm) cc_final: 0.8798 (mm) REVERT: C 298 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 321 LEU cc_start: 0.9752 (mm) cc_final: 0.9468 (mm) REVERT: C 395 GLU cc_start: 0.8857 (pm20) cc_final: 0.8460 (mp0) REVERT: C 450 LYS cc_start: 0.6845 (pttm) cc_final: 0.6315 (ptmm) REVERT: D 28 ASP cc_start: 0.9274 (t0) cc_final: 0.9035 (t0) REVERT: D 59 ILE cc_start: 0.9382 (pt) cc_final: 0.9155 (mp) REVERT: D 65 LEU cc_start: 0.8931 (pt) cc_final: 0.8698 (pt) REVERT: D 66 VAL cc_start: 0.9092 (m) cc_final: 0.8420 (m) REVERT: D 67 SER cc_start: 0.8769 (m) cc_final: 0.8423 (t) REVERT: D 78 MET cc_start: 0.7356 (mpp) cc_final: 0.6353 (mpp) REVERT: D 82 MET cc_start: 0.8876 (tpp) cc_final: 0.8477 (tpp) REVERT: D 88 ILE cc_start: 0.7663 (mt) cc_final: 0.7412 (mt) REVERT: D 103 GLU cc_start: 0.9127 (mp0) cc_final: 0.8792 (mp0) REVERT: D 109 LYS cc_start: 0.8896 (tptp) cc_final: 0.8457 (tptp) REVERT: D 134 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9097 (mmmt) REVERT: D 163 ILE cc_start: 0.9421 (pt) cc_final: 0.9037 (pt) REVERT: D 166 LEU cc_start: 0.8930 (pt) cc_final: 0.8140 (tp) REVERT: D 199 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9365 (mt-10) REVERT: D 261 ASP cc_start: 0.9237 (m-30) cc_final: 0.8500 (p0) REVERT: D 262 LEU cc_start: 0.9774 (tt) cc_final: 0.9281 (mt) REVERT: D 269 ASP cc_start: 0.9240 (t0) cc_final: 0.8314 (t0) REVERT: D 281 ILE cc_start: 0.9416 (mm) cc_final: 0.9152 (mm) REVERT: D 285 ASN cc_start: 0.9500 (m110) cc_final: 0.9210 (m110) REVERT: D 286 MET cc_start: 0.8660 (mtm) cc_final: 0.8393 (mtt) REVERT: D 296 ASN cc_start: 0.9439 (p0) cc_final: 0.8630 (p0) REVERT: D 298 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8131 (mm-40) REVERT: D 305 VAL cc_start: 0.8622 (m) cc_final: 0.7835 (p) REVERT: D 321 LEU cc_start: 0.9751 (mm) cc_final: 0.9446 (mm) REVERT: D 375 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9322 (ptpp) REVERT: D 395 GLU cc_start: 0.8816 (pm20) cc_final: 0.8208 (mp0) REVERT: D 401 PHE cc_start: 0.9302 (p90) cc_final: 0.9080 (p90) REVERT: D 492 LYS cc_start: 0.8517 (tptp) cc_final: 0.8259 (tptp) REVERT: D 493 ARG cc_start: 0.9306 (ttt90) cc_final: 0.9030 (ttm-80) REVERT: E 12 TYR cc_start: 0.9207 (t80) cc_final: 0.8522 (t80) REVERT: E 49 VAL cc_start: 0.8079 (t) cc_final: 0.7702 (m) REVERT: E 66 VAL cc_start: 0.9188 (m) cc_final: 0.8677 (m) REVERT: E 67 SER cc_start: 0.8769 (m) cc_final: 0.8386 (t) REVERT: E 78 MET cc_start: 0.7622 (mpp) cc_final: 0.6794 (mpp) REVERT: E 82 MET cc_start: 0.8900 (tpp) cc_final: 0.8510 (tpp) REVERT: E 93 HIS cc_start: 0.9275 (p90) cc_final: 0.8761 (p90) REVERT: E 94 ASN cc_start: 0.8850 (t0) cc_final: 0.8647 (t0) REVERT: E 105 ARG cc_start: 0.8774 (mtt90) cc_final: 0.8260 (ttp80) REVERT: E 106 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8865 (mtpt) REVERT: E 109 LYS cc_start: 0.8946 (tptp) cc_final: 0.8458 (tptp) REVERT: E 166 LEU cc_start: 0.8790 (pt) cc_final: 0.8086 (tp) REVERT: E 261 ASP cc_start: 0.9323 (m-30) cc_final: 0.8590 (p0) REVERT: E 262 LEU cc_start: 0.9772 (tt) cc_final: 0.9509 (tt) REVERT: E 269 ASP cc_start: 0.9160 (t0) cc_final: 0.8316 (t0) REVERT: E 276 SER cc_start: 0.9083 (m) cc_final: 0.8771 (p) REVERT: E 285 ASN cc_start: 0.9489 (m110) cc_final: 0.9280 (m110) REVERT: E 296 ASN cc_start: 0.9366 (p0) cc_final: 0.8675 (p0) REVERT: E 297 LEU cc_start: 0.9253 (mm) cc_final: 0.8739 (mm) REVERT: E 298 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8147 (mm-40) REVERT: E 321 LEU cc_start: 0.9723 (mm) cc_final: 0.9421 (mm) REVERT: E 489 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7521 (ttpt) REVERT: E 490 PHE cc_start: 0.8889 (m-80) cc_final: 0.8433 (m-80) REVERT: E 492 LYS cc_start: 0.8462 (tptp) cc_final: 0.8163 (tptp) REVERT: E 493 ARG cc_start: 0.9301 (ttt90) cc_final: 0.8993 (ttm-80) REVERT: F 16 ASP cc_start: 0.8346 (m-30) cc_final: 0.8129 (m-30) REVERT: F 65 LEU cc_start: 0.8930 (pt) cc_final: 0.8663 (pt) REVERT: F 66 VAL cc_start: 0.9137 (m) cc_final: 0.8586 (m) REVERT: F 67 SER cc_start: 0.8739 (m) cc_final: 0.8395 (t) REVERT: F 78 MET cc_start: 0.7764 (mpp) cc_final: 0.6901 (mpp) REVERT: F 82 MET cc_start: 0.8846 (tpp) cc_final: 0.8467 (tpp) REVERT: F 88 ILE cc_start: 0.7539 (mt) cc_final: 0.7243 (mp) REVERT: F 94 ASN cc_start: 0.9053 (t0) cc_final: 0.8739 (t0) REVERT: F 103 GLU cc_start: 0.9211 (mp0) cc_final: 0.8781 (mp0) REVERT: F 109 LYS cc_start: 0.8930 (tptp) cc_final: 0.8342 (tptp) REVERT: F 134 LYS cc_start: 0.9332 (mmmt) cc_final: 0.8928 (mmmt) REVERT: F 166 LEU cc_start: 0.8853 (pt) cc_final: 0.8101 (tp) REVERT: F 216 ASP cc_start: 0.9067 (t70) cc_final: 0.8779 (t0) REVERT: F 229 LYS cc_start: 0.9572 (mttm) cc_final: 0.9328 (mmtm) REVERT: F 232 ASP cc_start: 0.8982 (t70) cc_final: 0.8592 (t0) REVERT: F 253 HIS cc_start: 0.9048 (t-90) cc_final: 0.8843 (t-90) REVERT: F 261 ASP cc_start: 0.9321 (m-30) cc_final: 0.8662 (p0) REVERT: F 269 ASP cc_start: 0.9241 (t0) cc_final: 0.8296 (t0) REVERT: F 285 ASN cc_start: 0.9460 (m110) cc_final: 0.9210 (m110) REVERT: F 296 ASN cc_start: 0.9428 (p0) cc_final: 0.8726 (p0) REVERT: F 297 LEU cc_start: 0.9279 (mm) cc_final: 0.8698 (mm) REVERT: F 298 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8212 (mm-40) REVERT: F 321 LEU cc_start: 0.9770 (mm) cc_final: 0.9523 (mm) REVERT: F 351 SER cc_start: 0.9234 (m) cc_final: 0.9022 (p) REVERT: F 375 LYS cc_start: 0.9560 (ptpp) cc_final: 0.9336 (ptpp) REVERT: F 401 PHE cc_start: 0.9284 (p90) cc_final: 0.9077 (p90) REVERT: F 492 LYS cc_start: 0.8514 (tptp) cc_final: 0.8244 (tptp) REVERT: F 493 ARG cc_start: 0.9324 (ttt90) cc_final: 0.9040 (ttm-80) REVERT: G 28 ASP cc_start: 0.9182 (t0) cc_final: 0.8891 (t0) REVERT: G 65 LEU cc_start: 0.8925 (pt) cc_final: 0.8714 (pt) REVERT: G 66 VAL cc_start: 0.9110 (m) cc_final: 0.8516 (m) REVERT: G 67 SER cc_start: 0.8722 (m) cc_final: 0.8351 (t) REVERT: G 78 MET cc_start: 0.7647 (mpp) cc_final: 0.7067 (mpp) REVERT: G 82 MET cc_start: 0.8868 (tpp) cc_final: 0.8511 (tpp) REVERT: G 93 HIS cc_start: 0.9277 (p90) cc_final: 0.8710 (p90) REVERT: G 94 ASN cc_start: 0.8867 (t0) cc_final: 0.8584 (t0) REVERT: G 103 GLU cc_start: 0.9200 (mp0) cc_final: 0.8907 (mp0) REVERT: G 109 LYS cc_start: 0.9048 (tptp) cc_final: 0.8755 (tptp) REVERT: G 166 LEU cc_start: 0.8834 (pt) cc_final: 0.8185 (tp) REVERT: G 262 LEU cc_start: 0.9775 (tt) cc_final: 0.9451 (mt) REVERT: G 269 ASP cc_start: 0.9195 (t0) cc_final: 0.8317 (t0) REVERT: G 276 SER cc_start: 0.9109 (m) cc_final: 0.8809 (p) REVERT: G 285 ASN cc_start: 0.9548 (m110) cc_final: 0.9311 (m110) REVERT: G 296 ASN cc_start: 0.9337 (p0) cc_final: 0.8672 (p0) REVERT: G 297 LEU cc_start: 0.9213 (mm) cc_final: 0.8718 (mm) REVERT: G 298 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8325 (mm-40) REVERT: G 321 LEU cc_start: 0.9730 (mm) cc_final: 0.9441 (mm) REVERT: G 369 ASN cc_start: 0.9277 (p0) cc_final: 0.9021 (p0) REVERT: G 401 PHE cc_start: 0.9302 (p90) cc_final: 0.9043 (p90) REVERT: G 479 VAL cc_start: 0.9461 (p) cc_final: 0.9213 (t) REVERT: G 482 MET cc_start: 0.8930 (tmm) cc_final: 0.8722 (tmm) REVERT: G 490 PHE cc_start: 0.8794 (m-80) cc_final: 0.8011 (m-80) REVERT: G 493 ARG cc_start: 0.9293 (ttt90) cc_final: 0.8752 (ttm-80) REVERT: H 59 ILE cc_start: 0.9400 (pt) cc_final: 0.9150 (mp) REVERT: H 65 LEU cc_start: 0.8888 (pt) cc_final: 0.8644 (pt) REVERT: H 66 VAL cc_start: 0.9167 (m) cc_final: 0.8741 (m) REVERT: H 67 SER cc_start: 0.8733 (m) cc_final: 0.8390 (t) REVERT: H 78 MET cc_start: 0.7408 (mpp) cc_final: 0.6632 (mpp) REVERT: H 82 MET cc_start: 0.8862 (tpp) cc_final: 0.8467 (tpp) REVERT: H 109 LYS cc_start: 0.9014 (tptp) cc_final: 0.8591 (tptp) REVERT: H 130 VAL cc_start: 0.9509 (m) cc_final: 0.9087 (m) REVERT: H 134 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8896 (mmmt) REVERT: H 166 LEU cc_start: 0.8939 (pt) cc_final: 0.8179 (tp) REVERT: H 181 LYS cc_start: 0.9267 (mmpt) cc_final: 0.8959 (mmpt) REVERT: H 199 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9408 (pt0) REVERT: H 261 ASP cc_start: 0.9216 (m-30) cc_final: 0.8466 (p0) REVERT: H 262 LEU cc_start: 0.9738 (tt) cc_final: 0.9224 (mt) REVERT: H 269 ASP cc_start: 0.9203 (t0) cc_final: 0.8263 (t0) REVERT: H 285 ASN cc_start: 0.9497 (m110) cc_final: 0.9243 (m110) REVERT: H 286 MET cc_start: 0.8733 (mtm) cc_final: 0.8513 (mtt) REVERT: H 296 ASN cc_start: 0.9438 (p0) cc_final: 0.8719 (p0) REVERT: H 298 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8163 (mm-40) REVERT: H 321 LEU cc_start: 0.9738 (mm) cc_final: 0.9482 (mm) REVERT: H 352 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8326 (mm-30) REVERT: H 357 PHE cc_start: 0.9173 (m-80) cc_final: 0.8788 (m-10) REVERT: H 375 LYS cc_start: 0.9546 (ptpp) cc_final: 0.9320 (ptpp) REVERT: H 395 GLU cc_start: 0.8859 (pm20) cc_final: 0.8472 (mp0) REVERT: H 401 PHE cc_start: 0.9271 (p90) cc_final: 0.9068 (p90) REVERT: H 489 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7512 (ttpt) REVERT: H 490 PHE cc_start: 0.9022 (m-80) cc_final: 0.8656 (m-80) REVERT: H 493 ARG cc_start: 0.9340 (ttt90) cc_final: 0.8983 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 1324 average time/residue: 0.1640 time to fit residues: 348.5135 Evaluate side-chains 1052 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1052 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 0.6980 chunk 203 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 230 ASN A 343 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS 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 ** 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** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091324 restraints weight = 54072.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095399 restraints weight = 34658.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098480 restraints weight = 24916.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.100865 restraints weight = 19338.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102589 restraints weight = 15833.565| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28872 Z= 0.150 Angle : 0.871 10.641 39136 Z= 0.419 Chirality : 0.050 0.210 4472 Planarity : 0.004 0.038 4928 Dihedral : 17.036 169.076 4120 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.37 % 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: -2.83 (0.13), residues: 3576 helix: -1.27 (0.14), residues: 1224 sheet: -3.22 (0.19), residues: 424 loop : -1.95 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 480 TYR 0.024 0.002 TYR F 484 PHE 0.031 0.002 PHE E 456 HIS 0.009 0.001 HIS H 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (28864) covalent geometry : angle 0.87079 / 0.42 (39136) hydrogen bonds : bond 0.03775 / 2.54 ( 888) hydrogen bonds : angle 5.81380 / 3.90 ( 2448) Misc. bond : bond 0.00199 / 0.12 ( 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 1350 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1349 time to evaluate : 1.047 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: A 28 ASP cc_start: 0.9208 (t0) cc_final: 0.8971 (t0) REVERT: A 65 LEU cc_start: 0.8938 (pt) cc_final: 0.8728 (pt) REVERT: A 67 SER cc_start: 0.8622 (m) cc_final: 0.8240 (t) REVERT: A 78 MET cc_start: 0.7504 (mpp) cc_final: 0.7065 (mpp) REVERT: A 82 MET cc_start: 0.8991 (tpp) cc_final: 0.8626 (tpp) REVERT: A 93 HIS cc_start: 0.9311 (p90) cc_final: 0.8725 (p90) REVERT: A 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8563 (t0) REVERT: A 139 PHE cc_start: 0.8652 (p90) cc_final: 0.8010 (p90) REVERT: A 166 LEU cc_start: 0.8870 (pt) cc_final: 0.8163 (tp) REVERT: A 174 PHE cc_start: 0.8900 (m-80) cc_final: 0.8674 (m-80) REVERT: A 199 GLU cc_start: 0.9629 (mt-10) cc_final: 0.9426 (pt0) REVERT: A 230 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8720 (m-40) REVERT: A 241 LYS cc_start: 0.9396 (tptp) cc_final: 0.9102 (tptp) REVERT: A 262 LEU cc_start: 0.9786 (tt) cc_final: 0.9432 (mt) REVERT: A 269 ASP cc_start: 0.9163 (t0) cc_final: 0.8258 (t0) REVERT: A 276 SER cc_start: 0.9178 (m) cc_final: 0.8856 (p) REVERT: A 285 ASN cc_start: 0.9541 (m110) cc_final: 0.9295 (m110) REVERT: A 296 ASN cc_start: 0.9335 (p0) cc_final: 0.8580 (p0) REVERT: A 297 LEU cc_start: 0.9160 (mm) cc_final: 0.8737 (mm) REVERT: A 298 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8353 (mm110) REVERT: A 321 LEU cc_start: 0.9728 (mm) cc_final: 0.9463 (mm) REVERT: A 368 GLN cc_start: 0.9101 (mp10) cc_final: 0.8882 (mp-120) REVERT: A 479 VAL cc_start: 0.9460 (m) cc_final: 0.9201 (t) REVERT: A 489 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7022 (ttpt) REVERT: A 490 PHE cc_start: 0.8871 (m-80) cc_final: 0.8502 (m-80) REVERT: A 492 LYS cc_start: 0.8448 (tptp) cc_final: 0.8159 (tptp) REVERT: B 65 LEU cc_start: 0.8913 (pt) cc_final: 0.8552 (pt) REVERT: B 66 VAL cc_start: 0.9143 (m) cc_final: 0.8711 (m) REVERT: B 78 MET cc_start: 0.7574 (mpp) cc_final: 0.6632 (mpp) REVERT: B 82 MET cc_start: 0.8894 (tpp) cc_final: 0.8483 (tpp) REVERT: B 93 HIS cc_start: 0.9326 (p90) cc_final: 0.8754 (p90) REVERT: B 94 ASN cc_start: 0.8928 (t0) cc_final: 0.8704 (t0) REVERT: B 109 LYS cc_start: 0.8798 (tptp) cc_final: 0.8265 (tptp) REVERT: B 127 VAL cc_start: 0.9100 (t) cc_final: 0.8678 (t) REVERT: B 134 LYS cc_start: 0.9430 (tppt) cc_final: 0.9224 (mmtt) REVERT: B 139 PHE cc_start: 0.8399 (p90) cc_final: 0.8132 (p90) REVERT: B 166 LEU cc_start: 0.8904 (pt) cc_final: 0.8184 (tp) REVERT: B 199 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9379 (mt-10) REVERT: B 229 LYS cc_start: 0.9409 (mttt) cc_final: 0.9026 (mttt) REVERT: B 261 ASP cc_start: 0.9264 (m-30) cc_final: 0.8705 (p0) REVERT: B 269 ASP cc_start: 0.9271 (t0) cc_final: 0.8254 (t0) REVERT: B 281 ILE cc_start: 0.9379 (mm) cc_final: 0.9154 (mm) REVERT: B 285 ASN cc_start: 0.9494 (m110) cc_final: 0.9200 (m110) REVERT: B 286 MET cc_start: 0.8627 (mtm) cc_final: 0.8386 (mtt) REVERT: B 296 ASN cc_start: 0.9420 (p0) cc_final: 0.8704 (p0) REVERT: B 297 LEU cc_start: 0.9227 (mm) cc_final: 0.8737 (mm) REVERT: B 298 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8226 (mm110) REVERT: B 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9479 (mm) REVERT: B 364 ASP cc_start: 0.8391 (t0) cc_final: 0.8113 (t0) REVERT: B 372 HIS cc_start: 0.9465 (m90) cc_final: 0.9072 (m170) REVERT: B 375 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9276 (ptpp) REVERT: B 493 ARG cc_start: 0.9257 (ttt90) cc_final: 0.8999 (ttm-80) REVERT: C 65 LEU cc_start: 0.8962 (pt) cc_final: 0.8753 (pt) REVERT: C 67 SER cc_start: 0.8671 (m) cc_final: 0.8362 (t) REVERT: C 78 MET cc_start: 0.7845 (mpp) cc_final: 0.6878 (mpp) REVERT: C 82 MET cc_start: 0.9028 (tpp) cc_final: 0.8672 (tpp) REVERT: C 94 ASN cc_start: 0.8878 (t0) cc_final: 0.8664 (t0) REVERT: C 109 LYS cc_start: 0.9284 (tptp) cc_final: 0.9061 (tptp) REVERT: C 134 LYS cc_start: 0.9509 (tppt) cc_final: 0.9287 (mmtt) REVERT: C 139 PHE cc_start: 0.8758 (p90) cc_final: 0.8113 (p90) REVERT: C 162 ASP cc_start: 0.9154 (m-30) cc_final: 0.8947 (m-30) REVERT: C 166 LEU cc_start: 0.8765 (pt) cc_final: 0.8105 (tp) REVERT: C 181 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9169 (mmpt) REVERT: C 216 ASP cc_start: 0.8985 (t70) cc_final: 0.8685 (t70) REVERT: C 261 ASP cc_start: 0.9334 (m-30) cc_final: 0.8718 (p0) REVERT: C 262 LEU cc_start: 0.9756 (tt) cc_final: 0.9490 (tt) REVERT: C 269 ASP cc_start: 0.9165 (t0) cc_final: 0.8299 (t0) REVERT: C 276 SER cc_start: 0.9209 (m) cc_final: 0.8908 (p) REVERT: C 281 ILE cc_start: 0.9404 (mm) cc_final: 0.9199 (mm) REVERT: C 285 ASN cc_start: 0.9514 (m110) cc_final: 0.9246 (m110) REVERT: C 286 MET cc_start: 0.8852 (mtm) cc_final: 0.8506 (mtt) REVERT: C 297 LEU cc_start: 0.9156 (mm) cc_final: 0.8608 (mm) REVERT: C 298 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8250 (mm-40) REVERT: C 321 LEU cc_start: 0.9739 (mm) cc_final: 0.9462 (mm) REVERT: C 364 ASP cc_start: 0.8735 (t0) cc_final: 0.8171 (t0) REVERT: C 372 HIS cc_start: 0.9496 (m90) cc_final: 0.8968 (m90) REVERT: C 450 LYS cc_start: 0.6864 (pttm) cc_final: 0.6325 (ptmm) REVERT: C 489 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7078 (ttpt) REVERT: C 490 PHE cc_start: 0.8831 (m-80) cc_final: 0.8593 (m-80) REVERT: D 28 ASP cc_start: 0.9307 (t0) cc_final: 0.9035 (t0) REVERT: D 65 LEU cc_start: 0.8880 (pt) cc_final: 0.8526 (pt) REVERT: D 66 VAL cc_start: 0.9110 (m) cc_final: 0.8547 (m) REVERT: D 78 MET cc_start: 0.7856 (mpp) cc_final: 0.6937 (mpp) REVERT: D 82 MET cc_start: 0.8961 (tpp) cc_final: 0.8564 (tpp) REVERT: D 88 ILE cc_start: 0.7867 (mt) cc_final: 0.7643 (mt) REVERT: D 94 ASN cc_start: 0.8908 (t0) cc_final: 0.8692 (t0) REVERT: D 130 VAL cc_start: 0.9514 (m) cc_final: 0.9040 (m) REVERT: D 134 LYS cc_start: 0.9412 (mmmt) cc_final: 0.8984 (mmmt) REVERT: D 166 LEU cc_start: 0.8913 (pt) cc_final: 0.8163 (tp) REVERT: D 181 LYS cc_start: 0.9286 (mmpt) cc_final: 0.9048 (mmmt) REVERT: D 261 ASP cc_start: 0.9228 (m-30) cc_final: 0.8476 (p0) REVERT: D 262 LEU cc_start: 0.9757 (tt) cc_final: 0.9133 (mt) REVERT: D 269 ASP cc_start: 0.9232 (t0) cc_final: 0.8507 (t70) REVERT: D 276 SER cc_start: 0.9076 (m) cc_final: 0.8798 (p) REVERT: D 281 ILE cc_start: 0.9380 (mm) cc_final: 0.9130 (mm) REVERT: D 285 ASN cc_start: 0.9517 (m110) cc_final: 0.9218 (m110) REVERT: D 286 MET cc_start: 0.8664 (mtm) cc_final: 0.8315 (mtt) REVERT: D 296 ASN cc_start: 0.9471 (p0) cc_final: 0.8749 (p0) REVERT: D 297 LEU cc_start: 0.9163 (mm) cc_final: 0.8858 (mm) REVERT: D 298 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8268 (mm110) REVERT: D 321 LEU cc_start: 0.9736 (mm) cc_final: 0.9442 (mm) REVERT: D 353 TYR cc_start: 0.9261 (t80) cc_final: 0.8986 (t80) REVERT: D 364 ASP cc_start: 0.8453 (t0) cc_final: 0.8150 (t0) REVERT: D 372 HIS cc_start: 0.9496 (m90) cc_final: 0.8970 (m90) REVERT: D 395 GLU cc_start: 0.8911 (pm20) cc_final: 0.8653 (pm20) REVERT: D 401 PHE cc_start: 0.9334 (p90) cc_final: 0.9125 (p90) REVERT: D 489 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7242 (ttpt) REVERT: D 490 PHE cc_start: 0.8982 (m-80) cc_final: 0.8112 (m-80) REVERT: D 492 LYS cc_start: 0.8649 (tptp) cc_final: 0.8442 (tptp) REVERT: E 12 TYR cc_start: 0.9257 (t80) cc_final: 0.8553 (t80) REVERT: E 65 LEU cc_start: 0.8945 (pt) cc_final: 0.8739 (pt) REVERT: E 66 VAL cc_start: 0.9148 (m) cc_final: 0.8379 (m) REVERT: E 67 SER cc_start: 0.8707 (m) cc_final: 0.8152 (t) REVERT: E 78 MET cc_start: 0.7515 (mpp) cc_final: 0.7033 (mpp) REVERT: E 82 MET cc_start: 0.8945 (tpp) cc_final: 0.8565 (tpp) REVERT: E 93 HIS cc_start: 0.9282 (p90) cc_final: 0.8748 (p90) REVERT: E 94 ASN cc_start: 0.8827 (t0) cc_final: 0.8587 (t0) REVERT: E 103 GLU cc_start: 0.9325 (mp0) cc_final: 0.9114 (mp0) REVERT: E 109 LYS cc_start: 0.9092 (tptp) cc_final: 0.8850 (tptp) REVERT: E 139 PHE cc_start: 0.8566 (p90) cc_final: 0.8293 (p90) REVERT: E 166 LEU cc_start: 0.8836 (pt) cc_final: 0.8103 (tp) REVERT: E 174 PHE cc_start: 0.8837 (m-80) cc_final: 0.8623 (m-80) REVERT: E 229 LYS cc_start: 0.9421 (mttt) cc_final: 0.9016 (mttt) REVERT: E 261 ASP cc_start: 0.9306 (m-30) cc_final: 0.8645 (p0) REVERT: E 262 LEU cc_start: 0.9771 (tt) cc_final: 0.9544 (tt) REVERT: E 265 GLN cc_start: 0.9565 (tm-30) cc_final: 0.9291 (tm-30) REVERT: E 269 ASP cc_start: 0.9153 (t0) cc_final: 0.8278 (t0) REVERT: E 296 ASN cc_start: 0.9377 (p0) cc_final: 0.8674 (p0) REVERT: E 297 LEU cc_start: 0.9255 (mm) cc_final: 0.8754 (mm) REVERT: E 298 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8148 (mm-40) REVERT: E 364 ASP cc_start: 0.8995 (t0) cc_final: 0.8414 (t0) REVERT: E 450 LYS cc_start: 0.7266 (pttm) cc_final: 0.6129 (ptmm) REVERT: E 489 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7433 (ttpt) REVERT: E 490 PHE cc_start: 0.8984 (m-80) cc_final: 0.8533 (m-80) REVERT: E 492 LYS cc_start: 0.8610 (tptp) cc_final: 0.8273 (tptp) REVERT: F 65 LEU cc_start: 0.8865 (pt) cc_final: 0.8476 (pt) REVERT: F 66 VAL cc_start: 0.9099 (m) cc_final: 0.8400 (m) REVERT: F 78 MET cc_start: 0.8022 (mpp) cc_final: 0.7258 (mpp) REVERT: F 82 MET cc_start: 0.8905 (tpp) cc_final: 0.8525 (tpp) REVERT: F 88 ILE cc_start: 0.7926 (mt) cc_final: 0.7603 (mp) REVERT: F 103 GLU cc_start: 0.9421 (mp0) cc_final: 0.9141 (mp0) REVERT: F 134 LYS cc_start: 0.9341 (mmmt) cc_final: 0.8958 (mmmt) REVERT: F 166 LEU cc_start: 0.8872 (pt) cc_final: 0.8100 (tp) REVERT: F 216 ASP cc_start: 0.9050 (t70) cc_final: 0.8780 (t0) REVERT: F 261 ASP cc_start: 0.9231 (m-30) cc_final: 0.8615 (p0) REVERT: F 262 LEU cc_start: 0.9719 (tt) cc_final: 0.9467 (tt) REVERT: F 269 ASP cc_start: 0.9195 (t0) cc_final: 0.8274 (t0) REVERT: F 296 ASN cc_start: 0.9414 (p0) cc_final: 0.8664 (p0) REVERT: F 297 LEU cc_start: 0.9260 (mm) cc_final: 0.8769 (mm) REVERT: F 298 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8280 (mm110) REVERT: F 321 LEU cc_start: 0.9751 (mm) cc_final: 0.9505 (mm) REVERT: F 353 TYR cc_start: 0.9233 (t80) cc_final: 0.8834 (t80) REVERT: F 364 ASP cc_start: 0.8448 (t0) cc_final: 0.8164 (t0) REVERT: F 372 HIS cc_start: 0.9489 (m90) cc_final: 0.8949 (m90) REVERT: F 401 PHE cc_start: 0.9291 (p90) cc_final: 0.9071 (p90) REVERT: F 456 PHE cc_start: 0.9645 (t80) cc_final: 0.9434 (t80) REVERT: F 492 LYS cc_start: 0.8570 (tptp) cc_final: 0.8253 (tptp) REVERT: G 65 LEU cc_start: 0.8917 (pt) cc_final: 0.8709 (pt) REVERT: G 66 VAL cc_start: 0.9136 (m) cc_final: 0.8602 (m) REVERT: G 78 MET cc_start: 0.7487 (mpp) cc_final: 0.6641 (mpp) REVERT: G 82 MET cc_start: 0.8926 (tpp) cc_final: 0.8591 (tpp) REVERT: G 94 ASN cc_start: 0.8874 (t0) cc_final: 0.8623 (t0) REVERT: G 109 LYS cc_start: 0.9162 (tptp) cc_final: 0.8828 (tptp) REVERT: G 134 LYS cc_start: 0.9480 (tppt) cc_final: 0.9258 (mmtt) REVERT: G 139 PHE cc_start: 0.8536 (p90) cc_final: 0.8253 (p90) REVERT: G 166 LEU cc_start: 0.8855 (pt) cc_final: 0.8181 (tp) REVERT: G 174 PHE cc_start: 0.8944 (m-80) cc_final: 0.8736 (m-80) REVERT: G 178 ILE cc_start: 0.9335 (mp) cc_final: 0.9028 (mp) REVERT: G 262 LEU cc_start: 0.9779 (tt) cc_final: 0.9447 (mt) REVERT: G 269 ASP cc_start: 0.9193 (t0) cc_final: 0.8313 (t0) REVERT: G 276 SER cc_start: 0.9101 (m) cc_final: 0.8793 (p) REVERT: G 285 ASN cc_start: 0.9555 (m110) cc_final: 0.9333 (m110) REVERT: G 296 ASN cc_start: 0.9357 (p0) cc_final: 0.8687 (p0) REVERT: G 297 LEU cc_start: 0.9194 (mm) cc_final: 0.8750 (mm) REVERT: G 298 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8289 (mm110) REVERT: G 369 ASN cc_start: 0.9229 (p0) cc_final: 0.8988 (p0) REVERT: G 401 PHE cc_start: 0.9214 (p90) cc_final: 0.8977 (p90) REVERT: G 490 PHE cc_start: 0.8852 (m-80) cc_final: 0.8175 (m-80) REVERT: G 493 ARG cc_start: 0.9243 (ttt90) cc_final: 0.8989 (ttm-80) REVERT: H 28 ASP cc_start: 0.9312 (t0) cc_final: 0.9048 (t0) REVERT: H 58 LYS cc_start: 0.9690 (mmpt) cc_final: 0.9489 (mmmm) REVERT: H 66 VAL cc_start: 0.9132 (m) cc_final: 0.8717 (m) REVERT: H 67 SER cc_start: 0.8655 (m) cc_final: 0.8288 (t) REVERT: H 78 MET cc_start: 0.7535 (mpp) cc_final: 0.6359 (mpp) REVERT: H 82 MET cc_start: 0.8909 (tpp) cc_final: 0.8488 (tpp) REVERT: H 93 HIS cc_start: 0.9315 (p90) cc_final: 0.8742 (p90) REVERT: H 94 ASN cc_start: 0.8894 (t0) cc_final: 0.8653 (t0) REVERT: H 130 VAL cc_start: 0.9532 (m) cc_final: 0.9072 (m) REVERT: H 134 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9041 (mmmt) REVERT: H 161 ARG cc_start: 0.9475 (mtm180) cc_final: 0.9262 (mtm110) REVERT: H 166 LEU cc_start: 0.8774 (pt) cc_final: 0.7708 (tp) REVERT: H 181 LYS cc_start: 0.9241 (mmpt) cc_final: 0.8878 (mmpt) REVERT: H 199 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9354 (pt0) REVERT: H 214 GLU cc_start: 0.9221 (pm20) cc_final: 0.8972 (pm20) REVERT: H 261 ASP cc_start: 0.9184 (m-30) cc_final: 0.8509 (p0) REVERT: H 262 LEU cc_start: 0.9719 (tt) cc_final: 0.9384 (tt) REVERT: H 269 ASP cc_start: 0.9239 (t0) cc_final: 0.8228 (t0) REVERT: H 285 ASN cc_start: 0.9508 (m110) cc_final: 0.9298 (m110) REVERT: H 286 MET cc_start: 0.8740 (mtm) cc_final: 0.8514 (mtt) REVERT: H 296 ASN cc_start: 0.9431 (p0) cc_final: 0.8722 (p0) REVERT: H 297 LEU cc_start: 0.9227 (mm) cc_final: 0.8725 (mm) REVERT: H 298 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8208 (mm110) REVERT: H 364 ASP cc_start: 0.8863 (t0) cc_final: 0.8318 (t0) REVERT: H 372 HIS cc_start: 0.9530 (m170) cc_final: 0.9328 (m170) REVERT: H 395 GLU cc_start: 0.8882 (pm20) cc_final: 0.8139 (mp0) REVERT: H 450 LYS cc_start: 0.7177 (pttm) cc_final: 0.6113 (ptmm) REVERT: H 489 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7816 (ttpt) REVERT: H 490 PHE cc_start: 0.9115 (m-80) cc_final: 0.8693 (m-80) REVERT: H 493 ARG cc_start: 0.9280 (ttt90) cc_final: 0.9031 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 1349 average time/residue: 0.1647 time to fit residues: 361.4479 Evaluate side-chains 1065 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1064 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 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** ** 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 343 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091361 restraints weight = 54330.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095449 restraints weight = 34790.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098534 restraints weight = 25085.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100839 restraints weight = 19484.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102724 restraints weight = 16009.255| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28872 Z= 0.145 Angle : 0.867 11.224 39136 Z= 0.416 Chirality : 0.050 0.225 4472 Planarity : 0.005 0.063 4928 Dihedral : 16.739 169.582 4120 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.13), residues: 3576 helix: -1.12 (0.14), residues: 1224 sheet: -3.24 (0.21), residues: 344 loop : -1.90 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 480 TYR 0.028 0.002 TYR D 233 PHE 0.050 0.002 PHE A 456 HIS 0.004 0.001 HIS G 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (28864) covalent geometry : angle 0.86723 / 0.42 (39136) hydrogen bonds : bond 0.03676 / 2.43 ( 888) hydrogen bonds : angle 5.70235 / 3.83 ( 2448) Misc. bond : bond 0.00202 / 0.12 ( 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 1358 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1354 time to evaluate : 1.014 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: A 28 ASP cc_start: 0.9225 (t0) cc_final: 0.9002 (t0) REVERT: A 66 VAL cc_start: 0.8940 (m) cc_final: 0.8356 (m) REVERT: A 78 MET cc_start: 0.7530 (mpp) cc_final: 0.6884 (mpp) REVERT: A 82 MET cc_start: 0.8916 (tpp) cc_final: 0.8673 (tpp) REVERT: A 94 ASN cc_start: 0.8879 (t0) cc_final: 0.8633 (t0) REVERT: A 102 ASN cc_start: 0.9404 (t0) cc_final: 0.9176 (m-40) REVERT: A 105 ARG cc_start: 0.9010 (mmt-90) cc_final: 0.8798 (mmt90) REVERT: A 108 LYS cc_start: 0.9341 (tptp) cc_final: 0.9135 (ptpp) REVERT: A 158 ILE cc_start: 0.9103 (mm) cc_final: 0.8902 (mm) REVERT: A 166 LEU cc_start: 0.8966 (pt) cc_final: 0.8285 (tp) REVERT: A 199 GLU cc_start: 0.9622 (mt-10) cc_final: 0.9404 (mt-10) REVERT: A 229 LYS cc_start: 0.9465 (mttt) cc_final: 0.9127 (mttt) REVERT: A 241 LYS cc_start: 0.9423 (tptp) cc_final: 0.9138 (tptp) REVERT: A 262 LEU cc_start: 0.9795 (tt) cc_final: 0.9437 (mt) REVERT: A 269 ASP cc_start: 0.9164 (t0) cc_final: 0.8319 (t0) REVERT: A 276 SER cc_start: 0.9186 (m) cc_final: 0.8856 (p) REVERT: A 285 ASN cc_start: 0.9557 (m110) cc_final: 0.9319 (m110) REVERT: A 296 ASN cc_start: 0.9359 (p0) cc_final: 0.8649 (p0) REVERT: A 297 LEU cc_start: 0.9048 (mm) cc_final: 0.8593 (mm) REVERT: A 298 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8306 (mm110) REVERT: A 372 HIS cc_start: 0.9482 (m90) cc_final: 0.8849 (m90) REVERT: A 402 PHE cc_start: 0.8072 (m-80) cc_final: 0.7701 (m-80) REVERT: A 489 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7909 (ttmt) REVERT: A 490 PHE cc_start: 0.8850 (m-80) cc_final: 0.8452 (m-80) REVERT: B 66 VAL cc_start: 0.9073 (m) cc_final: 0.8675 (m) REVERT: B 67 SER cc_start: 0.9454 (t) cc_final: 0.9041 (t) REVERT: B 78 MET cc_start: 0.7508 (mpp) cc_final: 0.6714 (mpp) REVERT: B 82 MET cc_start: 0.8802 (tpp) cc_final: 0.8361 (tpp) REVERT: B 93 HIS cc_start: 0.9380 (p90) cc_final: 0.8746 (p90) REVERT: B 94 ASN cc_start: 0.8883 (t0) cc_final: 0.8663 (t0) REVERT: B 109 LYS cc_start: 0.8796 (tptp) cc_final: 0.8473 (tptp) REVERT: B 154 LEU cc_start: 0.9567 (mm) cc_final: 0.9364 (mm) REVERT: B 166 LEU cc_start: 0.8987 (pt) cc_final: 0.8296 (tp) REVERT: B 215 ASP cc_start: 0.9063 (m-30) cc_final: 0.8781 (t0) REVERT: B 216 ASP cc_start: 0.9044 (t0) cc_final: 0.8793 (t70) REVERT: B 229 LYS cc_start: 0.9443 (mttt) cc_final: 0.8814 (mttt) REVERT: B 242 LYS cc_start: 0.8777 (tptm) cc_final: 0.8448 (tptp) REVERT: B 253 HIS cc_start: 0.9015 (t-90) cc_final: 0.8646 (t70) REVERT: B 255 ASP cc_start: 0.9592 (p0) cc_final: 0.9254 (p0) REVERT: B 261 ASP cc_start: 0.9228 (m-30) cc_final: 0.8651 (p0) REVERT: B 269 ASP cc_start: 0.9182 (t0) cc_final: 0.8326 (t70) REVERT: B 292 ASP cc_start: 0.9723 (m-30) cc_final: 0.9487 (m-30) REVERT: B 296 ASN cc_start: 0.9449 (p0) cc_final: 0.8612 (p0) REVERT: B 297 LEU cc_start: 0.9084 (mm) cc_final: 0.8602 (mm) REVERT: B 298 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8267 (mm110) REVERT: B 372 HIS cc_start: 0.9460 (m90) cc_final: 0.8935 (m90) REVERT: B 465 GLN cc_start: 0.9184 (mt0) cc_final: 0.8841 (pt0) REVERT: B 489 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7264 (ttpt) REVERT: B 490 PHE cc_start: 0.8957 (m-80) cc_final: 0.8611 (m-80) REVERT: B 493 ARG cc_start: 0.9233 (ttt90) cc_final: 0.8885 (ttm-80) REVERT: C 65 LEU cc_start: 0.8826 (pt) cc_final: 0.8622 (pt) REVERT: C 66 VAL cc_start: 0.8844 (m) cc_final: 0.8165 (m) REVERT: C 75 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7595 (tm-30) REVERT: C 78 MET cc_start: 0.7977 (mpp) cc_final: 0.6809 (mpp) REVERT: C 82 MET cc_start: 0.8923 (tpp) cc_final: 0.8666 (tpp) REVERT: C 94 ASN cc_start: 0.8836 (t0) cc_final: 0.8615 (t0) REVERT: C 166 LEU cc_start: 0.8800 (pt) cc_final: 0.8087 (tp) REVERT: C 174 PHE cc_start: 0.9115 (m-80) cc_final: 0.8807 (m-80) REVERT: C 216 ASP cc_start: 0.8973 (t70) cc_final: 0.8693 (t70) REVERT: C 242 LYS cc_start: 0.8789 (tptm) cc_final: 0.8521 (tptp) REVERT: C 269 ASP cc_start: 0.9095 (t0) cc_final: 0.8184 (t70) REVERT: C 276 SER cc_start: 0.9230 (m) cc_final: 0.8887 (p) REVERT: C 286 MET cc_start: 0.8946 (mtm) cc_final: 0.8537 (mtt) REVERT: C 297 LEU cc_start: 0.9083 (mm) cc_final: 0.8582 (mm) REVERT: C 298 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8177 (mm110) REVERT: C 364 ASP cc_start: 0.8815 (t0) cc_final: 0.8610 (t0) REVERT: C 372 HIS cc_start: 0.9482 (m90) cc_final: 0.8901 (m90) REVERT: C 395 GLU cc_start: 0.9235 (pm20) cc_final: 0.8831 (pm20) REVERT: C 450 LYS cc_start: 0.6788 (pttm) cc_final: 0.6275 (ptmm) REVERT: C 489 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7844 (ttpt) REVERT: C 490 PHE cc_start: 0.8935 (m-80) cc_final: 0.8611 (m-80) REVERT: D 66 VAL cc_start: 0.9040 (m) cc_final: 0.8510 (m) REVERT: D 67 SER cc_start: 0.9500 (t) cc_final: 0.9086 (t) REVERT: D 75 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7256 (tm-30) REVERT: D 78 MET cc_start: 0.7769 (mpp) cc_final: 0.6952 (mpp) REVERT: D 82 MET cc_start: 0.8862 (tpp) cc_final: 0.8444 (tpp) REVERT: D 88 ILE cc_start: 0.8021 (mt) cc_final: 0.7755 (mt) REVERT: D 94 ASN cc_start: 0.8864 (t0) cc_final: 0.8645 (t0) REVERT: D 166 LEU cc_start: 0.8977 (pt) cc_final: 0.8238 (tp) REVERT: D 242 LYS cc_start: 0.8825 (tptm) cc_final: 0.8515 (tptp) REVERT: D 261 ASP cc_start: 0.9152 (m-30) cc_final: 0.8452 (p0) REVERT: D 262 LEU cc_start: 0.9720 (tt) cc_final: 0.9444 (tt) REVERT: D 269 ASP cc_start: 0.9303 (t0) cc_final: 0.8681 (t70) REVERT: D 276 SER cc_start: 0.9137 (m) cc_final: 0.8855 (p) REVERT: D 286 MET cc_start: 0.8709 (mtm) cc_final: 0.8499 (mtt) REVERT: D 296 ASN cc_start: 0.9503 (p0) cc_final: 0.8962 (p0) REVERT: D 297 LEU cc_start: 0.9049 (mm) cc_final: 0.8527 (mm) REVERT: D 298 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8323 (mm110) REVERT: D 353 TYR cc_start: 0.9182 (t80) cc_final: 0.8848 (t80) REVERT: D 372 HIS cc_start: 0.9484 (m90) cc_final: 0.8869 (m90) REVERT: D 490 PHE cc_start: 0.8980 (m-80) cc_final: 0.8105 (m-80) REVERT: E 12 TYR cc_start: 0.9291 (t80) cc_final: 0.8610 (t80) REVERT: E 78 MET cc_start: 0.7574 (mpp) cc_final: 0.6854 (mpp) REVERT: E 88 ILE cc_start: 0.7321 (pt) cc_final: 0.6798 (pt) REVERT: E 93 HIS cc_start: 0.9285 (p90) cc_final: 0.8731 (p90) REVERT: E 94 ASN cc_start: 0.8818 (t0) cc_final: 0.8592 (t0) REVERT: E 166 LEU cc_start: 0.8959 (pt) cc_final: 0.8269 (tp) REVERT: E 174 PHE cc_start: 0.8952 (m-80) cc_final: 0.8748 (m-80) REVERT: E 229 LYS cc_start: 0.9430 (mttt) cc_final: 0.8766 (mttt) REVERT: E 261 ASP cc_start: 0.9314 (m-30) cc_final: 0.8638 (p0) REVERT: E 262 LEU cc_start: 0.9758 (tt) cc_final: 0.9526 (tt) REVERT: E 269 ASP cc_start: 0.9168 (t0) cc_final: 0.8343 (t0) REVERT: E 296 ASN cc_start: 0.9384 (p0) cc_final: 0.8638 (p0) REVERT: E 298 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8219 (mm110) REVERT: E 372 HIS cc_start: 0.9379 (m90) cc_final: 0.8879 (m90) REVERT: E 450 LYS cc_start: 0.6958 (pttm) cc_final: 0.6178 (ptmm) REVERT: E 490 PHE cc_start: 0.8964 (m-80) cc_final: 0.8759 (m-80) REVERT: F 28 ASP cc_start: 0.9241 (t0) cc_final: 0.9007 (t0) REVERT: F 66 VAL cc_start: 0.8998 (m) cc_final: 0.8336 (m) REVERT: F 67 SER cc_start: 0.9455 (t) cc_final: 0.9032 (t) REVERT: F 75 GLU cc_start: 0.6736 (pp20) cc_final: 0.4981 (pp20) REVERT: F 78 MET cc_start: 0.7960 (mpp) cc_final: 0.6714 (mpp) REVERT: F 82 MET cc_start: 0.8822 (tpp) cc_final: 0.8414 (tpp) REVERT: F 88 ILE cc_start: 0.8025 (mt) cc_final: 0.7722 (mp) REVERT: F 94 ASN cc_start: 0.8873 (t0) cc_final: 0.8656 (t0) REVERT: F 127 VAL cc_start: 0.9307 (t) cc_final: 0.9089 (t) REVERT: F 130 VAL cc_start: 0.9632 (m) cc_final: 0.9351 (m) REVERT: F 134 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9065 (mmmt) REVERT: F 166 LEU cc_start: 0.8967 (pt) cc_final: 0.8248 (tp) REVERT: F 216 ASP cc_start: 0.9044 (t70) cc_final: 0.8774 (t0) REVERT: F 261 ASP cc_start: 0.9219 (m-30) cc_final: 0.8597 (p0) REVERT: F 262 LEU cc_start: 0.9733 (tt) cc_final: 0.9458 (tt) REVERT: F 269 ASP cc_start: 0.9218 (t0) cc_final: 0.8337 (t70) REVERT: F 296 ASN cc_start: 0.9411 (p0) cc_final: 0.8744 (p0) REVERT: F 297 LEU cc_start: 0.9109 (mm) cc_final: 0.8577 (mm) REVERT: F 298 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8262 (mm110) REVERT: F 353 TYR cc_start: 0.9216 (t80) cc_final: 0.8957 (t80) REVERT: F 372 HIS cc_start: 0.9495 (m90) cc_final: 0.8893 (m90) REVERT: F 395 GLU cc_start: 0.9081 (mp0) cc_final: 0.8438 (mp0) REVERT: F 450 LYS cc_start: 0.7472 (pttm) cc_final: 0.6356 (ptmm) REVERT: F 490 PHE cc_start: 0.8939 (m-80) cc_final: 0.8041 (m-80) REVERT: G 12 TYR cc_start: 0.9370 (t80) cc_final: 0.8820 (t80) REVERT: G 65 LEU cc_start: 0.8925 (pt) cc_final: 0.8703 (pt) REVERT: G 67 SER cc_start: 0.9373 (t) cc_final: 0.8944 (t) REVERT: G 78 MET cc_start: 0.7439 (mpp) cc_final: 0.6647 (mpp) REVERT: G 82 MET cc_start: 0.8900 (tpp) cc_final: 0.8538 (tpp) REVERT: G 94 ASN cc_start: 0.8883 (t0) cc_final: 0.8642 (t0) REVERT: G 105 ARG cc_start: 0.8993 (mmt-90) cc_final: 0.8757 (mmt90) REVERT: G 132 GLU cc_start: 0.9463 (pp20) cc_final: 0.9183 (pp20) REVERT: G 166 LEU cc_start: 0.8909 (pt) cc_final: 0.8175 (tp) REVERT: G 262 LEU cc_start: 0.9775 (tt) cc_final: 0.9440 (mt) REVERT: G 269 ASP cc_start: 0.9177 (t0) cc_final: 0.8349 (t0) REVERT: G 276 SER cc_start: 0.9120 (m) cc_final: 0.8796 (p) REVERT: G 285 ASN cc_start: 0.9574 (m110) cc_final: 0.9367 (m110) REVERT: G 296 ASN cc_start: 0.9373 (p0) cc_final: 0.8665 (p0) REVERT: G 297 LEU cc_start: 0.9089 (mm) cc_final: 0.8640 (mm) REVERT: G 298 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8213 (mm110) REVERT: G 401 PHE cc_start: 0.9322 (p90) cc_final: 0.9079 (p90) REVERT: G 402 PHE cc_start: 0.8091 (m-80) cc_final: 0.7701 (m-80) REVERT: G 490 PHE cc_start: 0.8905 (m-80) cc_final: 0.8213 (m-80) REVERT: G 493 ARG cc_start: 0.9210 (ttt90) cc_final: 0.8876 (ttm-80) REVERT: H 28 ASP cc_start: 0.9296 (t0) cc_final: 0.8970 (t0) REVERT: H 30 LEU cc_start: 0.8698 (mt) cc_final: 0.8410 (mt) REVERT: H 66 VAL cc_start: 0.8823 (m) cc_final: 0.8209 (m) REVERT: H 78 MET cc_start: 0.7595 (mpp) cc_final: 0.6367 (mpp) REVERT: H 82 MET cc_start: 0.8858 (tpp) cc_final: 0.8563 (tpp) REVERT: H 93 HIS cc_start: 0.9359 (p90) cc_final: 0.8713 (p90) REVERT: H 94 ASN cc_start: 0.8861 (t0) cc_final: 0.8614 (t0) REVERT: H 163 ILE cc_start: 0.9419 (pt) cc_final: 0.9052 (pt) REVERT: H 166 LEU cc_start: 0.8940 (pt) cc_final: 0.8144 (tp) REVERT: H 178 ILE cc_start: 0.9178 (mp) cc_final: 0.8694 (mp) REVERT: H 179 MET cc_start: 0.7692 (tpt) cc_final: 0.7453 (tpp) REVERT: H 181 LYS cc_start: 0.9243 (mmpt) cc_final: 0.9020 (mmpt) REVERT: H 199 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9406 (mt-10) REVERT: H 214 GLU cc_start: 0.9289 (pm20) cc_final: 0.9079 (pm20) REVERT: H 261 ASP cc_start: 0.9209 (m-30) cc_final: 0.8616 (p0) REVERT: H 269 ASP cc_start: 0.9169 (t0) cc_final: 0.8278 (t70) REVERT: H 285 ASN cc_start: 0.9475 (m110) cc_final: 0.9250 (m110) REVERT: H 286 MET cc_start: 0.8723 (mtm) cc_final: 0.8231 (mtt) REVERT: H 296 ASN cc_start: 0.9438 (p0) cc_final: 0.8771 (p0) REVERT: H 297 LEU cc_start: 0.9155 (mm) cc_final: 0.8612 (mm) REVERT: H 298 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8259 (mm110) REVERT: H 357 PHE cc_start: 0.9188 (m-80) cc_final: 0.8780 (m-10) REVERT: H 364 ASP cc_start: 0.8978 (t0) cc_final: 0.8773 (t0) REVERT: H 372 HIS cc_start: 0.9513 (m170) cc_final: 0.9288 (m170) REVERT: H 395 GLU cc_start: 0.8970 (pm20) cc_final: 0.8029 (mp0) REVERT: H 489 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7930 (ttpt) REVERT: H 490 PHE cc_start: 0.9100 (m-80) cc_final: 0.8673 (m-80) REVERT: H 493 ARG cc_start: 0.9249 (ttt90) cc_final: 0.9023 (ttm-80) outliers start: 4 outliers final: 3 residues processed: 1355 average time/residue: 0.1657 time to fit residues: 363.1946 Evaluate side-chains 1091 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1088 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 8.9990 chunk 300 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 142 optimal weight: 0.0070 chunk 94 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN 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 343 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090365 restraints weight = 55906.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094349 restraints weight = 36247.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097346 restraints weight = 26300.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099616 restraints weight = 20564.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101227 restraints weight = 16953.951| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4480 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= 0.162 Angle : 0.866 11.362 39136 Z= 0.418 Chirality : 0.050 0.271 4472 Planarity : 0.005 0.080 4928 Dihedral : 16.556 171.567 4120 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.13), residues: 3576 helix: -1.19 (0.14), residues: 1232 sheet: -3.10 (0.22), residues: 344 loop : -1.86 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 480 TYR 0.038 0.002 TYR B 484 PHE 0.029 0.002 PHE E 456 HIS 0.005 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (28864) covalent geometry : angle 0.86607 / 0.42 (39136) hydrogen bonds : bond 0.03593 / 2.40 ( 888) hydrogen bonds : angle 5.67552 / 3.83 ( 2448) Misc. bond : bond 0.00188 / 0.12 ( 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 1302 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1301 time to evaluate : 0.805 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: A 75 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 78 MET cc_start: 0.7807 (mpp) cc_final: 0.6954 (mpp) REVERT: A 94 ASN cc_start: 0.8893 (t0) cc_final: 0.8649 (t0) REVERT: A 105 ARG cc_start: 0.9046 (mmt-90) cc_final: 0.8769 (mmt90) REVERT: A 166 LEU cc_start: 0.9024 (pt) cc_final: 0.8364 (tp) REVERT: A 179 MET cc_start: 0.7685 (tpt) cc_final: 0.7333 (tpt) REVERT: A 229 LYS cc_start: 0.9491 (mttt) cc_final: 0.9126 (mttt) REVERT: A 261 ASP cc_start: 0.9369 (m-30) cc_final: 0.8698 (p0) REVERT: A 262 LEU cc_start: 0.9785 (tt) cc_final: 0.9114 (mt) REVERT: A 269 ASP cc_start: 0.9154 (t0) cc_final: 0.8199 (t0) REVERT: A 296 ASN cc_start: 0.9356 (p0) cc_final: 0.8661 (p0) REVERT: A 297 LEU cc_start: 0.9032 (mm) cc_final: 0.8576 (mm) REVERT: A 298 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8345 (mm110) REVERT: A 372 HIS cc_start: 0.9380 (m90) cc_final: 0.8837 (m90) REVERT: A 402 PHE cc_start: 0.8100 (m-80) cc_final: 0.7773 (m-80) REVERT: A 479 VAL cc_start: 0.9356 (p) cc_final: 0.9129 (t) REVERT: A 489 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7692 (ttmt) REVERT: A 490 PHE cc_start: 0.8888 (m-80) cc_final: 0.8559 (m-80) REVERT: B 66 VAL cc_start: 0.9180 (m) cc_final: 0.8788 (m) REVERT: B 67 SER cc_start: 0.9538 (t) cc_final: 0.9109 (t) REVERT: B 78 MET cc_start: 0.7992 (mpp) cc_final: 0.7690 (mpp) REVERT: B 82 MET cc_start: 0.8836 (tpp) cc_final: 0.8394 (tpp) REVERT: B 166 LEU cc_start: 0.9049 (pt) cc_final: 0.8412 (tp) REVERT: B 229 LYS cc_start: 0.9461 (mttt) cc_final: 0.8858 (mttt) REVERT: B 261 ASP cc_start: 0.9209 (m-30) cc_final: 0.8644 (p0) REVERT: B 269 ASP cc_start: 0.9188 (t0) cc_final: 0.8457 (t70) REVERT: B 296 ASN cc_start: 0.9432 (p0) cc_final: 0.8434 (p0) REVERT: B 298 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8300 (mm110) REVERT: B 372 HIS cc_start: 0.9468 (m90) cc_final: 0.9029 (m90) REVERT: B 465 GLN cc_start: 0.9233 (mt0) cc_final: 0.8905 (pt0) REVERT: B 490 PHE cc_start: 0.9047 (m-80) cc_final: 0.8612 (m-80) REVERT: B 493 ARG cc_start: 0.9181 (ttt90) cc_final: 0.8871 (ttm-80) REVERT: C 24 PHE cc_start: 0.8234 (m-80) cc_final: 0.8025 (m-10) REVERT: C 35 PHE cc_start: 0.9307 (p90) cc_final: 0.9071 (p90) REVERT: C 75 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 78 MET cc_start: 0.8071 (mpp) cc_final: 0.7009 (mpp) REVERT: C 82 MET cc_start: 0.9009 (tpp) cc_final: 0.8737 (tpp) REVERT: C 94 ASN cc_start: 0.8830 (t0) cc_final: 0.8574 (t0) REVERT: C 166 LEU cc_start: 0.8860 (pt) cc_final: 0.8146 (tp) REVERT: C 174 PHE cc_start: 0.9155 (m-80) cc_final: 0.8888 (m-80) REVERT: C 202 GLN cc_start: 0.9343 (mp10) cc_final: 0.8700 (mp10) REVERT: C 216 ASP cc_start: 0.9014 (t70) cc_final: 0.8737 (t70) REVERT: C 276 SER cc_start: 0.9327 (m) cc_final: 0.9028 (p) REVERT: C 286 MET cc_start: 0.8966 (mtm) cc_final: 0.8482 (mtt) REVERT: C 297 LEU cc_start: 0.9057 (mm) cc_final: 0.8732 (mm) REVERT: C 364 ASP cc_start: 0.8836 (t0) cc_final: 0.8587 (t0) REVERT: C 372 HIS cc_start: 0.9491 (m90) cc_final: 0.8912 (m90) REVERT: C 450 LYS cc_start: 0.6870 (pttm) cc_final: 0.6424 (ptmm) REVERT: C 489 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7682 (ttmt) REVERT: C 490 PHE cc_start: 0.9052 (m-80) cc_final: 0.8620 (m-80) REVERT: C 493 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8385 (ttm110) REVERT: D 28 ASP cc_start: 0.9345 (t0) cc_final: 0.9095 (t0) REVERT: D 66 VAL cc_start: 0.9063 (m) cc_final: 0.8195 (m) REVERT: D 67 SER cc_start: 0.9573 (t) cc_final: 0.9157 (t) REVERT: D 75 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7340 (tm-30) REVERT: D 78 MET cc_start: 0.7935 (mpp) cc_final: 0.7204 (mpp) REVERT: D 82 MET cc_start: 0.8909 (tpp) cc_final: 0.8401 (tpp) REVERT: D 88 ILE cc_start: 0.8061 (mt) cc_final: 0.7728 (pt) REVERT: D 94 ASN cc_start: 0.8885 (t0) cc_final: 0.8667 (t0) REVERT: D 109 LYS cc_start: 0.8748 (tptp) cc_final: 0.8152 (tptp) REVERT: D 130 VAL cc_start: 0.9579 (m) cc_final: 0.9161 (m) REVERT: D 134 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9127 (mmmt) REVERT: D 166 LEU cc_start: 0.8998 (pt) cc_final: 0.8285 (tp) REVERT: D 261 ASP cc_start: 0.9157 (m-30) cc_final: 0.8517 (p0) REVERT: D 269 ASP cc_start: 0.9277 (t0) cc_final: 0.8735 (t70) REVERT: D 286 MET cc_start: 0.8773 (mtm) cc_final: 0.8486 (mtt) REVERT: D 296 ASN cc_start: 0.9512 (p0) cc_final: 0.8874 (p0) REVERT: D 298 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8414 (mm110) REVERT: D 353 TYR cc_start: 0.9259 (t80) cc_final: 0.8943 (t80) REVERT: D 372 HIS cc_start: 0.9392 (m90) cc_final: 0.9050 (m90) REVERT: D 401 PHE cc_start: 0.9272 (p90) cc_final: 0.9071 (p90) REVERT: D 490 PHE cc_start: 0.9001 (m-80) cc_final: 0.8206 (m-80) REVERT: E 12 TYR cc_start: 0.9310 (t80) cc_final: 0.8608 (t80) REVERT: E 75 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7792 (tm-30) REVERT: E 78 MET cc_start: 0.7635 (mpp) cc_final: 0.6805 (mpp) REVERT: E 82 MET cc_start: 0.9059 (tpt) cc_final: 0.8691 (tpp) REVERT: E 88 ILE cc_start: 0.7371 (pt) cc_final: 0.7005 (pt) REVERT: E 93 HIS cc_start: 0.9312 (p90) cc_final: 0.8687 (p90) REVERT: E 94 ASN cc_start: 0.8851 (t0) cc_final: 0.8612 (t0) REVERT: E 103 GLU cc_start: 0.9366 (mp0) cc_final: 0.9166 (mp0) REVERT: E 106 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8820 (mmtm) REVERT: E 109 LYS cc_start: 0.8930 (tptp) cc_final: 0.8443 (tptp) REVERT: E 166 LEU cc_start: 0.9048 (pt) cc_final: 0.8326 (tp) REVERT: E 229 LYS cc_start: 0.9445 (mttt) cc_final: 0.8764 (mttt) REVERT: E 232 ASP cc_start: 0.8915 (m-30) cc_final: 0.8706 (m-30) REVERT: E 258 TYR cc_start: 0.9672 (t80) cc_final: 0.9153 (t80) REVERT: E 261 ASP cc_start: 0.9313 (m-30) cc_final: 0.8645 (p0) REVERT: E 265 GLN cc_start: 0.9576 (tm-30) cc_final: 0.9342 (tm-30) REVERT: E 297 LEU cc_start: 0.9176 (mm) cc_final: 0.8904 (mm) REVERT: E 364 ASP cc_start: 0.8607 (t0) cc_final: 0.8404 (t0) REVERT: E 372 HIS cc_start: 0.9204 (m90) cc_final: 0.8843 (m90) REVERT: E 482 MET cc_start: 0.8820 (tmm) cc_final: 0.8534 (tmm) REVERT: E 489 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7402 (mtpt) REVERT: E 490 PHE cc_start: 0.8987 (m-80) cc_final: 0.8697 (m-80) REVERT: F 12 TYR cc_start: 0.9525 (t80) cc_final: 0.8906 (t80) REVERT: F 28 ASP cc_start: 0.9274 (t0) cc_final: 0.9034 (t0) REVERT: F 65 LEU cc_start: 0.8827 (pt) cc_final: 0.8554 (pt) REVERT: F 66 VAL cc_start: 0.9067 (m) cc_final: 0.8194 (m) REVERT: F 67 SER cc_start: 0.9514 (t) cc_final: 0.8961 (t) REVERT: F 78 MET cc_start: 0.8217 (mpp) cc_final: 0.7681 (mpp) REVERT: F 82 MET cc_start: 0.8913 (tpp) cc_final: 0.8430 (tpp) REVERT: F 88 ILE cc_start: 0.8127 (mt) cc_final: 0.7880 (pt) REVERT: F 94 ASN cc_start: 0.8865 (t0) cc_final: 0.8605 (t0) REVERT: F 130 VAL cc_start: 0.9626 (m) cc_final: 0.9329 (m) REVERT: F 134 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9089 (mmmt) REVERT: F 166 LEU cc_start: 0.8972 (pt) cc_final: 0.8285 (tp) REVERT: F 174 PHE cc_start: 0.8803 (m-80) cc_final: 0.8593 (m-80) REVERT: F 216 ASP cc_start: 0.9077 (t70) cc_final: 0.8830 (t70) REVERT: F 261 ASP cc_start: 0.9221 (m-30) cc_final: 0.8595 (p0) REVERT: F 262 LEU cc_start: 0.9727 (tt) cc_final: 0.9457 (tt) REVERT: F 269 ASP cc_start: 0.9174 (t0) cc_final: 0.8155 (t70) REVERT: F 296 ASN cc_start: 0.9413 (p0) cc_final: 0.8495 (p0) REVERT: F 297 LEU cc_start: 0.9132 (mm) cc_final: 0.8715 (mm) REVERT: F 298 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8212 (mm110) REVERT: F 357 PHE cc_start: 0.9122 (m-80) cc_final: 0.8891 (m-10) REVERT: F 372 HIS cc_start: 0.9413 (m90) cc_final: 0.8904 (m90) REVERT: F 401 PHE cc_start: 0.9262 (p90) cc_final: 0.9036 (p90) REVERT: F 479 VAL cc_start: 0.9315 (p) cc_final: 0.9041 (t) REVERT: F 490 PHE cc_start: 0.8971 (m-80) cc_final: 0.8156 (m-80) REVERT: G 28 ASP cc_start: 0.9188 (t0) cc_final: 0.8987 (t0) REVERT: G 67 SER cc_start: 0.9504 (t) cc_final: 0.8896 (t) REVERT: G 78 MET cc_start: 0.7644 (mpp) cc_final: 0.6797 (mpp) REVERT: G 82 MET cc_start: 0.9012 (tpp) cc_final: 0.8564 (tpp) REVERT: G 88 ILE cc_start: 0.7685 (pt) cc_final: 0.7260 (pt) REVERT: G 94 ASN cc_start: 0.8887 (t0) cc_final: 0.8627 (t0) REVERT: G 166 LEU cc_start: 0.9036 (pt) cc_final: 0.8283 (tp) REVERT: G 174 PHE cc_start: 0.9034 (m-80) cc_final: 0.8811 (m-80) REVERT: G 261 ASP cc_start: 0.9373 (m-30) cc_final: 0.8701 (p0) REVERT: G 262 LEU cc_start: 0.9765 (tt) cc_final: 0.9220 (mt) REVERT: G 269 ASP cc_start: 0.9150 (t0) cc_final: 0.8203 (t0) REVERT: G 276 SER cc_start: 0.9188 (m) cc_final: 0.8855 (p) REVERT: G 296 ASN cc_start: 0.9369 (p0) cc_final: 0.8701 (p0) REVERT: G 297 LEU cc_start: 0.9050 (mm) cc_final: 0.8603 (mm) REVERT: G 298 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8215 (mm110) REVERT: G 364 ASP cc_start: 0.8755 (t0) cc_final: 0.8549 (t0) REVERT: G 401 PHE cc_start: 0.9295 (p90) cc_final: 0.9075 (p90) REVERT: G 402 PHE cc_start: 0.8109 (m-80) cc_final: 0.7693 (m-80) REVERT: G 479 VAL cc_start: 0.9207 (p) cc_final: 0.8942 (t) REVERT: G 489 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7112 (ttpt) REVERT: G 490 PHE cc_start: 0.8899 (m-80) cc_final: 0.8187 (m-80) REVERT: G 493 ARG cc_start: 0.9239 (ttt90) cc_final: 0.8925 (ttm-80) REVERT: H 28 ASP cc_start: 0.9285 (t0) cc_final: 0.8968 (t0) REVERT: H 30 LEU cc_start: 0.8755 (mt) cc_final: 0.8427 (mt) REVERT: H 66 VAL cc_start: 0.9135 (m) cc_final: 0.8692 (m) REVERT: H 78 MET cc_start: 0.7600 (mpp) cc_final: 0.6579 (mpp) REVERT: H 82 MET cc_start: 0.8857 (tpp) cc_final: 0.8603 (tpp) REVERT: H 88 ILE cc_start: 0.7522 (pt) cc_final: 0.7157 (pt) REVERT: H 105 ARG cc_start: 0.8884 (mmt180) cc_final: 0.8446 (mmt180) REVERT: H 130 VAL cc_start: 0.9610 (m) cc_final: 0.9157 (m) REVERT: H 134 LYS cc_start: 0.9500 (mmmt) cc_final: 0.9108 (mmmt) REVERT: H 163 ILE cc_start: 0.9440 (pt) cc_final: 0.9052 (pt) REVERT: H 166 LEU cc_start: 0.9002 (pt) cc_final: 0.8155 (tp) REVERT: H 178 ILE cc_start: 0.9162 (mp) cc_final: 0.8451 (mp) REVERT: H 179 MET cc_start: 0.7599 (tpt) cc_final: 0.7204 (tpt) REVERT: H 181 LYS cc_start: 0.9252 (mmpt) cc_final: 0.9032 (mmpt) REVERT: H 261 ASP cc_start: 0.9248 (m-30) cc_final: 0.8713 (p0) REVERT: H 269 ASP cc_start: 0.9177 (t0) cc_final: 0.8291 (t70) REVERT: H 286 MET cc_start: 0.8714 (mtm) cc_final: 0.8232 (mtt) REVERT: H 296 ASN cc_start: 0.9435 (p0) cc_final: 0.8783 (p0) REVERT: H 297 LEU cc_start: 0.9079 (mm) cc_final: 0.8545 (mm) REVERT: H 298 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8253 (mm110) REVERT: H 357 PHE cc_start: 0.9199 (m-80) cc_final: 0.8781 (m-10) REVERT: H 364 ASP cc_start: 0.8939 (t0) cc_final: 0.8690 (t0) REVERT: H 372 HIS cc_start: 0.9548 (m170) cc_final: 0.9215 (m170) REVERT: H 401 PHE cc_start: 0.9265 (p90) cc_final: 0.9050 (p90) REVERT: H 456 PHE cc_start: 0.9628 (t80) cc_final: 0.9353 (t80) REVERT: H 489 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7780 (ttpt) REVERT: H 490 PHE cc_start: 0.9100 (m-80) cc_final: 0.8667 (m-80) REVERT: H 493 ARG cc_start: 0.9241 (ttt90) cc_final: 0.8940 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 1301 average time/residue: 0.1687 time to fit residues: 353.5043 Evaluate side-chains 1071 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1071 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 325 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 348 optimal weight: 1.9990 chunk 315 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093055 restraints weight = 54457.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097246 restraints weight = 34623.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.100379 restraints weight = 24793.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.102819 restraints weight = 19172.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104524 restraints weight = 15680.917| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28872 Z= 0.147 Angle : 0.886 13.105 39136 Z= 0.421 Chirality : 0.050 0.282 4472 Planarity : 0.005 0.071 4928 Dihedral : 16.356 174.308 4120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -2.50 (0.13), residues: 3576 helix: -1.10 (0.14), residues: 1216 sheet: -2.78 (0.24), residues: 344 loop : -1.81 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 480 TYR 0.032 0.002 TYR E 233 PHE 0.037 0.002 PHE E 456 HIS 0.005 0.001 HIS E 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (28864) covalent geometry : angle 0.88606 / 0.42 (39136) hydrogen bonds : bond 0.03503 / 2.35 ( 888) hydrogen bonds : angle 5.66897 / 3.84 ( 2448) Misc. bond : bond 0.00199 / 0.12 ( 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 1354 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1354 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9120 (t0) cc_final: 0.8815 (t0) REVERT: A 75 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 78 MET cc_start: 0.7470 (mpp) cc_final: 0.6753 (mpp) REVERT: A 82 MET cc_start: 0.9086 (tpt) cc_final: 0.8688 (tpp) REVERT: A 94 ASN cc_start: 0.8882 (t0) cc_final: 0.8630 (t0) REVERT: A 134 LYS cc_start: 0.9318 (mmtt) cc_final: 0.9105 (mmtt) REVERT: A 166 LEU cc_start: 0.9003 (pt) cc_final: 0.8379 (tp) REVERT: A 179 MET cc_start: 0.7554 (tpt) cc_final: 0.7059 (tpt) REVERT: A 199 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9242 (mt-10) REVERT: A 202 GLN cc_start: 0.9305 (mp10) cc_final: 0.8500 (mp10) REVERT: A 203 ARG cc_start: 0.9464 (mmp80) cc_final: 0.9248 (mmp80) REVERT: A 216 ASP cc_start: 0.9134 (t70) cc_final: 0.8653 (t70) REVERT: A 229 LYS cc_start: 0.9439 (mttt) cc_final: 0.8775 (mttt) REVERT: A 241 LYS cc_start: 0.9408 (tptp) cc_final: 0.9107 (tptp) REVERT: A 261 ASP cc_start: 0.9342 (m-30) cc_final: 0.8899 (m-30) REVERT: A 269 ASP cc_start: 0.9172 (t0) cc_final: 0.8265 (t70) REVERT: A 296 ASN cc_start: 0.9355 (p0) cc_final: 0.8673 (p0) REVERT: A 297 LEU cc_start: 0.8934 (mm) cc_final: 0.8512 (mm) REVERT: A 298 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8309 (mm110) REVERT: A 372 HIS cc_start: 0.9214 (m90) cc_final: 0.8846 (m90) REVERT: A 399 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9128 (tm-30) REVERT: A 402 PHE cc_start: 0.8103 (m-80) cc_final: 0.7781 (m-80) REVERT: A 450 LYS cc_start: 0.7314 (pttm) cc_final: 0.6396 (ptmm) REVERT: A 479 VAL cc_start: 0.9338 (p) cc_final: 0.9067 (t) REVERT: A 489 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7772 (ttmt) REVERT: A 490 PHE cc_start: 0.8946 (m-80) cc_final: 0.8474 (m-80) REVERT: A 493 ARG cc_start: 0.9093 (ttm-80) cc_final: 0.8668 (ttm-80) REVERT: B 28 ASP cc_start: 0.9248 (t0) cc_final: 0.8987 (t0) REVERT: B 66 VAL cc_start: 0.9141 (m) cc_final: 0.8683 (m) REVERT: B 78 MET cc_start: 0.7594 (mpp) cc_final: 0.7001 (mpp) REVERT: B 82 MET cc_start: 0.8809 (tpp) cc_final: 0.8367 (tpp) REVERT: B 166 LEU cc_start: 0.8966 (pt) cc_final: 0.8344 (tp) REVERT: B 178 ILE cc_start: 0.9183 (mp) cc_final: 0.8692 (mp) REVERT: B 199 GLU cc_start: 0.9592 (mt-10) cc_final: 0.9062 (pt0) REVERT: B 202 GLN cc_start: 0.9337 (mp10) cc_final: 0.8829 (pp30) REVERT: B 203 ARG cc_start: 0.9446 (mmp80) cc_final: 0.9006 (mmm-85) REVERT: B 229 LYS cc_start: 0.9441 (mttt) cc_final: 0.8939 (mttt) REVERT: B 269 ASP cc_start: 0.9183 (t0) cc_final: 0.8327 (t70) REVERT: B 296 ASN cc_start: 0.9444 (p0) cc_final: 0.8626 (p0) REVERT: B 297 LEU cc_start: 0.8974 (mm) cc_final: 0.8545 (mm) REVERT: B 298 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8316 (mm110) REVERT: B 461 ILE cc_start: 0.9710 (pt) cc_final: 0.9506 (pt) REVERT: B 465 GLN cc_start: 0.9184 (mt0) cc_final: 0.8861 (pt0) REVERT: B 490 PHE cc_start: 0.8966 (m-80) cc_final: 0.8500 (m-80) REVERT: C 58 LYS cc_start: 0.9634 (mmpt) cc_final: 0.9402 (mmmm) REVERT: C 75 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 78 MET cc_start: 0.8007 (mpp) cc_final: 0.6943 (mpp) REVERT: C 82 MET cc_start: 0.9003 (tpp) cc_final: 0.8763 (tpp) REVERT: C 88 ILE cc_start: 0.7372 (pt) cc_final: 0.6847 (pt) REVERT: C 94 ASN cc_start: 0.8806 (t0) cc_final: 0.8548 (t0) REVERT: C 109 LYS cc_start: 0.9210 (tptp) cc_final: 0.9007 (tptp) REVERT: C 166 LEU cc_start: 0.8900 (pt) cc_final: 0.8156 (tp) REVERT: C 261 ASP cc_start: 0.9325 (m-30) cc_final: 0.9087 (m-30) REVERT: C 262 LEU cc_start: 0.9725 (tt) cc_final: 0.9517 (pp) REVERT: C 269 ASP cc_start: 0.9211 (t70) cc_final: 0.8719 (t70) REVERT: C 276 SER cc_start: 0.9243 (m) cc_final: 0.8915 (p) REVERT: C 286 MET cc_start: 0.8952 (mtm) cc_final: 0.8326 (mtt) REVERT: C 297 LEU cc_start: 0.8768 (mm) cc_final: 0.8369 (mm) REVERT: C 298 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8331 (mm-40) REVERT: C 372 HIS cc_start: 0.9458 (m90) cc_final: 0.8804 (m90) REVERT: C 399 GLU cc_start: 0.9302 (tm-30) cc_final: 0.9051 (tm-30) REVERT: C 450 LYS cc_start: 0.6839 (pttm) cc_final: 0.6394 (ptmm) REVERT: C 489 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7601 (ttpt) REVERT: C 490 PHE cc_start: 0.8998 (m-80) cc_final: 0.8571 (m-80) REVERT: C 493 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8189 (ttm110) REVERT: D 28 ASP cc_start: 0.9330 (t0) cc_final: 0.9064 (t0) REVERT: D 66 VAL cc_start: 0.9059 (m) cc_final: 0.8275 (m) REVERT: D 75 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 78 MET cc_start: 0.7830 (mpp) cc_final: 0.7154 (mpp) REVERT: D 82 MET cc_start: 0.8969 (tpp) cc_final: 0.8462 (tpp) REVERT: D 88 ILE cc_start: 0.8136 (mt) cc_final: 0.7911 (pt) REVERT: D 94 ASN cc_start: 0.8845 (t0) cc_final: 0.8612 (t0) REVERT: D 166 LEU cc_start: 0.9019 (pt) cc_final: 0.8302 (tp) REVERT: D 199 GLU cc_start: 0.9456 (pt0) cc_final: 0.9239 (pt0) REVERT: D 202 GLN cc_start: 0.9348 (mp10) cc_final: 0.8484 (mp10) REVERT: D 261 ASP cc_start: 0.9157 (m-30) cc_final: 0.8393 (p0) REVERT: D 262 LEU cc_start: 0.9689 (tt) cc_final: 0.9395 (tt) REVERT: D 265 GLN cc_start: 0.9434 (tt0) cc_final: 0.9108 (tm-30) REVERT: D 276 SER cc_start: 0.9185 (m) cc_final: 0.8877 (p) REVERT: D 286 MET cc_start: 0.8755 (mtm) cc_final: 0.8468 (mtt) REVERT: D 372 HIS cc_start: 0.9294 (m90) cc_final: 0.8842 (m90) REVERT: D 385 MET cc_start: 0.8709 (ttt) cc_final: 0.8487 (tpp) REVERT: D 489 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7058 (ttpt) REVERT: D 490 PHE cc_start: 0.8930 (m-80) cc_final: 0.8111 (m-80) REVERT: E 12 TYR cc_start: 0.9328 (t80) cc_final: 0.8629 (t80) REVERT: E 58 LYS cc_start: 0.9625 (mmpt) cc_final: 0.9423 (mmmm) REVERT: E 75 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 78 MET cc_start: 0.7522 (mpp) cc_final: 0.6723 (mpp) REVERT: E 82 MET cc_start: 0.9140 (tpt) cc_final: 0.8632 (tpp) REVERT: E 88 ILE cc_start: 0.7255 (pt) cc_final: 0.6804 (pt) REVERT: E 106 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8897 (mmtm) REVERT: E 166 LEU cc_start: 0.9067 (pt) cc_final: 0.8327 (tp) REVERT: E 178 ILE cc_start: 0.9243 (mp) cc_final: 0.8885 (mp) REVERT: E 229 LYS cc_start: 0.9413 (mttt) cc_final: 0.8806 (mttt) REVERT: E 296 ASN cc_start: 0.9412 (p0) cc_final: 0.8518 (p0) REVERT: E 297 LEU cc_start: 0.8972 (mm) cc_final: 0.8552 (mm) REVERT: E 298 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8281 (mm-40) REVERT: E 372 HIS cc_start: 0.9343 (m90) cc_final: 0.8786 (m90) REVERT: E 399 GLU cc_start: 0.9304 (tm-30) cc_final: 0.9043 (tm-30) REVERT: E 450 LYS cc_start: 0.7442 (pttm) cc_final: 0.6481 (ptmm) REVERT: E 489 LYS cc_start: 0.7605 (mtpt) cc_final: 0.7261 (mtpt) REVERT: E 490 PHE cc_start: 0.8965 (m-80) cc_final: 0.8669 (m-80) REVERT: E 493 ARG cc_start: 0.8955 (ttt90) cc_final: 0.8661 (ttm-80) REVERT: F 12 TYR cc_start: 0.9567 (t80) cc_final: 0.9090 (t80) REVERT: F 28 ASP cc_start: 0.9273 (t0) cc_final: 0.9035 (t0) REVERT: F 78 MET cc_start: 0.7989 (mpp) cc_final: 0.7336 (mpp) REVERT: F 82 MET cc_start: 0.8939 (tpp) cc_final: 0.8547 (tpp) REVERT: F 94 ASN cc_start: 0.8845 (t0) cc_final: 0.8575 (t0) REVERT: F 105 ARG cc_start: 0.8624 (mmt90) cc_final: 0.7889 (tpp-160) REVERT: F 130 VAL cc_start: 0.9610 (m) cc_final: 0.9302 (m) REVERT: F 134 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9066 (mmmt) REVERT: F 166 LEU cc_start: 0.8960 (pt) cc_final: 0.8268 (tp) REVERT: F 199 GLU cc_start: 0.9508 (pt0) cc_final: 0.9281 (pt0) REVERT: F 269 ASP cc_start: 0.9134 (t0) cc_final: 0.8171 (t70) REVERT: F 296 ASN cc_start: 0.9421 (p0) cc_final: 0.8599 (p0) REVERT: F 297 LEU cc_start: 0.9028 (mm) cc_final: 0.8602 (mm) REVERT: F 298 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8241 (mm110) REVERT: F 372 HIS cc_start: 0.9376 (m90) cc_final: 0.9054 (m90) REVERT: F 450 LYS cc_start: 0.7619 (pttm) cc_final: 0.6288 (ptmm) REVERT: F 479 VAL cc_start: 0.9374 (p) cc_final: 0.9118 (t) REVERT: F 490 PHE cc_start: 0.8910 (m-80) cc_final: 0.8092 (m-80) REVERT: G 12 TYR cc_start: 0.9412 (t80) cc_final: 0.8786 (t80) REVERT: G 28 ASP cc_start: 0.9140 (t0) cc_final: 0.8939 (t0) REVERT: G 78 MET cc_start: 0.7964 (mpp) cc_final: 0.7713 (mpp) REVERT: G 82 MET cc_start: 0.8932 (tpp) cc_final: 0.8526 (tpp) REVERT: G 88 ILE cc_start: 0.7561 (pt) cc_final: 0.7150 (pt) REVERT: G 94 ASN cc_start: 0.8914 (t0) cc_final: 0.8643 (t0) REVERT: G 158 ILE cc_start: 0.8909 (mm) cc_final: 0.8678 (mm) REVERT: G 166 LEU cc_start: 0.9026 (pt) cc_final: 0.8307 (tp) REVERT: G 232 ASP cc_start: 0.8956 (m-30) cc_final: 0.8732 (m-30) REVERT: G 261 ASP cc_start: 0.9351 (m-30) cc_final: 0.8926 (m-30) REVERT: G 269 ASP cc_start: 0.9176 (t0) cc_final: 0.8269 (t70) REVERT: G 276 SER cc_start: 0.9195 (m) cc_final: 0.8850 (p) REVERT: G 292 ASP cc_start: 0.9639 (m-30) cc_final: 0.9401 (m-30) REVERT: G 296 ASN cc_start: 0.9366 (p0) cc_final: 0.8779 (p0) REVERT: G 297 LEU cc_start: 0.8965 (mm) cc_final: 0.8509 (mm) REVERT: G 298 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8240 (mm110) REVERT: G 402 PHE cc_start: 0.7985 (m-80) cc_final: 0.7673 (m-80) REVERT: G 450 LYS cc_start: 0.7327 (pttm) cc_final: 0.6224 (ptmm) REVERT: G 479 VAL cc_start: 0.9251 (p) cc_final: 0.8987 (t) REVERT: G 489 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7919 (ttmt) REVERT: G 490 PHE cc_start: 0.8955 (m-80) cc_final: 0.8259 (m-80) REVERT: G 493 ARG cc_start: 0.9190 (ttt90) cc_final: 0.8871 (ttm-80) REVERT: H 28 ASP cc_start: 0.9234 (t0) cc_final: 0.8910 (t0) REVERT: H 30 LEU cc_start: 0.8702 (mt) cc_final: 0.8436 (mt) REVERT: H 66 VAL cc_start: 0.9105 (m) cc_final: 0.8746 (m) REVERT: H 82 MET cc_start: 0.8725 (tpp) cc_final: 0.8479 (tpp) REVERT: H 88 ILE cc_start: 0.7268 (pt) cc_final: 0.6908 (pt) REVERT: H 94 ASN cc_start: 0.8850 (t0) cc_final: 0.8636 (t0) REVERT: H 130 VAL cc_start: 0.9598 (m) cc_final: 0.9162 (m) REVERT: H 134 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9116 (mmmm) REVERT: H 166 LEU cc_start: 0.8947 (pt) cc_final: 0.8090 (tp) REVERT: H 179 MET cc_start: 0.7470 (tpt) cc_final: 0.7151 (tpt) REVERT: H 198 ASN cc_start: 0.9644 (m110) cc_final: 0.9414 (m110) REVERT: H 199 GLU cc_start: 0.9623 (mt-10) cc_final: 0.9160 (mm-30) REVERT: H 202 GLN cc_start: 0.9354 (mp10) cc_final: 0.8977 (mp10) REVERT: H 269 ASP cc_start: 0.9155 (t0) cc_final: 0.8278 (t70) REVERT: H 276 SER cc_start: 0.9183 (m) cc_final: 0.8862 (p) REVERT: H 286 MET cc_start: 0.8705 (mtm) cc_final: 0.8431 (mtt) REVERT: H 297 LEU cc_start: 0.8996 (mm) cc_final: 0.8478 (mm) REVERT: H 298 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8225 (mm110) REVERT: H 357 PHE cc_start: 0.9178 (m-80) cc_final: 0.8770 (m-10) REVERT: H 364 ASP cc_start: 0.8824 (t0) cc_final: 0.8571 (t0) REVERT: H 372 HIS cc_start: 0.9511 (m170) cc_final: 0.9195 (m170) REVERT: H 465 GLN cc_start: 0.9067 (pm20) cc_final: 0.8859 (mp10) REVERT: H 489 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7767 (tppt) REVERT: H 490 PHE cc_start: 0.9108 (m-80) cc_final: 0.8533 (m-80) outliers start: 0 outliers final: 0 residues processed: 1354 average time/residue: 0.1700 time to fit residues: 369.9579 Evaluate side-chains 1084 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1084 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092794 restraints weight = 54615.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096952 restraints weight = 34924.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100079 restraints weight = 25058.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102480 restraints weight = 19421.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104113 restraints weight = 15896.041| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28872 Z= 0.149 Angle : 0.887 12.489 39136 Z= 0.425 Chirality : 0.050 0.316 4472 Planarity : 0.005 0.074 4928 Dihedral : 16.264 175.514 4120 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: -2.50 (0.13), residues: 3576 helix: -1.18 (0.14), residues: 1224 sheet: -2.60 (0.25), residues: 344 loop : -1.79 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 480 TYR 0.032 0.002 TYR E 233 PHE 0.026 0.002 PHE C 24 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (28864) covalent geometry : angle 0.88714 / 0.42 (39136) hydrogen bonds : bond 0.03512 / 2.36 ( 888) hydrogen bonds : angle 5.73601 / 3.91 ( 2448) Misc. bond : bond 0.00206 / 0.13 ( 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 1326 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1326 time to evaluate : 1.143 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: A 28 ASP cc_start: 0.8918 (t0) cc_final: 0.8575 (t0) REVERT: A 58 LYS cc_start: 0.9645 (mmpt) cc_final: 0.9419 (mmmm) REVERT: A 75 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 78 MET cc_start: 0.7686 (mpp) cc_final: 0.6911 (mpp) REVERT: A 82 MET cc_start: 0.9190 (tpt) cc_final: 0.8751 (tpp) REVERT: A 88 ILE cc_start: 0.7378 (pt) cc_final: 0.6942 (pt) REVERT: A 94 ASN cc_start: 0.8927 (t0) cc_final: 0.8654 (t0) REVERT: A 166 LEU cc_start: 0.9070 (pt) cc_final: 0.8459 (tp) REVERT: A 199 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9300 (mt-10) REVERT: A 203 ARG cc_start: 0.9492 (mmp80) cc_final: 0.9278 (mmp80) REVERT: A 216 ASP cc_start: 0.9164 (t70) cc_final: 0.8710 (t70) REVERT: A 229 LYS cc_start: 0.9409 (mttt) cc_final: 0.8746 (mttt) REVERT: A 232 ASP cc_start: 0.8929 (m-30) cc_final: 0.8721 (m-30) REVERT: A 241 LYS cc_start: 0.9414 (tptp) cc_final: 0.9079 (tptp) REVERT: A 269 ASP cc_start: 0.9108 (t0) cc_final: 0.8253 (t70) REVERT: A 276 SER cc_start: 0.9192 (m) cc_final: 0.8855 (p) REVERT: A 286 MET cc_start: 0.8861 (mtm) cc_final: 0.8558 (mtt) REVERT: A 296 ASN cc_start: 0.9346 (p0) cc_final: 0.8800 (p0) REVERT: A 297 LEU cc_start: 0.8881 (mm) cc_final: 0.8433 (mm) REVERT: A 298 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8260 (mm110) REVERT: A 355 ARG cc_start: 0.9072 (ptm160) cc_final: 0.8819 (ptm160) REVERT: A 372 HIS cc_start: 0.9367 (m90) cc_final: 0.8810 (m90) REVERT: A 402 PHE cc_start: 0.8120 (m-80) cc_final: 0.7855 (m-80) REVERT: A 450 LYS cc_start: 0.7385 (pttm) cc_final: 0.6225 (ptmm) REVERT: A 479 VAL cc_start: 0.9315 (p) cc_final: 0.9076 (t) REVERT: A 489 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7731 (ttmt) REVERT: A 490 PHE cc_start: 0.8869 (m-80) cc_final: 0.8511 (m-80) REVERT: A 493 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8702 (ttm-80) REVERT: B 28 ASP cc_start: 0.9298 (t0) cc_final: 0.8910 (t0) REVERT: B 58 LYS cc_start: 0.9603 (mmpt) cc_final: 0.9369 (mmmm) REVERT: B 66 VAL cc_start: 0.9069 (m) cc_final: 0.8628 (m) REVERT: B 67 SER cc_start: 0.9524 (t) cc_final: 0.9045 (t) REVERT: B 78 MET cc_start: 0.7985 (mpp) cc_final: 0.7690 (mpp) REVERT: B 82 MET cc_start: 0.8824 (tpp) cc_final: 0.8262 (tpp) REVERT: B 94 ASN cc_start: 0.8940 (t0) cc_final: 0.8718 (t0) REVERT: B 105 ARG cc_start: 0.9129 (mmt180) cc_final: 0.8812 (mmt180) REVERT: B 108 LYS cc_start: 0.9431 (tptp) cc_final: 0.9230 (mtpt) REVERT: B 132 GLU cc_start: 0.9470 (pp20) cc_final: 0.9258 (pp20) REVERT: B 166 LEU cc_start: 0.9017 (pt) cc_final: 0.8418 (tp) REVERT: B 199 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9281 (mt-10) REVERT: B 229 LYS cc_start: 0.9414 (mttt) cc_final: 0.8921 (mttt) REVERT: B 269 ASP cc_start: 0.9118 (t0) cc_final: 0.8197 (t70) REVERT: B 276 SER cc_start: 0.9210 (m) cc_final: 0.8879 (p) REVERT: B 296 ASN cc_start: 0.9431 (p0) cc_final: 0.8576 (p0) REVERT: B 297 LEU cc_start: 0.9050 (mm) cc_final: 0.8604 (mm) REVERT: B 298 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8260 (mm110) REVERT: B 450 LYS cc_start: 0.7346 (pttm) cc_final: 0.6084 (ptmm) REVERT: B 461 ILE cc_start: 0.9713 (pt) cc_final: 0.9493 (pt) REVERT: B 465 GLN cc_start: 0.9194 (mt0) cc_final: 0.8848 (pt0) REVERT: B 490 PHE cc_start: 0.9070 (m-80) cc_final: 0.8589 (m-80) REVERT: C 58 LYS cc_start: 0.9634 (mmpt) cc_final: 0.9392 (mmmm) REVERT: C 75 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 78 MET cc_start: 0.8146 (mpp) cc_final: 0.7019 (mpp) REVERT: C 82 MET cc_start: 0.8924 (tpp) cc_final: 0.8720 (tpp) REVERT: C 88 ILE cc_start: 0.7445 (pt) cc_final: 0.6904 (pt) REVERT: C 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8572 (t0) REVERT: C 109 LYS cc_start: 0.9239 (tptp) cc_final: 0.8987 (tptp) REVERT: C 166 LEU cc_start: 0.8950 (pt) cc_final: 0.8227 (tp) REVERT: C 232 ASP cc_start: 0.8873 (m-30) cc_final: 0.8648 (m-30) REVERT: C 261 ASP cc_start: 0.9319 (m-30) cc_final: 0.8884 (m-30) REVERT: C 276 SER cc_start: 0.9257 (m) cc_final: 0.8938 (p) REVERT: C 286 MET cc_start: 0.8992 (mtm) cc_final: 0.8302 (mtt) REVERT: C 296 ASN cc_start: 0.9308 (p0) cc_final: 0.8598 (p0) REVERT: C 297 LEU cc_start: 0.8734 (mm) cc_final: 0.8528 (mm) REVERT: C 298 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8330 (mm-40) REVERT: C 372 HIS cc_start: 0.9462 (m90) cc_final: 0.8833 (m90) REVERT: C 489 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7675 (ttmt) REVERT: C 490 PHE cc_start: 0.9086 (m-80) cc_final: 0.8622 (m-80) REVERT: C 493 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8058 (ttm110) REVERT: D 28 ASP cc_start: 0.9368 (t0) cc_final: 0.9065 (t0) REVERT: D 65 LEU cc_start: 0.8848 (pt) cc_final: 0.8575 (pt) REVERT: D 66 VAL cc_start: 0.9107 (m) cc_final: 0.8231 (m) REVERT: D 75 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7286 (tm-30) REVERT: D 78 MET cc_start: 0.7922 (mpp) cc_final: 0.7266 (mpp) REVERT: D 82 MET cc_start: 0.8980 (tpp) cc_final: 0.8430 (tpp) REVERT: D 88 ILE cc_start: 0.8091 (mt) cc_final: 0.7865 (pt) REVERT: D 94 ASN cc_start: 0.8866 (t0) cc_final: 0.8628 (t0) REVERT: D 166 LEU cc_start: 0.9033 (pt) cc_final: 0.8302 (tp) REVERT: D 229 LYS cc_start: 0.9509 (mttm) cc_final: 0.8987 (mttm) REVERT: D 261 ASP cc_start: 0.9143 (m-30) cc_final: 0.8537 (p0) REVERT: D 262 LEU cc_start: 0.9677 (tt) cc_final: 0.9288 (pp) REVERT: D 276 SER cc_start: 0.9204 (m) cc_final: 0.8920 (p) REVERT: D 286 MET cc_start: 0.8806 (mtm) cc_final: 0.8464 (mtt) REVERT: D 372 HIS cc_start: 0.9177 (m90) cc_final: 0.8941 (m90) REVERT: D 385 MET cc_start: 0.8882 (ttt) cc_final: 0.8566 (tpp) REVERT: D 465 GLN cc_start: 0.9059 (mp10) cc_final: 0.8821 (pm20) REVERT: D 489 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7067 (ttpt) REVERT: D 490 PHE cc_start: 0.8980 (m-80) cc_final: 0.8126 (m-80) REVERT: D 493 ARG cc_start: 0.9027 (ttm-80) cc_final: 0.8769 (ttm-80) REVERT: E 12 TYR cc_start: 0.9374 (t80) cc_final: 0.8703 (t80) REVERT: E 58 LYS cc_start: 0.9626 (mmpt) cc_final: 0.9412 (mmmm) REVERT: E 66 VAL cc_start: 0.9237 (m) cc_final: 0.9020 (m) REVERT: E 67 SER cc_start: 0.9267 (m) cc_final: 0.8926 (m) REVERT: E 75 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 78 MET cc_start: 0.7637 (mpp) cc_final: 0.6793 (mpp) REVERT: E 82 MET cc_start: 0.9190 (tpt) cc_final: 0.8556 (tpp) REVERT: E 88 ILE cc_start: 0.7308 (pt) cc_final: 0.6969 (pt) REVERT: E 94 ASN cc_start: 0.8856 (t0) cc_final: 0.8644 (t0) REVERT: E 103 GLU cc_start: 0.9332 (mp0) cc_final: 0.9121 (mp0) REVERT: E 106 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8907 (mmtm) REVERT: E 166 LEU cc_start: 0.9101 (pt) cc_final: 0.8373 (tp) REVERT: E 174 PHE cc_start: 0.9270 (m-10) cc_final: 0.8902 (m-80) REVERT: E 229 LYS cc_start: 0.9428 (mttt) cc_final: 0.8826 (mttt) REVERT: E 261 ASP cc_start: 0.9323 (m-30) cc_final: 0.8903 (m-30) REVERT: E 296 ASN cc_start: 0.9376 (p0) cc_final: 0.8158 (p0) REVERT: E 297 LEU cc_start: 0.8881 (mm) cc_final: 0.8588 (mm) REVERT: E 298 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8244 (mm110) REVERT: E 372 HIS cc_start: 0.9157 (m90) cc_final: 0.8798 (m90) REVERT: E 399 GLU cc_start: 0.9324 (tm-30) cc_final: 0.9062 (tm-30) REVERT: E 456 PHE cc_start: 0.9622 (t80) cc_final: 0.9396 (t80) REVERT: E 493 ARG cc_start: 0.8953 (ttt90) cc_final: 0.8696 (ttm-80) REVERT: F 12 TYR cc_start: 0.9596 (t80) cc_final: 0.9184 (t80) REVERT: F 28 ASP cc_start: 0.9263 (t0) cc_final: 0.9034 (t0) REVERT: F 78 MET cc_start: 0.7976 (mpp) cc_final: 0.7419 (mpp) REVERT: F 82 MET cc_start: 0.8980 (tpp) cc_final: 0.8447 (tpp) REVERT: F 109 LYS cc_start: 0.8936 (tptp) cc_final: 0.8335 (tptp) REVERT: F 130 VAL cc_start: 0.9604 (m) cc_final: 0.9296 (m) REVERT: F 134 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9135 (mmmt) REVERT: F 166 LEU cc_start: 0.8974 (pt) cc_final: 0.8042 (tp) REVERT: F 168 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8830 (tp30) REVERT: F 199 GLU cc_start: 0.9509 (pt0) cc_final: 0.9295 (pt0) REVERT: F 202 GLN cc_start: 0.9336 (mp10) cc_final: 0.8628 (mp10) REVERT: F 203 ARG cc_start: 0.9412 (mmp80) cc_final: 0.9189 (mmp80) REVERT: F 214 GLU cc_start: 0.9429 (pm20) cc_final: 0.9135 (pm20) REVERT: F 269 ASP cc_start: 0.9175 (t0) cc_final: 0.8265 (t70) REVERT: F 296 ASN cc_start: 0.9402 (p0) cc_final: 0.8598 (p0) REVERT: F 297 LEU cc_start: 0.9019 (mm) cc_final: 0.8609 (mm) REVERT: F 298 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8238 (mm110) REVERT: F 353 TYR cc_start: 0.9220 (t80) cc_final: 0.9005 (t80) REVERT: F 456 PHE cc_start: 0.9641 (t80) cc_final: 0.9339 (t80) REVERT: F 460 LEU cc_start: 0.9834 (mt) cc_final: 0.9595 (mt) REVERT: G 12 TYR cc_start: 0.9441 (t80) cc_final: 0.9143 (t80) REVERT: G 28 ASP cc_start: 0.9174 (t0) cc_final: 0.8914 (t0) REVERT: G 58 LYS cc_start: 0.9643 (mmpt) cc_final: 0.9429 (mmmm) REVERT: G 65 LEU cc_start: 0.8960 (pt) cc_final: 0.8635 (pt) REVERT: G 78 MET cc_start: 0.7746 (mpp) cc_final: 0.7178 (mpp) REVERT: G 82 MET cc_start: 0.8874 (tpp) cc_final: 0.8491 (tpp) REVERT: G 88 ILE cc_start: 0.7521 (pt) cc_final: 0.6959 (pt) REVERT: G 94 ASN cc_start: 0.8958 (t0) cc_final: 0.8681 (t0) REVERT: G 166 LEU cc_start: 0.9097 (pt) cc_final: 0.8382 (tp) REVERT: G 261 ASP cc_start: 0.9343 (m-30) cc_final: 0.9005 (m-30) REVERT: G 269 ASP cc_start: 0.9129 (t0) cc_final: 0.8303 (t70) REVERT: G 276 SER cc_start: 0.9196 (m) cc_final: 0.8865 (p) REVERT: G 297 LEU cc_start: 0.8933 (mm) cc_final: 0.8508 (mm) REVERT: G 298 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8157 (mm110) REVERT: G 402 PHE cc_start: 0.8068 (m-80) cc_final: 0.7657 (m-80) REVERT: G 450 LYS cc_start: 0.7517 (pttm) cc_final: 0.6495 (ptmm) REVERT: G 489 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7768 (ttpt) REVERT: G 490 PHE cc_start: 0.8949 (m-80) cc_final: 0.8212 (m-80) REVERT: G 493 ARG cc_start: 0.9066 (ttt90) cc_final: 0.8740 (ttm-80) REVERT: H 28 ASP cc_start: 0.9262 (t0) cc_final: 0.8957 (t0) REVERT: H 30 LEU cc_start: 0.8720 (mt) cc_final: 0.8431 (mt) REVERT: H 58 LYS cc_start: 0.9618 (mmpt) cc_final: 0.9388 (mmmm) REVERT: H 66 VAL cc_start: 0.9091 (m) cc_final: 0.8755 (m) REVERT: H 82 MET cc_start: 0.8667 (tpp) cc_final: 0.8362 (tpp) REVERT: H 88 ILE cc_start: 0.7201 (pt) cc_final: 0.6829 (pt) REVERT: H 94 ASN cc_start: 0.8881 (t0) cc_final: 0.8666 (t0) REVERT: H 105 ARG cc_start: 0.8700 (mmt180) cc_final: 0.8364 (mmt180) REVERT: H 130 VAL cc_start: 0.9599 (m) cc_final: 0.9159 (m) REVERT: H 134 LYS cc_start: 0.9525 (mmmt) cc_final: 0.9160 (mmmm) REVERT: H 166 LEU cc_start: 0.8982 (pt) cc_final: 0.8131 (tp) REVERT: H 199 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9094 (mm-30) REVERT: H 229 LYS cc_start: 0.9545 (mttm) cc_final: 0.9060 (mttm) REVERT: H 269 ASP cc_start: 0.9098 (t0) cc_final: 0.8160 (t70) REVERT: H 276 SER cc_start: 0.9198 (m) cc_final: 0.8879 (p) REVERT: H 286 MET cc_start: 0.8718 (mtm) cc_final: 0.8428 (mtt) REVERT: H 297 LEU cc_start: 0.8969 (mm) cc_final: 0.8460 (mm) REVERT: H 298 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8164 (mm110) REVERT: H 353 TYR cc_start: 0.9257 (t80) cc_final: 0.9039 (t80) REVERT: H 357 PHE cc_start: 0.9196 (m-80) cc_final: 0.8953 (m-10) REVERT: H 372 HIS cc_start: 0.9538 (m170) cc_final: 0.9149 (m170) REVERT: H 489 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7807 (tppt) REVERT: H 490 PHE cc_start: 0.9127 (m-80) cc_final: 0.8658 (m-80) outliers start: 0 outliers final: 0 residues processed: 1326 average time/residue: 0.1806 time to fit residues: 382.7555 Evaluate side-chains 1082 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1082 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.7980 chunk 311 optimal weight: 0.8980 chunk 304 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 229 optimal weight: 0.3980 chunk 294 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN B 454 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 HIS F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN G 454 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090997 restraints weight = 55684.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094828 restraints weight = 36437.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097721 restraints weight = 26631.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099914 restraints weight = 20901.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101623 restraints weight = 17281.752| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28872 Z= 0.172 Angle : 0.880 13.028 39136 Z= 0.425 Chirality : 0.050 0.336 4472 Planarity : 0.005 0.068 4928 Dihedral : 16.316 177.866 4120 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % 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: -2.51 (0.13), residues: 3576 helix: -1.18 (0.13), residues: 1232 sheet: -2.52 (0.25), residues: 344 loop : -1.82 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 480 TYR 0.032 0.002 TYR E 233 PHE 0.023 0.002 PHE C 456 HIS 0.005 0.001 HIS G 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (28864) covalent geometry : angle 0.87991 / 0.42 (39136) hydrogen bonds : bond 0.03499 / 2.37 ( 888) hydrogen bonds : angle 5.75084 / 3.91 ( 2448) Misc. bond : bond 0.00194 / 0.12 ( 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 1292 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1292 time to evaluate : 1.062 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: A 28 ASP cc_start: 0.8930 (t0) cc_final: 0.8657 (t0) REVERT: A 67 SER cc_start: 0.9306 (m) cc_final: 0.8947 (m) REVERT: A 75 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 78 MET cc_start: 0.8018 (mpp) cc_final: 0.7268 (mpp) REVERT: A 82 MET cc_start: 0.9252 (tpt) cc_final: 0.8619 (tpp) REVERT: A 88 ILE cc_start: 0.7607 (pt) cc_final: 0.7161 (pt) REVERT: A 93 HIS cc_start: 0.9178 (p90) cc_final: 0.8712 (p90) REVERT: A 94 ASN cc_start: 0.8912 (t0) cc_final: 0.8495 (t0) REVERT: A 103 GLU cc_start: 0.9414 (mp0) cc_final: 0.9210 (mp0) REVERT: A 166 LEU cc_start: 0.9120 (pt) cc_final: 0.8525 (tp) REVERT: A 178 ILE cc_start: 0.9299 (mp) cc_final: 0.8518 (mp) REVERT: A 179 MET cc_start: 0.7344 (tpt) cc_final: 0.7084 (tpt) REVERT: A 199 GLU cc_start: 0.9625 (mt-10) cc_final: 0.9327 (mt-10) REVERT: A 202 GLN cc_start: 0.9343 (mp10) cc_final: 0.8665 (mp10) REVERT: A 203 ARG cc_start: 0.9521 (mmp80) cc_final: 0.9263 (mmp80) REVERT: A 216 ASP cc_start: 0.9173 (t70) cc_final: 0.8788 (t70) REVERT: A 229 LYS cc_start: 0.9406 (mttt) cc_final: 0.8801 (mttt) REVERT: A 232 ASP cc_start: 0.8949 (m-30) cc_final: 0.8738 (m-30) REVERT: A 241 LYS cc_start: 0.9428 (tptp) cc_final: 0.9143 (tptp) REVERT: A 269 ASP cc_start: 0.9112 (t0) cc_final: 0.8368 (t70) REVERT: A 276 SER cc_start: 0.9252 (m) cc_final: 0.8937 (p) REVERT: A 286 MET cc_start: 0.8824 (mtm) cc_final: 0.8615 (mtt) REVERT: A 296 ASN cc_start: 0.9362 (p0) cc_final: 0.8708 (p0) REVERT: A 298 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8275 (mm110) REVERT: A 355 ARG cc_start: 0.9046 (ptm160) cc_final: 0.8836 (ptm160) REVERT: A 372 HIS cc_start: 0.9248 (m90) cc_final: 0.8812 (m90) REVERT: A 399 GLU cc_start: 0.9392 (tm-30) cc_final: 0.9168 (tm-30) REVERT: A 402 PHE cc_start: 0.8127 (m-80) cc_final: 0.7893 (m-80) REVERT: A 450 LYS cc_start: 0.7488 (pttm) cc_final: 0.6424 (ptmm) REVERT: A 489 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7495 (ttmt) REVERT: A 490 PHE cc_start: 0.8804 (m-80) cc_final: 0.8410 (m-80) REVERT: B 28 ASP cc_start: 0.9266 (t0) cc_final: 0.8723 (t0) REVERT: B 66 VAL cc_start: 0.9076 (m) cc_final: 0.8708 (m) REVERT: B 82 MET cc_start: 0.8796 (tpp) cc_final: 0.8271 (tpp) REVERT: B 94 ASN cc_start: 0.8935 (t0) cc_final: 0.8709 (t0) REVERT: B 105 ARG cc_start: 0.9161 (mmt180) cc_final: 0.8838 (mmt180) REVERT: B 108 LYS cc_start: 0.9471 (tptp) cc_final: 0.9270 (mtpt) REVERT: B 132 GLU cc_start: 0.9463 (pp20) cc_final: 0.9247 (pp20) REVERT: B 166 LEU cc_start: 0.9036 (pt) cc_final: 0.8411 (tp) REVERT: B 199 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9286 (mt-10) REVERT: B 202 GLN cc_start: 0.9339 (mp10) cc_final: 0.8638 (mp10) REVERT: B 203 ARG cc_start: 0.9449 (mmp80) cc_final: 0.9161 (mmp80) REVERT: B 229 LYS cc_start: 0.9449 (mttt) cc_final: 0.8915 (mttt) REVERT: B 269 ASP cc_start: 0.9140 (t0) cc_final: 0.8320 (t70) REVERT: B 276 SER cc_start: 0.9298 (m) cc_final: 0.8999 (p) REVERT: B 296 ASN cc_start: 0.9438 (p0) cc_final: 0.8441 (p0) REVERT: B 298 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8297 (mm110) REVERT: B 401 PHE cc_start: 0.9239 (p90) cc_final: 0.9018 (p90) REVERT: B 450 LYS cc_start: 0.7235 (pttm) cc_final: 0.5682 (ptmm) REVERT: B 465 GLN cc_start: 0.9235 (mt0) cc_final: 0.8896 (pt0) REVERT: B 490 PHE cc_start: 0.9101 (m-80) cc_final: 0.8679 (m-80) REVERT: C 58 LYS cc_start: 0.9658 (mmpt) cc_final: 0.9418 (mmmm) REVERT: C 82 MET cc_start: 0.8905 (tpp) cc_final: 0.8660 (tpp) REVERT: C 88 ILE cc_start: 0.7445 (pt) cc_final: 0.6903 (pt) REVERT: C 94 ASN cc_start: 0.8842 (t0) cc_final: 0.8565 (t0) REVERT: C 166 LEU cc_start: 0.8980 (pt) cc_final: 0.8300 (tp) REVERT: C 261 ASP cc_start: 0.9327 (m-30) cc_final: 0.9063 (m-30) REVERT: C 276 SER cc_start: 0.9291 (m) cc_final: 0.8959 (p) REVERT: C 285 ASN cc_start: 0.9484 (m110) cc_final: 0.9191 (m110) REVERT: C 286 MET cc_start: 0.9005 (mtm) cc_final: 0.8347 (mtt) REVERT: C 296 ASN cc_start: 0.9323 (p0) cc_final: 0.8653 (p0) REVERT: C 297 LEU cc_start: 0.8716 (mm) cc_final: 0.8469 (mm) REVERT: C 298 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8355 (mm-40) REVERT: C 479 VAL cc_start: 0.9330 (p) cc_final: 0.9057 (t) REVERT: C 489 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7595 (tppt) REVERT: C 490 PHE cc_start: 0.9151 (m-80) cc_final: 0.8790 (m-80) REVERT: C 493 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8141 (ttm110) REVERT: D 28 ASP cc_start: 0.9347 (t0) cc_final: 0.9065 (t0) REVERT: D 65 LEU cc_start: 0.8834 (pt) cc_final: 0.8575 (pt) REVERT: D 75 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 78 MET cc_start: 0.8402 (mpp) cc_final: 0.7674 (mpp) REVERT: D 82 MET cc_start: 0.8913 (tpp) cc_final: 0.8341 (tpp) REVERT: D 88 ILE cc_start: 0.8214 (mt) cc_final: 0.7888 (pt) REVERT: D 94 ASN cc_start: 0.8871 (t0) cc_final: 0.8649 (t0) REVERT: D 166 LEU cc_start: 0.9080 (pt) cc_final: 0.8358 (tp) REVERT: D 199 GLU cc_start: 0.9463 (pt0) cc_final: 0.9184 (pt0) REVERT: D 202 GLN cc_start: 0.9315 (mp10) cc_final: 0.8414 (mp10) REVERT: D 203 ARG cc_start: 0.9439 (mmp80) cc_final: 0.9116 (mmp80) REVERT: D 261 ASP cc_start: 0.9144 (m-30) cc_final: 0.8522 (p0) REVERT: D 262 LEU cc_start: 0.9685 (tt) cc_final: 0.9473 (tt) REVERT: D 276 SER cc_start: 0.9278 (m) cc_final: 0.9003 (p) REVERT: D 281 ILE cc_start: 0.9529 (mp) cc_final: 0.9237 (mp) REVERT: D 285 ASN cc_start: 0.9498 (m110) cc_final: 0.9259 (m110) REVERT: D 286 MET cc_start: 0.8872 (mtm) cc_final: 0.8467 (mtt) REVERT: D 385 MET cc_start: 0.8841 (ttt) cc_final: 0.8538 (tpp) REVERT: D 465 GLN cc_start: 0.9026 (mp10) cc_final: 0.8815 (pm20) REVERT: D 482 MET cc_start: 0.8674 (tmm) cc_final: 0.8314 (tmm) REVERT: D 489 LYS cc_start: 0.7515 (ttpt) cc_final: 0.6998 (ttpt) REVERT: D 490 PHE cc_start: 0.8999 (m-80) cc_final: 0.8232 (m-80) REVERT: D 493 ARG cc_start: 0.9098 (ttm-80) cc_final: 0.8847 (ttm-80) REVERT: E 12 TYR cc_start: 0.9418 (t80) cc_final: 0.8721 (t80) REVERT: E 58 LYS cc_start: 0.9652 (mmpt) cc_final: 0.9427 (mmmm) REVERT: E 66 VAL cc_start: 0.9285 (m) cc_final: 0.9009 (m) REVERT: E 67 SER cc_start: 0.9336 (m) cc_final: 0.9062 (m) REVERT: E 75 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 78 MET cc_start: 0.7890 (mpp) cc_final: 0.7005 (mpp) REVERT: E 82 MET cc_start: 0.9098 (tpt) cc_final: 0.8387 (tpp) REVERT: E 88 ILE cc_start: 0.7255 (pt) cc_final: 0.6862 (pt) REVERT: E 94 ASN cc_start: 0.8868 (t0) cc_final: 0.8667 (t0) REVERT: E 103 GLU cc_start: 0.9345 (mp0) cc_final: 0.9136 (mp0) REVERT: E 106 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8979 (mmtm) REVERT: E 166 LEU cc_start: 0.9167 (pt) cc_final: 0.8491 (tp) REVERT: E 203 ARG cc_start: 0.9447 (mmp80) cc_final: 0.9181 (mmp80) REVERT: E 229 LYS cc_start: 0.9431 (mttt) cc_final: 0.8867 (mttt) REVERT: E 261 ASP cc_start: 0.9323 (m-30) cc_final: 0.8683 (p0) REVERT: E 262 LEU cc_start: 0.9682 (tt) cc_final: 0.9454 (tt) REVERT: E 286 MET cc_start: 0.8827 (mtm) cc_final: 0.8627 (mtt) REVERT: E 296 ASN cc_start: 0.9377 (p0) cc_final: 0.8059 (p0) REVERT: E 298 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8281 (mm110) REVERT: E 456 PHE cc_start: 0.9623 (t80) cc_final: 0.9391 (t80) REVERT: E 493 ARG cc_start: 0.8984 (ttt90) cc_final: 0.8612 (ttm-80) REVERT: F 12 TYR cc_start: 0.9557 (t80) cc_final: 0.9154 (t80) REVERT: F 28 ASP cc_start: 0.9261 (t0) cc_final: 0.9016 (t0) REVERT: F 78 MET cc_start: 0.8032 (mpp) cc_final: 0.7418 (mpp) REVERT: F 82 MET cc_start: 0.8990 (tpp) cc_final: 0.8392 (tpp) REVERT: F 88 ILE cc_start: 0.7242 (pt) cc_final: 0.6706 (pt) REVERT: F 105 ARG cc_start: 0.8703 (mmt180) cc_final: 0.8227 (mmt180) REVERT: F 109 LYS cc_start: 0.8970 (tptp) cc_final: 0.8356 (tptp) REVERT: F 134 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9082 (mmmm) REVERT: F 166 LEU cc_start: 0.9093 (pt) cc_final: 0.8297 (tp) REVERT: F 214 GLU cc_start: 0.9486 (pm20) cc_final: 0.9271 (pm20) REVERT: F 232 ASP cc_start: 0.8977 (t70) cc_final: 0.8773 (t0) REVERT: F 269 ASP cc_start: 0.9100 (t0) cc_final: 0.8144 (t70) REVERT: F 296 ASN cc_start: 0.9382 (p0) cc_final: 0.8458 (p0) REVERT: F 297 LEU cc_start: 0.9095 (mm) cc_final: 0.8544 (mm) REVERT: F 298 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8259 (mm110) REVERT: F 395 GLU cc_start: 0.8734 (pm20) cc_final: 0.8409 (mp0) REVERT: F 456 PHE cc_start: 0.9639 (t80) cc_final: 0.9273 (t80) REVERT: F 460 LEU cc_start: 0.9830 (mt) cc_final: 0.9550 (mt) REVERT: F 479 VAL cc_start: 0.9217 (p) cc_final: 0.8902 (t) REVERT: F 482 MET cc_start: 0.8565 (tmm) cc_final: 0.8214 (tmm) REVERT: F 489 LYS cc_start: 0.7369 (ttpt) cc_final: 0.7085 (ttpt) REVERT: F 490 PHE cc_start: 0.8668 (m-80) cc_final: 0.8409 (m-80) REVERT: G 12 TYR cc_start: 0.9438 (t80) cc_final: 0.9189 (t80) REVERT: G 28 ASP cc_start: 0.9268 (t0) cc_final: 0.8975 (t0) REVERT: G 30 LEU cc_start: 0.8819 (mt) cc_final: 0.8610 (mt) REVERT: G 58 LYS cc_start: 0.9668 (mmpt) cc_final: 0.9452 (mmmm) REVERT: G 66 VAL cc_start: 0.9226 (m) cc_final: 0.8750 (m) REVERT: G 82 MET cc_start: 0.8888 (tpp) cc_final: 0.8439 (tpp) REVERT: G 88 ILE cc_start: 0.7535 (pt) cc_final: 0.7052 (pt) REVERT: G 93 HIS cc_start: 0.9133 (p90) cc_final: 0.8666 (p90) REVERT: G 94 ASN cc_start: 0.8891 (t0) cc_final: 0.8467 (t0) REVERT: G 105 ARG cc_start: 0.9088 (mmt-90) cc_final: 0.8878 (mmt180) REVERT: G 154 LEU cc_start: 0.9609 (mm) cc_final: 0.9369 (mm) REVERT: G 166 LEU cc_start: 0.9107 (pt) cc_final: 0.8392 (tp) REVERT: G 261 ASP cc_start: 0.9327 (m-30) cc_final: 0.8975 (m-30) REVERT: G 269 ASP cc_start: 0.9109 (t0) cc_final: 0.8355 (t70) REVERT: G 276 SER cc_start: 0.9225 (m) cc_final: 0.8893 (p) REVERT: G 296 ASN cc_start: 0.9286 (p0) cc_final: 0.8515 (p0) REVERT: G 298 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8239 (mm110) REVERT: G 401 PHE cc_start: 0.9231 (p90) cc_final: 0.8989 (p90) REVERT: G 402 PHE cc_start: 0.8070 (m-80) cc_final: 0.7808 (m-80) REVERT: G 450 LYS cc_start: 0.7603 (pttm) cc_final: 0.6515 (ptmm) REVERT: G 479 VAL cc_start: 0.9138 (p) cc_final: 0.8807 (t) REVERT: G 489 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7978 (ttpt) REVERT: G 490 PHE cc_start: 0.8988 (m-80) cc_final: 0.8372 (m-80) REVERT: G 493 ARG cc_start: 0.9117 (ttt90) cc_final: 0.8915 (ttm-80) REVERT: H 28 ASP cc_start: 0.9273 (t0) cc_final: 0.8962 (t0) REVERT: H 30 LEU cc_start: 0.8785 (mt) cc_final: 0.8464 (mt) REVERT: H 66 VAL cc_start: 0.9163 (m) cc_final: 0.8776 (m) REVERT: H 82 MET cc_start: 0.8710 (tpp) cc_final: 0.8374 (tpp) REVERT: H 88 ILE cc_start: 0.7256 (pt) cc_final: 0.6880 (pt) REVERT: H 94 ASN cc_start: 0.8903 (t0) cc_final: 0.8680 (t0) REVERT: H 103 GLU cc_start: 0.9370 (mp0) cc_final: 0.9138 (pm20) REVERT: H 109 LYS cc_start: 0.8823 (tptp) cc_final: 0.8250 (tptp) REVERT: H 166 LEU cc_start: 0.9047 (pt) cc_final: 0.8262 (tp) REVERT: H 178 ILE cc_start: 0.9211 (mp) cc_final: 0.8620 (mm) REVERT: H 179 MET cc_start: 0.7232 (tpt) cc_final: 0.6950 (tpt) REVERT: H 199 GLU cc_start: 0.9615 (mt-10) cc_final: 0.9139 (mm-30) REVERT: H 203 ARG cc_start: 0.9461 (mmp80) cc_final: 0.9220 (mmp80) REVERT: H 269 ASP cc_start: 0.9096 (t0) cc_final: 0.8223 (t70) REVERT: H 276 SER cc_start: 0.9231 (m) cc_final: 0.8920 (p) REVERT: H 286 MET cc_start: 0.8725 (mtm) cc_final: 0.8436 (mtt) REVERT: H 296 ASN cc_start: 0.9384 (p0) cc_final: 0.8582 (p0) REVERT: H 298 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8307 (mm110) REVERT: H 353 TYR cc_start: 0.9243 (t80) cc_final: 0.9019 (t80) REVERT: H 364 ASP cc_start: 0.8745 (t0) cc_final: 0.8503 (t0) REVERT: H 372 HIS cc_start: 0.9534 (m170) cc_final: 0.9098 (m170) REVERT: H 482 MET cc_start: 0.8757 (tmm) cc_final: 0.8422 (tmm) REVERT: H 489 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7883 (ttmt) REVERT: H 490 PHE cc_start: 0.9109 (m-80) cc_final: 0.8735 (m-80) outliers start: 0 outliers final: 0 residues processed: 1292 average time/residue: 0.1781 time to fit residues: 368.0851 Evaluate side-chains 1084 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1084 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 262 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 5 optimal weight: 0.0070 chunk 227 optimal weight: 0.2980 chunk 198 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 310 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 247 optimal weight: 0.0070 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 448 GLN B 454 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.093400 restraints weight = 53666.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097499 restraints weight = 34352.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100575 restraints weight = 24642.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102890 restraints weight = 19102.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.104719 restraints weight = 15653.519| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28872 Z= 0.145 Angle : 0.919 13.933 39136 Z= 0.435 Chirality : 0.051 0.245 4472 Planarity : 0.005 0.059 4928 Dihedral : 16.261 179.768 4120 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % 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: -2.54 (0.13), residues: 3576 helix: -1.24 (0.13), residues: 1232 sheet: -2.45 (0.25), residues: 344 loop : -1.84 (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 E 233 PHE 0.026 0.002 PHE H 456 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (28864) covalent geometry : angle 0.91860 / 0.43 (39136) hydrogen bonds : bond 0.03455 / 2.33 ( 888) hydrogen bonds : angle 5.76238 / 3.91 ( 2448) Misc. bond : bond 0.00205 / 0.13 ( 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 1350 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1350 time to evaluate : 0.971 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: A 75 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 78 MET cc_start: 0.7700 (mpp) cc_final: 0.6844 (mpp) REVERT: A 82 MET cc_start: 0.9214 (tpt) cc_final: 0.8648 (tpp) REVERT: A 88 ILE cc_start: 0.7439 (pt) cc_final: 0.6970 (pt) REVERT: A 93 HIS cc_start: 0.9241 (p90) cc_final: 0.8828 (p90) REVERT: A 94 ASN cc_start: 0.8916 (t0) cc_final: 0.8492 (t0) REVERT: A 105 ARG cc_start: 0.8942 (mmt-90) cc_final: 0.8732 (mmt-90) REVERT: A 166 LEU cc_start: 0.9101 (pt) cc_final: 0.8531 (tp) REVERT: A 179 MET cc_start: 0.7414 (tpt) cc_final: 0.7168 (tpt) REVERT: A 199 GLU cc_start: 0.9605 (mt-10) cc_final: 0.9303 (mt-10) REVERT: A 202 GLN cc_start: 0.9318 (mp10) cc_final: 0.8663 (mp10) REVERT: A 203 ARG cc_start: 0.9505 (mmp80) cc_final: 0.9255 (mmp80) REVERT: A 216 ASP cc_start: 0.9099 (t70) cc_final: 0.8706 (t70) REVERT: A 229 LYS cc_start: 0.9378 (mttt) cc_final: 0.8789 (mttt) REVERT: A 232 ASP cc_start: 0.8838 (m-30) cc_final: 0.8636 (m-30) REVERT: A 241 LYS cc_start: 0.9387 (tptp) cc_final: 0.9091 (tptp) REVERT: A 261 ASP cc_start: 0.9107 (m-30) cc_final: 0.8853 (p0) REVERT: A 262 LEU cc_start: 0.9264 (pp) cc_final: 0.9005 (pp) REVERT: A 269 ASP cc_start: 0.9147 (t0) cc_final: 0.8377 (t70) REVERT: A 276 SER cc_start: 0.9250 (m) cc_final: 0.8909 (p) REVERT: A 296 ASN cc_start: 0.9388 (p0) cc_final: 0.8783 (p0) REVERT: A 297 LEU cc_start: 0.8730 (mm) cc_final: 0.8371 (mm) REVERT: A 298 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8297 (mm110) REVERT: A 372 HIS cc_start: 0.9232 (m90) cc_final: 0.8839 (m90) REVERT: A 402 PHE cc_start: 0.8025 (m-80) cc_final: 0.7823 (m-80) REVERT: A 450 LYS cc_start: 0.7555 (pttm) cc_final: 0.6507 (ptmm) REVERT: A 489 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7645 (ttmt) REVERT: A 490 PHE cc_start: 0.8872 (m-80) cc_final: 0.8648 (m-80) REVERT: A 493 ARG cc_start: 0.8890 (ttm-80) cc_final: 0.8499 (ttm-80) REVERT: B 19 THR cc_start: 0.9117 (p) cc_final: 0.8736 (p) REVERT: B 51 LEU cc_start: 0.7715 (mm) cc_final: 0.7455 (mm) REVERT: B 66 VAL cc_start: 0.9138 (m) cc_final: 0.8682 (m) REVERT: B 82 MET cc_start: 0.8769 (tpp) cc_final: 0.8352 (tpp) REVERT: B 94 ASN cc_start: 0.8924 (t0) cc_final: 0.8697 (t0) REVERT: B 105 ARG cc_start: 0.9141 (mmt180) cc_final: 0.8650 (mmt180) REVERT: B 132 GLU cc_start: 0.9444 (pp20) cc_final: 0.9232 (pp20) REVERT: B 158 ILE cc_start: 0.8965 (mm) cc_final: 0.8465 (mm) REVERT: B 166 LEU cc_start: 0.8981 (pt) cc_final: 0.8326 (tp) REVERT: B 216 ASP cc_start: 0.9088 (t0) cc_final: 0.8870 (t70) REVERT: B 229 LYS cc_start: 0.9421 (mttt) cc_final: 0.8874 (mttt) REVERT: B 269 ASP cc_start: 0.9155 (t0) cc_final: 0.8842 (t70) REVERT: B 276 SER cc_start: 0.9278 (m) cc_final: 0.8973 (p) REVERT: B 277 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 297 LEU cc_start: 0.8976 (mm) cc_final: 0.8664 (mm) REVERT: B 355 ARG cc_start: 0.9089 (ptm160) cc_final: 0.8821 (ptm160) REVERT: B 450 LYS cc_start: 0.6954 (pttm) cc_final: 0.5505 (ptmm) REVERT: B 465 GLN cc_start: 0.9177 (mt0) cc_final: 0.8167 (mm-40) REVERT: B 490 PHE cc_start: 0.9048 (m-80) cc_final: 0.8528 (m-80) REVERT: C 15 ASP cc_start: 0.9605 (t0) cc_final: 0.9401 (t0) REVERT: C 58 LYS cc_start: 0.9629 (mmpt) cc_final: 0.9356 (mmmm) REVERT: C 66 VAL cc_start: 0.9247 (m) cc_final: 0.8907 (m) REVERT: C 75 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 78 MET cc_start: 0.8223 (mpp) cc_final: 0.6952 (mpp) REVERT: C 82 MET cc_start: 0.8799 (tpp) cc_final: 0.8547 (tpp) REVERT: C 88 ILE cc_start: 0.7319 (pt) cc_final: 0.6974 (pt) REVERT: C 94 ASN cc_start: 0.8818 (t0) cc_final: 0.8533 (t0) REVERT: C 132 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9088 (pp20) REVERT: C 158 ILE cc_start: 0.8968 (mm) cc_final: 0.8619 (mm) REVERT: C 162 ASP cc_start: 0.9265 (m-30) cc_final: 0.9029 (m-30) REVERT: C 166 LEU cc_start: 0.8939 (pt) cc_final: 0.8273 (tp) REVERT: C 261 ASP cc_start: 0.9292 (m-30) cc_final: 0.8889 (m-30) REVERT: C 262 LEU cc_start: 0.9673 (tt) cc_final: 0.9435 (pp) REVERT: C 276 SER cc_start: 0.9261 (m) cc_final: 0.8912 (p) REVERT: C 285 ASN cc_start: 0.9454 (m110) cc_final: 0.9192 (m110) REVERT: C 286 MET cc_start: 0.8979 (mtm) cc_final: 0.8640 (mtt) REVERT: C 296 ASN cc_start: 0.9338 (p0) cc_final: 0.8705 (p0) REVERT: C 297 LEU cc_start: 0.8553 (mm) cc_final: 0.8340 (mm) REVERT: C 298 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8289 (mm-40) REVERT: C 450 LYS cc_start: 0.6996 (pttp) cc_final: 0.6224 (ptmm) REVERT: C 479 VAL cc_start: 0.9290 (p) cc_final: 0.9051 (t) REVERT: C 489 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7651 (ttmt) REVERT: C 490 PHE cc_start: 0.9005 (m-80) cc_final: 0.8711 (m-80) REVERT: C 493 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8043 (ttm110) REVERT: D 28 ASP cc_start: 0.9328 (t0) cc_final: 0.9086 (t0) REVERT: D 30 LEU cc_start: 0.8458 (mt) cc_final: 0.8107 (mp) REVERT: D 66 VAL cc_start: 0.9130 (m) cc_final: 0.8058 (m) REVERT: D 67 SER cc_start: 0.9341 (t) cc_final: 0.9039 (t) REVERT: D 75 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 78 MET cc_start: 0.8252 (mpp) cc_final: 0.7624 (mpp) REVERT: D 82 MET cc_start: 0.8935 (tpp) cc_final: 0.8354 (tpp) REVERT: D 94 ASN cc_start: 0.8859 (t0) cc_final: 0.8639 (t0) REVERT: D 166 LEU cc_start: 0.9061 (pt) cc_final: 0.8384 (tp) REVERT: D 175 LEU cc_start: 0.9360 (mt) cc_final: 0.8928 (mt) REVERT: D 199 GLU cc_start: 0.9453 (pt0) cc_final: 0.9216 (pt0) REVERT: D 203 ARG cc_start: 0.9410 (mmp80) cc_final: 0.9139 (mmp80) REVERT: D 276 SER cc_start: 0.9272 (m) cc_final: 0.8984 (p) REVERT: D 286 MET cc_start: 0.8828 (mtm) cc_final: 0.8504 (mtt) REVERT: D 372 HIS cc_start: 0.9337 (m90) cc_final: 0.8878 (m90) REVERT: D 385 MET cc_start: 0.8811 (ttt) cc_final: 0.8168 (tpp) REVERT: D 465 GLN cc_start: 0.8952 (mp10) cc_final: 0.8736 (pt0) REVERT: D 482 MET cc_start: 0.8642 (tmm) cc_final: 0.8280 (tmm) REVERT: D 489 LYS cc_start: 0.7354 (ttpt) cc_final: 0.6861 (ttpt) REVERT: D 490 PHE cc_start: 0.8881 (m-80) cc_final: 0.8131 (m-80) REVERT: D 493 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8759 (ttm-80) REVERT: E 12 TYR cc_start: 0.9426 (t80) cc_final: 0.8790 (t80) REVERT: E 58 LYS cc_start: 0.9633 (mmpt) cc_final: 0.9386 (mmmm) REVERT: E 75 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 78 MET cc_start: 0.7632 (mpp) cc_final: 0.6758 (mpp) REVERT: E 82 MET cc_start: 0.9154 (tpt) cc_final: 0.8418 (tpp) REVERT: E 88 ILE cc_start: 0.7151 (pt) cc_final: 0.6835 (pt) REVERT: E 93 HIS cc_start: 0.9178 (p90) cc_final: 0.8790 (p90) REVERT: E 94 ASN cc_start: 0.8875 (t0) cc_final: 0.8612 (t0) REVERT: E 103 GLU cc_start: 0.9285 (mp0) cc_final: 0.9081 (mp0) REVERT: E 166 LEU cc_start: 0.9133 (pt) cc_final: 0.8462 (tp) REVERT: E 175 LEU cc_start: 0.9269 (mt) cc_final: 0.8856 (mt) REVERT: E 203 ARG cc_start: 0.9429 (mmp80) cc_final: 0.9144 (mmp80) REVERT: E 229 LYS cc_start: 0.9412 (mttt) cc_final: 0.8887 (mttt) REVERT: E 261 ASP cc_start: 0.9279 (m-30) cc_final: 0.8812 (m-30) REVERT: E 276 SER cc_start: 0.9252 (m) cc_final: 0.8914 (p) REVERT: E 296 ASN cc_start: 0.9387 (p0) cc_final: 0.8190 (p0) REVERT: E 297 LEU cc_start: 0.8755 (mm) cc_final: 0.8405 (mm) REVERT: E 298 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8226 (mm-40) REVERT: E 456 PHE cc_start: 0.9611 (t80) cc_final: 0.9400 (t80) REVERT: E 493 ARG cc_start: 0.8928 (ttt90) cc_final: 0.8561 (ttm-80) REVERT: F 12 TYR cc_start: 0.9551 (t80) cc_final: 0.9172 (t80) REVERT: F 28 ASP cc_start: 0.9260 (t0) cc_final: 0.9029 (t0) REVERT: F 66 VAL cc_start: 0.9177 (m) cc_final: 0.8660 (m) REVERT: F 78 MET cc_start: 0.7868 (mpp) cc_final: 0.7089 (mpp) REVERT: F 82 MET cc_start: 0.8967 (tpp) cc_final: 0.8381 (tpp) REVERT: F 88 ILE cc_start: 0.7320 (pt) cc_final: 0.6832 (pt) REVERT: F 109 LYS cc_start: 0.8892 (tptp) cc_final: 0.8248 (tptp) REVERT: F 158 ILE cc_start: 0.8879 (mm) cc_final: 0.8384 (mm) REVERT: F 166 LEU cc_start: 0.9040 (pt) cc_final: 0.8197 (tp) REVERT: F 215 ASP cc_start: 0.9449 (m-30) cc_final: 0.9012 (t0) REVERT: F 217 GLU cc_start: 0.9136 (mp0) cc_final: 0.8725 (mm-30) REVERT: F 254 GLU cc_start: 0.9250 (tp30) cc_final: 0.8898 (pm20) REVERT: F 269 ASP cc_start: 0.9138 (t0) cc_final: 0.8199 (t70) REVERT: F 276 SER cc_start: 0.9213 (m) cc_final: 0.8882 (p) REVERT: F 296 ASN cc_start: 0.9394 (p0) cc_final: 0.8528 (p0) REVERT: F 297 LEU cc_start: 0.9028 (mm) cc_final: 0.8585 (mm) REVERT: F 298 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8230 (mm110) REVERT: F 456 PHE cc_start: 0.9615 (t80) cc_final: 0.9296 (t80) REVERT: F 460 LEU cc_start: 0.9830 (mt) cc_final: 0.9564 (mt) REVERT: F 465 GLN cc_start: 0.9103 (mt0) cc_final: 0.8793 (pt0) REVERT: F 489 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6644 (ttpt) REVERT: F 490 PHE cc_start: 0.8894 (m-80) cc_final: 0.8500 (m-80) REVERT: G 28 ASP cc_start: 0.9188 (t0) cc_final: 0.8687 (t0) REVERT: G 30 LEU cc_start: 0.8898 (mt) cc_final: 0.8697 (mt) REVERT: G 65 LEU cc_start: 0.8961 (pt) cc_final: 0.8658 (pt) REVERT: G 66 VAL cc_start: 0.9250 (m) cc_final: 0.8775 (m) REVERT: G 75 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7707 (tm-30) REVERT: G 78 MET cc_start: 0.7652 (mpp) cc_final: 0.6062 (mpp) REVERT: G 82 MET cc_start: 0.8842 (tpp) cc_final: 0.8450 (tpp) REVERT: G 88 ILE cc_start: 0.7549 (pt) cc_final: 0.7191 (pt) REVERT: G 93 HIS cc_start: 0.9163 (p90) cc_final: 0.8752 (p90) REVERT: G 94 ASN cc_start: 0.8906 (t0) cc_final: 0.8455 (t0) REVERT: G 105 ARG cc_start: 0.9099 (mmt-90) cc_final: 0.8873 (mmt180) REVERT: G 166 LEU cc_start: 0.9130 (pt) cc_final: 0.8475 (tp) REVERT: G 261 ASP cc_start: 0.9297 (m-30) cc_final: 0.8923 (m-30) REVERT: G 269 ASP cc_start: 0.9144 (t0) cc_final: 0.8398 (t70) REVERT: G 276 SER cc_start: 0.9189 (m) cc_final: 0.8858 (p) REVERT: G 296 ASN cc_start: 0.9341 (p0) cc_final: 0.8549 (p0) REVERT: G 298 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8272 (mm110) REVERT: G 318 VAL cc_start: 0.8708 (p) cc_final: 0.8462 (m) REVERT: G 368 GLN cc_start: 0.9392 (mm110) cc_final: 0.9093 (mp10) REVERT: G 401 PHE cc_start: 0.9222 (p90) cc_final: 0.9006 (p90) REVERT: G 402 PHE cc_start: 0.7960 (m-80) cc_final: 0.7734 (m-80) REVERT: G 450 LYS cc_start: 0.7468 (pttm) cc_final: 0.6413 (ptmm) REVERT: G 489 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7709 (ttpt) REVERT: G 490 PHE cc_start: 0.8979 (m-80) cc_final: 0.8313 (m-80) REVERT: H 28 ASP cc_start: 0.9237 (t0) cc_final: 0.8949 (t0) REVERT: H 30 LEU cc_start: 0.8713 (mt) cc_final: 0.8497 (mt) REVERT: H 66 VAL cc_start: 0.9152 (m) cc_final: 0.8788 (m) REVERT: H 75 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7476 (tm-30) REVERT: H 82 MET cc_start: 0.8739 (tpp) cc_final: 0.8484 (tpp) REVERT: H 88 ILE cc_start: 0.7335 (pt) cc_final: 0.6879 (pt) REVERT: H 94 ASN cc_start: 0.8880 (t0) cc_final: 0.8648 (t0) REVERT: H 109 LYS cc_start: 0.8833 (tptp) cc_final: 0.8302 (tptp) REVERT: H 166 LEU cc_start: 0.9021 (pt) cc_final: 0.8235 (tp) REVERT: H 178 ILE cc_start: 0.9185 (mp) cc_final: 0.8590 (mm) REVERT: H 199 GLU cc_start: 0.9604 (mt-10) cc_final: 0.9206 (mm-30) REVERT: H 202 GLN cc_start: 0.9307 (mp10) cc_final: 0.8978 (mp10) REVERT: H 229 LYS cc_start: 0.9549 (mttm) cc_final: 0.9032 (mttm) REVERT: H 261 ASP cc_start: 0.9125 (m-30) cc_final: 0.8796 (m-30) REVERT: H 269 ASP cc_start: 0.9165 (t0) cc_final: 0.8369 (t70) REVERT: H 276 SER cc_start: 0.9275 (m) cc_final: 0.8959 (p) REVERT: H 286 MET cc_start: 0.8698 (mtm) cc_final: 0.8414 (mtt) REVERT: H 296 ASN cc_start: 0.9403 (p0) cc_final: 0.8651 (p0) REVERT: H 298 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8312 (mm110) REVERT: H 372 HIS cc_start: 0.9515 (m170) cc_final: 0.9042 (m170) REVERT: H 489 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7822 (tppt) REVERT: H 490 PHE cc_start: 0.9069 (m-80) cc_final: 0.8601 (m-80) outliers start: 0 outliers final: 0 residues processed: 1350 average time/residue: 0.1779 time to fit residues: 387.3310 Evaluate side-chains 1097 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1097 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 101 optimal weight: 8.9990 chunk 229 optimal weight: 0.1980 chunk 280 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 336 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 59 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS B 21 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN B 454 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** 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 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** F 454 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093647 restraints weight = 54457.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097808 restraints weight = 34889.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100932 restraints weight = 25083.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103329 restraints weight = 19449.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105178 restraints weight = 15936.730| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5486 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 : 0.902 13.823 39136 Z= 0.431 Chirality : 0.051 0.242 4472 Planarity : 0.005 0.078 4928 Dihedral : 15.980 179.432 4120 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % 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 : 0.14 % 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: -2.58 (0.13), residues: 3576 helix: -1.28 (0.13), residues: 1232 sheet: -2.44 (0.25), residues: 344 loop : -1.87 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 153 TYR 0.026 0.002 TYR E 233 PHE 0.019 0.002 PHE D 456 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28864) covalent geometry : angle 0.90219 / 0.43 (39136) hydrogen bonds : bond 0.03469 / 2.35 ( 888) hydrogen bonds : angle 5.79960 / 3.94 ( 2448) Misc. bond : bond 0.00210 / 0.13 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6786.00 seconds wall clock time: 117 minutes 41.31 seconds (7061.31 seconds total)