Starting phenix.real_space_refine on Thu Mar 5 16:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l7i_0844/03_2026/6l7i_0844.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l7i_0844/03_2026/6l7i_0844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l7i_0844/03_2026/6l7i_0844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l7i_0844/03_2026/6l7i_0844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l7i_0844/03_2026/6l7i_0844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l7i_0844/03_2026/6l7i_0844.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 14794 2.51 5 N 4110 2.21 5 O 4600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23561 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1344 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Chain: "B" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1344 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Chain: "C" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1344 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Chain: "D" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1344 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Chain: "E" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1344 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Chain: "F" Number of atoms: 11478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1451, 11478 Classifications: {'peptide': 1451} Link IDs: {'PTRANS': 87, 'TRANS': 1363} Chain breaks: 3 Chain: "G" Number of atoms: 5242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5242 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 26, 'TRANS': 633} Chain breaks: 1 Chain: "H" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 4.82, per 1000 atoms: 0.20 Number of scatterers: 23561 At special positions: 0 Unit cell: (131.124, 116.406, 187.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 4600 8.00 N 4110 7.00 C 14794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 291 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5558 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 34 sheets defined 10.7% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 2337 through 2342 Processing helix chain 'A' and resid 2352 through 2363 Processing helix chain 'A' and resid 2397 through 2401 removed outlier: 3.547A pdb=" N GLU A2400 " --> pdb=" O LYS A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2403 through 2407 removed outlier: 3.649A pdb=" N LEU A2406 " --> pdb=" O PRO A2403 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A2407 " --> pdb=" O ALA A2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2403 through 2407' Processing helix chain 'A' and resid 2497 through 2502 removed outlier: 4.097A pdb=" N LYS A2502 " --> pdb=" O ALA A2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2337 through 2342 Processing helix chain 'B' and resid 2352 through 2363 removed outlier: 3.856A pdb=" N ASP B2358 " --> pdb=" O ALA B2354 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B2362 " --> pdb=" O ASP B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2394 through 2396 No H-bonds generated for 'chain 'B' and resid 2394 through 2396' Processing helix chain 'B' and resid 2397 through 2402 removed outlier: 3.993A pdb=" N TYR B2402 " --> pdb=" O ARG B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2497 through 2502 removed outlier: 3.530A pdb=" N LYS B2502 " --> pdb=" O ALA B2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2337 through 2342 Processing helix chain 'C' and resid 2352 through 2363 removed outlier: 3.590A pdb=" N SER C2362 " --> pdb=" O ASP C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2397 through 2401 Processing helix chain 'D' and resid 2337 through 2343 Processing helix chain 'D' and resid 2352 through 2363 removed outlier: 4.233A pdb=" N ASP D2358 " --> pdb=" O ALA D2354 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D2359 " --> pdb=" O GLN D2355 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D2362 " --> pdb=" O ASP D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2397 through 2401 removed outlier: 3.544A pdb=" N GLU D2400 " --> pdb=" O LYS D2397 " (cutoff:3.500A) Processing helix chain 'D' and resid 2497 through 2502 removed outlier: 3.718A pdb=" N LYS D2502 " --> pdb=" O ALA D2498 " (cutoff:3.500A) Processing helix chain 'E' and resid 2337 through 2343 Processing helix chain 'E' and resid 2352 through 2364 Processing helix chain 'E' and resid 2397 through 2401 removed outlier: 3.512A pdb=" N GLU E2400 " --> pdb=" O LYS E2397 " (cutoff:3.500A) Processing helix chain 'E' and resid 2403 through 2407 Processing helix chain 'E' and resid 2497 through 2503 removed outlier: 3.591A pdb=" N LYS E2502 " --> pdb=" O ALA E2498 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E2503 " --> pdb=" O THR E2499 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 219 through 226 removed outlier: 3.655A pdb=" N ALA F 225 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 501 through 504 Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 723 through 735 removed outlier: 3.564A pdb=" N GLU F 730 " --> pdb=" O PHE F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 825 Processing helix chain 'F' and resid 826 through 830 removed outlier: 3.599A pdb=" N ALA F 829 " --> pdb=" O ALA F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 871 Processing helix chain 'F' and resid 975 through 979 removed outlier: 4.116A pdb=" N PHE F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) Processing helix chain 'F' and resid 1034 through 1039 Processing helix chain 'F' and resid 1090 through 1095 removed outlier: 3.544A pdb=" N SER F1093 " --> pdb=" O SER F1090 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F1095 " --> pdb=" O LEU F1092 " (cutoff:3.500A) Processing helix chain 'F' and resid 1103 through 1111 removed outlier: 3.526A pdb=" N THR F1109 " --> pdb=" O PRO F1105 " (cutoff:3.500A) Processing helix chain 'F' and resid 1242 through 1248 removed outlier: 3.602A pdb=" N ASN F1248 " --> pdb=" O ASP F1244 " (cutoff:3.500A) Processing helix chain 'F' and resid 1263 through 1267 removed outlier: 4.512A pdb=" N TRP F1266 " --> pdb=" O PRO F1263 " (cutoff:3.500A) Processing helix chain 'F' and resid 1271 through 1276 Processing helix chain 'F' and resid 1279 through 1288 removed outlier: 3.654A pdb=" N THR F1285 " --> pdb=" O GLU F1281 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F1286 " --> pdb=" O GLU F1282 " (cutoff:3.500A) Processing helix chain 'F' and resid 1299 through 1310 removed outlier: 3.916A pdb=" N GLN F1308 " --> pdb=" O ARG F1304 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER F1309 " --> pdb=" O ARG F1305 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN F1310 " --> pdb=" O TRP F1306 " (cutoff:3.500A) Processing helix chain 'F' and resid 1314 through 1322 removed outlier: 4.005A pdb=" N ASN F1322 " --> pdb=" O LYS F1318 " (cutoff:3.500A) Processing helix chain 'F' and resid 1421 through 1428 removed outlier: 3.572A pdb=" N LYS F1427 " --> pdb=" O ASP F1423 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 removed outlier: 3.783A pdb=" N ILE G 8 " --> pdb=" O ASN G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 65 removed outlier: 3.760A pdb=" N LYS G 64 " --> pdb=" O PRO G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 155 removed outlier: 3.986A pdb=" N TYR G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 removed outlier: 3.774A pdb=" N PHE G 444 " --> pdb=" O ASP G 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 669 through 673 removed outlier: 3.523A pdb=" N LYS H 673 " --> pdb=" O LYS H 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2329 through 2336 removed outlier: 5.814A pdb=" N THR A2514 " --> pdb=" O ILE A2412 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE A2412 " --> pdb=" O THR A2514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2368 through 2370 removed outlier: 4.031A pdb=" N SER A2370 " --> pdb=" O ASN A2373 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A2373 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2329 through 2336 removed outlier: 5.812A pdb=" N THR B2514 " --> pdb=" O ILE B2412 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE B2412 " --> pdb=" O THR B2514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2369 through 2370 removed outlier: 3.992A pdb=" N SER B2370 " --> pdb=" O ASN B2373 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B2373 " --> pdb=" O SER B2370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2422 through 2423 Processing sheet with id=AA6, first strand: chain 'C' and resid 2329 through 2336 removed outlier: 5.799A pdb=" N THR C2514 " --> pdb=" O ILE C2412 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE C2412 " --> pdb=" O THR C2514 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS C2516 " --> pdb=" O ARG C2410 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ARG C2410 " --> pdb=" O LYS C2516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2369 through 2370 removed outlier: 3.548A pdb=" N THR C2483 " --> pdb=" O SER C2434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 2330 through 2336 removed outlier: 5.971A pdb=" N THR D2514 " --> pdb=" O ILE D2412 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D2412 " --> pdb=" O THR D2514 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LYS D2516 " --> pdb=" O ARG D2410 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG D2410 " --> pdb=" O LYS D2516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 2375 through 2377 Processing sheet with id=AB1, first strand: chain 'E' and resid 2329 through 2336 removed outlier: 5.686A pdb=" N THR E2514 " --> pdb=" O ILE E2412 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE E2412 " --> pdb=" O THR E2514 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS E2516 " --> pdb=" O ARG E2410 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG E2410 " --> pdb=" O LYS E2516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 2369 through 2370 removed outlier: 3.653A pdb=" N SER E2370 " --> pdb=" O ASN E2373 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E2374 " --> pdb=" O SER E2390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AB4, first strand: chain 'F' and resid 65 through 66 removed outlier: 3.680A pdb=" N GLY F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.754A pdb=" N VAL F 170 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER F 198 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU F 172 " --> pdb=" O GLU F 196 " (cutoff:3.500A) removed outlier: 16.029A pdb=" N GLN F 192 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 12.592A pdb=" N ALA F 212 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N LEU F 194 " --> pdb=" O TYR F 210 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TYR F 210 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU F 196 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN F 205 " --> pdb=" O GLY F 241 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY F 241 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG F 211 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU F 235 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLN F 236 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN F 242 " --> pdb=" O TRP F 262 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP F 262 " --> pdb=" O ASN F 242 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 314 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG F 338 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET F 316 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL F 336 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS F 360 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 338 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP F 344 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU F 352 " --> pdb=" O ASP F 344 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N THR F 351 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR F 376 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL F 353 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER F 706 " --> pdb=" O LEU F 718 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG F 721 " --> pdb=" O LEU F 752 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU F 752 " --> pdb=" O ARG F 721 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N THR F 751 " --> pdb=" O TYR F 772 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N TYR F 772 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP F 753 " --> pdb=" O LEU F 770 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR F 768 " --> pdb=" O THR F 755 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY F 775 " --> pdb=" O PHE F 787 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE F 787 " --> pdb=" O GLY F 775 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TRP F 777 " --> pdb=" O ARG F 785 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG F 785 " --> pdb=" O TRP F 777 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY F 788 " --> pdb=" O TYR F 816 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA F 817 " --> pdb=" O PRO F 876 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N GLN F 875 " --> pdb=" O PRO F 901 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU F 877 " --> pdb=" O SER F 899 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR F 895 " --> pdb=" O LEU F 881 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN F 907 " --> pdb=" O TRP F 849 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 116 through 122 removed outlier: 5.426A pdb=" N SER F 121 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N ALA F 129 " --> pdb=" O SER F 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 170 through 173 current: chain 'F' and resid 96 through 97 Processing sheet with id=AB7, first strand: chain 'F' and resid 180 through 182 removed outlier: 6.619A pdb=" N ILE F 181 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 16.029A pdb=" N GLN F 192 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 12.592A pdb=" N ALA F 212 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N LEU F 194 " --> pdb=" O TYR F 210 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TYR F 210 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU F 196 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN F 205 " --> pdb=" O GLY F 241 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY F 241 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG F 211 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU F 235 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLN F 236 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN F 242 " --> pdb=" O TRP F 262 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP F 262 " --> pdb=" O ASN F 242 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 314 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG F 338 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET F 316 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL F 336 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS F 360 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 338 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP F 344 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU F 352 " --> pdb=" O ASP F 344 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR F 365 " --> pdb=" O GLU F 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 853 through 856 removed outlier: 6.311A pdb=" N GLN F 907 " --> pdb=" O TRP F 849 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU F 922 " --> pdb=" O ARG F 900 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN F 902 " --> pdb=" O VAL F 920 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL F 920 " --> pdb=" O GLN F 902 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG F 904 " --> pdb=" O ALA F 918 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA F 918 " --> pdb=" O ARG F 904 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU F 906 " --> pdb=" O LEU F 916 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU F 916 " --> pdb=" O LEU F 906 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N SER F 919 " --> pdb=" O SER F 944 " (cutoff:3.500A) removed outlier: 11.658A pdb=" N SER F 944 " --> pdb=" O SER F 919 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 921 " --> pdb=" O THR F 942 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS F 953 " --> pdb=" O LEU F 943 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER F 945 " --> pdb=" O PRO F 951 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU F 952 " --> pdb=" O SER F 997 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F1015 " --> pdb=" O SER F 998 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS F1000 " --> pdb=" O PRO F1013 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N LEU F1002 " --> pdb=" O GLY F1011 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLY F1011 " --> pdb=" O LEU F1002 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY F1004 " --> pdb=" O VAL F1009 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL F1009 " --> pdb=" O GLY F1004 " (cutoff:3.500A) removed outlier: 14.459A pdb=" N LEU F1010 " --> pdb=" O THR F1062 " (cutoff:3.500A) removed outlier: 14.738A pdb=" N THR F1062 " --> pdb=" O LEU F1010 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N LEU F1012 " --> pdb=" O PHE F1060 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N PHE F1060 " --> pdb=" O LEU F1012 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP F1014 " --> pdb=" O ARG F1058 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG F1058 " --> pdb=" O ASP F1014 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR F1016 " --> pdb=" O GLN F1056 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN F1056 " --> pdb=" O THR F1016 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER F1018 " --> pdb=" O LEU F1054 " (cutoff:3.500A) removed outlier: 13.910A pdb=" N GLU F1052 " --> pdb=" O THR F1088 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N THR F1088 " --> pdb=" O GLU F1052 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N LEU F1054 " --> pdb=" O VAL F1086 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL F1086 " --> pdb=" O LEU F1054 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN F1056 " --> pdb=" O THR F1084 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR F1084 " --> pdb=" O GLN F1056 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG F1058 " --> pdb=" O THR F1082 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR F1082 " --> pdb=" O ARG F1058 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE F1060 " --> pdb=" O ALA F1080 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU F1078 " --> pdb=" O THR F1062 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU F1083 " --> pdb=" O GLN F1133 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN F1133 " --> pdb=" O GLU F1083 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA F1085 " --> pdb=" O ALA F1131 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA F1131 " --> pdb=" O ALA F1085 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 386 through 390 removed outlier: 3.927A pdb=" N HIS F 692 " --> pdb=" O MET F 390 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 402 through 405 Processing sheet with id=AC2, first strand: chain 'F' and resid 428 through 430 Processing sheet with id=AC3, first strand: chain 'F' and resid 457 through 460 removed outlier: 3.586A pdb=" N SER F 458 " --> pdb=" O VAL F 471 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 508 through 510 Processing sheet with id=AC5, first strand: chain 'F' and resid 562 through 566 removed outlier: 3.935A pdb=" N VAL F 584 " --> pdb=" O LEU F 601 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 589 through 591 removed outlier: 5.596A pdb=" N ARG F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 616 through 619 Processing sheet with id=AC8, first strand: chain 'F' and resid 1135 through 1138 removed outlier: 6.898A pdb=" N TYR F1135 " --> pdb=" O GLN F1150 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN F1150 " --> pdb=" O TYR F1135 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP F1137 " --> pdb=" O VAL F1148 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 1173 through 1174 removed outlier: 3.534A pdb=" N GLN F1194 " --> pdb=" O ASN F1184 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR F1193 " --> pdb=" O ILE F1205 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F1202 " --> pdb=" O PHE F1218 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE F1218 " --> pdb=" O VAL F1202 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F1204 " --> pdb=" O GLN F1216 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN F1216 " --> pdb=" O LEU F1204 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR F1206 " --> pdb=" O VAL F1214 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 1257 through 1262 removed outlier: 5.348A pdb=" N GLN F1348 " --> pdb=" O ARG F1365 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN F1361 " --> pdb=" O PHE F1352 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG F1390 " --> pdb=" O HIS F1366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR F1412 " --> pdb=" O VAL F1393 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 1369 through 1374 removed outlier: 6.173A pdb=" N GLY F1369 " --> pdb=" O GLU F1385 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU F1385 " --> pdb=" O GLY F1369 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA F1371 " --> pdb=" O LYS F1383 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS F1383 " --> pdb=" O ALA F1371 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1397 through 1399 removed outlier: 6.477A pdb=" N GLU F1398 " --> pdb=" O ILE F1406 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE F1406 " --> pdb=" O HIS F1434 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG F1444 " --> pdb=" O ILE F1435 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE F1443 " --> pdb=" O SER F1455 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL G 25 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL G 55 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE G 72 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU G 84 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL G 74 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU G 82 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL G 103 " --> pdb=" O HIS G 115 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU G 127 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU G 131 " --> pdb=" O THR G 139 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N THR G 139 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG G 163 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL G 162 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER G 184 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU G 176 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL G 182 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU G 183 " --> pdb=" O ASN G 219 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN G 218 " --> pdb=" O GLN G 230 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN G 230 " --> pdb=" O GLN G 218 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS G 220 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU G 228 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 250 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS G 249 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS G 265 " --> pdb=" O LYS G 249 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS G 251 " --> pdb=" O ILE G 263 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 277 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU G 276 " --> pdb=" O TYR G 288 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE G 298 " --> pdb=" O ARG G 315 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG G 315 " --> pdb=" O ILE G 298 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE G 300 " --> pdb=" O ASP G 313 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP G 313 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR G 302 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN G 326 " --> pdb=" O GLN G 317 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE G 325 " --> pdb=" O TYR G 348 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER G 347 " --> pdb=" O ALA G 359 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA G 359 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR G 349 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE G 357 " --> pdb=" O TYR G 393 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR G 402 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER G 408 " --> pdb=" O ASN G 413 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN G 413 " --> pdb=" O SER G 408 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 458 through 461 Processing sheet with id=AD5, first strand: chain 'G' and resid 477 through 481 removed outlier: 6.642A pdb=" N TRP G 478 " --> pdb=" O LYS G 490 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS G 490 " --> pdb=" O TRP G 478 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG G 480 " --> pdb=" O GLN G 488 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN G 488 " --> pdb=" O TYR G 507 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR G 507 " --> pdb=" O GLN G 488 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 546 " --> pdb=" O GLU G 525 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS G 527 " --> pdb=" O TRP G 544 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TRP G 544 " --> pdb=" O HIS G 527 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE G 529 " --> pdb=" O LEU G 542 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU G 542 " --> pdb=" O ILE G 529 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU G 531 " --> pdb=" O ARG G 540 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG G 540 " --> pdb=" O LEU G 531 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN G 569 " --> pdb=" O GLU G 581 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU G 581 " --> pdb=" O GLN G 569 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU G 571 " --> pdb=" O ILE G 579 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 606 through 608 removed outlier: 5.538A pdb=" N LYS G 611 " --> pdb=" O ARG G 607 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU G 612 " --> pdb=" O TYR G 620 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 659 through 660 768 hydrogen bonds defined for protein. 2013 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: 6.69 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7912 1.34 - 1.46: 5459 1.46 - 1.58: 10591 1.58 - 1.71: 0 1.71 - 1.83: 91 Bond restraints: 24053 Sorted by residual: bond pdb=" N ASN G 383 " pdb=" CA ASN G 383 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.33e+00 bond pdb=" C GLN F 958 " pdb=" N TYR F 959 " ideal model delta sigma weight residual 1.340 1.227 0.113 5.87e-02 2.90e+02 3.70e+00 bond pdb=" C GLY F1211 " pdb=" N ARG F1212 " ideal model delta sigma weight residual 1.329 1.302 0.027 1.60e-02 3.91e+03 2.89e+00 bond pdb=" CB ARG D2327 " pdb=" CG ARG D2327 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CG LEU F 916 " pdb=" CD2 LEU F 916 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 24048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 32552 3.93 - 7.86: 127 7.86 - 11.78: 10 11.78 - 15.71: 2 15.71 - 19.64: 1 Bond angle restraints: 32692 Sorted by residual: angle pdb=" C HIS F 687 " pdb=" N MET F 688 " pdb=" CA MET F 688 " ideal model delta sigma weight residual 121.54 133.97 -12.43 1.91e+00 2.74e-01 4.23e+01 angle pdb=" C ASP F1339 " pdb=" N ARG F1340 " pdb=" CA ARG F1340 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLY F 409 " pdb=" N GLU F 410 " pdb=" CA GLU F 410 " ideal model delta sigma weight residual 121.54 130.62 -9.08 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C THR B2381 " pdb=" N ASP B2382 " pdb=" CA ASP B2382 " ideal model delta sigma weight residual 122.08 128.93 -6.85 1.47e+00 4.63e-01 2.17e+01 angle pdb=" C GLN F1310 " pdb=" N LYS F1311 " pdb=" CA LYS F1311 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 ... (remaining 32687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13083 17.96 - 35.93: 1078 35.93 - 53.89: 164 53.89 - 71.85: 33 71.85 - 89.81: 22 Dihedral angle restraints: 14380 sinusoidal: 5704 harmonic: 8676 Sorted by residual: dihedral pdb=" CA ASP F 406 " pdb=" C ASP F 406 " pdb=" N LEU F 407 " pdb=" CA LEU F 407 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA TYR F 970 " pdb=" C TYR F 970 " pdb=" N PRO F 971 " pdb=" CA PRO F 971 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLN G 497 " pdb=" C GLN G 497 " pdb=" N ASN G 498 " pdb=" CA ASN G 498 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 14377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2478 0.049 - 0.099: 845 0.099 - 0.148: 268 0.148 - 0.198: 26 0.198 - 0.247: 9 Chirality restraints: 3626 Sorted by residual: chirality pdb=" CB THR G 254 " pdb=" CA THR G 254 " pdb=" OG1 THR G 254 " pdb=" CG2 THR G 254 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE D2409 " pdb=" CA ILE D2409 " pdb=" CG1 ILE D2409 " pdb=" CG2 ILE D2409 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL F 912 " pdb=" CA VAL F 912 " pdb=" CG1 VAL F 912 " pdb=" CG2 VAL F 912 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 3623 not shown) Planarity restraints: 4305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F1437 " -0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO F1438 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO F1438 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F1438 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 625 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO F 626 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 626 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 626 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 462 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO G 463 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " 0.039 5.00e-02 4.00e+02 ... (remaining 4302 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4847 2.78 - 3.31: 19271 3.31 - 3.84: 39614 3.84 - 4.37: 48728 4.37 - 4.90: 84655 Nonbonded interactions: 197115 Sorted by model distance: nonbonded pdb=" OD2 ASP G 59 " pdb=" OG SER G 398 " model vdw 2.246 3.040 nonbonded pdb=" O PHE G 587 " pdb=" OH TYR G 626 " model vdw 2.255 3.040 nonbonded pdb=" OG SER F 165 " pdb=" OD1 ASP F 167 " model vdw 2.267 3.040 nonbonded pdb=" O SER F 610 " pdb=" OG SER F 610 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR E2341 " pdb=" O SER E2390 " model vdw 2.283 3.040 ... (remaining 197110 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.800 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.007 0.113 24054 Z= 0.307 Angle : 0.828 19.641 32694 Z= 0.455 Chirality : 0.054 0.247 3626 Planarity : 0.007 0.087 4305 Dihedral : 13.829 89.814 8819 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 0.28 % Allowed : 5.46 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.13), residues: 2978 helix: -4.64 (0.10), residues: 289 sheet: -1.30 (0.16), residues: 944 loop : -2.18 (0.12), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 211 TYR 0.027 0.002 TYR G 621 PHE 0.018 0.003 PHE F 296 TRP 0.013 0.002 TRP G 593 HIS 0.009 0.002 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00727 (24053) covalent geometry : angle 0.82776 (32692) SS BOND : bond 0.00794 ( 1) SS BOND : angle 2.39106 ( 2) hydrogen bonds : bond 0.24199 ( 719) hydrogen bonds : angle 10.32701 ( 2013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 391 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2388 GLN cc_start: 0.8644 (mt0) cc_final: 0.8021 (mm110) REVERT: A 2397 LYS cc_start: 0.8134 (mttt) cc_final: 0.7927 (mttm) REVERT: A 2477 ILE cc_start: 0.8015 (mm) cc_final: 0.7772 (tp) REVERT: A 2479 GLN cc_start: 0.8254 (mt0) cc_final: 0.7779 (pt0) REVERT: B 2327 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7207 (mtt-85) REVERT: B 2346 LYS cc_start: 0.7706 (tttm) cc_final: 0.7344 (tptt) REVERT: B 2426 TYR cc_start: 0.8095 (m-80) cc_final: 0.7601 (m-80) REVERT: B 2456 ASP cc_start: 0.8498 (t0) cc_final: 0.8248 (t0) REVERT: B 2491 MET cc_start: 0.8338 (ttm) cc_final: 0.8094 (ttp) REVERT: B 2500 MET cc_start: 0.8584 (tmm) cc_final: 0.8226 (ttp) REVERT: B 2505 ASN cc_start: 0.8485 (t0) cc_final: 0.8117 (t0) REVERT: C 2359 LYS cc_start: 0.8368 (tttt) cc_final: 0.8110 (ttmm) REVERT: C 2427 GLN cc_start: 0.8422 (mm110) cc_final: 0.7831 (mm-40) REVERT: C 2461 GLN cc_start: 0.8405 (pt0) cc_final: 0.8204 (pt0) REVERT: C 2478 ASP cc_start: 0.8094 (m-30) cc_final: 0.7719 (m-30) REVERT: C 2500 MET cc_start: 0.8419 (tmm) cc_final: 0.8016 (tmm) REVERT: C 2516 LYS cc_start: 0.8282 (ptpt) cc_final: 0.6300 (tptm) REVERT: D 2339 GLU cc_start: 0.7818 (tt0) cc_final: 0.7605 (tt0) REVERT: D 2399 ARG cc_start: 0.9132 (ttm-80) cc_final: 0.8843 (ttt-90) REVERT: D 2493 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7921 (mm-30) REVERT: D 2512 ARG cc_start: 0.8252 (mtt180) cc_final: 0.8043 (mtt90) REVERT: E 2355 GLN cc_start: 0.8168 (mt0) cc_final: 0.7817 (mt0) REVERT: E 2359 LYS cc_start: 0.8117 (tttt) cc_final: 0.7916 (ttmt) REVERT: E 2408 LYS cc_start: 0.8095 (tttm) cc_final: 0.7502 (pptt) REVERT: E 2427 GLN cc_start: 0.8369 (mm110) cc_final: 0.8124 (mm-40) REVERT: E 2446 GLU cc_start: 0.8467 (pm20) cc_final: 0.8131 (pm20) REVERT: E 2505 ASN cc_start: 0.8346 (m110) cc_final: 0.8059 (m-40) REVERT: F 420 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7505 (ttp80) REVERT: F 467 GLN cc_start: 0.8426 (pt0) cc_final: 0.8088 (pt0) REVERT: F 513 MET cc_start: 0.8390 (mmm) cc_final: 0.8153 (mmm) REVERT: F 550 ILE cc_start: 0.8049 (mt) cc_final: 0.7821 (mt) REVERT: F 712 MET cc_start: 0.9076 (mtp) cc_final: 0.8689 (mtp) REVERT: F 771 ARG cc_start: 0.8092 (ttp-170) cc_final: 0.7814 (tmt-80) REVERT: F 1041 GLU cc_start: 0.6864 (mp0) cc_final: 0.6462 (mp0) REVERT: F 1290 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7286 (mtt90) REVERT: F 1337 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8352 (mtt180) REVERT: F 1407 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7904 (mmt90) REVERT: F 1430 TYR cc_start: 0.6963 (p90) cc_final: 0.5966 (p90) REVERT: G 16 LYS cc_start: 0.8303 (mttt) cc_final: 0.8035 (mtmt) REVERT: G 131 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7217 (mt-10) REVERT: G 148 ASN cc_start: 0.7584 (p0) cc_final: 0.7316 (p0) REVERT: G 383 ASN cc_start: 0.8189 (p0) cc_final: 0.7925 (p0) outliers start: 7 outliers final: 3 residues processed: 397 average time/residue: 0.7673 time to fit residues: 341.2153 Evaluate side-chains 270 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 254 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2348 ASN A2355 GLN A2452 HIS A2461 GLN A2497 GLN B2348 ASN B2452 HIS C2452 HIS C2497 GLN D2363 GLN D2452 HIS D2461 GLN D2465 ASN D2497 GLN E2348 ASN E2452 HIS E2455 ASN E2497 GLN E2505 ASN F 171 HIS F 189 GLN F 226 HIS F 239 HIS F 313 GLN F 360 HIS F 403 GLN F 421 ASN F 454 GLN F 456 ASN F 481 HIS F 508 GLN F 597 GLN F 617 HIS F 692 HIS F 792 GLN F 890 GLN F 936 GLN F 986 GLN F1000 HIS F1201 ASN F1330 ASN F1366 HIS G 54 GLN G 80 GLN G 148 ASN G 207 GLN G 340 GLN G 471 ASN G 527 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107459 restraints weight = 39073.418| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.65 r_work: 0.3219 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24054 Z= 0.162 Angle : 0.589 14.745 32694 Z= 0.310 Chirality : 0.044 0.149 3626 Planarity : 0.005 0.070 4305 Dihedral : 5.378 27.682 3282 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.24 % Allowed : 11.79 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.14), residues: 2978 helix: -3.41 (0.19), residues: 293 sheet: -0.78 (0.16), residues: 954 loop : -1.63 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E2411 TYR 0.016 0.001 TYR F 343 PHE 0.013 0.001 PHE G 48 TRP 0.016 0.001 TRP F1296 HIS 0.006 0.001 HIS F 481 Details of bonding type rmsd covalent geometry : bond 0.00371 (24053) covalent geometry : angle 0.58918 (32692) SS BOND : bond 0.00465 ( 1) SS BOND : angle 1.71241 ( 2) hydrogen bonds : bond 0.04195 ( 719) hydrogen bonds : angle 6.56874 ( 2013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2455 ASN cc_start: 0.9095 (t0) cc_final: 0.8855 (t0) REVERT: A 2463 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7735 (t70) REVERT: A 2479 GLN cc_start: 0.8552 (mt0) cc_final: 0.8256 (pt0) REVERT: B 2346 LYS cc_start: 0.7952 (tttm) cc_final: 0.7532 (tptt) REVERT: B 2388 GLN cc_start: 0.8708 (mt0) cc_final: 0.8331 (mp10) REVERT: B 2426 TYR cc_start: 0.8073 (m-80) cc_final: 0.7872 (m-80) REVERT: B 2456 ASP cc_start: 0.8391 (t0) cc_final: 0.8099 (t0) REVERT: B 2500 MET cc_start: 0.8888 (tmm) cc_final: 0.8457 (ttp) REVERT: B 2505 ASN cc_start: 0.8403 (t0) cc_final: 0.8158 (t0) REVERT: C 2427 GLN cc_start: 0.8647 (mm110) cc_final: 0.8396 (mp-120) REVERT: C 2478 ASP cc_start: 0.8331 (m-30) cc_final: 0.8019 (m-30) REVERT: C 2500 MET cc_start: 0.8535 (tmm) cc_final: 0.8242 (tmm) REVERT: C 2516 LYS cc_start: 0.8514 (ptpt) cc_final: 0.6737 (tptm) REVERT: D 2459 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: D 2491 MET cc_start: 0.8387 (ttm) cc_final: 0.8169 (tpt) REVERT: D 2493 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8438 (mm-30) REVERT: D 2512 ARG cc_start: 0.8732 (mtt180) cc_final: 0.8507 (mtt90) REVERT: E 2330 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: E 2385 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (p) REVERT: E 2408 LYS cc_start: 0.8127 (tttm) cc_final: 0.7493 (pptt) REVERT: E 2427 GLN cc_start: 0.8641 (mm110) cc_final: 0.8218 (mm-40) REVERT: E 2446 GLU cc_start: 0.8557 (pm20) cc_final: 0.8323 (pm20) REVERT: E 2500 MET cc_start: 0.8583 (tmm) cc_final: 0.8292 (tmt) REVERT: F 16 LYS cc_start: 0.7131 (ptmt) cc_final: 0.6849 (ptmm) REVERT: F 187 VAL cc_start: 0.8123 (p) cc_final: 0.7821 (p) REVERT: F 219 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: F 420 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.7575 (ttp80) REVERT: F 467 GLN cc_start: 0.8620 (pt0) cc_final: 0.8333 (pt0) REVERT: F 550 ILE cc_start: 0.8438 (mt) cc_final: 0.8207 (mt) REVERT: F 676 LEU cc_start: 0.8312 (mt) cc_final: 0.8101 (mt) REVERT: F 688 MET cc_start: 0.8622 (mmm) cc_final: 0.8389 (mmm) REVERT: F 712 MET cc_start: 0.9177 (mtp) cc_final: 0.8632 (mtp) REVERT: F 771 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.7889 (tmt-80) REVERT: F 794 ASP cc_start: 0.7594 (m-30) cc_final: 0.7377 (p0) REVERT: F 988 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: F 995 ARG cc_start: 0.8249 (tpt-90) cc_final: 0.7965 (ttm-80) REVERT: F 1041 GLU cc_start: 0.7312 (mp0) cc_final: 0.6956 (mp0) REVERT: F 1191 THR cc_start: 0.9375 (m) cc_final: 0.9047 (m) REVERT: F 1290 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7226 (mtt90) REVERT: F 1336 ASP cc_start: 0.8060 (m-30) cc_final: 0.7806 (t70) REVERT: F 1430 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.5728 (p90) REVERT: G 99 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: G 152 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8516 (mt-10) REVERT: H 670 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8354 (mmmt) outliers start: 57 outliers final: 12 residues processed: 342 average time/residue: 0.7270 time to fit residues: 281.1449 Evaluate side-chains 287 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2429 VAL Chi-restraints excluded: chain D residue 2459 GLN Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 756 GLU Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1279 THR Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain H residue 670 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 129 optimal weight: 1.9990 chunk 55 optimal weight: 0.0000 chunk 30 optimal weight: 0.0070 chunk 91 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2348 ASN E2505 ASN F 236 GLN F 431 GLN F1166 HIS F1329 HIS G 24 ASN G 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109593 restraints weight = 38916.968| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.67 r_work: 0.3238 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24054 Z= 0.099 Angle : 0.508 11.322 32694 Z= 0.267 Chirality : 0.042 0.147 3626 Planarity : 0.004 0.066 4305 Dihedral : 4.797 28.689 3280 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.48 % Allowed : 13.63 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.14), residues: 2978 helix: -2.53 (0.24), residues: 292 sheet: -0.49 (0.16), residues: 955 loop : -1.39 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.013 0.001 TYR G 621 PHE 0.009 0.001 PHE F 652 TRP 0.016 0.001 TRP F1296 HIS 0.004 0.001 HIS F1000 Details of bonding type rmsd covalent geometry : bond 0.00221 (24053) covalent geometry : angle 0.50781 (32692) SS BOND : bond 0.00440 ( 1) SS BOND : angle 1.25296 ( 2) hydrogen bonds : bond 0.03247 ( 719) hydrogen bonds : angle 5.81319 ( 2013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 323 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2455 ASN cc_start: 0.9001 (t0) cc_final: 0.8733 (t0) REVERT: A 2479 GLN cc_start: 0.8559 (mt0) cc_final: 0.8321 (pt0) REVERT: B 2346 LYS cc_start: 0.7994 (tttm) cc_final: 0.7543 (tptt) REVERT: B 2388 GLN cc_start: 0.8821 (mt0) cc_final: 0.8382 (mp10) REVERT: B 2456 ASP cc_start: 0.8430 (t0) cc_final: 0.8117 (t0) REVERT: B 2500 MET cc_start: 0.8797 (tmm) cc_final: 0.8203 (ttp) REVERT: B 2505 ASN cc_start: 0.8372 (t0) cc_final: 0.8158 (t0) REVERT: C 2427 GLN cc_start: 0.8508 (mm110) cc_final: 0.8305 (mp-120) REVERT: C 2478 ASP cc_start: 0.8354 (m-30) cc_final: 0.8031 (m-30) REVERT: C 2500 MET cc_start: 0.8605 (tmm) cc_final: 0.8332 (tmm) REVERT: C 2512 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8223 (mtm-85) REVERT: C 2516 LYS cc_start: 0.8437 (ptpt) cc_final: 0.6634 (tptm) REVERT: D 2455 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7679 (m110) REVERT: D 2493 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8450 (mm-30) REVERT: D 2512 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8454 (mtt90) REVERT: E 2357 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8174 (tt) REVERT: E 2408 LYS cc_start: 0.8132 (tttm) cc_final: 0.7508 (pptt) REVERT: E 2427 GLN cc_start: 0.8645 (mm110) cc_final: 0.8185 (mm-40) REVERT: E 2493 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: F 390 MET cc_start: 0.8738 (ttt) cc_final: 0.8507 (ttt) REVERT: F 420 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7478 (ttp80) REVERT: F 435 GLU cc_start: 0.7114 (mp0) cc_final: 0.6896 (mp0) REVERT: F 443 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8274 (mtmt) REVERT: F 467 GLN cc_start: 0.8336 (pt0) cc_final: 0.8022 (pt0) REVERT: F 676 LEU cc_start: 0.8401 (mt) cc_final: 0.8058 (mt) REVERT: F 688 MET cc_start: 0.8346 (mmm) cc_final: 0.8103 (mmm) REVERT: F 712 MET cc_start: 0.9116 (mtp) cc_final: 0.8604 (mtp) REVERT: F 771 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7952 (tmt-80) REVERT: F 988 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: F 1041 GLU cc_start: 0.7406 (mp0) cc_final: 0.7101 (mp0) REVERT: F 1191 THR cc_start: 0.9304 (m) cc_final: 0.8999 (m) REVERT: F 1290 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7113 (mtt90) REVERT: F 1430 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5607 (p90) REVERT: G 116 ARG cc_start: 0.8190 (ptm-80) cc_final: 0.7958 (ptt-90) REVERT: G 152 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8675 (mt-10) outliers start: 63 outliers final: 19 residues processed: 356 average time/residue: 0.6828 time to fit residues: 276.6425 Evaluate side-chains 307 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2383 THR Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain E residue 2493 GLU Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1168 CYS Chi-restraints excluded: chain F residue 1332 THR Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2348 ASN F 113 GLN F 397 ASN F 431 GLN F 936 GLN G 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106077 restraints weight = 39267.523| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.66 r_work: 0.3201 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24054 Z= 0.206 Angle : 0.593 11.831 32694 Z= 0.306 Chirality : 0.046 0.152 3626 Planarity : 0.005 0.066 4305 Dihedral : 5.125 45.034 3280 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.99 % Allowed : 14.62 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 2978 helix: -2.21 (0.26), residues: 291 sheet: -0.42 (0.16), residues: 960 loop : -1.26 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D2399 TYR 0.017 0.002 TYR G 621 PHE 0.013 0.002 PHE F 652 TRP 0.011 0.001 TRP F1296 HIS 0.009 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00481 (24053) covalent geometry : angle 0.59335 (32692) SS BOND : bond 0.00518 ( 1) SS BOND : angle 1.57608 ( 2) hydrogen bonds : bond 0.03577 ( 719) hydrogen bonds : angle 5.78554 ( 2013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2455 ASN cc_start: 0.9051 (t0) cc_final: 0.8840 (t0) REVERT: A 2463 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7755 (t70) REVERT: A 2477 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 2479 GLN cc_start: 0.8608 (mt0) cc_final: 0.8302 (pt0) REVERT: B 2346 LYS cc_start: 0.7953 (tttm) cc_final: 0.7508 (tptt) REVERT: B 2388 GLN cc_start: 0.8770 (mt0) cc_final: 0.8376 (mp10) REVERT: B 2456 ASP cc_start: 0.8483 (t0) cc_final: 0.8283 (t0) REVERT: B 2500 MET cc_start: 0.8874 (tmm) cc_final: 0.8521 (ttp) REVERT: C 2427 GLN cc_start: 0.8459 (mm110) cc_final: 0.8232 (mp-120) REVERT: C 2500 MET cc_start: 0.8592 (tmm) cc_final: 0.8323 (tmm) REVERT: C 2516 LYS cc_start: 0.8488 (ptpt) cc_final: 0.6696 (tptm) REVERT: D 2491 MET cc_start: 0.8289 (tpt) cc_final: 0.7920 (tpt) REVERT: D 2493 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8447 (mm-30) REVERT: E 2357 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8159 (tt) REVERT: E 2397 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7660 (mtpp) REVERT: E 2408 LYS cc_start: 0.8183 (tttm) cc_final: 0.7524 (pptt) REVERT: E 2427 GLN cc_start: 0.8659 (mm110) cc_final: 0.8287 (mm-40) REVERT: E 2456 ASP cc_start: 0.9003 (t0) cc_final: 0.8675 (t0) REVERT: F 219 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: F 243 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (mt) REVERT: F 405 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8679 (pt) REVERT: F 420 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7574 (ttp80) REVERT: F 435 GLU cc_start: 0.7333 (mp0) cc_final: 0.7034 (mp0) REVERT: F 443 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8317 (mtmt) REVERT: F 467 GLN cc_start: 0.8410 (pt0) cc_final: 0.8127 (pt0) REVERT: F 688 MET cc_start: 0.8414 (mmm) cc_final: 0.8185 (mmm) REVERT: F 771 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.7928 (tmt-80) REVERT: F 988 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: F 1019 ASP cc_start: 0.8654 (m-30) cc_final: 0.8431 (m-30) REVERT: F 1041 GLU cc_start: 0.7345 (mp0) cc_final: 0.7007 (mp0) REVERT: F 1191 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9020 (m) REVERT: F 1290 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7174 (mtt90) REVERT: F 1430 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.5590 (p90) REVERT: G 116 ARG cc_start: 0.8219 (ptm-80) cc_final: 0.7883 (ptt-90) REVERT: G 152 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: G 173 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8335 (OUTLIER) REVERT: H 670 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8453 (mmmt) outliers start: 76 outliers final: 34 residues processed: 339 average time/residue: 0.6911 time to fit residues: 266.7157 Evaluate side-chains 325 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2383 THR Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2477 ILE Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2418 THR Chi-restraints excluded: chain C residue 2429 VAL Chi-restraints excluded: chain C residue 2494 LYS Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2367 SER Chi-restraints excluded: chain E residue 2397 LYS Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain E residue 2423 LEU Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 755 THR Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1031 ASP Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1168 CYS Chi-restraints excluded: chain F residue 1191 THR Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain H residue 670 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 0.0030 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 92 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 258 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 233 optimal weight: 0.5980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2348 ASN A2427 GLN B2505 ASN F 113 GLN F 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109117 restraints weight = 38602.862| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.65 r_work: 0.3241 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24054 Z= 0.108 Angle : 0.512 11.753 32694 Z= 0.267 Chirality : 0.043 0.258 3626 Planarity : 0.004 0.064 4305 Dihedral : 4.781 46.679 3280 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.08 % Allowed : 15.99 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 2978 helix: -1.86 (0.27), residues: 292 sheet: -0.26 (0.16), residues: 964 loop : -1.14 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2411 TYR 0.014 0.001 TYR F 926 PHE 0.009 0.001 PHE F 652 TRP 0.012 0.001 TRP F1296 HIS 0.005 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00246 (24053) covalent geometry : angle 0.51164 (32692) SS BOND : bond 0.00420 ( 1) SS BOND : angle 1.15524 ( 2) hydrogen bonds : bond 0.02951 ( 719) hydrogen bonds : angle 5.48541 ( 2013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2388 GLN cc_start: 0.8659 (mm110) cc_final: 0.8420 (mm110) REVERT: A 2463 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7800 (t70) REVERT: A 2479 GLN cc_start: 0.8603 (mt0) cc_final: 0.8299 (pt0) REVERT: B 2346 LYS cc_start: 0.7939 (tttm) cc_final: 0.7510 (tptt) REVERT: B 2388 GLN cc_start: 0.8752 (mt0) cc_final: 0.8344 (mp10) REVERT: B 2397 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8075 (mtpt) REVERT: B 2400 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8002 (mp0) REVERT: B 2456 ASP cc_start: 0.8407 (t0) cc_final: 0.8141 (t0) REVERT: B 2505 ASN cc_start: 0.8295 (t0) cc_final: 0.7988 (t0) REVERT: C 2400 GLU cc_start: 0.8468 (mp0) cc_final: 0.7991 (mp0) REVERT: C 2500 MET cc_start: 0.8629 (tmm) cc_final: 0.8359 (tmm) REVERT: C 2512 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8195 (mtm180) REVERT: C 2516 LYS cc_start: 0.8336 (ptpt) cc_final: 0.6654 (tptm) REVERT: D 2455 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.7890 (m110) REVERT: D 2491 MET cc_start: 0.8318 (tpt) cc_final: 0.8117 (tpt) REVERT: D 2493 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8425 (mm-30) REVERT: E 2357 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8037 (tt) REVERT: E 2372 ASN cc_start: 0.8675 (m-40) cc_final: 0.8275 (m110) REVERT: E 2408 LYS cc_start: 0.8127 (tttm) cc_final: 0.7491 (pptt) REVERT: E 2427 GLN cc_start: 0.8654 (mm110) cc_final: 0.8245 (mm-40) REVERT: F 219 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: F 243 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8249 (mt) REVERT: F 408 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8421 (mmtp) REVERT: F 420 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.7549 (ttp80) REVERT: F 443 LYS cc_start: 0.8415 (mmtp) cc_final: 0.8198 (mtmt) REVERT: F 467 GLN cc_start: 0.8307 (pt0) cc_final: 0.8017 (pt0) REVERT: F 676 LEU cc_start: 0.8419 (mt) cc_final: 0.8070 (mt) REVERT: F 688 MET cc_start: 0.8292 (mmm) cc_final: 0.8017 (mmm) REVERT: F 988 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: F 1019 ASP cc_start: 0.8604 (m-30) cc_final: 0.8336 (m-30) REVERT: F 1041 GLU cc_start: 0.7427 (mp0) cc_final: 0.7113 (mp0) REVERT: F 1191 THR cc_start: 0.9321 (m) cc_final: 0.9023 (m) REVERT: F 1290 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7104 (mtt90) REVERT: F 1430 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.5334 (p90) REVERT: G 116 ARG cc_start: 0.8202 (ptm-80) cc_final: 0.7871 (ptt-90) REVERT: G 152 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: G 173 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8260 (OUTLIER) REVERT: G 317 GLN cc_start: 0.8344 (mt0) cc_final: 0.7856 (tt0) outliers start: 53 outliers final: 28 residues processed: 340 average time/residue: 0.6885 time to fit residues: 266.7982 Evaluate side-chains 319 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2397 LYS Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2461 GLN Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1168 CYS Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1279 THR Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 173 optimal weight: 2.9990 chunk 139 optimal weight: 0.0070 chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 0.0270 chunk 42 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 83 optimal weight: 0.0050 chunk 11 optimal weight: 5.9990 overall best weight: 0.3270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D2459 GLN F 113 GLN F 242 ASN F 383 GLN F1376 GLN G 24 ASN G 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109983 restraints weight = 39057.606| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.66 r_work: 0.3255 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24054 Z= 0.095 Angle : 0.496 10.882 32694 Z= 0.259 Chirality : 0.042 0.195 3626 Planarity : 0.004 0.064 4305 Dihedral : 4.575 46.991 3280 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.36 % Allowed : 16.62 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 2978 helix: -1.51 (0.28), residues: 288 sheet: -0.16 (0.17), residues: 958 loop : -1.04 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1287 TYR 0.013 0.001 TYR F 926 PHE 0.009 0.001 PHE F 640 TRP 0.011 0.001 TRP F1296 HIS 0.005 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00214 (24053) covalent geometry : angle 0.49614 (32692) SS BOND : bond 0.00411 ( 1) SS BOND : angle 1.18421 ( 2) hydrogen bonds : bond 0.02738 ( 719) hydrogen bonds : angle 5.27966 ( 2013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2463 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7773 (t70) REVERT: A 2479 GLN cc_start: 0.8581 (mt0) cc_final: 0.8295 (pt0) REVERT: B 2346 LYS cc_start: 0.7997 (tttm) cc_final: 0.7576 (tptt) REVERT: B 2388 GLN cc_start: 0.8799 (mt0) cc_final: 0.8426 (mp10) REVERT: B 2397 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8138 (mtpt) REVERT: B 2400 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7949 (mp0) REVERT: B 2500 MET cc_start: 0.8853 (tmm) cc_final: 0.8127 (ttp) REVERT: B 2512 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8421 (mtt180) REVERT: C 2500 MET cc_start: 0.8618 (tmm) cc_final: 0.8373 (tmm) REVERT: C 2512 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8211 (mtm180) REVERT: C 2516 LYS cc_start: 0.8528 (ptpt) cc_final: 0.6894 (tptm) REVERT: D 2455 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.7904 (m110) REVERT: D 2491 MET cc_start: 0.8353 (tpt) cc_final: 0.8069 (tpt) REVERT: D 2493 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8377 (mm-30) REVERT: E 2357 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (tt) REVERT: E 2372 ASN cc_start: 0.8637 (m-40) cc_final: 0.8408 (m110) REVERT: E 2397 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7518 (mtpp) REVERT: E 2408 LYS cc_start: 0.8101 (tttm) cc_final: 0.7489 (pptt) REVERT: E 2427 GLN cc_start: 0.8626 (mm110) cc_final: 0.8232 (mm-40) REVERT: F 408 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8415 (mmtp) REVERT: F 420 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7504 (ttp80) REVERT: F 467 GLN cc_start: 0.8323 (pt0) cc_final: 0.8069 (pt0) REVERT: F 676 LEU cc_start: 0.8359 (mt) cc_final: 0.8036 (mt) REVERT: F 688 MET cc_start: 0.8162 (mmm) cc_final: 0.7958 (mmm) REVERT: F 730 GLU cc_start: 0.8180 (tt0) cc_final: 0.7924 (tt0) REVERT: F 771 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7450 (tmt-80) REVERT: F 988 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: F 1041 GLU cc_start: 0.7403 (mp0) cc_final: 0.7116 (mp0) REVERT: F 1191 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8981 (m) REVERT: F 1290 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7141 (mtt90) REVERT: F 1337 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8464 (mtt-85) REVERT: F 1430 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.5381 (p90) REVERT: G 116 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7889 (ptt-90) REVERT: G 152 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: G 173 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8290 (mt) REVERT: G 317 GLN cc_start: 0.8339 (mt0) cc_final: 0.7852 (tt0) REVERT: G 412 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6839 (tp-100) REVERT: G 642 ILE cc_start: 0.8857 (tt) cc_final: 0.8590 (tt) outliers start: 60 outliers final: 27 residues processed: 342 average time/residue: 0.7019 time to fit residues: 272.9549 Evaluate side-chains 321 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2397 LYS Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2397 LYS Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1191 THR Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1284 GLU Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1337 ARG Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 211 optimal weight: 2.9990 chunk 165 optimal weight: 0.0970 chunk 164 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 260 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 269 optimal weight: 3.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2355 GLN A2363 GLN B2505 ASN F 113 GLN ** F 397 ASN ** 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 = 0.3442 r_free = 0.3442 target = 0.119032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109759 restraints weight = 38947.808| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.66 r_work: 0.3239 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24054 Z= 0.106 Angle : 0.506 10.610 32694 Z= 0.263 Chirality : 0.043 0.170 3626 Planarity : 0.004 0.064 4305 Dihedral : 4.549 47.046 3280 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.12 % Allowed : 17.41 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 2978 helix: -1.25 (0.29), residues: 288 sheet: -0.08 (0.17), residues: 969 loop : -0.98 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 424 TYR 0.013 0.001 TYR F 926 PHE 0.009 0.001 PHE F 652 TRP 0.010 0.001 TRP F1296 HIS 0.006 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00243 (24053) covalent geometry : angle 0.50567 (32692) SS BOND : bond 0.00428 ( 1) SS BOND : angle 1.09845 ( 2) hydrogen bonds : bond 0.02768 ( 719) hydrogen bonds : angle 5.19860 ( 2013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2358 ASP cc_start: 0.7828 (t0) cc_final: 0.7588 (t0) REVERT: A 2463 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7777 (t70) REVERT: A 2479 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: B 2346 LYS cc_start: 0.8088 (tttm) cc_final: 0.7667 (tptt) REVERT: B 2388 GLN cc_start: 0.8790 (mt0) cc_final: 0.8386 (mp10) REVERT: B 2455 ASN cc_start: 0.8861 (t0) cc_final: 0.8661 (t0) REVERT: B 2500 MET cc_start: 0.8863 (tmm) cc_final: 0.8191 (ttp) REVERT: B 2505 ASN cc_start: 0.8206 (t0) cc_final: 0.7931 (t0) REVERT: B 2512 ARG cc_start: 0.8686 (mtt180) cc_final: 0.8396 (mtt180) REVERT: C 2400 GLU cc_start: 0.8348 (mp0) cc_final: 0.8014 (mp0) REVERT: C 2500 MET cc_start: 0.8630 (tmm) cc_final: 0.8387 (tmm) REVERT: C 2512 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8247 (mtm180) REVERT: C 2516 LYS cc_start: 0.8510 (ptpt) cc_final: 0.6871 (tptm) REVERT: D 2455 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.7938 (m110) REVERT: D 2491 MET cc_start: 0.8343 (tpt) cc_final: 0.8023 (tpt) REVERT: D 2493 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8359 (mm-30) REVERT: E 2357 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8101 (tt) REVERT: E 2372 ASN cc_start: 0.8637 (m-40) cc_final: 0.8293 (m110) REVERT: E 2397 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7454 (mtpp) REVERT: E 2408 LYS cc_start: 0.8069 (tttm) cc_final: 0.7462 (pptt) REVERT: E 2427 GLN cc_start: 0.8605 (mm110) cc_final: 0.8208 (mm-40) REVERT: E 2456 ASP cc_start: 0.8990 (t0) cc_final: 0.8759 (t0) REVERT: F 242 ASN cc_start: 0.7567 (t0) cc_final: 0.7232 (t0) REVERT: F 258 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8091 (mp) REVERT: F 408 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8478 (mmtp) REVERT: F 420 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7720 (ttp80) REVERT: F 467 GLN cc_start: 0.8319 (pt0) cc_final: 0.8075 (pt0) REVERT: F 676 LEU cc_start: 0.8313 (mt) cc_final: 0.8006 (mt) REVERT: F 688 MET cc_start: 0.8117 (mmm) cc_final: 0.7880 (mmm) REVERT: F 730 GLU cc_start: 0.8194 (tt0) cc_final: 0.7939 (tt0) REVERT: F 771 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7456 (tmt-80) REVERT: F 988 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: F 1041 GLU cc_start: 0.7416 (mp0) cc_final: 0.7144 (mp0) REVERT: F 1191 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8999 (m) REVERT: F 1290 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7153 (mtt90) REVERT: F 1430 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.5281 (p90) REVERT: G 116 ARG cc_start: 0.8215 (ptm-80) cc_final: 0.7889 (ptt-90) REVERT: G 152 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: G 173 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8282 (mt) REVERT: G 317 GLN cc_start: 0.8328 (mt0) cc_final: 0.7849 (tt0) REVERT: G 412 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6803 (tp-100) outliers start: 54 outliers final: 27 residues processed: 323 average time/residue: 0.6858 time to fit residues: 252.5626 Evaluate side-chains 322 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2479 GLN Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2397 LYS Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1191 THR Chi-restraints excluded: chain F residue 1233 GLU Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1279 THR Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 99 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 228 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2355 GLN B2461 GLN F 113 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1376 GLN G 34 GLN G 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108641 restraints weight = 38875.495| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.65 r_work: 0.3229 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24054 Z= 0.132 Angle : 0.526 9.623 32694 Z= 0.273 Chirality : 0.043 0.168 3626 Planarity : 0.004 0.063 4305 Dihedral : 4.624 46.598 3280 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.40 % Allowed : 17.41 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2978 helix: -1.20 (0.29), residues: 288 sheet: -0.07 (0.17), residues: 969 loop : -0.95 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 424 TYR 0.014 0.001 TYR F 926 PHE 0.011 0.001 PHE F1021 TRP 0.010 0.001 TRP F1296 HIS 0.007 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00309 (24053) covalent geometry : angle 0.52624 (32692) SS BOND : bond 0.00445 ( 1) SS BOND : angle 1.18126 ( 2) hydrogen bonds : bond 0.02901 ( 719) hydrogen bonds : angle 5.22932 ( 2013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 286 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2358 ASP cc_start: 0.7833 (t0) cc_final: 0.7585 (t0) REVERT: A 2388 GLN cc_start: 0.8656 (mm110) cc_final: 0.8360 (mm110) REVERT: A 2463 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7791 (t70) REVERT: A 2479 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: B 2346 LYS cc_start: 0.8085 (tttm) cc_final: 0.7679 (tptt) REVERT: B 2388 GLN cc_start: 0.8755 (mt0) cc_final: 0.8364 (mp10) REVERT: B 2500 MET cc_start: 0.8880 (tmm) cc_final: 0.8153 (ttp) REVERT: B 2512 ARG cc_start: 0.8704 (mtt180) cc_final: 0.8413 (mtt180) REVERT: C 2400 GLU cc_start: 0.8384 (mp0) cc_final: 0.8055 (mp0) REVERT: C 2500 MET cc_start: 0.8625 (tmm) cc_final: 0.8377 (tmm) REVERT: C 2512 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8228 (mtm180) REVERT: C 2516 LYS cc_start: 0.8534 (ptpt) cc_final: 0.6891 (tptm) REVERT: D 2455 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.7977 (m110) REVERT: D 2491 MET cc_start: 0.8287 (tpt) cc_final: 0.7933 (tpt) REVERT: D 2493 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8378 (mm-30) REVERT: E 2357 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8220 (tt) REVERT: E 2372 ASN cc_start: 0.8647 (m-40) cc_final: 0.8411 (m110) REVERT: E 2397 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7602 (mtpp) REVERT: E 2408 LYS cc_start: 0.8063 (tttm) cc_final: 0.7466 (pptt) REVERT: E 2427 GLN cc_start: 0.8614 (mm110) cc_final: 0.8221 (mm-40) REVERT: E 2456 ASP cc_start: 0.8999 (t0) cc_final: 0.8763 (t0) REVERT: F 242 ASN cc_start: 0.7608 (t0) cc_final: 0.7283 (t0) REVERT: F 258 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8122 (mp) REVERT: F 405 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8672 (pt) REVERT: F 408 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8382 (mmtp) REVERT: F 420 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7317 (ttp80) REVERT: F 771 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7490 (tmt-80) REVERT: F 988 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: F 1041 GLU cc_start: 0.7431 (mp0) cc_final: 0.7174 (mp0) REVERT: F 1191 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9014 (m) REVERT: F 1290 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7174 (mtt90) REVERT: F 1430 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5424 (p90) REVERT: G 34 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: G 116 ARG cc_start: 0.8225 (ptm-80) cc_final: 0.7940 (ptt-90) REVERT: G 173 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8413 (OUTLIER) REVERT: G 317 GLN cc_start: 0.8334 (mt0) cc_final: 0.7881 (tt0) REVERT: G 412 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6795 (tp-100) outliers start: 61 outliers final: 33 residues processed: 323 average time/residue: 0.6798 time to fit residues: 250.1976 Evaluate side-chains 322 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2479 GLN Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2397 LYS Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain E residue 2423 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1168 CYS Chi-restraints excluded: chain F residue 1191 THR Chi-restraints excluded: chain F residue 1233 GLU Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1279 THR Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2355 GLN B2461 GLN B2505 ASN D2465 ASN F 113 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1376 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108960 restraints weight = 38962.391| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.65 r_work: 0.3241 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24054 Z= 0.131 Angle : 0.530 10.064 32694 Z= 0.275 Chirality : 0.044 0.195 3626 Planarity : 0.004 0.063 4305 Dihedral : 4.626 46.761 3280 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.24 % Allowed : 17.45 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 2978 helix: -1.20 (0.29), residues: 288 sheet: -0.05 (0.17), residues: 975 loop : -0.93 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2411 TYR 0.014 0.001 TYR F 926 PHE 0.010 0.001 PHE F1021 TRP 0.010 0.001 TRP F1296 HIS 0.006 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00306 (24053) covalent geometry : angle 0.52989 (32692) SS BOND : bond 0.00436 ( 1) SS BOND : angle 1.17530 ( 2) hydrogen bonds : bond 0.02889 ( 719) hydrogen bonds : angle 5.22050 ( 2013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2358 ASP cc_start: 0.7842 (t70) cc_final: 0.7598 (t0) REVERT: A 2463 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7783 (t70) REVERT: A 2479 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: B 2388 GLN cc_start: 0.8751 (mt0) cc_final: 0.8352 (mp10) REVERT: B 2500 MET cc_start: 0.8883 (tmm) cc_final: 0.8213 (ttp) REVERT: B 2505 ASN cc_start: 0.8217 (t0) cc_final: 0.7991 (t0) REVERT: B 2512 ARG cc_start: 0.8683 (mtt180) cc_final: 0.8383 (mtt180) REVERT: C 2500 MET cc_start: 0.8579 (tmm) cc_final: 0.8313 (tmm) REVERT: C 2512 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8216 (mtm180) REVERT: C 2516 LYS cc_start: 0.8520 (ptpt) cc_final: 0.6876 (tptm) REVERT: D 2455 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8100 (m110) REVERT: D 2491 MET cc_start: 0.8334 (tpt) cc_final: 0.8041 (tpt) REVERT: D 2493 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 2357 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8223 (tt) REVERT: E 2359 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8450 (ttpt) REVERT: E 2372 ASN cc_start: 0.8649 (m-40) cc_final: 0.8404 (m110) REVERT: E 2397 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7586 (mtpp) REVERT: E 2408 LYS cc_start: 0.8081 (tttm) cc_final: 0.7460 (pptt) REVERT: E 2427 GLN cc_start: 0.8627 (mm110) cc_final: 0.8233 (mm-40) REVERT: E 2456 ASP cc_start: 0.9013 (t0) cc_final: 0.8784 (t0) REVERT: F 113 GLN cc_start: 0.5509 (OUTLIER) cc_final: 0.5302 (mp10) REVERT: F 242 ASN cc_start: 0.7605 (t0) cc_final: 0.7267 (t0) REVERT: F 405 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8674 (pt) REVERT: F 408 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8277 (mmtp) REVERT: F 420 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7302 (ttp80) REVERT: F 771 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7474 (tmt-80) REVERT: F 988 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: F 1041 GLU cc_start: 0.7472 (mp0) cc_final: 0.7207 (mp0) REVERT: F 1071 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8079 (mptt) REVERT: F 1191 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9019 (m) REVERT: F 1290 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7151 (mtt90) REVERT: F 1430 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.5397 (p90) REVERT: G 116 ARG cc_start: 0.8221 (ptm-80) cc_final: 0.7955 (ptt-90) REVERT: G 173 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8429 (OUTLIER) REVERT: G 317 GLN cc_start: 0.8322 (mt0) cc_final: 0.7878 (tt0) outliers start: 57 outliers final: 36 residues processed: 315 average time/residue: 0.6752 time to fit residues: 242.5679 Evaluate side-chains 321 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2479 GLN Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2461 GLN Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2359 LYS Chi-restraints excluded: chain E residue 2397 LYS Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 755 THR Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1030 VAL Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1071 LYS Chi-restraints excluded: chain F residue 1168 CYS Chi-restraints excluded: chain F residue 1191 THR Chi-restraints excluded: chain F residue 1233 GLU Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1279 THR Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 110 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 255 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2461 GLN D2459 GLN F 113 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1376 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108641 restraints weight = 39065.383| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.65 r_work: 0.3230 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24054 Z= 0.138 Angle : 0.537 9.064 32694 Z= 0.279 Chirality : 0.044 0.204 3626 Planarity : 0.004 0.063 4305 Dihedral : 4.662 46.692 3280 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.16 % Allowed : 17.72 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 2978 helix: -1.22 (0.29), residues: 287 sheet: -0.05 (0.17), residues: 975 loop : -0.90 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 424 TYR 0.014 0.001 TYR F 926 PHE 0.010 0.001 PHE F 652 TRP 0.010 0.001 TRP F1296 HIS 0.007 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00325 (24053) covalent geometry : angle 0.53725 (32692) SS BOND : bond 0.00454 ( 1) SS BOND : angle 1.19725 ( 2) hydrogen bonds : bond 0.02933 ( 719) hydrogen bonds : angle 5.23251 ( 2013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2358 ASP cc_start: 0.7854 (t70) cc_final: 0.7612 (t0) REVERT: A 2388 GLN cc_start: 0.8625 (mm110) cc_final: 0.8371 (mm110) REVERT: A 2463 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7807 (t70) REVERT: A 2479 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8312 (pt0) REVERT: B 2347 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: B 2388 GLN cc_start: 0.8733 (mt0) cc_final: 0.8358 (mp10) REVERT: B 2500 MET cc_start: 0.8885 (tmm) cc_final: 0.8219 (ttp) REVERT: B 2512 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8406 (mtt180) REVERT: C 2400 GLU cc_start: 0.8332 (mp0) cc_final: 0.8057 (mp0) REVERT: C 2408 LYS cc_start: 0.8415 (mppt) cc_final: 0.7709 (tmmt) REVERT: C 2500 MET cc_start: 0.8591 (tmm) cc_final: 0.8333 (tmm) REVERT: C 2512 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8241 (mtm180) REVERT: C 2516 LYS cc_start: 0.8500 (ptpt) cc_final: 0.6831 (tptm) REVERT: D 2455 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8110 (m110) REVERT: D 2491 MET cc_start: 0.8354 (tpt) cc_final: 0.8047 (tpt) REVERT: D 2493 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8402 (mm-30) REVERT: E 2357 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8309 (tt) REVERT: E 2359 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8340 (ttpt) REVERT: E 2372 ASN cc_start: 0.8643 (m-40) cc_final: 0.8401 (m110) REVERT: E 2397 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7619 (mtpp) REVERT: E 2408 LYS cc_start: 0.8155 (tttm) cc_final: 0.7490 (pptt) REVERT: E 2427 GLN cc_start: 0.8615 (mm110) cc_final: 0.8230 (mm-40) REVERT: E 2456 ASP cc_start: 0.9018 (t0) cc_final: 0.8791 (t0) REVERT: F 219 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: F 242 ASN cc_start: 0.7541 (t0) cc_final: 0.7195 (t0) REVERT: F 405 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8630 (pt) REVERT: F 408 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8221 (mmtp) REVERT: F 420 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.7319 (ttp80) REVERT: F 620 ASP cc_start: 0.8424 (t0) cc_final: 0.8150 (t0) REVERT: F 771 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7486 (tmt-80) REVERT: F 988 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: F 1041 GLU cc_start: 0.7414 (mp0) cc_final: 0.7136 (mp0) REVERT: F 1071 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8109 (mptt) REVERT: F 1191 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9032 (m) REVERT: F 1290 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7178 (mtt90) REVERT: F 1430 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5090 (p90) REVERT: G 116 ARG cc_start: 0.8228 (ptm-80) cc_final: 0.7970 (ptt-90) REVERT: G 173 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (mt) REVERT: G 274 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6699 (mm-40) REVERT: G 317 GLN cc_start: 0.8324 (mt0) cc_final: 0.7880 (tt0) outliers start: 55 outliers final: 36 residues processed: 311 average time/residue: 0.6826 time to fit residues: 241.7919 Evaluate side-chains 320 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2479 GLN Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 2347 ASP Chi-restraints excluded: chain B residue 2357 ILE Chi-restraints excluded: chain B residue 2483 THR Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain C residue 2417 VAL Chi-restraints excluded: chain C residue 2461 GLN Chi-restraints excluded: chain D residue 2454 MET Chi-restraints excluded: chain D residue 2455 ASN Chi-restraints excluded: chain D residue 2499 THR Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2359 LYS Chi-restraints excluded: chain E residue 2397 LYS Chi-restraints excluded: chain E residue 2409 ILE Chi-restraints excluded: chain E residue 2418 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 755 THR Chi-restraints excluded: chain F residue 988 GLN Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1030 VAL Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1071 LYS Chi-restraints excluded: chain F residue 1168 CYS Chi-restraints excluded: chain F residue 1191 THR Chi-restraints excluded: chain F residue 1233 GLU Chi-restraints excluded: chain F residue 1274 THR Chi-restraints excluded: chain F residue 1279 THR Chi-restraints excluded: chain F residue 1294 GLU Chi-restraints excluded: chain F residue 1334 THR Chi-restraints excluded: chain F residue 1364 VAL Chi-restraints excluded: chain F residue 1430 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 274 GLN Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 364 MET Chi-restraints excluded: chain G residue 411 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 233 optimal weight: 0.8980 chunk 133 optimal weight: 0.0270 chunk 214 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 144 optimal weight: 0.0470 chunk 109 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2452 HIS B2461 GLN B2505 ASN D2459 GLN F 209 GLN F 236 GLN ** F 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1376 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109511 restraints weight = 38941.548| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.66 r_work: 0.3207 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24054 Z= 0.119 Angle : 0.525 9.916 32694 Z= 0.272 Chirality : 0.043 0.186 3626 Planarity : 0.004 0.064 4305 Dihedral : 4.593 46.771 3280 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.04 % Allowed : 17.92 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2978 helix: -1.19 (0.29), residues: 293 sheet: -0.03 (0.17), residues: 961 loop : -0.90 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 424 TYR 0.014 0.001 TYR F 926 PHE 0.010 0.001 PHE F 652 TRP 0.011 0.001 TRP F1296 HIS 0.005 0.001 HIS F 687 Details of bonding type rmsd covalent geometry : bond 0.00277 (24053) covalent geometry : angle 0.52450 (32692) SS BOND : bond 0.00430 ( 1) SS BOND : angle 1.09026 ( 2) hydrogen bonds : bond 0.02823 ( 719) hydrogen bonds : angle 5.17993 ( 2013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8138.52 seconds wall clock time: 139 minutes 0.93 seconds (8340.93 seconds total)