Starting phenix.real_space_refine on Fri Aug 7 15:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pu0_17927/08_2026/8pu0_17927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pu0_17927/08_2026/8pu0_17927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pu0_17927/08_2026/8pu0_17927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pu0_17927/08_2026/8pu0_17927.map" model { file = "/net/cci-nas-00/data/ceres_data/8pu0_17927/08_2026/8pu0_17927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pu0_17927/08_2026/8pu0_17927.cif" } resolution = 4.25 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= 0.002 sd= 0.024 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 73 5.49 5 S 129 5.16 5 C 14011 2.51 5 N 3851 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22416 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9209 Classifications: {'peptide': 1157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1107} Chain breaks: 7 Chain: "B" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5380 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 26, 'TRANS': 650} Chain breaks: 10 Chain: "C" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4296 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 29, 'TRANS': 508} Chain: "E" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1942 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "X" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1507 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 58} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {'5AD': 1, 'DCA': 1, 'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15348 SG CYS C 109 39.338 64.555 69.080 1.00354.93 S ATOM 15273 SG CYS C 99 40.853 68.791 63.985 1.00322.40 S ATOM 15373 SG CYS C 112 37.703 69.692 69.335 1.00338.59 S Time building chain proxies: 5.05, per 1000 atoms: 0.23 Number of scatterers: 22416 At special positions: 0 Unit cell: (112.66, 166.84, 206.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 129 16.00 P 73 15.00 O 4348 8.00 N 3851 7.00 C 14011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 602 " pdb="FE4 SF4 C 602 " - pdb=" SG CYS C 112 " pdb="FE2 SF4 C 602 " - pdb=" SG CYS C 109 " pdb="FE3 SF4 C 602 " - pdb=" SG CYS C 99 " Number of angles added : 9 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4924 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 32 sheets defined 33.2% alpha, 21.4% beta 22 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.635A pdb=" N ASP A 667 " --> pdb=" O CYS A 664 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 668' Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 679 through 682 Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.696A pdb=" N VAL A 725 " --> pdb=" O HIS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 747 removed outlier: 3.675A pdb=" N ALA A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 759 removed outlier: 4.468A pdb=" N ASN A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 765 removed outlier: 3.825A pdb=" N GLY A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 775 Processing helix chain 'A' and resid 776 through 785 Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.829A pdb=" N VAL A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 845 Processing helix chain 'A' and resid 850 through 864 removed outlier: 3.599A pdb=" N VAL A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 886 removed outlier: 3.618A pdb=" N HIS A 883 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 884 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 897 Processing helix chain 'A' and resid 899 through 909 removed outlier: 3.721A pdb=" N VAL A 903 " --> pdb=" O ASP A 899 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 909 " --> pdb=" O MET A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 927 Proline residue: A 919 - end of helix Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.783A pdb=" N LYS A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 968 Processing helix chain 'A' and resid 970 through 978 removed outlier: 3.809A pdb=" N LYS A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 977 " --> pdb=" O GLU A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.840A pdb=" N LEU A 996 " --> pdb=" O TYR A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1012 Processing helix chain 'A' and resid 1029 through 1037 Processing helix chain 'A' and resid 1046 through 1059 Processing helix chain 'A' and resid 1062 through 1072 removed outlier: 4.087A pdb=" N ALA A1066 " --> pdb=" O HIS A1062 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A1070 " --> pdb=" O ALA A1066 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A1071 " --> pdb=" O MET A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1086 Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.613A pdb=" N ALA A1092 " --> pdb=" O ALA A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.488A pdb=" N GLU A1106 " --> pdb=" O ASP A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1141 removed outlier: 4.050A pdb=" N VAL A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1230 removed outlier: 3.515A pdb=" N VAL A1225 " --> pdb=" O ALA A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1246 removed outlier: 3.560A pdb=" N LYS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A1246 " --> pdb=" O VAL A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1274 Proline residue: A1271 - end of helix Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 467 through 479 Processing helix chain 'B' and resid 547 through 554 removed outlier: 3.679A pdb=" N LEU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 32 removed outlier: 3.521A pdb=" N GLN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 65 through 73 removed outlier: 5.554A pdb=" N VAL C 71 " --> pdb=" O GLN C 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.877A pdb=" N LEU C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.642A pdb=" N LEU C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.591A pdb=" N ALA C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.847A pdb=" N ALA C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.510A pdb=" N VAL C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 307 removed outlier: 3.857A pdb=" N PHE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.723A pdb=" N GLU C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.790A pdb=" N LEU C 373 " --> pdb=" O PRO C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.856A pdb=" N LEU C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 532 Processing helix chain 'E' and resid 932 through 940 Processing helix chain 'E' and resid 942 through 953 Processing helix chain 'E' and resid 954 through 956 No H-bonds generated for 'chain 'E' and resid 954 through 956' Processing helix chain 'E' and resid 957 through 968 removed outlier: 3.626A pdb=" N LYS E 968 " --> pdb=" O LEU E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 970 through 978 Processing helix chain 'E' and resid 982 through 997 removed outlier: 3.835A pdb=" N GLN E 986 " --> pdb=" O SER E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1011 Processing helix chain 'E' and resid 1021 through 1026 Processing helix chain 'E' and resid 1027 through 1037 Processing helix chain 'E' and resid 1045 through 1059 Processing helix chain 'E' and resid 1066 through 1072 removed outlier: 4.157A pdb=" N CYS E1072 " --> pdb=" O VAL E1068 " (cutoff:3.500A) Processing helix chain 'E' and resid 1075 through 1087 Processing helix chain 'E' and resid 1108 through 1130 removed outlier: 3.744A pdb=" N THR E1130 " --> pdb=" O SER E1126 " (cutoff:3.500A) Processing helix chain 'E' and resid 1131 through 1131 No H-bonds generated for 'chain 'E' and resid 1131 through 1131' Processing helix chain 'E' and resid 1228 through 1229 No H-bonds generated for 'chain 'E' and resid 1228 through 1229' Processing helix chain 'E' and resid 1230 through 1245 removed outlier: 3.996A pdb=" N ASP E1234 " --> pdb=" O GLU E1230 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E1236 " --> pdb=" O LEU E1232 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR E1237 " --> pdb=" O LYS E1233 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS E1241 " --> pdb=" O TYR E1237 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL E1242 " --> pdb=" O HIS E1238 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU E1243 " --> pdb=" O ILE E1239 " (cutoff:3.500A) Processing helix chain 'E' and resid 1250 through 1262 removed outlier: 3.570A pdb=" N GLU E1254 " --> pdb=" O GLU E1250 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ALA E1258 " --> pdb=" O GLU E1254 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE E1259 " --> pdb=" O LEU E1255 " (cutoff:3.500A) Processing helix chain 'E' and resid 1263 through 1265 No H-bonds generated for 'chain 'E' and resid 1263 through 1265' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 5.194A pdb=" N LEU A 4 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR A 376 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU A 6 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS A 374 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 8 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.467A pdb=" N GLY A 36 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 42 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 41 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 54 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU A 43 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 50 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 75 removed outlier: 4.168A pdb=" N GLY A 73 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 75 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 84 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 94 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N CYS A 104 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117 removed outlier: 3.975A pdb=" N VAL A 114 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 124 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A 136 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.617A pdb=" N ASN A 225 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 230 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 246 removed outlier: 5.043A pdb=" N GLY A 276 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 294 removed outlier: 4.518A pdb=" N TRP A 304 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU A 292 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 302 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 301 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 320 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER A 335 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 322 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 390 through 395 Processing sheet with id=AA9, first strand: chain 'A' and resid 424 through 429 removed outlier: 3.750A pdb=" N GLN A 426 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 439 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 451 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE A 448 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 485 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 450 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU A 545 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS A 487 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 507 through 510 removed outlier: 6.671A pdb=" N VAL A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 525 through 527 Processing sheet with id=AB3, first strand: chain 'A' and resid 557 through 563 removed outlier: 4.070A pdb=" N VAL A 569 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 609 through 612 removed outlier: 4.066A pdb=" N GLN A 609 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 624 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 623 " --> pdb=" O PHE A 631 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 631 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 638 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 641 through 646 removed outlier: 6.452A pdb=" N THR A 654 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 652 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 653 " --> pdb=" O GLN A 661 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A 661 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 699 through 701 removed outlier: 3.879A pdb=" N ASN A 715 " --> pdb=" O MET A 711 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 12 removed outlier: 6.666A pdb=" N ILE B 818 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 11 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 816 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 784 " --> pdb=" O CYS B 810 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 22 through 24 removed outlier: 6.397A pdb=" N VAL B 40 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN B 53 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 42 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.538A pdb=" N VAL B 87 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N HIS B 102 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS B 89 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 100 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 91 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 116 removed outlier: 3.942A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER B 143 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N CYS B 151 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS B 145 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 162 through 169 removed outlier: 3.637A pdb=" N CYS B 166 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 187 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 202 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 189 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 210 through 218 removed outlier: 3.601A pdb=" N GLY B 212 " --> pdb=" O CYS B 227 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP B 236 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 226 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B 234 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 233 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 278 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 235 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 270 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 291 removed outlier: 6.831A pdb=" N ALA B 310 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 289 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 308 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 347 through 349 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 7.018A pdb=" N VAL B 406 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 394 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 404 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 414 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 441 through 446 removed outlier: 3.903A pdb=" N ARG B 462 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 463 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN B 561 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER B 465 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU B 559 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 570 through 575 removed outlier: 3.521A pdb=" N SER B 584 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 608 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN B 600 " --> pdb=" O GLN B 606 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN B 606 " --> pdb=" O ASN B 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 617 through 622 removed outlier: 3.536A pdb=" N LEU B 629 " --> pdb=" O TRP B 641 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP B 641 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP B 638 " --> pdb=" O PHE B 660 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 660 " --> pdb=" O TRP B 638 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 640 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 672 through 676 removed outlier: 6.871A pdb=" N GLY B 687 " --> pdb=" O TRP B 673 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 675 " --> pdb=" O PHE B 685 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE B 685 " --> pdb=" O CYS B 675 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 684 " --> pdb=" O TRP B 696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 686 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 694 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 723 through 728 removed outlier: 3.520A pdb=" N CYS B 750 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE B 749 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU B 771 " --> pdb=" O ILE B 749 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU B 751 " --> pdb=" O CYS B 769 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 769 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.452A pdb=" N VAL C 90 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 165 " --> pdb=" O CYS C 215 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 217 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 219 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 169 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU C 221 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C 241 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE C 218 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 243 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 220 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 241 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL C 282 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU C 243 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS C 284 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU C 315 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 365 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 317 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 421 through 429 removed outlier: 3.613A pdb=" N TYR C 427 " --> pdb=" O GLU C 434 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP C 433 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG C 454 " --> pdb=" O TRP C 433 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C 435 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG C 452 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 437 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 450 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR C 439 " --> pdb=" O ILE C 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 469 through 472 removed outlier: 3.545A pdb=" N SER C 470 " --> pdb=" O LYS C 517 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 9379 1.40 - 1.62: 13498 1.62 - 1.84: 182 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 23071 Sorted by residual: bond pdb=" C1B DCA C 601 " pdb=" O4B DCA C 601 " ideal model delta sigma weight residual 1.416 1.646 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1B DCA C 601 " pdb=" C2B DCA C 601 " ideal model delta sigma weight residual 1.537 1.322 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C ALA C 53 " pdb=" N GLN C 54 " ideal model delta sigma weight residual 1.331 1.446 -0.115 1.48e-02 4.57e+03 6.05e+01 bond pdb=" C5P DCA C 601 " pdb=" N4P DCA C 601 " ideal model delta sigma weight residual 1.343 1.488 -0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C4B DCA C 601 " pdb=" O4B DCA C 601 " ideal model delta sigma weight residual 1.450 1.305 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 23066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 31291 2.81 - 5.61: 291 5.61 - 8.42: 28 8.42 - 11.23: 8 11.23 - 14.04: 2 Bond angle restraints: 31620 Sorted by residual: angle pdb=" O3' C X 70 " pdb=" C3' C X 70 " pdb=" C2' C X 70 " ideal model delta sigma weight residual 113.70 105.08 8.62 1.60e+00 3.91e-01 2.90e+01 angle pdb=" N ASP A1075 " pdb=" CA ASP A1075 " pdb=" C ASP A1075 " ideal model delta sigma weight residual 112.93 107.41 5.52 1.12e+00 7.97e-01 2.43e+01 angle pdb=" N1A DCA C 601 " pdb=" C6A DCA C 601 " pdb=" N6A DCA C 601 " ideal model delta sigma weight residual 119.05 105.01 14.04 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N1 U X 53 " pdb=" C2 U X 53 " pdb=" O2 U X 53 " ideal model delta sigma weight residual 122.80 125.80 -3.00 7.00e-01 2.04e+00 1.83e+01 angle pdb=" O5' U X 33 " pdb=" C5' U X 33 " pdb=" C4' U X 33 " ideal model delta sigma weight residual 109.40 112.72 -3.32 8.00e-01 1.56e+00 1.72e+01 ... (remaining 31615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 12380 18.14 - 36.28: 1063 36.28 - 54.43: 290 54.43 - 72.57: 148 72.57 - 90.71: 41 Dihedral angle restraints: 13922 sinusoidal: 6324 harmonic: 7598 Sorted by residual: dihedral pdb=" CA ASP A 886 " pdb=" C ASP A 886 " pdb=" N VAL A 887 " pdb=" CA VAL A 887 " ideal model delta harmonic sigma weight residual 180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA MET A 927 " pdb=" C MET A 927 " pdb=" N GLU A 928 " pdb=" CA GLU A 928 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ASP C 488 " pdb=" C ASP C 488 " pdb=" N PRO C 489 " pdb=" CA PRO C 489 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 13919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3435 0.108 - 0.216: 151 0.216 - 0.324: 2 0.324 - 0.432: 0 0.432 - 0.540: 5 Chirality restraints: 3593 Sorted by residual: chirality pdb=" P C X 70 " pdb=" OP1 C X 70 " pdb=" OP2 C X 70 " pdb=" O5' C X 70 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" P C X 71 " pdb=" OP1 C X 71 " pdb=" OP2 C X 71 " pdb=" O5' C X 71 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" P C X 49 " pdb=" OP1 C X 49 " pdb=" OP2 C X 49 " pdb=" O5' C X 49 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 3590 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 604 " -0.015 2.00e-02 2.50e+03 1.22e-02 3.75e+00 pdb=" CG TRP B 604 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 604 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 604 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 604 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 604 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 604 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 604 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 604 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 604 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 32 " -0.022 2.00e-02 2.50e+03 1.15e-02 2.95e+00 pdb=" N1 C X 32 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C X 32 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C X 32 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C X 32 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C X 32 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C X 32 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C X 32 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C X 32 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 265 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C LYS C 265 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS C 265 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA C 266 " 0.009 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2529 2.74 - 3.28: 25081 3.28 - 3.82: 40757 3.82 - 4.36: 46858 4.36 - 4.90: 73417 Nonbonded interactions: 188642 Sorted by model distance: nonbonded pdb=" OP1 U X 59 " pdb=" N4 C X 60 " model vdw 2.202 3.120 nonbonded pdb=" NH2 ARG A1011 " pdb=" O ALA A1014 " model vdw 2.209 3.120 nonbonded pdb=" OG SER B 688 " pdb=" OD1 ASP B 690 " model vdw 2.211 3.040 nonbonded pdb=" NZ LYS A 247 " pdb=" O GLY A 250 " model vdw 2.213 3.120 nonbonded pdb=" OG SER C 194 " pdb=" OG SER C 208 " model vdw 2.218 3.040 ... (remaining 188637 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.005 0.230 23074 Z= 0.274 Angle : 0.746 22.085 31629 Z= 0.417 Chirality : 0.050 0.540 3593 Planarity : 0.004 0.039 3753 Dihedral : 16.628 90.708 8998 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.61 % Allowed : 0.44 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.73 (0.17), residues: 2567 helix: 0.16 (0.19), residues: 735 sheet: -1.63 (0.20), residues: 608 loop : -1.65 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1011 TYR 0.026 0.002 TYR A 931 PHE 0.018 0.002 PHE B 388 TRP 0.029 0.002 TRP B 604 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.27 (23071) covalent geometry : angle 0.71254 / 0.42 (31620) hydrogen bonds : bond 0.17724 / 11.46 ( 855) hydrogen bonds : angle 7.19734 / 5.08 ( 2328) metal coordination : bond 0.01119 / 0.56 ( 3) metal coordination : angle 13.18050 / 6.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 820 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7152 (tmm) cc_final: 0.6793 (tmm) REVERT: A 4 LEU cc_start: 0.7337 (mt) cc_final: 0.6925 (mp) REVERT: A 33 VAL cc_start: 0.7579 (t) cc_final: 0.7085 (m) REVERT: A 43 GLU cc_start: 0.6691 (tt0) cc_final: 0.6483 (tp30) REVERT: A 122 GLU cc_start: 0.7506 (tp30) cc_final: 0.7221 (tp30) REVERT: A 136 MET cc_start: 0.8062 (pmm) cc_final: 0.7265 (pmm) REVERT: A 234 SER cc_start: 0.8091 (t) cc_final: 0.7710 (p) REVERT: A 337 SER cc_start: 0.7624 (p) cc_final: 0.7378 (t) REVERT: A 378 ASP cc_start: 0.7083 (m-30) cc_final: 0.6343 (m-30) REVERT: A 476 CYS cc_start: 0.7371 (m) cc_final: 0.7015 (t) REVERT: A 487 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7387 (mmmt) REVERT: A 529 HIS cc_start: 0.7340 (m-70) cc_final: 0.6958 (m90) REVERT: A 573 LEU cc_start: 0.6646 (tp) cc_final: 0.6219 (mp) REVERT: A 610 THR cc_start: 0.8489 (p) cc_final: 0.7709 (p) REVERT: A 612 LEU cc_start: 0.8220 (mt) cc_final: 0.7871 (tp) REVERT: A 617 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 640 ASN cc_start: 0.4926 (t0) cc_final: 0.4716 (t0) REVERT: A 660 CYS cc_start: 0.7400 (t) cc_final: 0.6385 (p) REVERT: A 661 GLN cc_start: 0.7545 (pm20) cc_final: 0.6963 (pm20) REVERT: A 731 LYS cc_start: 0.8352 (mmpt) cc_final: 0.7602 (tptp) REVERT: A 744 CYS cc_start: 0.8516 (t) cc_final: 0.7817 (p) REVERT: A 745 MET cc_start: 0.7752 (tmm) cc_final: 0.7141 (tmm) REVERT: A 774 ILE cc_start: 0.8493 (mm) cc_final: 0.8201 (tp) REVERT: A 893 HIS cc_start: 0.8287 (m90) cc_final: 0.8017 (m90) REVERT: A 898 TYR cc_start: 0.7206 (t80) cc_final: 0.6876 (t80) REVERT: A 908 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 931 TYR cc_start: 0.7524 (t80) cc_final: 0.7233 (t80) REVERT: A 1121 MET cc_start: 0.8292 (mmp) cc_final: 0.8077 (mmm) REVERT: A 1254 GLU cc_start: 0.8681 (tt0) cc_final: 0.8416 (tt0) REVERT: B 17 ARG cc_start: 0.7231 (ptm-80) cc_final: 0.6814 (ptm-80) REVERT: B 31 LEU cc_start: 0.6898 (mt) cc_final: 0.6579 (mt) REVERT: B 32 LEU cc_start: 0.5899 (mt) cc_final: 0.5545 (mt) REVERT: B 77 GLU cc_start: 0.7381 (mp0) cc_final: 0.6777 (mp0) REVERT: B 83 SER cc_start: 0.6003 (t) cc_final: 0.5752 (m) REVERT: B 91 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6359 (mt-10) REVERT: B 156 ASN cc_start: 0.7821 (p0) cc_final: 0.7618 (p0) REVERT: B 169 PHE cc_start: 0.7329 (m-10) cc_final: 0.7123 (m-80) REVERT: B 391 VAL cc_start: 0.5329 (m) cc_final: 0.4593 (p) REVERT: B 394 LEU cc_start: 0.6069 (pt) cc_final: 0.5698 (pt) REVERT: B 395 VAL cc_start: 0.6472 (p) cc_final: 0.6260 (p) REVERT: B 415 PHE cc_start: 0.6634 (m-80) cc_final: 0.6245 (m-80) REVERT: B 443 CYS cc_start: 0.4247 (m) cc_final: 0.3693 (m) REVERT: B 566 HIS cc_start: 0.4325 (m90) cc_final: 0.3980 (m-70) REVERT: B 628 PHE cc_start: 0.5804 (m-80) cc_final: 0.4840 (m-80) REVERT: B 638 TRP cc_start: 0.5796 (p-90) cc_final: 0.5450 (p-90) REVERT: B 675 CYS cc_start: 0.6011 (p) cc_final: 0.4993 (p) REVERT: B 696 TRP cc_start: 0.5293 (m100) cc_final: 0.5079 (m100) REVERT: B 785 LEU cc_start: 0.7492 (mt) cc_final: 0.7232 (mt) REVERT: B 817 LYS cc_start: 0.7083 (mtmt) cc_final: 0.6857 (mtmt) REVERT: C 28 GLU cc_start: 0.8756 (tt0) cc_final: 0.8269 (tp30) REVERT: C 31 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8078 (mt-10) REVERT: C 32 GLN cc_start: 0.6949 (mp10) cc_final: 0.6621 (mp10) REVERT: C 73 MET cc_start: 0.8149 (mmp) cc_final: 0.7929 (mmp) REVERT: C 87 ILE cc_start: 0.8038 (mm) cc_final: 0.7755 (mp) REVERT: C 154 GLN cc_start: 0.7452 (tt0) cc_final: 0.7212 (tt0) REVERT: C 213 THR cc_start: 0.5189 (p) cc_final: 0.4730 (p) REVERT: C 219 THR cc_start: 0.5934 (p) cc_final: 0.5622 (p) REVERT: C 279 PHE cc_start: 0.7368 (m-80) cc_final: 0.6835 (m-80) REVERT: C 288 ASP cc_start: 0.7940 (t0) cc_final: 0.6916 (t70) REVERT: C 300 GLN cc_start: 0.8531 (pp30) cc_final: 0.8123 (pp30) REVERT: C 330 GLU cc_start: 0.7607 (mp0) cc_final: 0.7328 (mp0) REVERT: C 337 TYR cc_start: 0.7666 (t80) cc_final: 0.7429 (t80) REVERT: C 340 TYR cc_start: 0.8086 (m-10) cc_final: 0.7635 (m-10) REVERT: C 345 LEU cc_start: 0.8225 (mt) cc_final: 0.7900 (mm) REVERT: C 370 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: C 373 LEU cc_start: 0.8425 (mp) cc_final: 0.8096 (mp) REVERT: C 382 ASN cc_start: 0.7935 (p0) cc_final: 0.6844 (p0) REVERT: C 385 GLU cc_start: 0.7983 (mp0) cc_final: 0.7754 (mp0) REVERT: C 402 ARG cc_start: 0.6808 (tmm-80) cc_final: 0.6313 (tpt-90) REVERT: C 474 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6158 (tm-30) REVERT: C 497 PHE cc_start: 0.5428 (m-80) cc_final: 0.4642 (m-10) REVERT: C 532 LYS cc_start: 0.8155 (mttp) cc_final: 0.7775 (mttp) REVERT: C 535 TYR cc_start: 0.7204 (m-80) cc_final: 0.6831 (m-80) REVERT: C 542 MET cc_start: 0.6032 (tpp) cc_final: 0.5797 (tpp) REVERT: C 545 MET cc_start: 0.7471 (tpt) cc_final: 0.7173 (tpt) REVERT: E 939 TYR cc_start: 0.7566 (m-10) cc_final: 0.7362 (m-10) REVERT: E 987 ASP cc_start: 0.7569 (m-30) cc_final: 0.7288 (m-30) REVERT: E 992 TYR cc_start: 0.7941 (t80) cc_final: 0.7610 (t80) REVERT: E 996 LEU cc_start: 0.6882 (tp) cc_final: 0.6493 (tp) REVERT: E 1008 MET cc_start: 0.6958 (mmp) cc_final: 0.6219 (mmp) REVERT: E 1095 LEU cc_start: 0.7610 (mt) cc_final: 0.7345 (mt) REVERT: E 1110 LYS cc_start: 0.8018 (tttt) cc_final: 0.7725 (tttt) REVERT: E 1127 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8128 (mp10) outliers start: 14 outliers final: 5 residues processed: 830 average time/residue: 0.1734 time to fit residues: 218.3037 Evaluate side-chains 693 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 688 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 HIS A 529 HIS A 530 HIS ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 118 GLN B 192 GLN B 613 HIS C 476 HIS ** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN C 538 GLN ** E1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1264 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.125295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100209 restraints weight = 44467.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104215 restraints weight = 23710.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106317 restraints weight = 12660.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107696 restraints weight = 8906.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108011 restraints weight = 7183.067| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23074 Z= 0.178 Angle : 0.732 20.819 31629 Z= 0.368 Chirality : 0.047 0.271 3593 Planarity : 0.005 0.084 3753 Dihedral : 15.002 74.231 3988 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.66 (0.17), residues: 2567 helix: 0.14 (0.19), residues: 764 sheet: -1.50 (0.21), residues: 610 loop : -1.65 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 473 TYR 0.016 0.002 TYR B 117 PHE 0.031 0.002 PHE C 461 TRP 0.026 0.002 TRP B 787 HIS 0.010 0.001 HIS A1238 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (23071) covalent geometry : angle 0.69890 / 0.37 (31620) hydrogen bonds : bond 0.05451 / 3.68 ( 855) hydrogen bonds : angle 5.98901 / 4.22 ( 2328) metal coordination : bond 0.01616 / 0.82 ( 3) metal coordination : angle 12.92866 / 6.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 758 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7297 (ttp-170) cc_final: 0.6977 (ttp80) REVERT: A 43 GLU cc_start: 0.7407 (tt0) cc_final: 0.7202 (tp30) REVERT: A 115 MET cc_start: 0.6842 (ppp) cc_final: 0.6604 (ppp) REVERT: A 121 GLN cc_start: 0.8210 (mp10) cc_final: 0.7761 (mp10) REVERT: A 131 GLN cc_start: 0.8402 (mp-120) cc_final: 0.8143 (mp10) REVERT: A 136 MET cc_start: 0.7870 (pmm) cc_final: 0.7200 (pmm) REVERT: A 150 GLN cc_start: 0.7755 (pm20) cc_final: 0.7301 (pm20) REVERT: A 193 ASP cc_start: 0.7578 (t0) cc_final: 0.7092 (t0) REVERT: A 234 SER cc_start: 0.8361 (t) cc_final: 0.8119 (p) REVERT: A 257 GLN cc_start: 0.8807 (tt0) cc_final: 0.8598 (tt0) REVERT: A 259 LYS cc_start: 0.8424 (tppt) cc_final: 0.8211 (tptt) REVERT: A 274 LEU cc_start: 0.8748 (pp) cc_final: 0.8430 (tp) REVERT: A 286 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7560 (tt0) REVERT: A 378 ASP cc_start: 0.7306 (m-30) cc_final: 0.6772 (m-30) REVERT: A 414 CYS cc_start: 0.7603 (p) cc_final: 0.7396 (p) REVERT: A 443 ASP cc_start: 0.7553 (t0) cc_final: 0.7345 (t0) REVERT: A 474 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8180 (mmtt) REVERT: A 478 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7703 (ttm-80) REVERT: A 483 GLU cc_start: 0.7745 (tp30) cc_final: 0.7085 (tp30) REVERT: A 572 GLN cc_start: 0.7659 (tt0) cc_final: 0.5834 (tt0) REVERT: A 573 LEU cc_start: 0.7907 (tp) cc_final: 0.7437 (mp) REVERT: A 578 ILE cc_start: 0.8413 (mm) cc_final: 0.8166 (mm) REVERT: A 580 LYS cc_start: 0.8298 (tmmt) cc_final: 0.7855 (tmmt) REVERT: A 620 CYS cc_start: 0.8306 (p) cc_final: 0.8026 (p) REVERT: A 626 ASP cc_start: 0.8489 (p0) cc_final: 0.8214 (p0) REVERT: A 640 ASN cc_start: 0.6740 (t0) cc_final: 0.6335 (t0) REVERT: A 660 CYS cc_start: 0.8368 (t) cc_final: 0.7611 (p) REVERT: A 661 GLN cc_start: 0.8389 (pm20) cc_final: 0.7879 (pm20) REVERT: A 689 ARG cc_start: 0.7544 (tmt-80) cc_final: 0.7209 (tmt-80) REVERT: A 725 VAL cc_start: 0.8586 (t) cc_final: 0.8357 (t) REVERT: A 731 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8183 (tptp) REVERT: A 743 GLU cc_start: 0.8209 (pt0) cc_final: 0.7938 (pt0) REVERT: A 749 ARG cc_start: 0.8660 (tpt170) cc_final: 0.8364 (tpp80) REVERT: A 753 ASN cc_start: 0.8428 (m-40) cc_final: 0.8216 (m-40) REVERT: A 767 VAL cc_start: 0.8661 (m) cc_final: 0.8433 (m) REVERT: A 771 ILE cc_start: 0.8968 (mm) cc_final: 0.8760 (mm) REVERT: A 774 ILE cc_start: 0.9038 (mm) cc_final: 0.8665 (tp) REVERT: A 794 LYS cc_start: 0.8690 (mppt) cc_final: 0.8424 (mmtt) REVERT: A 796 MET cc_start: 0.8494 (ttm) cc_final: 0.8204 (mtt) REVERT: A 834 LYS cc_start: 0.7187 (mttm) cc_final: 0.6607 (mttm) REVERT: A 841 THR cc_start: 0.8635 (m) cc_final: 0.8285 (p) REVERT: A 850 GLU cc_start: 0.7797 (mp0) cc_final: 0.7293 (mp0) REVERT: A 882 LEU cc_start: 0.8849 (mt) cc_final: 0.8635 (mt) REVERT: A 931 TYR cc_start: 0.8169 (t80) cc_final: 0.7806 (t80) REVERT: A 939 TYR cc_start: 0.7264 (t80) cc_final: 0.6898 (t80) REVERT: A 1001 MET cc_start: 0.5923 (mmp) cc_final: 0.5537 (mmp) REVERT: A 1089 TRP cc_start: 0.7527 (m100) cc_final: 0.7312 (m100) REVERT: A 1121 MET cc_start: 0.8280 (mmp) cc_final: 0.8042 (mmp) REVERT: B 7 GLU cc_start: 0.7218 (pt0) cc_final: 0.6774 (pm20) REVERT: B 22 LEU cc_start: 0.7806 (tp) cc_final: 0.7601 (tp) REVERT: B 98 LEU cc_start: 0.8594 (tp) cc_final: 0.7442 (tp) REVERT: B 150 MET cc_start: 0.7159 (ptp) cc_final: 0.6208 (ppp) REVERT: B 156 ASN cc_start: 0.8161 (p0) cc_final: 0.7780 (p0) REVERT: B 183 ASP cc_start: 0.7054 (p0) cc_final: 0.6412 (p0) REVERT: B 237 LYS cc_start: 0.6057 (tmmt) cc_final: 0.5699 (ttpt) REVERT: B 377 GLU cc_start: 0.7714 (tt0) cc_final: 0.6641 (pt0) REVERT: B 394 LEU cc_start: 0.8431 (pt) cc_final: 0.8099 (pt) REVERT: B 395 VAL cc_start: 0.8483 (p) cc_final: 0.8164 (p) REVERT: B 435 GLN cc_start: 0.8654 (pp30) cc_final: 0.8378 (pp30) REVERT: B 447 ILE cc_start: 0.7534 (mm) cc_final: 0.7092 (mm) REVERT: B 586 CYS cc_start: 0.7941 (p) cc_final: 0.7705 (p) REVERT: B 625 ASN cc_start: 0.8385 (t0) cc_final: 0.7602 (t0) REVERT: B 627 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7688 (mmmt) REVERT: B 628 PHE cc_start: 0.7208 (m-80) cc_final: 0.6580 (m-80) REVERT: B 638 TRP cc_start: 0.7661 (p-90) cc_final: 0.7263 (p-90) REVERT: B 684 PHE cc_start: 0.7185 (p90) cc_final: 0.6780 (p90) REVERT: B 786 CYS cc_start: 0.6954 (t) cc_final: 0.6654 (t) REVERT: B 817 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7751 (mtmt) REVERT: C 17 LEU cc_start: 0.8791 (mt) cc_final: 0.8458 (mt) REVERT: C 28 GLU cc_start: 0.8549 (tt0) cc_final: 0.8024 (tt0) REVERT: C 31 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7987 (mt-10) REVERT: C 40 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8256 (mmtt) REVERT: C 87 ILE cc_start: 0.8396 (mm) cc_final: 0.8060 (mp) REVERT: C 154 GLN cc_start: 0.7731 (tt0) cc_final: 0.7121 (tt0) REVERT: C 167 PHE cc_start: 0.7951 (m-80) cc_final: 0.7501 (m-80) REVERT: C 223 ARG cc_start: 0.7673 (ptm160) cc_final: 0.7466 (ptp-170) REVERT: C 242 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7676 (mtm110) REVERT: C 244 GLU cc_start: 0.7352 (mp0) cc_final: 0.6570 (mm-30) REVERT: C 280 LYS cc_start: 0.7285 (mmpt) cc_final: 0.6551 (mmmt) REVERT: C 285 MET cc_start: 0.7889 (mmm) cc_final: 0.7420 (mmm) REVERT: C 288 ASP cc_start: 0.8042 (t0) cc_final: 0.6383 (t70) REVERT: C 300 GLN cc_start: 0.8514 (pp30) cc_final: 0.8032 (pp30) REVERT: C 330 GLU cc_start: 0.8147 (mp0) cc_final: 0.7864 (mp0) REVERT: C 337 TYR cc_start: 0.7635 (t80) cc_final: 0.7275 (t80) REVERT: C 340 TYR cc_start: 0.8082 (m-10) cc_final: 0.7826 (m-10) REVERT: C 345 LEU cc_start: 0.8546 (mt) cc_final: 0.8175 (mm) REVERT: C 391 MET cc_start: 0.7006 (ppp) cc_final: 0.6579 (ppp) REVERT: C 411 ILE cc_start: 0.8674 (tt) cc_final: 0.8422 (mm) REVERT: C 428 VAL cc_start: 0.8432 (t) cc_final: 0.8111 (m) REVERT: C 445 ASP cc_start: 0.7574 (m-30) cc_final: 0.7256 (m-30) REVERT: C 459 GLU cc_start: 0.7594 (pm20) cc_final: 0.6763 (pm20) REVERT: C 464 GLU cc_start: 0.8266 (mp0) cc_final: 0.7751 (pm20) REVERT: C 497 PHE cc_start: 0.7417 (m-80) cc_final: 0.6771 (m-10) REVERT: C 507 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7704 (tmm-80) REVERT: C 508 ILE cc_start: 0.8539 (tp) cc_final: 0.8259 (tp) REVERT: C 518 ILE cc_start: 0.8682 (mt) cc_final: 0.8417 (mt) REVERT: C 529 TYR cc_start: 0.8038 (t80) cc_final: 0.7321 (t80) REVERT: C 532 LYS cc_start: 0.8440 (mttp) cc_final: 0.7994 (mttp) REVERT: C 535 TYR cc_start: 0.8246 (m-80) cc_final: 0.7792 (m-80) REVERT: C 538 GLN cc_start: 0.7960 (tt0) cc_final: 0.7516 (tt0) REVERT: C 543 VAL cc_start: 0.8628 (p) cc_final: 0.7374 (t) REVERT: E 939 TYR cc_start: 0.7232 (m-10) cc_final: 0.6942 (m-10) REVERT: E 983 GLN cc_start: 0.6035 (pp30) cc_final: 0.5498 (pp30) REVERT: E 985 TYR cc_start: 0.7701 (t80) cc_final: 0.7065 (t80) REVERT: E 992 TYR cc_start: 0.7359 (t80) cc_final: 0.6651 (t80) REVERT: E 996 LEU cc_start: 0.7565 (tp) cc_final: 0.7109 (tp) REVERT: E 997 MET cc_start: 0.7526 (mmt) cc_final: 0.6908 (mmt) REVERT: E 1038 LEU cc_start: 0.7592 (mt) cc_final: 0.7244 (mt) REVERT: E 1052 LEU cc_start: 0.8962 (tp) cc_final: 0.8722 (tp) REVERT: E 1059 GLN cc_start: 0.8180 (mm110) cc_final: 0.7790 (mm110) REVERT: E 1064 ASP cc_start: 0.7452 (p0) cc_final: 0.7130 (t0) REVERT: E 1095 LEU cc_start: 0.8449 (mt) cc_final: 0.8007 (mt) REVERT: E 1097 TYR cc_start: 0.7535 (m-80) cc_final: 0.7270 (m-80) REVERT: E 1103 ASP cc_start: 0.7993 (m-30) cc_final: 0.7713 (m-30) REVERT: E 1115 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8448 (tm-30) outliers start: 2 outliers final: 1 residues processed: 758 average time/residue: 0.1715 time to fit residues: 197.3622 Evaluate side-chains 692 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 691 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 245 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN A 271 ASN A 321 GLN A 422 HIS A 530 HIS ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 192 GLN ** B 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN ** E1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1264 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098495 restraints weight = 44118.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102368 restraints weight = 23335.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.104159 restraints weight = 12818.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105466 restraints weight = 8888.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105800 restraints weight = 7165.227| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23074 Z= 0.174 Angle : 0.726 31.464 31629 Z= 0.359 Chirality : 0.046 0.218 3593 Planarity : 0.005 0.055 3753 Dihedral : 14.669 75.878 3988 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.74 (0.16), residues: 2567 helix: 0.11 (0.19), residues: 763 sheet: -1.43 (0.21), residues: 590 loop : -1.82 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 462 TYR 0.036 0.002 TYR A 931 PHE 0.030 0.002 PHE A 62 TRP 0.031 0.002 TRP B 24 HIS 0.013 0.002 HIS A1238 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (23071) covalent geometry : angle 0.67637 / 0.36 (31620) hydrogen bonds : bond 0.05434 / 3.71 ( 855) hydrogen bonds : angle 5.70830 / 4.03 ( 2328) metal coordination : bond 0.02163 / 1.06 ( 3) metal coordination : angle 15.58406 / 6.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 752 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7201 (ttp-170) cc_final: 0.6956 (ptt-90) REVERT: A 52 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8841 (mmtm) REVERT: A 121 GLN cc_start: 0.8180 (mp10) cc_final: 0.7837 (mp10) REVERT: A 131 GLN cc_start: 0.8417 (mp-120) cc_final: 0.8158 (mp10) REVERT: A 136 MET cc_start: 0.7866 (pmm) cc_final: 0.7412 (pmm) REVERT: A 189 LEU cc_start: 0.9170 (tp) cc_final: 0.8102 (tp) REVERT: A 262 GLN cc_start: 0.7968 (pm20) cc_final: 0.7632 (pm20) REVERT: A 263 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6281 (mm-40) REVERT: A 274 LEU cc_start: 0.8795 (pp) cc_final: 0.8555 (tp) REVERT: A 285 ASP cc_start: 0.8305 (t0) cc_final: 0.8081 (t70) REVERT: A 286 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7658 (tt0) REVERT: A 327 ASN cc_start: 0.8480 (m-40) cc_final: 0.8208 (m-40) REVERT: A 377 THR cc_start: 0.8014 (p) cc_final: 0.7706 (p) REVERT: A 378 ASP cc_start: 0.7314 (m-30) cc_final: 0.6844 (m-30) REVERT: A 443 ASP cc_start: 0.7530 (t0) cc_final: 0.7204 (t0) REVERT: A 474 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8171 (mmtt) REVERT: A 478 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7735 (ttm-80) REVERT: A 483 GLU cc_start: 0.7821 (tp30) cc_final: 0.7059 (tp30) REVERT: A 487 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7824 (mmmt) REVERT: A 573 LEU cc_start: 0.8035 (tp) cc_final: 0.7782 (mp) REVERT: A 580 LYS cc_start: 0.8288 (tmmt) cc_final: 0.7881 (tmmt) REVERT: A 640 ASN cc_start: 0.6872 (t0) cc_final: 0.6489 (t0) REVERT: A 654 THR cc_start: 0.7391 (m) cc_final: 0.7033 (p) REVERT: A 660 CYS cc_start: 0.8453 (t) cc_final: 0.7732 (p) REVERT: A 661 GLN cc_start: 0.8411 (pm20) cc_final: 0.7907 (pm20) REVERT: A 677 LEU cc_start: 0.8538 (tp) cc_final: 0.8202 (tp) REVERT: A 689 ARG cc_start: 0.7684 (tmt-80) cc_final: 0.7278 (tmt-80) REVERT: A 731 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8188 (tptp) REVERT: A 737 MET cc_start: 0.6304 (pmm) cc_final: 0.6005 (pmm) REVERT: A 740 GLU cc_start: 0.8078 (mp0) cc_final: 0.7634 (mp0) REVERT: A 743 GLU cc_start: 0.8238 (pt0) cc_final: 0.7996 (pt0) REVERT: A 745 MET cc_start: 0.8388 (ttp) cc_final: 0.8182 (ttp) REVERT: A 753 ASN cc_start: 0.8506 (m-40) cc_final: 0.8273 (m-40) REVERT: A 767 VAL cc_start: 0.8694 (m) cc_final: 0.8460 (m) REVERT: A 771 ILE cc_start: 0.8951 (mm) cc_final: 0.8725 (mm) REVERT: A 774 ILE cc_start: 0.9047 (mm) cc_final: 0.8749 (tp) REVERT: A 815 LYS cc_start: 0.7998 (ptmt) cc_final: 0.7774 (ptmm) REVERT: A 827 MET cc_start: 0.8246 (ppp) cc_final: 0.7970 (ppp) REVERT: A 850 GLU cc_start: 0.7761 (mp0) cc_final: 0.7266 (mp0) REVERT: A 882 LEU cc_start: 0.8892 (mt) cc_final: 0.8427 (tt) REVERT: A 909 LYS cc_start: 0.8334 (mppt) cc_final: 0.8027 (mmtm) REVERT: A 913 ASP cc_start: 0.8182 (t0) cc_final: 0.7689 (t0) REVERT: A 922 ASN cc_start: 0.8552 (m110) cc_final: 0.8280 (m110) REVERT: A 958 PHE cc_start: 0.6774 (t80) cc_final: 0.6506 (t80) REVERT: A 973 GLU cc_start: 0.8398 (mp0) cc_final: 0.8146 (mp0) REVERT: A 1001 MET cc_start: 0.6110 (mmp) cc_final: 0.5793 (mmp) REVERT: A 1008 MET cc_start: 0.7264 (ppp) cc_final: 0.6849 (ppp) REVERT: A 1032 LEU cc_start: 0.8175 (tp) cc_final: 0.7877 (tp) REVERT: A 1089 TRP cc_start: 0.7482 (m100) cc_final: 0.7012 (m100) REVERT: A 1121 MET cc_start: 0.8349 (mmp) cc_final: 0.7737 (mmt) REVERT: A 1228 ASN cc_start: 0.9032 (m110) cc_final: 0.8750 (m-40) REVERT: A 1238 HIS cc_start: 0.8151 (p90) cc_final: 0.7939 (p-80) REVERT: B 7 GLU cc_start: 0.7513 (pt0) cc_final: 0.6973 (pm20) REVERT: B 13 CYS cc_start: 0.7950 (p) cc_final: 0.7659 (t) REVERT: B 32 LEU cc_start: 0.8059 (mt) cc_final: 0.7338 (mp) REVERT: B 78 LEU cc_start: 0.7873 (mt) cc_final: 0.7574 (mt) REVERT: B 91 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6715 (tm-30) REVERT: B 93 GLU cc_start: 0.5937 (pm20) cc_final: 0.5635 (pm20) REVERT: B 144 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7371 (tptp) REVERT: B 150 MET cc_start: 0.7356 (ptp) cc_final: 0.6619 (ppp) REVERT: B 156 ASN cc_start: 0.8255 (p0) cc_final: 0.7881 (p0) REVERT: B 377 GLU cc_start: 0.7926 (tt0) cc_final: 0.6911 (tt0) REVERT: B 381 GLU cc_start: 0.7840 (tp30) cc_final: 0.7556 (tp30) REVERT: B 394 LEU cc_start: 0.8667 (pt) cc_final: 0.8383 (pt) REVERT: B 430 GLU cc_start: 0.8285 (pm20) cc_final: 0.7794 (pm20) REVERT: B 433 ARG cc_start: 0.8254 (ptp-110) cc_final: 0.7696 (mtp85) REVERT: B 443 CYS cc_start: 0.7120 (m) cc_final: 0.6830 (m) REVERT: B 447 ILE cc_start: 0.7619 (mm) cc_final: 0.7269 (mm) REVERT: B 462 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7141 (mtt90) REVERT: B 473 ASN cc_start: 0.8681 (t0) cc_final: 0.8281 (t0) REVERT: B 566 HIS cc_start: 0.7295 (m90) cc_final: 0.7047 (m90) REVERT: B 586 CYS cc_start: 0.8071 (p) cc_final: 0.7803 (p) REVERT: B 597 ILE cc_start: 0.8058 (mt) cc_final: 0.7853 (mt) REVERT: B 612 PHE cc_start: 0.7756 (t80) cc_final: 0.7407 (t80) REVERT: B 619 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7302 (tp-100) REVERT: B 625 ASN cc_start: 0.8408 (t0) cc_final: 0.8064 (t0) REVERT: B 628 PHE cc_start: 0.7257 (m-80) cc_final: 0.6716 (m-80) REVERT: B 638 TRP cc_start: 0.7731 (p-90) cc_final: 0.7429 (p-90) REVERT: B 641 TRP cc_start: 0.7386 (m100) cc_final: 0.6628 (m100) REVERT: B 643 LYS cc_start: 0.8434 (tmmt) cc_final: 0.7820 (tppt) REVERT: B 684 PHE cc_start: 0.7131 (p90) cc_final: 0.6877 (p90) REVERT: B 786 CYS cc_start: 0.7264 (t) cc_final: 0.6807 (t) REVERT: B 817 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7940 (mtmt) REVERT: C 17 LEU cc_start: 0.8844 (mt) cc_final: 0.8445 (mt) REVERT: C 28 GLU cc_start: 0.8487 (tt0) cc_final: 0.6974 (tm-30) REVERT: C 32 GLN cc_start: 0.7449 (mp10) cc_final: 0.6857 (mp10) REVERT: C 40 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8291 (mmtt) REVERT: C 87 ILE cc_start: 0.8264 (mm) cc_final: 0.7974 (mm) REVERT: C 154 GLN cc_start: 0.7675 (tt0) cc_final: 0.7011 (tt0) REVERT: C 225 ASP cc_start: 0.8314 (p0) cc_final: 0.8001 (p0) REVERT: C 234 ASP cc_start: 0.7729 (t0) cc_final: 0.7516 (t0) REVERT: C 235 MET cc_start: 0.7000 (mmm) cc_final: 0.6737 (mmm) REVERT: C 285 MET cc_start: 0.8000 (mmm) cc_final: 0.7556 (mmm) REVERT: C 288 ASP cc_start: 0.8050 (t0) cc_final: 0.5954 (t0) REVERT: C 300 GLN cc_start: 0.8574 (pp30) cc_final: 0.8057 (pp30) REVERT: C 330 GLU cc_start: 0.8299 (mp0) cc_final: 0.7953 (mp0) REVERT: C 338 LYS cc_start: 0.8755 (mmpt) cc_final: 0.8509 (mmpt) REVERT: C 340 TYR cc_start: 0.8111 (m-10) cc_final: 0.7593 (m-10) REVERT: C 345 LEU cc_start: 0.8517 (mt) cc_final: 0.8244 (mm) REVERT: C 347 GLU cc_start: 0.8106 (mp0) cc_final: 0.7890 (pm20) REVERT: C 391 MET cc_start: 0.7111 (ppp) cc_final: 0.6687 (ppp) REVERT: C 411 ILE cc_start: 0.8677 (tt) cc_final: 0.8455 (mm) REVERT: C 421 GLU cc_start: 0.7385 (mp0) cc_final: 0.7037 (mp0) REVERT: C 428 VAL cc_start: 0.8527 (t) cc_final: 0.8208 (m) REVERT: C 445 ASP cc_start: 0.7715 (m-30) cc_final: 0.7383 (m-30) REVERT: C 458 GLU cc_start: 0.7526 (tp30) cc_final: 0.7282 (tp30) REVERT: C 459 GLU cc_start: 0.7565 (pm20) cc_final: 0.7339 (pm20) REVERT: C 461 PHE cc_start: 0.6982 (t80) cc_final: 0.6764 (t80) REVERT: C 464 GLU cc_start: 0.8298 (mp0) cc_final: 0.7379 (mp0) REVERT: C 474 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 504 GLU cc_start: 0.7892 (tp30) cc_final: 0.7542 (tp30) REVERT: C 508 ILE cc_start: 0.8449 (tp) cc_final: 0.8067 (tp) REVERT: C 518 ILE cc_start: 0.8712 (mt) cc_final: 0.8452 (mt) REVERT: C 528 ASN cc_start: 0.8593 (m-40) cc_final: 0.8362 (m110) REVERT: C 529 TYR cc_start: 0.8091 (t80) cc_final: 0.7282 (t80) REVERT: C 532 LYS cc_start: 0.8461 (mttp) cc_final: 0.8000 (mttp) REVERT: C 538 GLN cc_start: 0.7822 (tt0) cc_final: 0.7461 (tt0) REVERT: E 939 TYR cc_start: 0.7331 (m-10) cc_final: 0.7022 (m-10) REVERT: E 985 TYR cc_start: 0.7742 (t80) cc_final: 0.7068 (t80) REVERT: E 992 TYR cc_start: 0.7345 (t80) cc_final: 0.6643 (t80) REVERT: E 996 LEU cc_start: 0.7698 (tp) cc_final: 0.7216 (tp) REVERT: E 997 MET cc_start: 0.7393 (mmt) cc_final: 0.6780 (mmt) REVERT: E 1055 LYS cc_start: 0.8923 (tppt) cc_final: 0.8622 (tppt) REVERT: E 1059 GLN cc_start: 0.8100 (mm110) cc_final: 0.7797 (mm110) REVERT: E 1064 ASP cc_start: 0.7274 (p0) cc_final: 0.7019 (t0) REVERT: E 1095 LEU cc_start: 0.8405 (mt) cc_final: 0.8052 (mt) REVERT: E 1097 TYR cc_start: 0.7382 (m-80) cc_final: 0.7150 (m-80) REVERT: E 1115 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8481 (tm-30) REVERT: E 1230 GLU cc_start: 0.8542 (mp0) cc_final: 0.8270 (pm20) REVERT: E 1241 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8391 (mmtp) outliers start: 3 outliers final: 1 residues processed: 754 average time/residue: 0.1561 time to fit residues: 179.5575 Evaluate side-chains 675 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 674 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 9 optimal weight: 3.9990 chunk 232 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 292 GLN ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN C 380 HIS C 495 GLN E1015 HIS ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1264 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093144 restraints weight = 44912.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097502 restraints weight = 23327.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099982 restraints weight = 12150.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100872 restraints weight = 8170.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101295 restraints weight = 7058.092| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23074 Z= 0.234 Angle : 0.744 22.564 31629 Z= 0.382 Chirality : 0.048 0.254 3593 Planarity : 0.005 0.050 3753 Dihedral : 14.502 77.800 3988 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.04 % Allowed : 4.96 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.88 (0.16), residues: 2567 helix: -0.01 (0.19), residues: 768 sheet: -1.35 (0.21), residues: 598 loop : -1.99 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1094 TYR 0.022 0.002 TYR B 239 PHE 0.029 0.002 PHE B 197 TRP 0.026 0.003 TRP A 373 HIS 0.014 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (23071) covalent geometry : angle 0.71486 / 0.38 (31620) hydrogen bonds : bond 0.05915 / 4.06 ( 855) hydrogen bonds : angle 5.68932 / 4.02 ( 2328) metal coordination : bond 0.01243 / 0.63 ( 3) metal coordination : angle 12.15477 / 5.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 766 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6814 (ptt-90) REVERT: A 34 LEU cc_start: 0.8309 (mt) cc_final: 0.8030 (mt) REVERT: A 43 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6488 (tm-30) REVERT: A 52 LYS cc_start: 0.9061 (mmpt) cc_final: 0.8799 (mmtm) REVERT: A 121 GLN cc_start: 0.8344 (mp10) cc_final: 0.7723 (mp10) REVERT: A 122 GLU cc_start: 0.7782 (tp30) cc_final: 0.7525 (tp30) REVERT: A 128 THR cc_start: 0.9138 (p) cc_final: 0.8790 (p) REVERT: A 131 GLN cc_start: 0.8556 (mp-120) cc_final: 0.8219 (mp10) REVERT: A 136 MET cc_start: 0.7858 (pmm) cc_final: 0.7470 (pmm) REVERT: A 189 LEU cc_start: 0.8742 (tp) cc_final: 0.8502 (tp) REVERT: A 193 ASP cc_start: 0.7583 (p0) cc_final: 0.7170 (p0) REVERT: A 205 GLN cc_start: 0.8154 (mt0) cc_final: 0.7939 (mt0) REVERT: A 258 ASP cc_start: 0.7155 (t0) cc_final: 0.6811 (t0) REVERT: A 263 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6614 (mm-40) REVERT: A 285 ASP cc_start: 0.8415 (t0) cc_final: 0.8064 (t70) REVERT: A 286 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7689 (tt0) REVERT: A 288 LYS cc_start: 0.7568 (ttmt) cc_final: 0.7328 (ttpp) REVERT: A 327 ASN cc_start: 0.8578 (m-40) cc_final: 0.8330 (m-40) REVERT: A 377 THR cc_start: 0.8092 (p) cc_final: 0.7747 (p) REVERT: A 378 ASP cc_start: 0.7468 (m-30) cc_final: 0.7021 (m-30) REVERT: A 443 ASP cc_start: 0.7592 (t0) cc_final: 0.7333 (t0) REVERT: A 474 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8097 (mmtt) REVERT: A 478 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7769 (ttm-80) REVERT: A 487 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7929 (mmmt) REVERT: A 573 LEU cc_start: 0.8136 (tp) cc_final: 0.7830 (mp) REVERT: A 580 LYS cc_start: 0.8318 (tmmt) cc_final: 0.7839 (tmmt) REVERT: A 619 GLU cc_start: 0.7960 (mp0) cc_final: 0.7730 (mp0) REVERT: A 622 LEU cc_start: 0.8442 (mp) cc_final: 0.8204 (mt) REVERT: A 640 ASN cc_start: 0.7039 (t0) cc_final: 0.6484 (t0) REVERT: A 654 THR cc_start: 0.7497 (m) cc_final: 0.7138 (p) REVERT: A 655 THR cc_start: 0.8446 (p) cc_final: 0.8067 (p) REVERT: A 659 THR cc_start: 0.7942 (m) cc_final: 0.7548 (p) REVERT: A 660 CYS cc_start: 0.8487 (t) cc_final: 0.7630 (p) REVERT: A 661 GLN cc_start: 0.8465 (pm20) cc_final: 0.7585 (pm20) REVERT: A 677 LEU cc_start: 0.8567 (tp) cc_final: 0.8307 (tp) REVERT: A 689 ARG cc_start: 0.7776 (tmt-80) cc_final: 0.7256 (tmt-80) REVERT: A 731 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8185 (tptp) REVERT: A 737 MET cc_start: 0.6420 (pmm) cc_final: 0.6054 (pmm) REVERT: A 739 LYS cc_start: 0.8796 (ttpt) cc_final: 0.7988 (ptmm) REVERT: A 740 GLU cc_start: 0.8122 (mp0) cc_final: 0.7589 (mp0) REVERT: A 743 GLU cc_start: 0.8316 (pt0) cc_final: 0.7856 (pt0) REVERT: A 745 MET cc_start: 0.8533 (ttp) cc_final: 0.8235 (ttp) REVERT: A 749 ARG cc_start: 0.9037 (mmm-85) cc_final: 0.8787 (tpp80) REVERT: A 753 ASN cc_start: 0.8640 (m-40) cc_final: 0.8327 (m-40) REVERT: A 767 VAL cc_start: 0.8697 (m) cc_final: 0.8152 (t) REVERT: A 771 ILE cc_start: 0.8976 (mm) cc_final: 0.8763 (mm) REVERT: A 774 ILE cc_start: 0.9067 (mm) cc_final: 0.8853 (tp) REVERT: A 782 LEU cc_start: 0.9110 (tp) cc_final: 0.8905 (tp) REVERT: A 796 MET cc_start: 0.8623 (ttm) cc_final: 0.8223 (mtt) REVERT: A 823 MET cc_start: 0.8429 (ptm) cc_final: 0.8210 (ptm) REVERT: A 827 MET cc_start: 0.8778 (ppp) cc_final: 0.8386 (ppp) REVERT: A 833 HIS cc_start: 0.7632 (m90) cc_final: 0.7425 (m90) REVERT: A 834 LYS cc_start: 0.7355 (mttm) cc_final: 0.6773 (mttm) REVERT: A 860 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 882 LEU cc_start: 0.8883 (mt) cc_final: 0.8466 (tt) REVERT: A 909 LYS cc_start: 0.8412 (mppt) cc_final: 0.8050 (mmtm) REVERT: A 913 ASP cc_start: 0.8203 (t0) cc_final: 0.7845 (t0) REVERT: A 922 ASN cc_start: 0.8646 (m110) cc_final: 0.8402 (m110) REVERT: A 924 LEU cc_start: 0.8705 (tt) cc_final: 0.8501 (mp) REVERT: A 958 PHE cc_start: 0.6879 (t80) cc_final: 0.6641 (t80) REVERT: A 973 GLU cc_start: 0.8500 (mp0) cc_final: 0.8162 (mp0) REVERT: A 985 TYR cc_start: 0.7490 (t80) cc_final: 0.7169 (t80) REVERT: A 1001 MET cc_start: 0.6280 (mmp) cc_final: 0.5837 (mmp) REVERT: A 1008 MET cc_start: 0.7319 (ppp) cc_final: 0.6905 (ppp) REVERT: A 1032 LEU cc_start: 0.8080 (tp) cc_final: 0.7616 (tp) REVERT: A 1125 ASP cc_start: 0.7830 (t0) cc_final: 0.7568 (m-30) REVERT: A 1135 LYS cc_start: 0.7528 (pttp) cc_final: 0.7300 (pttp) REVERT: A 1228 ASN cc_start: 0.9012 (m110) cc_final: 0.8777 (m-40) REVERT: A 1238 HIS cc_start: 0.8117 (p90) cc_final: 0.7867 (p-80) REVERT: A 1266 MET cc_start: 0.8093 (mpp) cc_final: 0.7877 (mpp) REVERT: B 55 ASN cc_start: 0.8109 (m110) cc_final: 0.7864 (m110) REVERT: B 98 LEU cc_start: 0.8240 (tp) cc_final: 0.7944 (tp) REVERT: B 99 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8145 (mtmm) REVERT: B 150 MET cc_start: 0.7702 (ptp) cc_final: 0.6664 (ppp) REVERT: B 151 CYS cc_start: 0.7788 (t) cc_final: 0.7382 (t) REVERT: B 152 LEU cc_start: 0.9005 (mt) cc_final: 0.8769 (mt) REVERT: B 156 ASN cc_start: 0.8296 (p0) cc_final: 0.7986 (p0) REVERT: B 184 ASP cc_start: 0.7221 (t0) cc_final: 0.7012 (t0) REVERT: B 237 LYS cc_start: 0.6330 (ttpt) cc_final: 0.5777 (ttpt) REVERT: B 316 MET cc_start: 0.6868 (mtp) cc_final: 0.6225 (mtp) REVERT: B 328 TRP cc_start: 0.8026 (m-10) cc_final: 0.6821 (m100) REVERT: B 377 GLU cc_start: 0.7968 (tt0) cc_final: 0.7046 (tt0) REVERT: B 381 GLU cc_start: 0.7897 (tp30) cc_final: 0.7667 (tp30) REVERT: B 395 VAL cc_start: 0.8606 (t) cc_final: 0.8091 (p) REVERT: B 430 GLU cc_start: 0.8322 (pm20) cc_final: 0.8006 (pm20) REVERT: B 433 ARG cc_start: 0.8250 (ptp-110) cc_final: 0.7835 (ptp-170) REVERT: B 443 CYS cc_start: 0.7055 (m) cc_final: 0.6801 (m) REVERT: B 447 ILE cc_start: 0.7640 (mm) cc_final: 0.7244 (mm) REVERT: B 462 ARG cc_start: 0.7420 (mtt90) cc_final: 0.6798 (mtt90) REVERT: B 473 ASN cc_start: 0.8723 (t0) cc_final: 0.8395 (t0) REVERT: B 474 PHE cc_start: 0.8187 (t80) cc_final: 0.7844 (t80) REVERT: B 478 THR cc_start: 0.6493 (t) cc_final: 0.6272 (t) REVERT: B 586 CYS cc_start: 0.8223 (p) cc_final: 0.7999 (p) REVERT: B 597 ILE cc_start: 0.8093 (mt) cc_final: 0.7887 (mt) REVERT: B 612 PHE cc_start: 0.8049 (t80) cc_final: 0.7802 (t80) REVERT: B 618 THR cc_start: 0.6950 (m) cc_final: 0.6664 (m) REVERT: B 620 MET cc_start: 0.6864 (mmp) cc_final: 0.6635 (mmp) REVERT: B 625 ASN cc_start: 0.8465 (t0) cc_final: 0.7852 (t0) REVERT: B 627 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7765 (mmtt) REVERT: B 628 PHE cc_start: 0.7243 (m-80) cc_final: 0.6641 (m-80) REVERT: B 638 TRP cc_start: 0.7848 (p-90) cc_final: 0.7399 (p-90) REVERT: B 643 LYS cc_start: 0.8407 (tmmt) cc_final: 0.7832 (tppt) REVERT: B 691 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7579 (ptpt) REVERT: B 786 CYS cc_start: 0.7419 (t) cc_final: 0.7026 (t) REVERT: B 812 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 817 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7882 (mtmt) REVERT: C 17 LEU cc_start: 0.8905 (mt) cc_final: 0.8458 (mt) REVERT: C 28 GLU cc_start: 0.8612 (tt0) cc_final: 0.7168 (tm-30) REVERT: C 32 GLN cc_start: 0.7544 (mp10) cc_final: 0.7027 (mp10) REVERT: C 40 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8311 (mmtt) REVERT: C 87 ILE cc_start: 0.8234 (mm) cc_final: 0.8002 (mm) REVERT: C 154 GLN cc_start: 0.7746 (tt0) cc_final: 0.6948 (tt0) REVERT: C 168 ILE cc_start: 0.8502 (tp) cc_final: 0.8115 (mm) REVERT: C 225 ASP cc_start: 0.8254 (p0) cc_final: 0.8004 (p0) REVERT: C 235 MET cc_start: 0.7189 (mmm) cc_final: 0.6977 (mmt) REVERT: C 288 ASP cc_start: 0.8081 (t0) cc_final: 0.5981 (t0) REVERT: C 297 ASP cc_start: 0.8050 (m-30) cc_final: 0.7659 (m-30) REVERT: C 300 GLN cc_start: 0.8664 (pp30) cc_final: 0.8252 (pp30) REVERT: C 340 TYR cc_start: 0.8214 (m-10) cc_final: 0.7769 (m-10) REVERT: C 347 GLU cc_start: 0.8208 (mp0) cc_final: 0.7920 (mp0) REVERT: C 348 LEU cc_start: 0.8869 (mp) cc_final: 0.8585 (mp) REVERT: C 411 ILE cc_start: 0.8734 (tt) cc_final: 0.8518 (mm) REVERT: C 421 GLU cc_start: 0.7135 (mp0) cc_final: 0.6880 (mp0) REVERT: C 428 VAL cc_start: 0.8531 (t) cc_final: 0.8221 (m) REVERT: C 434 GLU cc_start: 0.7789 (mp0) cc_final: 0.7107 (mp0) REVERT: C 443 ASP cc_start: 0.8620 (m-30) cc_final: 0.8355 (m-30) REVERT: C 445 ASP cc_start: 0.7682 (m-30) cc_final: 0.7435 (m-30) REVERT: C 464 GLU cc_start: 0.8414 (mp0) cc_final: 0.7745 (mp0) REVERT: C 497 PHE cc_start: 0.7715 (m-80) cc_final: 0.7197 (m-80) REVERT: C 504 GLU cc_start: 0.8169 (tp30) cc_final: 0.7773 (tp30) REVERT: C 507 ARG cc_start: 0.8217 (tmm-80) cc_final: 0.7849 (tmm-80) REVERT: C 508 ILE cc_start: 0.8504 (tp) cc_final: 0.8016 (tp) REVERT: C 529 TYR cc_start: 0.8143 (t80) cc_final: 0.7686 (t80) REVERT: C 532 LYS cc_start: 0.8492 (mttp) cc_final: 0.8009 (mttp) REVERT: C 535 TYR cc_start: 0.8556 (m-80) cc_final: 0.8124 (m-10) REVERT: C 538 GLN cc_start: 0.7984 (tt0) cc_final: 0.7714 (tt0) REVERT: C 542 MET cc_start: 0.7433 (tpt) cc_final: 0.6890 (tpt) REVERT: E 935 THR cc_start: 0.5103 (p) cc_final: 0.4855 (p) REVERT: E 939 TYR cc_start: 0.7392 (m-10) cc_final: 0.7116 (m-10) REVERT: E 985 TYR cc_start: 0.7811 (t80) cc_final: 0.7148 (t80) REVERT: E 992 TYR cc_start: 0.7401 (t80) cc_final: 0.6713 (t80) REVERT: E 996 LEU cc_start: 0.7803 (tp) cc_final: 0.7344 (tp) REVERT: E 997 MET cc_start: 0.7533 (mmt) cc_final: 0.6859 (mmt) REVERT: E 1052 LEU cc_start: 0.9031 (tp) cc_final: 0.8807 (tp) REVERT: E 1055 LYS cc_start: 0.8863 (tppt) cc_final: 0.8649 (tppt) REVERT: E 1059 GLN cc_start: 0.8168 (mm110) cc_final: 0.7917 (mm110) REVERT: E 1064 ASP cc_start: 0.7251 (p0) cc_final: 0.6956 (t0) REVERT: E 1095 LEU cc_start: 0.8438 (mt) cc_final: 0.8191 (mt) REVERT: E 1115 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8536 (tm-30) REVERT: E 1230 GLU cc_start: 0.8576 (mp0) cc_final: 0.8367 (pm20) REVERT: E 1241 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8370 (mmtp) outliers start: 1 outliers final: 0 residues processed: 767 average time/residue: 0.1597 time to fit residues: 186.8441 Evaluate side-chains 689 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 689 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 112 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 207 optimal weight: 0.3980 chunk 253 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN A 715 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 291 ASN C 495 GLN E1030 GLN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1100 ASN E1264 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.122180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096067 restraints weight = 43955.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100109 restraints weight = 22725.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102143 restraints weight = 12324.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104282 restraints weight = 8736.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104311 restraints weight = 6484.916| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23074 Z= 0.140 Angle : 0.699 23.616 31629 Z= 0.349 Chirality : 0.046 0.218 3593 Planarity : 0.005 0.059 3753 Dihedral : 14.346 76.521 3988 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.71 (0.16), residues: 2567 helix: 0.13 (0.18), residues: 767 sheet: -1.15 (0.20), residues: 608 loop : -1.96 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 69 TYR 0.028 0.002 TYR A 917 PHE 0.037 0.002 PHE A1009 TRP 0.038 0.002 TRP B 142 HIS 0.012 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (23071) covalent geometry : angle 0.66572 / 0.35 (31620) hydrogen bonds : bond 0.05104 / 3.50 ( 855) hydrogen bonds : angle 5.48217 / 3.86 ( 2328) metal coordination : bond 0.01325 / 0.66 ( 3) metal coordination : angle 12.61793 / 5.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6833 (ptt-90) REVERT: A 75 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 121 GLN cc_start: 0.8300 (mp10) cc_final: 0.7895 (mp10) REVERT: A 122 GLU cc_start: 0.7713 (tp30) cc_final: 0.7436 (tp30) REVERT: A 131 GLN cc_start: 0.8498 (mp-120) cc_final: 0.8183 (mp10) REVERT: A 136 MET cc_start: 0.7896 (pmm) cc_final: 0.7472 (pmm) REVERT: A 150 GLN cc_start: 0.7352 (pm20) cc_final: 0.7062 (pm20) REVERT: A 189 LEU cc_start: 0.8657 (tp) cc_final: 0.8434 (tp) REVERT: A 193 ASP cc_start: 0.7680 (p0) cc_final: 0.7366 (p0) REVERT: A 263 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6663 (mm-40) REVERT: A 285 ASP cc_start: 0.8337 (t0) cc_final: 0.8126 (t0) REVERT: A 286 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7807 (tt0) REVERT: A 288 LYS cc_start: 0.7527 (ttmt) cc_final: 0.7080 (ttmt) REVERT: A 327 ASN cc_start: 0.8509 (m-40) cc_final: 0.8233 (m-40) REVERT: A 377 THR cc_start: 0.8067 (p) cc_final: 0.7777 (p) REVERT: A 378 ASP cc_start: 0.7378 (m-30) cc_final: 0.6969 (m-30) REVERT: A 427 VAL cc_start: 0.7937 (p) cc_final: 0.7485 (t) REVERT: A 443 ASP cc_start: 0.7504 (t0) cc_final: 0.7216 (t0) REVERT: A 474 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8106 (mmtt) REVERT: A 478 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7730 (ttm-80) REVERT: A 487 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8052 (mmmt) REVERT: A 573 LEU cc_start: 0.8079 (tp) cc_final: 0.7824 (mp) REVERT: A 580 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7801 (tmmt) REVERT: A 619 GLU cc_start: 0.7899 (mp0) cc_final: 0.7669 (mp0) REVERT: A 622 LEU cc_start: 0.8495 (mp) cc_final: 0.8204 (mt) REVERT: A 660 CYS cc_start: 0.8432 (t) cc_final: 0.7717 (p) REVERT: A 661 GLN cc_start: 0.8493 (pm20) cc_final: 0.7877 (pm20) REVERT: A 677 LEU cc_start: 0.8507 (tp) cc_final: 0.8250 (tp) REVERT: A 689 ARG cc_start: 0.7655 (tmt-80) cc_final: 0.7069 (tmt-80) REVERT: A 728 GLN cc_start: 0.8435 (tp40) cc_final: 0.8092 (tp40) REVERT: A 731 LYS cc_start: 0.8820 (mmpt) cc_final: 0.8131 (tptp) REVERT: A 736 LEU cc_start: 0.8604 (mt) cc_final: 0.8336 (mt) REVERT: A 737 MET cc_start: 0.6329 (pmm) cc_final: 0.5959 (pmm) REVERT: A 739 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8180 (ptmm) REVERT: A 740 GLU cc_start: 0.8107 (mp0) cc_final: 0.7807 (mp0) REVERT: A 743 GLU cc_start: 0.8284 (pt0) cc_final: 0.8048 (pt0) REVERT: A 745 MET cc_start: 0.8436 (ttp) cc_final: 0.8117 (ttm) REVERT: A 753 ASN cc_start: 0.8608 (m-40) cc_final: 0.8273 (m-40) REVERT: A 767 VAL cc_start: 0.8667 (m) cc_final: 0.8155 (t) REVERT: A 771 ILE cc_start: 0.8933 (mm) cc_final: 0.8698 (mm) REVERT: A 823 MET cc_start: 0.8388 (ptm) cc_final: 0.8102 (ptm) REVERT: A 827 MET cc_start: 0.8779 (ppp) cc_final: 0.8224 (ppp) REVERT: A 833 HIS cc_start: 0.7616 (m90) cc_final: 0.7250 (m90) REVERT: A 834 LYS cc_start: 0.7339 (mttm) cc_final: 0.6738 (mttm) REVERT: A 850 GLU cc_start: 0.7658 (mp0) cc_final: 0.7189 (mp0) REVERT: A 860 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8550 (tm-30) REVERT: A 882 LEU cc_start: 0.8866 (mt) cc_final: 0.8458 (tt) REVERT: A 893 HIS cc_start: 0.8329 (m90) cc_final: 0.8017 (m90) REVERT: A 909 LYS cc_start: 0.8452 (mppt) cc_final: 0.8183 (mmtm) REVERT: A 913 ASP cc_start: 0.8276 (t0) cc_final: 0.7892 (t0) REVERT: A 985 TYR cc_start: 0.7452 (t80) cc_final: 0.7131 (t80) REVERT: A 1001 MET cc_start: 0.6330 (mmp) cc_final: 0.6045 (mmp) REVERT: A 1008 MET cc_start: 0.7540 (ppp) cc_final: 0.7137 (ppp) REVERT: A 1112 SER cc_start: 0.8373 (p) cc_final: 0.8083 (p) REVERT: A 1115 GLU cc_start: 0.8669 (pt0) cc_final: 0.8386 (pp20) REVERT: A 1121 MET cc_start: 0.8440 (mmp) cc_final: 0.8136 (mmt) REVERT: A 1125 ASP cc_start: 0.7842 (t0) cc_final: 0.7604 (m-30) REVERT: A 1235 GLU cc_start: 0.8452 (mp0) cc_final: 0.8016 (mp0) REVERT: A 1237 TYR cc_start: 0.8190 (t80) cc_final: 0.7716 (t80) REVERT: A 1241 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8469 (ptpp) REVERT: B 78 LEU cc_start: 0.7883 (mt) cc_final: 0.7635 (mt) REVERT: B 91 GLU cc_start: 0.7504 (pt0) cc_final: 0.6611 (pt0) REVERT: B 98 LEU cc_start: 0.8357 (tp) cc_final: 0.8125 (tp) REVERT: B 99 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8194 (mtmm) REVERT: B 150 MET cc_start: 0.7558 (ptp) cc_final: 0.7034 (ptp) REVERT: B 156 ASN cc_start: 0.8306 (p0) cc_final: 0.8032 (p0) REVERT: B 184 ASP cc_start: 0.7310 (t0) cc_final: 0.7042 (t0) REVERT: B 237 LYS cc_start: 0.6400 (ttpt) cc_final: 0.5871 (ttpt) REVERT: B 239 TYR cc_start: 0.7767 (p90) cc_final: 0.7515 (p90) REVERT: B 316 MET cc_start: 0.6723 (mtp) cc_final: 0.6480 (mtm) REVERT: B 328 TRP cc_start: 0.8047 (m-10) cc_final: 0.7150 (m100) REVERT: B 377 GLU cc_start: 0.7987 (tt0) cc_final: 0.7048 (tt0) REVERT: B 430 GLU cc_start: 0.8326 (pm20) cc_final: 0.7904 (pm20) REVERT: B 433 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7598 (ptp-110) REVERT: B 443 CYS cc_start: 0.6831 (m) cc_final: 0.6599 (m) REVERT: B 462 ARG cc_start: 0.7297 (mtt90) cc_final: 0.6688 (mtt90) REVERT: B 473 ASN cc_start: 0.8722 (t0) cc_final: 0.8347 (t0) REVERT: B 474 PHE cc_start: 0.8105 (t80) cc_final: 0.7788 (t80) REVERT: B 478 THR cc_start: 0.6441 (t) cc_final: 0.6218 (t) REVERT: B 586 CYS cc_start: 0.8206 (p) cc_final: 0.7920 (p) REVERT: B 612 PHE cc_start: 0.7779 (t80) cc_final: 0.7470 (t80) REVERT: B 625 ASN cc_start: 0.8428 (t0) cc_final: 0.7816 (t0) REVERT: B 627 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7820 (mmtt) REVERT: B 628 PHE cc_start: 0.7282 (m-80) cc_final: 0.6688 (m-80) REVERT: B 638 TRP cc_start: 0.7812 (p-90) cc_final: 0.7419 (p-90) REVERT: B 641 TRP cc_start: 0.7436 (m100) cc_final: 0.6590 (m100) REVERT: B 691 LYS cc_start: 0.8151 (ptpp) cc_final: 0.7494 (ptpt) REVERT: B 782 ILE cc_start: 0.8750 (mm) cc_final: 0.8525 (mm) REVERT: B 783 ARG cc_start: 0.8209 (mmt180) cc_final: 0.7549 (mmm-85) REVERT: B 786 CYS cc_start: 0.7290 (t) cc_final: 0.6886 (t) REVERT: B 812 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 817 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7680 (mtpp) REVERT: C 17 LEU cc_start: 0.8895 (mt) cc_final: 0.8416 (mt) REVERT: C 28 GLU cc_start: 0.8612 (tt0) cc_final: 0.7924 (tt0) REVERT: C 37 ASP cc_start: 0.8532 (t70) cc_final: 0.7368 (t70) REVERT: C 40 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8326 (mmtt) REVERT: C 59 ASP cc_start: 0.8339 (m-30) cc_final: 0.7893 (m-30) REVERT: C 69 ARG cc_start: 0.8073 (ptp-170) cc_final: 0.7190 (ptp-170) REVERT: C 87 ILE cc_start: 0.8233 (mm) cc_final: 0.7961 (mp) REVERT: C 143 ASP cc_start: 0.7893 (t0) cc_final: 0.7427 (t0) REVERT: C 153 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6466 (tm-30) REVERT: C 154 GLN cc_start: 0.7665 (tt0) cc_final: 0.6898 (tt0) REVERT: C 168 ILE cc_start: 0.8559 (tp) cc_final: 0.8147 (mm) REVERT: C 225 ASP cc_start: 0.8216 (p0) cc_final: 0.7909 (p0) REVERT: C 235 MET cc_start: 0.7234 (mmm) cc_final: 0.6861 (mmt) REVERT: C 244 GLU cc_start: 0.7146 (mp0) cc_final: 0.6773 (mp0) REVERT: C 285 MET cc_start: 0.7946 (mmp) cc_final: 0.7704 (mmm) REVERT: C 288 ASP cc_start: 0.8066 (t0) cc_final: 0.7064 (t0) REVERT: C 294 LEU cc_start: 0.7991 (mp) cc_final: 0.7584 (mm) REVERT: C 297 ASP cc_start: 0.8031 (m-30) cc_final: 0.7684 (m-30) REVERT: C 300 GLN cc_start: 0.8502 (pp30) cc_final: 0.8100 (pp30) REVERT: C 348 LEU cc_start: 0.8772 (mp) cc_final: 0.8563 (mp) REVERT: C 352 ILE cc_start: 0.9086 (mt) cc_final: 0.8885 (mm) REVERT: C 391 MET cc_start: 0.7020 (ppp) cc_final: 0.6644 (ppp) REVERT: C 411 ILE cc_start: 0.8695 (tt) cc_final: 0.8482 (mt) REVERT: C 421 GLU cc_start: 0.7140 (mp0) cc_final: 0.6910 (mp0) REVERT: C 443 ASP cc_start: 0.8589 (m-30) cc_final: 0.8353 (m-30) REVERT: C 444 GLN cc_start: 0.8513 (mp10) cc_final: 0.7442 (mp10) REVERT: C 445 ASP cc_start: 0.7824 (m-30) cc_final: 0.7329 (m-30) REVERT: C 458 GLU cc_start: 0.7859 (tp30) cc_final: 0.7597 (tp30) REVERT: C 459 GLU cc_start: 0.7724 (pm20) cc_final: 0.6815 (pm20) REVERT: C 464 GLU cc_start: 0.8428 (mp0) cc_final: 0.7765 (pm20) REVERT: C 504 GLU cc_start: 0.8067 (tp30) cc_final: 0.7345 (tp30) REVERT: C 507 ARG cc_start: 0.8219 (tmm-80) cc_final: 0.7754 (tmm-80) REVERT: C 508 ILE cc_start: 0.8527 (tp) cc_final: 0.8226 (tp) REVERT: C 512 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7051 (mt-10) REVERT: C 529 TYR cc_start: 0.8090 (t80) cc_final: 0.7559 (t80) REVERT: C 532 LYS cc_start: 0.8440 (mttp) cc_final: 0.8107 (mttp) REVERT: C 535 TYR cc_start: 0.8473 (m-80) cc_final: 0.8161 (m-10) REVERT: C 538 GLN cc_start: 0.7918 (tt0) cc_final: 0.7536 (tt0) REVERT: C 542 MET cc_start: 0.7457 (tpt) cc_final: 0.6914 (tpt) REVERT: E 935 THR cc_start: 0.5019 (p) cc_final: 0.4765 (p) REVERT: E 939 TYR cc_start: 0.7440 (m-10) cc_final: 0.7141 (m-10) REVERT: E 983 GLN cc_start: 0.6445 (pp30) cc_final: 0.6183 (pp30) REVERT: E 985 TYR cc_start: 0.7845 (t80) cc_final: 0.7145 (t80) REVERT: E 992 TYR cc_start: 0.7483 (t80) cc_final: 0.6703 (t80) REVERT: E 996 LEU cc_start: 0.7793 (tp) cc_final: 0.7333 (tp) REVERT: E 997 MET cc_start: 0.7448 (mmt) cc_final: 0.6849 (mmt) REVERT: E 1052 LEU cc_start: 0.8984 (tp) cc_final: 0.8761 (tp) REVERT: E 1056 LEU cc_start: 0.8588 (mt) cc_final: 0.8344 (mt) REVERT: E 1064 ASP cc_start: 0.7240 (p0) cc_final: 0.6959 (t0) REVERT: E 1115 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8552 (pp20) REVERT: E 1241 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8361 (mmtp) outliers start: 0 outliers final: 0 residues processed: 745 average time/residue: 0.1572 time to fit residues: 178.2835 Evaluate side-chains 685 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 106 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 177 optimal weight: 0.0030 chunk 257 optimal weight: 0.0970 chunk 187 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS C 291 ASN C 495 GLN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096084 restraints weight = 43759.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100965 restraints weight = 22531.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102851 restraints weight = 11471.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103814 restraints weight = 8168.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104404 restraints weight = 6770.926| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23074 Z= 0.136 Angle : 0.694 22.200 31629 Z= 0.347 Chirality : 0.046 0.248 3593 Planarity : 0.005 0.057 3753 Dihedral : 14.239 76.490 3988 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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 (0.16), residues: 2567 helix: 0.22 (0.19), residues: 766 sheet: -1.13 (0.21), residues: 601 loop : -1.91 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 449 TYR 0.030 0.002 TYR A 917 PHE 0.033 0.002 PHE A1009 TRP 0.041 0.002 TRP B 428 HIS 0.010 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (23071) covalent geometry : angle 0.66295 / 0.35 (31620) hydrogen bonds : bond 0.04923 / 3.38 ( 855) hydrogen bonds : angle 5.37483 / 3.79 ( 2328) metal coordination : bond 0.01032 / 0.52 ( 3) metal coordination : angle 12.12131 / 5.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 735 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.6882 (ptt-90) REVERT: A 75 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 121 GLN cc_start: 0.8351 (mp10) cc_final: 0.7891 (mp10) REVERT: A 122 GLU cc_start: 0.7711 (tp30) cc_final: 0.7281 (tp30) REVERT: A 131 GLN cc_start: 0.8516 (mp-120) cc_final: 0.8180 (mp10) REVERT: A 136 MET cc_start: 0.7919 (pmm) cc_final: 0.7569 (pmm) REVERT: A 189 LEU cc_start: 0.8647 (tp) cc_final: 0.8265 (tp) REVERT: A 258 ASP cc_start: 0.7220 (t70) cc_final: 0.6601 (t70) REVERT: A 263 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6494 (mm-40) REVERT: A 286 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7847 (tt0) REVERT: A 288 LYS cc_start: 0.7328 (ttmt) cc_final: 0.6769 (ttmm) REVERT: A 327 ASN cc_start: 0.8508 (m-40) cc_final: 0.8269 (m-40) REVERT: A 377 THR cc_start: 0.7982 (p) cc_final: 0.7651 (p) REVERT: A 378 ASP cc_start: 0.7326 (m-30) cc_final: 0.6909 (m-30) REVERT: A 415 THR cc_start: 0.8291 (m) cc_final: 0.7989 (t) REVERT: A 427 VAL cc_start: 0.7978 (p) cc_final: 0.7442 (t) REVERT: A 443 ASP cc_start: 0.7506 (t0) cc_final: 0.7254 (t0) REVERT: A 474 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8105 (mmtt) REVERT: A 487 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8064 (mmmt) REVERT: A 573 LEU cc_start: 0.8043 (tp) cc_final: 0.7832 (mp) REVERT: A 580 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7776 (tmmt) REVERT: A 619 GLU cc_start: 0.7949 (mp0) cc_final: 0.7722 (mp0) REVERT: A 622 LEU cc_start: 0.8510 (mp) cc_final: 0.8252 (mt) REVERT: A 660 CYS cc_start: 0.8322 (t) cc_final: 0.7728 (p) REVERT: A 661 GLN cc_start: 0.8418 (pm20) cc_final: 0.7819 (pm20) REVERT: A 677 LEU cc_start: 0.8535 (tp) cc_final: 0.8303 (tp) REVERT: A 689 ARG cc_start: 0.7582 (tmt-80) cc_final: 0.7087 (tmt-80) REVERT: A 728 GLN cc_start: 0.8408 (tp40) cc_final: 0.8074 (tp40) REVERT: A 731 LYS cc_start: 0.8824 (mmpt) cc_final: 0.8122 (tptp) REVERT: A 739 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8141 (ptmm) REVERT: A 740 GLU cc_start: 0.8057 (mp0) cc_final: 0.7723 (mp0) REVERT: A 745 MET cc_start: 0.8402 (ttp) cc_final: 0.8094 (ttm) REVERT: A 753 ASN cc_start: 0.8650 (m-40) cc_final: 0.8262 (m-40) REVERT: A 767 VAL cc_start: 0.8683 (m) cc_final: 0.8147 (t) REVERT: A 827 MET cc_start: 0.8759 (ppp) cc_final: 0.8207 (ppp) REVERT: A 833 HIS cc_start: 0.7582 (m90) cc_final: 0.7234 (m-70) REVERT: A 834 LYS cc_start: 0.7369 (mttm) cc_final: 0.6805 (mttm) REVERT: A 850 GLU cc_start: 0.7631 (mp0) cc_final: 0.7208 (mp0) REVERT: A 860 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 882 LEU cc_start: 0.8877 (mt) cc_final: 0.8457 (tt) REVERT: A 893 HIS cc_start: 0.8303 (m90) cc_final: 0.7986 (m90) REVERT: A 909 LYS cc_start: 0.8462 (mppt) cc_final: 0.8044 (mmtm) REVERT: A 913 ASP cc_start: 0.8288 (t0) cc_final: 0.7983 (t0) REVERT: A 922 ASN cc_start: 0.8634 (m110) cc_final: 0.8355 (m110) REVERT: A 924 LEU cc_start: 0.8959 (mp) cc_final: 0.8714 (mp) REVERT: A 985 TYR cc_start: 0.7412 (t80) cc_final: 0.7124 (t80) REVERT: A 1001 MET cc_start: 0.6314 (mmp) cc_final: 0.6070 (mmp) REVERT: A 1008 MET cc_start: 0.7529 (ppp) cc_final: 0.7165 (ppp) REVERT: A 1121 MET cc_start: 0.8424 (mmp) cc_final: 0.8139 (mmm) REVERT: A 1125 ASP cc_start: 0.7840 (t0) cc_final: 0.7600 (m-30) REVERT: A 1228 ASN cc_start: 0.8966 (m110) cc_final: 0.8726 (m110) REVERT: A 1239 ILE cc_start: 0.9185 (mm) cc_final: 0.8940 (mm) REVERT: B 32 LEU cc_start: 0.8126 (mt) cc_final: 0.7291 (mt) REVERT: B 55 ASN cc_start: 0.8006 (m110) cc_final: 0.7800 (m110) REVERT: B 78 LEU cc_start: 0.7824 (mt) cc_final: 0.7548 (mt) REVERT: B 91 GLU cc_start: 0.7542 (pt0) cc_final: 0.6548 (pt0) REVERT: B 98 LEU cc_start: 0.8377 (tp) cc_final: 0.8157 (tp) REVERT: B 99 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8183 (mtmm) REVERT: B 150 MET cc_start: 0.7594 (ptp) cc_final: 0.6961 (ptp) REVERT: B 156 ASN cc_start: 0.8353 (p0) cc_final: 0.8066 (p0) REVERT: B 184 ASP cc_start: 0.7298 (t0) cc_final: 0.6995 (t0) REVERT: B 193 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 328 TRP cc_start: 0.8060 (m-10) cc_final: 0.6893 (m100) REVERT: B 377 GLU cc_start: 0.7930 (tt0) cc_final: 0.6964 (tt0) REVERT: B 430 GLU cc_start: 0.8310 (pm20) cc_final: 0.7846 (pm20) REVERT: B 433 ARG cc_start: 0.8085 (ptp-110) cc_final: 0.7548 (ptp-110) REVERT: B 443 CYS cc_start: 0.6794 (m) cc_final: 0.6512 (m) REVERT: B 450 PHE cc_start: 0.8184 (m-80) cc_final: 0.7981 (m-80) REVERT: B 462 ARG cc_start: 0.7449 (mtt90) cc_final: 0.6972 (mtt90) REVERT: B 473 ASN cc_start: 0.8694 (t0) cc_final: 0.8362 (t0) REVERT: B 474 PHE cc_start: 0.8144 (t80) cc_final: 0.7774 (t80) REVERT: B 478 THR cc_start: 0.6394 (t) cc_final: 0.6169 (t) REVERT: B 566 HIS cc_start: 0.7378 (m90) cc_final: 0.7057 (m90) REVERT: B 569 GLU cc_start: 0.7664 (pm20) cc_final: 0.7430 (mp0) REVERT: B 570 ILE cc_start: 0.8545 (tp) cc_final: 0.8215 (tp) REVERT: B 586 CYS cc_start: 0.8187 (p) cc_final: 0.7930 (p) REVERT: B 612 PHE cc_start: 0.7937 (t80) cc_final: 0.7736 (t80) REVERT: B 625 ASN cc_start: 0.8448 (t0) cc_final: 0.7963 (t0) REVERT: B 638 TRP cc_start: 0.7810 (p-90) cc_final: 0.7359 (p-90) REVERT: B 680 ASP cc_start: 0.7822 (t0) cc_final: 0.7188 (t70) REVERT: B 691 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7498 (ptpt) REVERT: B 742 VAL cc_start: 0.8361 (t) cc_final: 0.7940 (p) REVERT: B 782 ILE cc_start: 0.8768 (mm) cc_final: 0.8545 (mm) REVERT: B 783 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7563 (mmm-85) REVERT: B 786 CYS cc_start: 0.7321 (t) cc_final: 0.6932 (t) REVERT: B 812 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 817 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7744 (mtpp) REVERT: C 17 LEU cc_start: 0.8915 (mt) cc_final: 0.8403 (mt) REVERT: C 22 VAL cc_start: 0.9089 (t) cc_final: 0.8580 (t) REVERT: C 25 GLN cc_start: 0.8702 (mt0) cc_final: 0.8419 (mt0) REVERT: C 28 GLU cc_start: 0.8605 (tt0) cc_final: 0.8077 (tt0) REVERT: C 69 ARG cc_start: 0.8081 (ptp-170) cc_final: 0.7227 (ptp-170) REVERT: C 87 ILE cc_start: 0.8204 (mm) cc_final: 0.7962 (mm) REVERT: C 143 ASP cc_start: 0.7812 (t0) cc_final: 0.7506 (t0) REVERT: C 150 HIS cc_start: 0.7065 (t70) cc_final: 0.6860 (t70) REVERT: C 153 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6607 (tm-30) REVERT: C 154 GLN cc_start: 0.7829 (tt0) cc_final: 0.6926 (tt0) REVERT: C 168 ILE cc_start: 0.8507 (tp) cc_final: 0.7854 (mm) REVERT: C 219 THR cc_start: 0.7446 (m) cc_final: 0.6840 (p) REVERT: C 234 ASP cc_start: 0.7914 (t0) cc_final: 0.6894 (t0) REVERT: C 235 MET cc_start: 0.7334 (mmm) cc_final: 0.6882 (mmt) REVERT: C 244 GLU cc_start: 0.7147 (mp0) cc_final: 0.6861 (mp0) REVERT: C 280 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7045 (mmmt) REVERT: C 285 MET cc_start: 0.7930 (mmp) cc_final: 0.7660 (mmm) REVERT: C 294 LEU cc_start: 0.8009 (mp) cc_final: 0.7515 (mp) REVERT: C 295 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7408 (mt-10) REVERT: C 297 ASP cc_start: 0.7973 (m-30) cc_final: 0.7512 (m-30) REVERT: C 300 GLN cc_start: 0.8550 (pp30) cc_final: 0.8230 (pp30) REVERT: C 313 ASP cc_start: 0.7393 (m-30) cc_final: 0.7146 (m-30) REVERT: C 347 GLU cc_start: 0.8103 (mp0) cc_final: 0.7901 (mp0) REVERT: C 348 LEU cc_start: 0.8691 (mp) cc_final: 0.8399 (mp) REVERT: C 391 MET cc_start: 0.6998 (ppp) cc_final: 0.6604 (ppp) REVERT: C 411 ILE cc_start: 0.8682 (tt) cc_final: 0.8481 (mt) REVERT: C 421 GLU cc_start: 0.7130 (mp0) cc_final: 0.6877 (mp0) REVERT: C 444 GLN cc_start: 0.8498 (mp10) cc_final: 0.7469 (mp10) REVERT: C 445 ASP cc_start: 0.7757 (m-30) cc_final: 0.7416 (m-30) REVERT: C 458 GLU cc_start: 0.7911 (tp30) cc_final: 0.7654 (tp30) REVERT: C 459 GLU cc_start: 0.7753 (pm20) cc_final: 0.6988 (pm20) REVERT: C 464 GLU cc_start: 0.8429 (mp0) cc_final: 0.7790 (pm20) REVERT: C 497 PHE cc_start: 0.7838 (m-80) cc_final: 0.7355 (m-80) REVERT: C 504 GLU cc_start: 0.8112 (tp30) cc_final: 0.7444 (tp30) REVERT: C 507 ARG cc_start: 0.8240 (tmm-80) cc_final: 0.7765 (tmm-80) REVERT: C 508 ILE cc_start: 0.8466 (tp) cc_final: 0.8173 (tp) REVERT: C 529 TYR cc_start: 0.7998 (t80) cc_final: 0.7599 (t80) REVERT: C 532 LYS cc_start: 0.8458 (mttp) cc_final: 0.8145 (mttp) REVERT: C 535 TYR cc_start: 0.8400 (m-80) cc_final: 0.8174 (m-80) REVERT: C 538 GLN cc_start: 0.7934 (tt0) cc_final: 0.7299 (tt0) REVERT: C 542 MET cc_start: 0.7046 (mmm) cc_final: 0.6827 (mmm) REVERT: E 935 THR cc_start: 0.4947 (p) cc_final: 0.4682 (p) REVERT: E 939 TYR cc_start: 0.7443 (m-10) cc_final: 0.7160 (m-10) REVERT: E 976 LYS cc_start: 0.8169 (pttm) cc_final: 0.7949 (pttm) REVERT: E 983 GLN cc_start: 0.6578 (pp30) cc_final: 0.6285 (pp30) REVERT: E 985 TYR cc_start: 0.7803 (t80) cc_final: 0.7101 (t80) REVERT: E 992 TYR cc_start: 0.7405 (t80) cc_final: 0.6676 (t80) REVERT: E 996 LEU cc_start: 0.7804 (tp) cc_final: 0.7338 (tp) REVERT: E 997 MET cc_start: 0.7395 (mmt) cc_final: 0.6755 (mmt) REVERT: E 1052 LEU cc_start: 0.8955 (tp) cc_final: 0.8737 (tp) REVERT: E 1056 LEU cc_start: 0.8500 (mt) cc_final: 0.8271 (mt) REVERT: E 1115 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8454 (pp20) REVERT: E 1120 TYR cc_start: 0.8289 (t80) cc_final: 0.7716 (t80) REVERT: E 1241 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8374 (mmtp) outliers start: 1 outliers final: 0 residues processed: 736 average time/residue: 0.1527 time to fit residues: 171.3383 Evaluate side-chains 678 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 143 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 222 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN C 291 ASN C 495 GLN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095618 restraints weight = 43766.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100401 restraints weight = 22569.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102256 restraints weight = 11409.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103611 restraints weight = 8231.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103922 restraints weight = 6852.683| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23074 Z= 0.155 Angle : 0.705 21.650 31629 Z= 0.356 Chirality : 0.046 0.232 3593 Planarity : 0.005 0.056 3753 Dihedral : 14.162 76.754 3988 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.72 (0.16), residues: 2567 helix: 0.08 (0.18), residues: 782 sheet: -1.07 (0.21), residues: 612 loop : -2.02 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 449 TYR 0.027 0.002 TYR B 239 PHE 0.040 0.002 PHE A1131 TRP 0.079 0.003 TRP B 428 HIS 0.016 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (23071) covalent geometry : angle 0.67575 / 0.36 (31620) hydrogen bonds : bond 0.04981 / 3.43 ( 855) hydrogen bonds : angle 5.31974 / 3.75 ( 2328) metal coordination : bond 0.01015 / 0.51 ( 3) metal coordination : angle 11.88522 / 5.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 742 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7227 (ttp-170) cc_final: 0.6935 (ttp80) REVERT: A 34 LEU cc_start: 0.8252 (mm) cc_final: 0.7908 (tp) REVERT: A 75 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 117 TRP cc_start: 0.7804 (m100) cc_final: 0.7567 (m100) REVERT: A 121 GLN cc_start: 0.8322 (mp10) cc_final: 0.7884 (mp10) REVERT: A 122 GLU cc_start: 0.7744 (tp30) cc_final: 0.7459 (tp30) REVERT: A 131 GLN cc_start: 0.8490 (mp-120) cc_final: 0.8196 (mp10) REVERT: A 136 MET cc_start: 0.7900 (pmm) cc_final: 0.7649 (pmm) REVERT: A 150 GLN cc_start: 0.7443 (pm20) cc_final: 0.7100 (pm20) REVERT: A 189 LEU cc_start: 0.8791 (tp) cc_final: 0.8255 (tp) REVERT: A 263 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6581 (mm110) REVERT: A 285 ASP cc_start: 0.8301 (t0) cc_final: 0.8097 (t0) REVERT: A 286 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7764 (tt0) REVERT: A 288 LYS cc_start: 0.7344 (ttmt) cc_final: 0.6981 (ttpt) REVERT: A 289 VAL cc_start: 0.8270 (p) cc_final: 0.7986 (p) REVERT: A 304 TRP cc_start: 0.7444 (t60) cc_final: 0.7137 (t60) REVERT: A 377 THR cc_start: 0.7936 (p) cc_final: 0.7574 (p) REVERT: A 378 ASP cc_start: 0.7391 (m-30) cc_final: 0.6931 (m-30) REVERT: A 414 CYS cc_start: 0.7692 (p) cc_final: 0.7491 (p) REVERT: A 427 VAL cc_start: 0.7968 (p) cc_final: 0.7548 (t) REVERT: A 443 ASP cc_start: 0.7603 (t0) cc_final: 0.7164 (t0) REVERT: A 474 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8044 (mmtt) REVERT: A 487 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8033 (mmmt) REVERT: A 573 LEU cc_start: 0.8062 (tp) cc_final: 0.7839 (mp) REVERT: A 580 LYS cc_start: 0.8260 (tmmt) cc_final: 0.7775 (tmmt) REVERT: A 619 GLU cc_start: 0.7953 (mp0) cc_final: 0.7726 (mp0) REVERT: A 622 LEU cc_start: 0.8540 (mp) cc_final: 0.8267 (mt) REVERT: A 660 CYS cc_start: 0.8348 (t) cc_final: 0.7628 (p) REVERT: A 661 GLN cc_start: 0.8379 (pm20) cc_final: 0.7664 (pm20) REVERT: A 677 LEU cc_start: 0.8562 (tp) cc_final: 0.8299 (tp) REVERT: A 689 ARG cc_start: 0.7671 (tmt-80) cc_final: 0.7118 (tmt-80) REVERT: A 731 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8147 (tptp) REVERT: A 739 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8054 (ptmm) REVERT: A 740 GLU cc_start: 0.8103 (mp0) cc_final: 0.7701 (mp0) REVERT: A 743 GLU cc_start: 0.8264 (pt0) cc_final: 0.7958 (pt0) REVERT: A 753 ASN cc_start: 0.8685 (m-40) cc_final: 0.8295 (m-40) REVERT: A 767 VAL cc_start: 0.8691 (m) cc_final: 0.8184 (t) REVERT: A 794 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8495 (mmtt) REVERT: A 833 HIS cc_start: 0.7621 (m90) cc_final: 0.7292 (m90) REVERT: A 834 LYS cc_start: 0.7428 (mttm) cc_final: 0.6937 (mttm) REVERT: A 850 GLU cc_start: 0.7458 (mp0) cc_final: 0.6631 (mp0) REVERT: A 860 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8552 (tm-30) REVERT: A 882 LEU cc_start: 0.8875 (mt) cc_final: 0.8493 (tt) REVERT: A 893 HIS cc_start: 0.8259 (m90) cc_final: 0.7959 (m90) REVERT: A 909 LYS cc_start: 0.8427 (mppt) cc_final: 0.8206 (mppt) REVERT: A 913 ASP cc_start: 0.8277 (t0) cc_final: 0.7938 (t0) REVERT: A 922 ASN cc_start: 0.8617 (m110) cc_final: 0.8334 (m110) REVERT: A 924 LEU cc_start: 0.8978 (mp) cc_final: 0.8465 (mt) REVERT: A 927 MET cc_start: 0.6660 (tmm) cc_final: 0.6448 (tmm) REVERT: A 985 TYR cc_start: 0.7416 (t80) cc_final: 0.7122 (t80) REVERT: A 1001 MET cc_start: 0.6412 (mmp) cc_final: 0.6150 (mmp) REVERT: A 1008 MET cc_start: 0.7569 (ppp) cc_final: 0.7240 (ppp) REVERT: A 1112 SER cc_start: 0.8407 (p) cc_final: 0.8187 (p) REVERT: A 1125 ASP cc_start: 0.7919 (t0) cc_final: 0.7642 (m-30) REVERT: A 1228 ASN cc_start: 0.9027 (m110) cc_final: 0.8777 (m110) REVERT: A 1238 HIS cc_start: 0.8286 (p-80) cc_final: 0.7849 (p-80) REVERT: A 1239 ILE cc_start: 0.9169 (mm) cc_final: 0.8856 (mm) REVERT: A 1266 MET cc_start: 0.7909 (mpp) cc_final: 0.7635 (mpp) REVERT: B 43 TYR cc_start: 0.8123 (t80) cc_final: 0.7737 (t80) REVERT: B 55 ASN cc_start: 0.8019 (m110) cc_final: 0.7802 (m110) REVERT: B 91 GLU cc_start: 0.7586 (pt0) cc_final: 0.6471 (pt0) REVERT: B 98 LEU cc_start: 0.8381 (tp) cc_final: 0.8149 (tp) REVERT: B 99 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8230 (mtmm) REVERT: B 150 MET cc_start: 0.7636 (ptp) cc_final: 0.7141 (ptp) REVERT: B 156 ASN cc_start: 0.8365 (p0) cc_final: 0.8077 (p0) REVERT: B 184 ASP cc_start: 0.7334 (t0) cc_final: 0.6823 (t0) REVERT: B 237 LYS cc_start: 0.6456 (ttpt) cc_final: 0.5837 (ttpt) REVERT: B 328 TRP cc_start: 0.8121 (m-10) cc_final: 0.6895 (m100) REVERT: B 347 CYS cc_start: 0.6232 (t) cc_final: 0.5880 (t) REVERT: B 377 GLU cc_start: 0.7934 (tt0) cc_final: 0.7073 (tt0) REVERT: B 430 GLU cc_start: 0.8310 (pm20) cc_final: 0.7881 (pm20) REVERT: B 433 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7795 (ptp-170) REVERT: B 462 ARG cc_start: 0.7444 (mtt90) cc_final: 0.6987 (mtt90) REVERT: B 473 ASN cc_start: 0.8713 (t0) cc_final: 0.8381 (t0) REVERT: B 474 PHE cc_start: 0.8128 (t80) cc_final: 0.7750 (t80) REVERT: B 478 THR cc_start: 0.6486 (t) cc_final: 0.6250 (t) REVERT: B 566 HIS cc_start: 0.7327 (m90) cc_final: 0.7002 (m90) REVERT: B 569 GLU cc_start: 0.7763 (pm20) cc_final: 0.7402 (mp0) REVERT: B 570 ILE cc_start: 0.8562 (tp) cc_final: 0.8206 (tp) REVERT: B 586 CYS cc_start: 0.8223 (p) cc_final: 0.7941 (p) REVERT: B 625 ASN cc_start: 0.8430 (t0) cc_final: 0.7901 (t0) REVERT: B 638 TRP cc_start: 0.7854 (p-90) cc_final: 0.7447 (p-90) REVERT: B 691 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7524 (ptpt) REVERT: B 742 VAL cc_start: 0.8410 (t) cc_final: 0.7973 (p) REVERT: B 774 GLN cc_start: 0.8463 (tp40) cc_final: 0.8218 (tp-100) REVERT: B 812 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 817 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7835 (mtpp) REVERT: C 17 LEU cc_start: 0.8926 (mt) cc_final: 0.8403 (mt) REVERT: C 25 GLN cc_start: 0.8713 (mt0) cc_final: 0.8454 (mt0) REVERT: C 28 GLU cc_start: 0.8629 (tt0) cc_final: 0.7749 (tt0) REVERT: C 40 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8272 (mmtt) REVERT: C 42 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7956 (tttp) REVERT: C 69 ARG cc_start: 0.8077 (ptp-170) cc_final: 0.7243 (ptp-170) REVERT: C 77 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8228 (ptpt) REVERT: C 143 ASP cc_start: 0.7811 (t0) cc_final: 0.7492 (t0) REVERT: C 150 HIS cc_start: 0.7080 (t70) cc_final: 0.6876 (t70) REVERT: C 153 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6553 (tm-30) REVERT: C 154 GLN cc_start: 0.7789 (tt0) cc_final: 0.6867 (tt0) REVERT: C 173 THR cc_start: 0.7628 (m) cc_final: 0.7406 (p) REVERT: C 199 ASN cc_start: 0.7246 (t0) cc_final: 0.6882 (t0) REVERT: C 234 ASP cc_start: 0.7897 (t0) cc_final: 0.6836 (t0) REVERT: C 235 MET cc_start: 0.7345 (mmm) cc_final: 0.6676 (mmt) REVERT: C 238 TYR cc_start: 0.8064 (m-80) cc_final: 0.7748 (m-10) REVERT: C 244 GLU cc_start: 0.7068 (mp0) cc_final: 0.6819 (mp0) REVERT: C 285 MET cc_start: 0.7941 (mmp) cc_final: 0.7702 (mmm) REVERT: C 295 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 297 ASP cc_start: 0.8032 (m-30) cc_final: 0.7602 (m-30) REVERT: C 300 GLN cc_start: 0.8576 (pp30) cc_final: 0.8007 (pp30) REVERT: C 313 ASP cc_start: 0.7238 (m-30) cc_final: 0.6751 (m-30) REVERT: C 347 GLU cc_start: 0.8128 (mp0) cc_final: 0.7814 (mp0) REVERT: C 348 LEU cc_start: 0.8717 (mp) cc_final: 0.8345 (mp) REVERT: C 391 MET cc_start: 0.7044 (ppp) cc_final: 0.6582 (ppp) REVERT: C 411 ILE cc_start: 0.8705 (tt) cc_final: 0.8488 (tt) REVERT: C 421 GLU cc_start: 0.7118 (mp0) cc_final: 0.6848 (mp0) REVERT: C 428 VAL cc_start: 0.8503 (t) cc_final: 0.8217 (m) REVERT: C 444 GLN cc_start: 0.8494 (mp10) cc_final: 0.7454 (mp10) REVERT: C 445 ASP cc_start: 0.7768 (m-30) cc_final: 0.7388 (m-30) REVERT: C 459 GLU cc_start: 0.7782 (pm20) cc_final: 0.7247 (pm20) REVERT: C 464 GLU cc_start: 0.8452 (mp0) cc_final: 0.7835 (pm20) REVERT: C 504 GLU cc_start: 0.8092 (tp30) cc_final: 0.7623 (tp30) REVERT: C 507 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.7865 (tmm-80) REVERT: C 508 ILE cc_start: 0.8453 (tp) cc_final: 0.8140 (tp) REVERT: C 511 GLU cc_start: 0.8145 (tp30) cc_final: 0.7897 (tp30) REVERT: C 533 ILE cc_start: 0.9138 (mp) cc_final: 0.8827 (tp) REVERT: C 538 GLN cc_start: 0.7942 (tt0) cc_final: 0.7220 (tt0) REVERT: E 939 TYR cc_start: 0.7472 (m-10) cc_final: 0.7228 (m-10) REVERT: E 976 LYS cc_start: 0.8198 (pttm) cc_final: 0.7905 (pttm) REVERT: E 983 GLN cc_start: 0.6715 (pp30) cc_final: 0.6406 (pp30) REVERT: E 985 TYR cc_start: 0.7842 (t80) cc_final: 0.7132 (t80) REVERT: E 992 TYR cc_start: 0.7437 (t80) cc_final: 0.6726 (t80) REVERT: E 996 LEU cc_start: 0.7835 (tp) cc_final: 0.7369 (tp) REVERT: E 997 MET cc_start: 0.7497 (mmt) cc_final: 0.6857 (mmt) REVERT: E 1008 MET cc_start: 0.7825 (mmp) cc_final: 0.7031 (mmp) REVERT: E 1033 CYS cc_start: 0.8309 (m) cc_final: 0.8092 (m) REVERT: E 1056 LEU cc_start: 0.8491 (mt) cc_final: 0.8274 (tp) REVERT: E 1094 ARG cc_start: 0.7110 (ptt180) cc_final: 0.6901 (ptt180) REVERT: E 1115 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8462 (pp20) REVERT: E 1120 TYR cc_start: 0.8386 (t80) cc_final: 0.7773 (t80) REVERT: E 1241 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8397 (mmtp) outliers start: 0 outliers final: 0 residues processed: 742 average time/residue: 0.1575 time to fit residues: 178.6023 Evaluate side-chains 682 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 205 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 776 GLN C 190 HIS C 291 ASN ** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1264 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094101 restraints weight = 43300.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098880 restraints weight = 22609.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100851 restraints weight = 11500.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101896 restraints weight = 8102.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102295 restraints weight = 6788.183| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23074 Z= 0.189 Angle : 0.730 21.019 31629 Z= 0.372 Chirality : 0.047 0.252 3593 Planarity : 0.005 0.055 3753 Dihedral : 14.135 77.153 3988 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.04 % Allowed : 1.13 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.80 (0.16), residues: 2567 helix: -0.03 (0.18), residues: 786 sheet: -1.00 (0.21), residues: 597 loop : -2.09 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1268 TYR 0.035 0.002 TYR A 917 PHE 0.030 0.002 PHE A1009 TRP 0.059 0.003 TRP A 191 HIS 0.019 0.002 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (23071) covalent geometry : angle 0.70297 / 0.37 (31620) hydrogen bonds : bond 0.05333 / 3.66 ( 855) hydrogen bonds : angle 5.39593 / 3.80 ( 2328) metal coordination : bond 0.01178 / 0.59 ( 3) metal coordination : angle 11.70139 / 5.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 751 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6945 (ttp80) REVERT: A 34 LEU cc_start: 0.8265 (mm) cc_final: 0.7954 (tt) REVERT: A 75 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 121 GLN cc_start: 0.8288 (mp10) cc_final: 0.7788 (mp10) REVERT: A 122 GLU cc_start: 0.7803 (tp30) cc_final: 0.7355 (tp30) REVERT: A 131 GLN cc_start: 0.8535 (mp-120) cc_final: 0.8166 (mp10) REVERT: A 136 MET cc_start: 0.8013 (pmm) cc_final: 0.7623 (pmm) REVERT: A 189 LEU cc_start: 0.8723 (tp) cc_final: 0.8233 (tp) REVERT: A 193 ASP cc_start: 0.8374 (p0) cc_final: 0.7391 (p0) REVERT: A 203 ASP cc_start: 0.8084 (p0) cc_final: 0.7881 (p0) REVERT: A 224 TRP cc_start: 0.7422 (m100) cc_final: 0.7204 (m100) REVERT: A 230 LEU cc_start: 0.8494 (pt) cc_final: 0.8110 (pt) REVERT: A 258 ASP cc_start: 0.7156 (t70) cc_final: 0.6598 (t70) REVERT: A 261 ASN cc_start: 0.8083 (m110) cc_final: 0.7356 (t0) REVERT: A 263 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6433 (mm-40) REVERT: A 286 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7981 (tt0) REVERT: A 304 TRP cc_start: 0.7447 (t60) cc_final: 0.7221 (t60) REVERT: A 377 THR cc_start: 0.7945 (p) cc_final: 0.7630 (p) REVERT: A 378 ASP cc_start: 0.7515 (m-30) cc_final: 0.7030 (m-30) REVERT: A 414 CYS cc_start: 0.7715 (p) cc_final: 0.7469 (p) REVERT: A 443 ASP cc_start: 0.7607 (t0) cc_final: 0.7168 (t0) REVERT: A 474 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8083 (mmtt) REVERT: A 487 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8029 (mmmt) REVERT: A 573 LEU cc_start: 0.8000 (tp) cc_final: 0.7780 (mp) REVERT: A 580 LYS cc_start: 0.8273 (tmmt) cc_final: 0.7759 (tmmt) REVERT: A 617 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8652 (mm-30) REVERT: A 619 GLU cc_start: 0.7967 (mp0) cc_final: 0.7681 (mp0) REVERT: A 622 LEU cc_start: 0.8529 (mp) cc_final: 0.8249 (mt) REVERT: A 660 CYS cc_start: 0.8354 (t) cc_final: 0.7540 (p) REVERT: A 661 GLN cc_start: 0.8402 (pm20) cc_final: 0.7650 (pm20) REVERT: A 689 ARG cc_start: 0.7650 (tmt-80) cc_final: 0.7037 (tmt-80) REVERT: A 697 ILE cc_start: 0.8664 (tp) cc_final: 0.8292 (tt) REVERT: A 728 GLN cc_start: 0.8448 (tp40) cc_final: 0.8161 (tp40) REVERT: A 731 LYS cc_start: 0.8798 (mmpt) cc_final: 0.8122 (tptp) REVERT: A 739 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8463 (ttpt) REVERT: A 740 GLU cc_start: 0.8153 (mp0) cc_final: 0.7801 (mp0) REVERT: A 745 MET cc_start: 0.8533 (ttm) cc_final: 0.7497 (mmm) REVERT: A 753 ASN cc_start: 0.8750 (m-40) cc_final: 0.8341 (m-40) REVERT: A 767 VAL cc_start: 0.8689 (m) cc_final: 0.8178 (t) REVERT: A 796 MET cc_start: 0.8777 (ttm) cc_final: 0.8571 (tpp) REVERT: A 833 HIS cc_start: 0.7708 (m90) cc_final: 0.7422 (m90) REVERT: A 834 LYS cc_start: 0.7469 (mttm) cc_final: 0.6938 (mttm) REVERT: A 850 GLU cc_start: 0.8020 (mp0) cc_final: 0.7584 (mp0) REVERT: A 878 LEU cc_start: 0.8766 (tp) cc_final: 0.8539 (tp) REVERT: A 882 LEU cc_start: 0.8871 (mt) cc_final: 0.8604 (mt) REVERT: A 893 HIS cc_start: 0.8290 (m90) cc_final: 0.7928 (m90) REVERT: A 909 LYS cc_start: 0.8411 (mppt) cc_final: 0.7884 (mmtm) REVERT: A 913 ASP cc_start: 0.8304 (t0) cc_final: 0.7929 (t0) REVERT: A 918 LEU cc_start: 0.7550 (tp) cc_final: 0.7217 (tp) REVERT: A 922 ASN cc_start: 0.8673 (m110) cc_final: 0.8434 (m110) REVERT: A 924 LEU cc_start: 0.8971 (mp) cc_final: 0.8462 (mt) REVERT: A 927 MET cc_start: 0.6697 (tmm) cc_final: 0.6477 (tmm) REVERT: A 985 TYR cc_start: 0.7505 (t80) cc_final: 0.7223 (t80) REVERT: A 1001 MET cc_start: 0.6476 (mmp) cc_final: 0.6246 (mmp) REVERT: A 1008 MET cc_start: 0.7631 (ppp) cc_final: 0.7268 (ppp) REVERT: A 1125 ASP cc_start: 0.7912 (t0) cc_final: 0.7666 (m-30) REVERT: A 1228 ASN cc_start: 0.9011 (m110) cc_final: 0.8773 (m110) REVERT: A 1238 HIS cc_start: 0.8298 (p-80) cc_final: 0.7789 (p-80) REVERT: A 1239 ILE cc_start: 0.9098 (mm) cc_final: 0.8792 (mm) REVERT: A 1266 MET cc_start: 0.7891 (mpp) cc_final: 0.7678 (mpp) REVERT: B 43 TYR cc_start: 0.8274 (t80) cc_final: 0.7892 (t80) REVERT: B 55 ASN cc_start: 0.7961 (m110) cc_final: 0.7627 (m110) REVERT: B 91 GLU cc_start: 0.7661 (pt0) cc_final: 0.6800 (pt0) REVERT: B 98 LEU cc_start: 0.8344 (tp) cc_final: 0.8095 (tp) REVERT: B 99 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8222 (mtmm) REVERT: B 150 MET cc_start: 0.7670 (ptp) cc_final: 0.7166 (ptp) REVERT: B 156 ASN cc_start: 0.8393 (p0) cc_final: 0.8114 (p0) REVERT: B 184 ASP cc_start: 0.7397 (t0) cc_final: 0.6807 (t0) REVERT: B 237 LYS cc_start: 0.6518 (ttpt) cc_final: 0.5860 (ttpt) REVERT: B 377 GLU cc_start: 0.7982 (tt0) cc_final: 0.7029 (tt0) REVERT: B 393 ASP cc_start: 0.7709 (m-30) cc_final: 0.7485 (m-30) REVERT: B 430 GLU cc_start: 0.8366 (pm20) cc_final: 0.7946 (pm20) REVERT: B 433 ARG cc_start: 0.8100 (ptp-110) cc_final: 0.7463 (ptp-170) REVERT: B 473 ASN cc_start: 0.8757 (t0) cc_final: 0.8436 (t0) REVERT: B 474 PHE cc_start: 0.8170 (t80) cc_final: 0.7778 (t80) REVERT: B 478 THR cc_start: 0.6624 (t) cc_final: 0.6423 (t) REVERT: B 566 HIS cc_start: 0.7430 (m90) cc_final: 0.7088 (m90) REVERT: B 569 GLU cc_start: 0.7784 (pm20) cc_final: 0.7390 (mp0) REVERT: B 570 ILE cc_start: 0.8519 (tp) cc_final: 0.8146 (tp) REVERT: B 586 CYS cc_start: 0.8258 (p) cc_final: 0.8002 (p) REVERT: B 604 TRP cc_start: 0.8233 (m-10) cc_final: 0.7663 (m-10) REVERT: B 625 ASN cc_start: 0.8453 (t0) cc_final: 0.7905 (t0) REVERT: B 638 TRP cc_start: 0.7855 (p-90) cc_final: 0.7408 (p-90) REVERT: B 680 ASP cc_start: 0.7946 (t0) cc_final: 0.7237 (t70) REVERT: B 691 LYS cc_start: 0.8138 (ptpp) cc_final: 0.7484 (ptpt) REVERT: B 812 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 817 LYS cc_start: 0.8456 (mtmt) cc_final: 0.7788 (mtpp) REVERT: C 25 GLN cc_start: 0.8779 (mt0) cc_final: 0.8507 (mt0) REVERT: C 28 GLU cc_start: 0.8677 (tt0) cc_final: 0.8211 (tt0) REVERT: C 40 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8288 (mmtt) REVERT: C 69 ARG cc_start: 0.8088 (ptp-170) cc_final: 0.7282 (ptp-170) REVERT: C 77 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8219 (ptpt) REVERT: C 143 ASP cc_start: 0.7827 (t0) cc_final: 0.7493 (t0) REVERT: C 150 HIS cc_start: 0.7184 (t70) cc_final: 0.6981 (t70) REVERT: C 153 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6664 (tm-30) REVERT: C 154 GLN cc_start: 0.7795 (tt0) cc_final: 0.6857 (tt0) REVERT: C 168 ILE cc_start: 0.8588 (tp) cc_final: 0.8303 (tp) REVERT: C 173 THR cc_start: 0.7702 (m) cc_final: 0.7474 (p) REVERT: C 234 ASP cc_start: 0.7904 (t0) cc_final: 0.6899 (t0) REVERT: C 235 MET cc_start: 0.7278 (mmm) cc_final: 0.6837 (mmm) REVERT: C 244 GLU cc_start: 0.7076 (mp0) cc_final: 0.6831 (mp0) REVERT: C 294 LEU cc_start: 0.8119 (mp) cc_final: 0.7661 (mp) REVERT: C 295 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 297 ASP cc_start: 0.8110 (m-30) cc_final: 0.7591 (m-30) REVERT: C 300 GLN cc_start: 0.8722 (pp30) cc_final: 0.8410 (pp30) REVERT: C 336 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7673 (mtp-110) REVERT: C 340 TYR cc_start: 0.8140 (m-10) cc_final: 0.7637 (m-10) REVERT: C 347 GLU cc_start: 0.8209 (mp0) cc_final: 0.7843 (mp0) REVERT: C 348 LEU cc_start: 0.8740 (mp) cc_final: 0.8364 (mp) REVERT: C 351 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: C 411 ILE cc_start: 0.8702 (tt) cc_final: 0.8487 (tt) REVERT: C 416 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8281 (mmm-85) REVERT: C 421 GLU cc_start: 0.6846 (mp0) cc_final: 0.6624 (mp0) REVERT: C 428 VAL cc_start: 0.8491 (t) cc_final: 0.8220 (m) REVERT: C 434 GLU cc_start: 0.7660 (mp0) cc_final: 0.7050 (mp0) REVERT: C 440 GLU cc_start: 0.6889 (pm20) cc_final: 0.6594 (pm20) REVERT: C 444 GLN cc_start: 0.8527 (mp10) cc_final: 0.7469 (mp10) REVERT: C 445 ASP cc_start: 0.7831 (m-30) cc_final: 0.7511 (m-30) REVERT: C 448 ILE cc_start: 0.8115 (pt) cc_final: 0.7885 (pt) REVERT: C 458 GLU cc_start: 0.8056 (tp30) cc_final: 0.7808 (tp30) REVERT: C 464 GLU cc_start: 0.8492 (mp0) cc_final: 0.7823 (pm20) REVERT: C 504 GLU cc_start: 0.8230 (tp30) cc_final: 0.7729 (tp30) REVERT: C 507 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.7861 (tmm-80) REVERT: C 511 GLU cc_start: 0.8200 (tp30) cc_final: 0.7969 (tp30) REVERT: C 526 THR cc_start: 0.8227 (p) cc_final: 0.7921 (p) REVERT: C 532 LYS cc_start: 0.8513 (mttp) cc_final: 0.7963 (mttp) REVERT: C 533 ILE cc_start: 0.9190 (mp) cc_final: 0.8869 (tp) REVERT: C 538 GLN cc_start: 0.7798 (tt0) cc_final: 0.7043 (tt0) REVERT: E 935 THR cc_start: 0.5077 (p) cc_final: 0.4874 (p) REVERT: E 939 TYR cc_start: 0.7500 (m-10) cc_final: 0.7263 (m-10) REVERT: E 976 LYS cc_start: 0.8185 (pttm) cc_final: 0.7916 (pttm) REVERT: E 983 GLN cc_start: 0.6852 (pp30) cc_final: 0.6484 (pp30) REVERT: E 985 TYR cc_start: 0.7875 (t80) cc_final: 0.7164 (t80) REVERT: E 992 TYR cc_start: 0.7480 (t80) cc_final: 0.6745 (t80) REVERT: E 996 LEU cc_start: 0.7879 (tp) cc_final: 0.7416 (tp) REVERT: E 997 MET cc_start: 0.7521 (mmt) cc_final: 0.6962 (mmt) REVERT: E 1033 CYS cc_start: 0.8285 (m) cc_final: 0.8071 (m) REVERT: E 1056 LEU cc_start: 0.8647 (mt) cc_final: 0.8422 (tp) REVERT: E 1094 ARG cc_start: 0.6864 (ptt180) cc_final: 0.6474 (ptt180) REVERT: E 1095 LEU cc_start: 0.8310 (mt) cc_final: 0.7996 (mt) REVERT: E 1097 TYR cc_start: 0.7389 (m-80) cc_final: 0.7116 (m-80) REVERT: E 1115 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8505 (pp20) REVERT: E 1120 TYR cc_start: 0.8409 (t80) cc_final: 0.7784 (t80) REVERT: E 1241 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8412 (mmtp) outliers start: 1 outliers final: 0 residues processed: 752 average time/residue: 0.1675 time to fit residues: 192.4996 Evaluate side-chains 687 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 41 optimal weight: 0.7980 chunk 148 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN C 291 ASN E 949 HIS E 969 ASN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095325 restraints weight = 43844.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099983 restraints weight = 22662.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102065 restraints weight = 11943.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103621 restraints weight = 8463.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103962 restraints weight = 6642.789| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23074 Z= 0.174 Angle : 0.718 21.077 31629 Z= 0.366 Chirality : 0.047 0.210 3593 Planarity : 0.005 0.054 3753 Dihedral : 14.101 76.908 3988 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.76 (0.16), residues: 2567 helix: 0.04 (0.18), residues: 770 sheet: -1.00 (0.21), residues: 587 loop : -2.06 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 462 TYR 0.025 0.002 TYR C 207 PHE 0.040 0.002 PHE A 784 TRP 0.061 0.003 TRP B 428 HIS 0.021 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (23071) covalent geometry : angle 0.69100 / 0.37 (31620) hydrogen bonds : bond 0.05207 / 3.60 ( 855) hydrogen bonds : angle 5.32340 / 3.74 ( 2328) metal coordination : bond 0.01094 / 0.55 ( 3) metal coordination : angle 11.59198 / 5.27 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 764 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6899 (ptt-90) REVERT: A 34 LEU cc_start: 0.8250 (mm) cc_final: 0.7979 (tt) REVERT: A 43 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6411 (tm-30) REVERT: A 52 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8661 (mmtm) REVERT: A 75 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 121 GLN cc_start: 0.8319 (mp10) cc_final: 0.7775 (mp10) REVERT: A 122 GLU cc_start: 0.7796 (tp30) cc_final: 0.7392 (tp30) REVERT: A 131 GLN cc_start: 0.8502 (mp-120) cc_final: 0.8107 (mp10) REVERT: A 136 MET cc_start: 0.7975 (pmm) cc_final: 0.7635 (pmm) REVERT: A 189 LEU cc_start: 0.8627 (tp) cc_final: 0.8224 (tp) REVERT: A 224 TRP cc_start: 0.7380 (m100) cc_final: 0.7028 (m100) REVERT: A 230 LEU cc_start: 0.8486 (pt) cc_final: 0.8089 (pt) REVERT: A 258 ASP cc_start: 0.7136 (t70) cc_final: 0.6620 (t70) REVERT: A 261 ASN cc_start: 0.8123 (m110) cc_final: 0.7420 (t0) REVERT: A 263 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6428 (mm-40) REVERT: A 285 ASP cc_start: 0.8275 (t0) cc_final: 0.7937 (t0) REVERT: A 286 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7938 (tt0) REVERT: A 288 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6683 (ttmm) REVERT: A 289 VAL cc_start: 0.8318 (p) cc_final: 0.8051 (p) REVERT: A 304 TRP cc_start: 0.7373 (t60) cc_final: 0.7150 (t60) REVERT: A 377 THR cc_start: 0.7949 (p) cc_final: 0.7640 (p) REVERT: A 378 ASP cc_start: 0.7525 (m-30) cc_final: 0.7036 (m-30) REVERT: A 414 CYS cc_start: 0.7788 (p) cc_final: 0.7515 (p) REVERT: A 443 ASP cc_start: 0.7622 (t0) cc_final: 0.7233 (t0) REVERT: A 487 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7932 (mmmt) REVERT: A 573 LEU cc_start: 0.8028 (tp) cc_final: 0.7826 (mp) REVERT: A 580 LYS cc_start: 0.8238 (tmmt) cc_final: 0.7739 (tmmt) REVERT: A 617 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8625 (mm-30) REVERT: A 619 GLU cc_start: 0.7955 (mp0) cc_final: 0.7674 (mp0) REVERT: A 660 CYS cc_start: 0.8395 (t) cc_final: 0.7624 (p) REVERT: A 661 GLN cc_start: 0.8372 (pm20) cc_final: 0.7636 (pm20) REVERT: A 689 ARG cc_start: 0.7673 (tmt-80) cc_final: 0.7073 (tmt-80) REVERT: A 697 ILE cc_start: 0.8650 (tp) cc_final: 0.8335 (tt) REVERT: A 728 GLN cc_start: 0.8402 (tp40) cc_final: 0.8131 (tp40) REVERT: A 731 LYS cc_start: 0.8808 (mmpt) cc_final: 0.8169 (tptp) REVERT: A 739 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8106 (ttpt) REVERT: A 740 GLU cc_start: 0.8061 (mp0) cc_final: 0.7642 (mp0) REVERT: A 743 GLU cc_start: 0.8285 (pt0) cc_final: 0.7969 (pt0) REVERT: A 745 MET cc_start: 0.8391 (ttm) cc_final: 0.7539 (mmm) REVERT: A 753 ASN cc_start: 0.8740 (m-40) cc_final: 0.8357 (m-40) REVERT: A 794 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8657 (mmtt) REVERT: A 796 MET cc_start: 0.8773 (ttm) cc_final: 0.8527 (tpp) REVERT: A 827 MET cc_start: 0.8790 (ppp) cc_final: 0.8504 (ppp) REVERT: A 833 HIS cc_start: 0.7671 (m90) cc_final: 0.7422 (m90) REVERT: A 834 LYS cc_start: 0.7444 (mttm) cc_final: 0.6938 (mttm) REVERT: A 850 GLU cc_start: 0.7916 (mp0) cc_final: 0.7472 (mp0) REVERT: A 860 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 878 LEU cc_start: 0.8786 (tp) cc_final: 0.8520 (tp) REVERT: A 882 LEU cc_start: 0.8884 (mt) cc_final: 0.8595 (mt) REVERT: A 893 HIS cc_start: 0.8305 (m90) cc_final: 0.8035 (m90) REVERT: A 909 LYS cc_start: 0.8401 (mppt) cc_final: 0.7848 (mmtm) REVERT: A 911 GLN cc_start: 0.7815 (tt0) cc_final: 0.7528 (tp40) REVERT: A 913 ASP cc_start: 0.8317 (t0) cc_final: 0.7947 (t0) REVERT: A 915 LYS cc_start: 0.8718 (tttt) cc_final: 0.8410 (ttpt) REVERT: A 918 LEU cc_start: 0.7512 (tp) cc_final: 0.7180 (tp) REVERT: A 922 ASN cc_start: 0.8608 (m110) cc_final: 0.8372 (m110) REVERT: A 924 LEU cc_start: 0.9016 (mp) cc_final: 0.8633 (mt) REVERT: A 927 MET cc_start: 0.6694 (tmm) cc_final: 0.6478 (tmm) REVERT: A 985 TYR cc_start: 0.7474 (t80) cc_final: 0.7165 (t80) REVERT: A 1001 MET cc_start: 0.6488 (mmp) cc_final: 0.6258 (mmp) REVERT: A 1008 MET cc_start: 0.7618 (ppp) cc_final: 0.7197 (ppp) REVERT: A 1032 LEU cc_start: 0.7860 (tp) cc_final: 0.7646 (tp) REVERT: A 1125 ASP cc_start: 0.7919 (t0) cc_final: 0.7670 (m-30) REVERT: A 1228 ASN cc_start: 0.8999 (m110) cc_final: 0.8764 (m110) REVERT: A 1238 HIS cc_start: 0.8248 (p-80) cc_final: 0.7740 (p-80) REVERT: A 1239 ILE cc_start: 0.9089 (mm) cc_final: 0.8781 (mm) REVERT: A 1266 MET cc_start: 0.7897 (mpp) cc_final: 0.7560 (mpp) REVERT: B 17 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.7006 (ptm-80) REVERT: B 43 TYR cc_start: 0.8198 (t80) cc_final: 0.7893 (t80) REVERT: B 55 ASN cc_start: 0.7940 (m110) cc_final: 0.7677 (m110) REVERT: B 91 GLU cc_start: 0.7859 (pt0) cc_final: 0.6928 (pt0) REVERT: B 99 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8224 (mtmm) REVERT: B 150 MET cc_start: 0.7667 (ptp) cc_final: 0.7159 (ptp) REVERT: B 156 ASN cc_start: 0.8370 (p0) cc_final: 0.8078 (p0) REVERT: B 184 ASP cc_start: 0.7392 (t0) cc_final: 0.6871 (t0) REVERT: B 377 GLU cc_start: 0.7678 (tt0) cc_final: 0.6760 (tt0) REVERT: B 393 ASP cc_start: 0.7742 (m-30) cc_final: 0.7506 (m-30) REVERT: B 420 ARG cc_start: 0.7612 (ppt170) cc_final: 0.7217 (ppt170) REVERT: B 430 GLU cc_start: 0.8375 (pm20) cc_final: 0.8059 (pm20) REVERT: B 433 ARG cc_start: 0.8151 (ptp-110) cc_final: 0.7843 (ptp-170) REVERT: B 462 ARG cc_start: 0.7669 (mtt90) cc_final: 0.6977 (mtt90) REVERT: B 473 ASN cc_start: 0.8760 (t0) cc_final: 0.8451 (t0) REVERT: B 474 PHE cc_start: 0.8128 (t80) cc_final: 0.7753 (t80) REVERT: B 478 THR cc_start: 0.6703 (t) cc_final: 0.6494 (t) REVERT: B 566 HIS cc_start: 0.7248 (m90) cc_final: 0.6897 (m90) REVERT: B 569 GLU cc_start: 0.7807 (pm20) cc_final: 0.7320 (mp0) REVERT: B 570 ILE cc_start: 0.8552 (tp) cc_final: 0.8182 (tp) REVERT: B 586 CYS cc_start: 0.8285 (p) cc_final: 0.8059 (p) REVERT: B 604 TRP cc_start: 0.8276 (m-10) cc_final: 0.7840 (m-10) REVERT: B 625 ASN cc_start: 0.8423 (t0) cc_final: 0.7887 (t0) REVERT: B 638 TRP cc_start: 0.7834 (p-90) cc_final: 0.7444 (p-90) REVERT: B 691 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7527 (ptpt) REVERT: B 742 VAL cc_start: 0.8488 (t) cc_final: 0.7998 (p) REVERT: B 774 GLN cc_start: 0.8504 (tp40) cc_final: 0.8274 (tp-100) REVERT: B 788 LYS cc_start: 0.8532 (pttt) cc_final: 0.8212 (ttmm) REVERT: B 789 ASN cc_start: 0.8792 (t0) cc_final: 0.8567 (t0) REVERT: B 812 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 817 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7868 (mtpp) REVERT: C 25 GLN cc_start: 0.8770 (mt0) cc_final: 0.8449 (mt0) REVERT: C 28 GLU cc_start: 0.8685 (tt0) cc_final: 0.8156 (tt0) REVERT: C 40 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8266 (mmtt) REVERT: C 69 ARG cc_start: 0.8074 (ptp-170) cc_final: 0.7275 (ptp-170) REVERT: C 77 LYS cc_start: 0.8415 (ptpt) cc_final: 0.8190 (ptpt) REVERT: C 143 ASP cc_start: 0.7819 (t0) cc_final: 0.7454 (t0) REVERT: C 153 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6650 (tm-30) REVERT: C 154 GLN cc_start: 0.7789 (tt0) cc_final: 0.6857 (tt0) REVERT: C 168 ILE cc_start: 0.8554 (tp) cc_final: 0.8339 (tp) REVERT: C 203 GLU cc_start: 0.8026 (pt0) cc_final: 0.7687 (pt0) REVERT: C 234 ASP cc_start: 0.7880 (t0) cc_final: 0.7088 (t0) REVERT: C 235 MET cc_start: 0.7252 (mmm) cc_final: 0.6808 (mmm) REVERT: C 238 TYR cc_start: 0.8061 (m-80) cc_final: 0.7812 (m-10) REVERT: C 244 GLU cc_start: 0.7073 (mp0) cc_final: 0.6761 (mp0) REVERT: C 294 LEU cc_start: 0.8141 (mp) cc_final: 0.7715 (mp) REVERT: C 295 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7378 (mt-10) REVERT: C 297 ASP cc_start: 0.8119 (m-30) cc_final: 0.7603 (m-30) REVERT: C 300 GLN cc_start: 0.8634 (pp30) cc_final: 0.8401 (pp30) REVERT: C 330 GLU cc_start: 0.8542 (mp0) cc_final: 0.8200 (mp0) REVERT: C 336 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: C 340 TYR cc_start: 0.8160 (m-10) cc_final: 0.7631 (m-10) REVERT: C 347 GLU cc_start: 0.8172 (mp0) cc_final: 0.7781 (mp0) REVERT: C 348 LEU cc_start: 0.8737 (mp) cc_final: 0.8365 (mp) REVERT: C 351 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.8060 (mmm-85) REVERT: C 411 ILE cc_start: 0.8734 (tt) cc_final: 0.8520 (tt) REVERT: C 416 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8243 (mmm-85) REVERT: C 421 GLU cc_start: 0.6832 (mp0) cc_final: 0.6610 (mp0) REVERT: C 428 VAL cc_start: 0.8450 (t) cc_final: 0.8218 (m) REVERT: C 434 GLU cc_start: 0.7591 (mp0) cc_final: 0.7049 (mp0) REVERT: C 441 ASP cc_start: 0.7028 (t0) cc_final: 0.6794 (t0) REVERT: C 444 GLN cc_start: 0.8496 (mp10) cc_final: 0.7452 (mp10) REVERT: C 445 ASP cc_start: 0.7844 (m-30) cc_final: 0.7430 (m-30) REVERT: C 446 ILE cc_start: 0.7944 (tt) cc_final: 0.7706 (tt) REVERT: C 448 ILE cc_start: 0.8151 (pt) cc_final: 0.7877 (pt) REVERT: C 458 GLU cc_start: 0.8101 (tp30) cc_final: 0.7879 (tp30) REVERT: C 464 GLU cc_start: 0.8485 (mp0) cc_final: 0.7842 (pm20) REVERT: C 504 GLU cc_start: 0.8149 (tp30) cc_final: 0.7456 (tp30) REVERT: C 507 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.7770 (tmm-80) REVERT: C 511 GLU cc_start: 0.8178 (tp30) cc_final: 0.7969 (tp30) REVERT: C 526 THR cc_start: 0.8156 (p) cc_final: 0.7933 (p) REVERT: C 533 ILE cc_start: 0.9153 (mp) cc_final: 0.8844 (tp) REVERT: C 538 GLN cc_start: 0.7863 (tt0) cc_final: 0.7139 (tt0) REVERT: C 542 MET cc_start: 0.6988 (tpt) cc_final: 0.6486 (tpt) REVERT: E 939 TYR cc_start: 0.7534 (m-10) cc_final: 0.7280 (m-10) REVERT: E 976 LYS cc_start: 0.8191 (pttm) cc_final: 0.7919 (pttm) REVERT: E 983 GLN cc_start: 0.6873 (pp30) cc_final: 0.6486 (pp30) REVERT: E 985 TYR cc_start: 0.7873 (t80) cc_final: 0.7168 (t80) REVERT: E 992 TYR cc_start: 0.7465 (t80) cc_final: 0.6769 (t80) REVERT: E 996 LEU cc_start: 0.7897 (tp) cc_final: 0.7432 (tp) REVERT: E 997 MET cc_start: 0.7484 (mmt) cc_final: 0.6940 (mmt) REVERT: E 1008 MET cc_start: 0.7958 (mmp) cc_final: 0.7201 (mmp) REVERT: E 1033 CYS cc_start: 0.8279 (m) cc_final: 0.8058 (m) REVERT: E 1052 LEU cc_start: 0.8917 (tp) cc_final: 0.8705 (tp) REVERT: E 1056 LEU cc_start: 0.8644 (mt) cc_final: 0.8409 (mt) REVERT: E 1094 ARG cc_start: 0.6888 (ptt180) cc_final: 0.6460 (ptt180) REVERT: E 1095 LEU cc_start: 0.8229 (mt) cc_final: 0.7929 (mt) REVERT: E 1097 TYR cc_start: 0.7435 (m-80) cc_final: 0.7148 (m-80) REVERT: E 1115 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8494 (pp20) REVERT: E 1120 TYR cc_start: 0.8428 (t80) cc_final: 0.7777 (t80) REVERT: E 1241 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8429 (mmtp) outliers start: 0 outliers final: 0 residues processed: 764 average time/residue: 0.1703 time to fit residues: 198.1813 Evaluate side-chains 713 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 173 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 59 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 776 GLN C 97 HIS C 190 HIS C 291 ASN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.123185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.094955 restraints weight = 43729.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098821 restraints weight = 23357.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101513 restraints weight = 14593.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103323 restraints weight = 10150.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104508 restraints weight = 7696.394| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23074 Z= 0.149 Angle : 0.726 20.532 31629 Z= 0.368 Chirality : 0.047 0.213 3593 Planarity : 0.005 0.052 3753 Dihedral : 14.051 76.441 3988 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.71 (0.16), residues: 2567 helix: 0.05 (0.18), residues: 777 sheet: -0.99 (0.21), residues: 601 loop : -2.01 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1268 TYR 0.025 0.002 TYR A 917 PHE 0.037 0.002 PHE A1131 TRP 0.069 0.003 TRP B 378 HIS 0.018 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (23071) covalent geometry : angle 0.70058 / 0.37 (31620) hydrogen bonds : bond 0.04946 / 3.42 ( 855) hydrogen bonds : angle 5.23242 / 3.68 ( 2328) metal coordination : bond 0.00944 / 0.48 ( 3) metal coordination : angle 11.33823 / 5.16 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 768 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7256 (ttp-170) cc_final: 0.6884 (ptt-90) REVERT: A 34 LEU cc_start: 0.8236 (mm) cc_final: 0.7975 (tt) REVERT: A 43 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6385 (tm-30) REVERT: A 52 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8666 (mmtm) REVERT: A 75 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 121 GLN cc_start: 0.8301 (mp10) cc_final: 0.7761 (mp10) REVERT: A 122 GLU cc_start: 0.7792 (tp30) cc_final: 0.7376 (tp30) REVERT: A 131 GLN cc_start: 0.8525 (mp-120) cc_final: 0.8161 (mp10) REVERT: A 134 ILE cc_start: 0.8581 (tp) cc_final: 0.8227 (pt) REVERT: A 136 MET cc_start: 0.8040 (pmm) cc_final: 0.7749 (pmm) REVERT: A 189 LEU cc_start: 0.8740 (tp) cc_final: 0.8238 (tp) REVERT: A 193 ASP cc_start: 0.8540 (p0) cc_final: 0.7724 (p0) REVERT: A 258 ASP cc_start: 0.7145 (t70) cc_final: 0.6607 (t70) REVERT: A 261 ASN cc_start: 0.8156 (m110) cc_final: 0.7438 (t0) REVERT: A 263 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6452 (mm-40) REVERT: A 285 ASP cc_start: 0.8231 (t0) cc_final: 0.7925 (t0) REVERT: A 286 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8075 (tt0) REVERT: A 304 TRP cc_start: 0.7365 (t60) cc_final: 0.7152 (t60) REVERT: A 333 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8611 (mmtt) REVERT: A 377 THR cc_start: 0.7960 (p) cc_final: 0.7676 (p) REVERT: A 378 ASP cc_start: 0.7479 (m-30) cc_final: 0.6999 (m-30) REVERT: A 414 CYS cc_start: 0.7654 (p) cc_final: 0.7453 (p) REVERT: A 443 ASP cc_start: 0.7598 (t0) cc_final: 0.7191 (t0) REVERT: A 474 LYS cc_start: 0.8964 (tppt) cc_final: 0.8657 (tppt) REVERT: A 487 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7957 (mmmt) REVERT: A 573 LEU cc_start: 0.8012 (tp) cc_final: 0.7807 (mp) REVERT: A 580 LYS cc_start: 0.8232 (tmmt) cc_final: 0.7762 (tmmt) REVERT: A 617 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 619 GLU cc_start: 0.7960 (mp0) cc_final: 0.7686 (mp0) REVERT: A 660 CYS cc_start: 0.8379 (t) cc_final: 0.7590 (p) REVERT: A 661 GLN cc_start: 0.8351 (pm20) cc_final: 0.7588 (pm20) REVERT: A 689 ARG cc_start: 0.7675 (tmt-80) cc_final: 0.7073 (tmt-80) REVERT: A 697 ILE cc_start: 0.8606 (tp) cc_final: 0.8301 (tt) REVERT: A 728 GLN cc_start: 0.8348 (tp40) cc_final: 0.8075 (tp40) REVERT: A 731 LYS cc_start: 0.8795 (mmpt) cc_final: 0.8135 (tptp) REVERT: A 739 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8416 (ttpp) REVERT: A 745 MET cc_start: 0.8361 (ttm) cc_final: 0.7575 (mmm) REVERT: A 753 ASN cc_start: 0.8750 (m-40) cc_final: 0.8350 (m-40) REVERT: A 796 MET cc_start: 0.8784 (ttm) cc_final: 0.8580 (tpp) REVERT: A 827 MET cc_start: 0.8808 (ppp) cc_final: 0.8375 (ppp) REVERT: A 833 HIS cc_start: 0.7656 (m90) cc_final: 0.7452 (m90) REVERT: A 834 LYS cc_start: 0.7491 (mttm) cc_final: 0.6992 (mttm) REVERT: A 850 GLU cc_start: 0.7875 (mp0) cc_final: 0.7457 (mp0) REVERT: A 860 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8493 (tm-30) REVERT: A 878 LEU cc_start: 0.8808 (tp) cc_final: 0.8559 (tp) REVERT: A 882 LEU cc_start: 0.8863 (mt) cc_final: 0.8573 (mt) REVERT: A 893 HIS cc_start: 0.8294 (m90) cc_final: 0.8046 (m90) REVERT: A 909 LYS cc_start: 0.8367 (mppt) cc_final: 0.7806 (mmtm) REVERT: A 911 GLN cc_start: 0.7768 (tt0) cc_final: 0.7501 (tp40) REVERT: A 913 ASP cc_start: 0.8291 (t0) cc_final: 0.7909 (t0) REVERT: A 915 LYS cc_start: 0.8703 (tttt) cc_final: 0.8406 (ttpt) REVERT: A 916 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 924 LEU cc_start: 0.8968 (mp) cc_final: 0.8539 (mt) REVERT: A 927 MET cc_start: 0.6670 (tmm) cc_final: 0.6431 (tmm) REVERT: A 947 ILE cc_start: 0.7991 (mm) cc_final: 0.7782 (mm) REVERT: A 985 TYR cc_start: 0.7425 (t80) cc_final: 0.7145 (t80) REVERT: A 1001 MET cc_start: 0.6493 (mmp) cc_final: 0.6250 (mmp) REVERT: A 1008 MET cc_start: 0.7445 (ppp) cc_final: 0.7081 (ppp) REVERT: A 1032 LEU cc_start: 0.7813 (tp) cc_final: 0.7596 (tp) REVERT: A 1089 TRP cc_start: 0.7414 (m100) cc_final: 0.6409 (m100) REVERT: A 1125 ASP cc_start: 0.7926 (t0) cc_final: 0.7672 (m-30) REVERT: A 1228 ASN cc_start: 0.9000 (m110) cc_final: 0.8765 (m110) REVERT: A 1237 TYR cc_start: 0.8156 (t80) cc_final: 0.7805 (t80) REVERT: A 1238 HIS cc_start: 0.8249 (p-80) cc_final: 0.7903 (p-80) REVERT: A 1239 ILE cc_start: 0.9108 (mm) cc_final: 0.8814 (mm) REVERT: A 1266 MET cc_start: 0.7895 (mpp) cc_final: 0.7599 (mpp) REVERT: B 32 LEU cc_start: 0.7856 (mt) cc_final: 0.7385 (mt) REVERT: B 43 TYR cc_start: 0.8197 (t80) cc_final: 0.7892 (t80) REVERT: B 55 ASN cc_start: 0.7868 (m110) cc_final: 0.7063 (m110) REVERT: B 73 SER cc_start: 0.8725 (m) cc_final: 0.8506 (t) REVERT: B 78 LEU cc_start: 0.7946 (mt) cc_final: 0.7727 (mt) REVERT: B 91 GLU cc_start: 0.7714 (pt0) cc_final: 0.7298 (pt0) REVERT: B 144 LYS cc_start: 0.7461 (tmtt) cc_final: 0.6681 (tmtt) REVERT: B 150 MET cc_start: 0.7659 (ptp) cc_final: 0.7002 (ppp) REVERT: B 151 CYS cc_start: 0.7644 (t) cc_final: 0.7141 (t) REVERT: B 152 LEU cc_start: 0.9067 (mt) cc_final: 0.8737 (mm) REVERT: B 156 ASN cc_start: 0.8378 (p0) cc_final: 0.8039 (p0) REVERT: B 184 ASP cc_start: 0.7408 (t0) cc_final: 0.6873 (t0) REVERT: B 314 LYS cc_start: 0.6403 (mmtt) cc_final: 0.6161 (mmtt) REVERT: B 348 GLN cc_start: 0.7785 (tp-100) cc_final: 0.6847 (tp-100) REVERT: B 377 GLU cc_start: 0.7651 (tt0) cc_final: 0.6776 (tt0) REVERT: B 393 ASP cc_start: 0.7758 (m-30) cc_final: 0.7481 (m-30) REVERT: B 430 GLU cc_start: 0.8351 (pm20) cc_final: 0.8023 (pm20) REVERT: B 433 ARG cc_start: 0.8132 (ptp-110) cc_final: 0.7540 (ptp-110) REVERT: B 450 PHE cc_start: 0.8358 (m-80) cc_final: 0.8097 (m-10) REVERT: B 473 ASN cc_start: 0.8753 (t0) cc_final: 0.8434 (t0) REVERT: B 474 PHE cc_start: 0.8101 (t80) cc_final: 0.7737 (t80) REVERT: B 478 THR cc_start: 0.6604 (t) cc_final: 0.6393 (t) REVERT: B 566 HIS cc_start: 0.7189 (m90) cc_final: 0.6869 (m90) REVERT: B 569 GLU cc_start: 0.7791 (pm20) cc_final: 0.7226 (mp0) REVERT: B 586 CYS cc_start: 0.8307 (p) cc_final: 0.8071 (p) REVERT: B 604 TRP cc_start: 0.8316 (m-10) cc_final: 0.7851 (m-10) REVERT: B 619 GLN cc_start: 0.7491 (tp-100) cc_final: 0.6837 (tm-30) REVERT: B 620 MET cc_start: 0.7087 (mmp) cc_final: 0.6721 (mmp) REVERT: B 625 ASN cc_start: 0.8406 (t0) cc_final: 0.7868 (t0) REVERT: B 638 TRP cc_start: 0.7813 (p-90) cc_final: 0.7422 (p-90) REVERT: B 643 LYS cc_start: 0.8313 (tmmt) cc_final: 0.7860 (mmmt) REVERT: B 682 LYS cc_start: 0.8069 (mptt) cc_final: 0.7329 (tttp) REVERT: B 691 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7545 (ptpt) REVERT: B 774 GLN cc_start: 0.8505 (tp40) cc_final: 0.7517 (tm-30) REVERT: B 783 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7947 (tpp-160) REVERT: B 812 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 25 GLN cc_start: 0.8757 (mt0) cc_final: 0.8438 (mt0) REVERT: C 28 GLU cc_start: 0.8716 (tt0) cc_final: 0.7509 (tm-30) REVERT: C 32 GLN cc_start: 0.7667 (pm20) cc_final: 0.6955 (pm20) REVERT: C 40 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8243 (mmtt) REVERT: C 42 LYS cc_start: 0.8198 (tttp) cc_final: 0.7991 (tptp) REVERT: C 69 ARG cc_start: 0.8029 (ptp-170) cc_final: 0.7225 (ptp-170) REVERT: C 77 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8198 (ptpt) REVERT: C 143 ASP cc_start: 0.7707 (t0) cc_final: 0.7401 (t0) REVERT: C 153 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6614 (tm-30) REVERT: C 154 GLN cc_start: 0.7748 (tt0) cc_final: 0.6838 (tt0) REVERT: C 166 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 167 PHE cc_start: 0.8143 (m-10) cc_final: 0.7634 (m-10) REVERT: C 200 ASN cc_start: 0.8818 (p0) cc_final: 0.7859 (p0) REVERT: C 234 ASP cc_start: 0.7858 (t0) cc_final: 0.7056 (t0) REVERT: C 235 MET cc_start: 0.7268 (mmm) cc_final: 0.6844 (mmm) REVERT: C 238 TYR cc_start: 0.8056 (m-80) cc_final: 0.7788 (m-10) REVERT: C 244 GLU cc_start: 0.7049 (mp0) cc_final: 0.6771 (mp0) REVERT: C 294 LEU cc_start: 0.8096 (mp) cc_final: 0.7781 (mp) REVERT: C 295 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7357 (mt-10) REVERT: C 297 ASP cc_start: 0.8096 (m-30) cc_final: 0.7694 (m-30) REVERT: C 300 GLN cc_start: 0.8567 (pp30) cc_final: 0.8357 (pp30) REVERT: C 330 GLU cc_start: 0.8557 (mp0) cc_final: 0.8341 (mp0) REVERT: C 336 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7707 (mtp-110) REVERT: C 338 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8507 (mmpt) REVERT: C 340 TYR cc_start: 0.8082 (m-10) cc_final: 0.7458 (m-10) REVERT: C 347 GLU cc_start: 0.8163 (mp0) cc_final: 0.7731 (mp0) REVERT: C 348 LEU cc_start: 0.8705 (mp) cc_final: 0.8367 (mp) REVERT: C 351 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8056 (mmm-85) REVERT: C 411 ILE cc_start: 0.8715 (tt) cc_final: 0.8490 (tt) REVERT: C 416 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8263 (mmm-85) REVERT: C 428 VAL cc_start: 0.8409 (t) cc_final: 0.8202 (m) REVERT: C 434 GLU cc_start: 0.7542 (mp0) cc_final: 0.6977 (mp0) REVERT: C 441 ASP cc_start: 0.6971 (t0) cc_final: 0.6688 (t0) REVERT: C 444 GLN cc_start: 0.8479 (mp10) cc_final: 0.7404 (mp10) REVERT: C 445 ASP cc_start: 0.7844 (m-30) cc_final: 0.7436 (m-30) REVERT: C 446 ILE cc_start: 0.7923 (tt) cc_final: 0.7648 (tt) REVERT: C 448 ILE cc_start: 0.8140 (pt) cc_final: 0.7896 (pt) REVERT: C 459 GLU cc_start: 0.7875 (pm20) cc_final: 0.6972 (pm20) REVERT: C 464 GLU cc_start: 0.8497 (mp0) cc_final: 0.8167 (mp0) REVERT: C 504 GLU cc_start: 0.8124 (tp30) cc_final: 0.7885 (tp30) REVERT: C 512 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7151 (mt-10) REVERT: C 526 THR cc_start: 0.8176 (p) cc_final: 0.7909 (p) REVERT: C 533 ILE cc_start: 0.9138 (mp) cc_final: 0.8905 (tp) REVERT: C 538 GLN cc_start: 0.7846 (tt0) cc_final: 0.7212 (tt0) REVERT: C 542 MET cc_start: 0.6934 (tpt) cc_final: 0.6336 (tpt) REVERT: E 939 TYR cc_start: 0.7548 (m-10) cc_final: 0.7303 (m-10) REVERT: E 976 LYS cc_start: 0.8365 (pttm) cc_final: 0.8097 (pttm) REVERT: E 983 GLN cc_start: 0.6905 (pp30) cc_final: 0.6504 (pp30) REVERT: E 985 TYR cc_start: 0.7869 (t80) cc_final: 0.7160 (t80) REVERT: E 992 TYR cc_start: 0.7504 (t80) cc_final: 0.6797 (t80) REVERT: E 997 MET cc_start: 0.7488 (mmt) cc_final: 0.6922 (mmt) REVERT: E 1008 MET cc_start: 0.7948 (mmp) cc_final: 0.7150 (mmp) REVERT: E 1033 CYS cc_start: 0.8253 (m) cc_final: 0.8022 (m) REVERT: E 1052 LEU cc_start: 0.8917 (tp) cc_final: 0.8697 (tp) REVERT: E 1056 LEU cc_start: 0.8650 (mt) cc_final: 0.8399 (mt) REVERT: E 1094 ARG cc_start: 0.6841 (ptt180) cc_final: 0.6385 (ptt180) REVERT: E 1095 LEU cc_start: 0.8202 (mt) cc_final: 0.7902 (mt) REVERT: E 1097 TYR cc_start: 0.7433 (m-80) cc_final: 0.7126 (m-80) REVERT: E 1115 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8440 (pp20) REVERT: E 1120 TYR cc_start: 0.8451 (t80) cc_final: 0.7781 (t80) REVERT: E 1241 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8447 (mmtp) outliers start: 1 outliers final: 0 residues processed: 769 average time/residue: 0.1699 time to fit residues: 199.2290 Evaluate side-chains 701 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 701 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 130 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 204 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN C 291 ASN ** E1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094546 restraints weight = 43937.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098469 restraints weight = 23383.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101118 restraints weight = 14579.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102924 restraints weight = 10125.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104228 restraints weight = 7651.545| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23074 Z= 0.158 Angle : 0.729 20.472 31629 Z= 0.372 Chirality : 0.047 0.215 3593 Planarity : 0.005 0.072 3753 Dihedral : 14.020 76.553 3988 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.75 (0.16), residues: 2567 helix: 0.04 (0.18), residues: 777 sheet: -0.94 (0.21), residues: 600 loop : -2.09 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 462 TYR 0.043 0.002 TYR A 978 PHE 0.040 0.002 PHE A1131 TRP 0.104 0.003 TRP A 224 HIS 0.017 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (23071) covalent geometry : angle 0.70407 / 0.37 (31620) hydrogen bonds : bond 0.05013 / 3.46 ( 855) hydrogen bonds : angle 5.22646 / 3.68 ( 2328) metal coordination : bond 0.00961 / 0.48 ( 3) metal coordination : angle 11.22742 / 5.10 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4648.53 seconds wall clock time: 81 minutes 3.72 seconds (4863.72 seconds total)