Starting phenix.real_space_refine on Thu Jun 19 15:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pu0_17927/06_2025/8pu0_17927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pu0_17927/06_2025/8pu0_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_17927/06_2025/8pu0_17927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pu0_17927/06_2025/8pu0_17927.map" model { file = "/net/cci-nas-00/data/ceres_data/8pu0_17927/06_2025/8pu0_17927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pu0_17927/06_2025/8pu0_17927.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.18, per 1000 atoms: 0.59 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: 5.99 Conformation dependent library (CDL) restraints added in 2.8 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: 9.43 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: 10.43 Time building geometry restraints manager: 6.77 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: 31296 2.81 - 5.61: 286 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 1.50e+00 4.44e-01 3.30e+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=" O TYR C 49 " pdb=" C TYR C 49 " pdb=" N GLY C 50 " ideal model delta sigma weight residual 122.25 117.32 4.93 1.19e+00 7.06e-01 1.72e+01 angle pdb=" C5A DCA C 601 " pdb=" C6A DCA C 601 " pdb=" N6A DCA C 601 " ideal model delta sigma weight residual 122.85 134.75 -11.90 3.00e+00 1.11e-01 1.57e+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: 3490 0.108 - 0.216: 96 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: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 63.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 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= 0.260 Angle : 0.727 22.085 31629 Z= 0.367 Chirality : 0.047 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.002 TRP B 604 HIS 0.006 0.001 HIS C 101 PHE 0.018 0.002 PHE B 388 TYR 0.026 0.002 TYR A 931 ARG 0.004 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.17724 ( 855) hydrogen bonds : angle 7.19734 ( 2328) metal coordination : bond 0.01119 ( 3) metal coordination : angle 13.18050 ( 9) covalent geometry : bond 0.00488 (23071) covalent geometry : angle 0.69225 (31620) *********************** 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 : 2.218 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: 0.7711 (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: 0.6957 (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: 0.7870 (tp) REVERT: A 617 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 640 ASN cc_start: 0.4925 (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: 0.6002 (t) cc_final: 0.5751 (m) REVERT: B 91 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6360 (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: 0.5328 (m) cc_final: 0.4593 (p) REVERT: B 394 LEU cc_start: 0.6069 (pt) cc_final: 0.5697 (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: 0.3981 (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: 0.4992 (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: 0.6856 (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: 0.8079 (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: 0.7211 (tt0) REVERT: C 213 THR cc_start: 0.5189 (p) cc_final: 0.4729 (p) REVERT: C 219 THR cc_start: 0.5934 (p) cc_final: 0.5628 (p) REVERT: C 279 PHE cc_start: 0.7367 (m-80) cc_final: 0.6836 (m-80) REVERT: C 288 ASP cc_start: 0.7939 (t0) cc_final: 0.6917 (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: 0.7329 (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: 0.6843 (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: 0.6317 (tpt-90) REVERT: C 474 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6159 (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: 0.6033 (tpp) cc_final: 0.5798 (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: 0.8127 (mp10) outliers start: 14 outliers final: 5 residues processed: 830 average time/residue: 0.3926 time to fit residues: 488.6415 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 : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 263 GLN A 271 ASN A 530 HIS ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 96 GLN B 106 HIS B 118 GLN B 192 GLN B 292 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095391 restraints weight = 44464.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099363 restraints weight = 23270.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101197 restraints weight = 13074.440| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 23074 Z= 0.261 Angle : 0.799 23.362 31629 Z= 0.406 Chirality : 0.049 0.191 3593 Planarity : 0.005 0.056 3753 Dihedral : 14.744 79.626 3988 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2567 helix: 0.14 (0.19), residues: 753 sheet: -1.51 (0.21), residues: 603 loop : -1.94 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 787 HIS 0.011 0.002 HIS C 476 PHE 0.035 0.003 PHE B 349 TYR 0.019 0.002 TYR E 978 ARG 0.013 0.001 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.06292 ( 855) hydrogen bonds : angle 5.87955 ( 2328) metal coordination : bond 0.01811 ( 3) metal coordination : angle 12.78421 ( 9) covalent geometry : bond 0.00555 (23071) covalent geometry : angle 0.76956 (31620) *********************** 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 791 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 790 time to evaluate : 2.399 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: 0.7236 (ttp-170) cc_final: 0.6851 (ttp80) REVERT: A 34 LEU cc_start: 0.8400 (mt) cc_final: 0.8173 (mt) REVERT: A 43 GLU cc_start: 0.7662 (tt0) cc_final: 0.7286 (tp30) REVERT: A 80 GLN cc_start: 0.8569 (mt0) cc_final: 0.8358 (mt0) REVERT: A 121 GLN cc_start: 0.8302 (mp10) cc_final: 0.7780 (mp10) REVERT: A 122 GLU cc_start: 0.7744 (tp30) cc_final: 0.7532 (tp30) REVERT: A 136 MET cc_start: 0.7907 (pmm) cc_final: 0.7293 (pmm) REVERT: A 189 LEU cc_start: 0.9092 (tp) cc_final: 0.7894 (tp) REVERT: A 257 GLN cc_start: 0.8893 (tt0) cc_final: 0.8627 (tt0) REVERT: A 259 LYS cc_start: 0.8525 (tppt) cc_final: 0.8173 (tppt) REVERT: A 269 GLU cc_start: 0.8000 (pt0) cc_final: 0.7730 (pt0) REVERT: A 274 LEU cc_start: 0.8890 (pp) cc_final: 0.8632 (tp) REVERT: A 285 ASP cc_start: 0.8397 (t0) cc_final: 0.8098 (t70) REVERT: A 286 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7697 (tt0) REVERT: A 327 ASN cc_start: 0.8574 (m-40) cc_final: 0.8278 (m-40) REVERT: A 377 THR cc_start: 0.8155 (p) cc_final: 0.7862 (p) REVERT: A 378 ASP cc_start: 0.7550 (m-30) cc_final: 0.7081 (m-30) REVERT: A 443 ASP cc_start: 0.7668 (t0) cc_final: 0.7390 (t0) REVERT: A 474 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8008 (mmtt) REVERT: A 476 CYS cc_start: 0.7495 (m) cc_final: 0.7252 (t) REVERT: A 487 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7914 (mmmt) REVERT: A 489 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7880 (tp-100) REVERT: A 529 HIS cc_start: 0.8065 (m-70) cc_final: 0.7779 (m90) REVERT: A 545 LEU cc_start: 0.8079 (mt) cc_final: 0.7819 (mt) REVERT: A 572 GLN cc_start: 0.7824 (tt0) cc_final: 0.5741 (tt0) REVERT: A 573 LEU cc_start: 0.8151 (tp) cc_final: 0.7645 (mp) REVERT: A 580 LYS cc_start: 0.8429 (tmmt) cc_final: 0.7919 (tmmt) REVERT: A 614 MET cc_start: 0.8600 (tpt) cc_final: 0.8046 (tpt) REVERT: A 619 GLU cc_start: 0.7922 (mp0) cc_final: 0.7698 (mp0) REVERT: A 620 CYS cc_start: 0.8342 (p) cc_final: 0.8025 (p) REVERT: A 640 ASN cc_start: 0.7096 (t0) cc_final: 0.6685 (t0) REVERT: A 660 CYS cc_start: 0.8536 (t) cc_final: 0.7648 (p) REVERT: A 661 GLN cc_start: 0.8504 (pm20) cc_final: 0.7808 (pm20) REVERT: A 689 ARG cc_start: 0.7821 (tmt-80) cc_final: 0.7400 (tmt-80) REVERT: A 707 LEU cc_start: 0.8074 (pt) cc_final: 0.7848 (pt) REVERT: A 728 GLN cc_start: 0.8509 (tp40) cc_final: 0.8209 (tp40) REVERT: A 731 LYS cc_start: 0.8917 (mmpt) cc_final: 0.8239 (tptp) REVERT: A 737 MET cc_start: 0.6514 (pmm) cc_final: 0.5884 (pmm) REVERT: A 744 CYS cc_start: 0.8124 (t) cc_final: 0.7699 (p) REVERT: A 753 ASN cc_start: 0.8671 (m-40) cc_final: 0.8369 (m-40) REVERT: A 767 VAL cc_start: 0.8746 (m) cc_final: 0.8503 (m) REVERT: A 794 LYS cc_start: 0.8793 (mppt) cc_final: 0.8476 (mmtt) REVERT: A 796 MET cc_start: 0.8539 (ttm) cc_final: 0.8248 (mtt) REVERT: A 834 LYS cc_start: 0.7353 (mttm) cc_final: 0.6829 (mttm) REVERT: A 841 THR cc_start: 0.8684 (m) cc_final: 0.8365 (p) REVERT: A 850 GLU cc_start: 0.7804 (mp0) cc_final: 0.6846 (mp0) REVERT: A 873 SER cc_start: 0.8360 (m) cc_final: 0.8142 (t) REVERT: A 882 LEU cc_start: 0.8903 (mt) cc_final: 0.8437 (tt) REVERT: A 922 ASN cc_start: 0.8615 (m110) cc_final: 0.8368 (m110) REVERT: A 931 TYR cc_start: 0.8289 (t80) cc_final: 0.7700 (t80) REVERT: A 973 GLU cc_start: 0.8432 (mp0) cc_final: 0.8143 (mp0) REVERT: A 985 TYR cc_start: 0.7509 (t80) cc_final: 0.7218 (t80) REVERT: A 1001 MET cc_start: 0.6281 (mmp) cc_final: 0.5852 (mmp) REVERT: A 1032 LEU cc_start: 0.8164 (tp) cc_final: 0.7715 (tp) REVERT: A 1121 MET cc_start: 0.8434 (mmp) cc_final: 0.8088 (mmm) REVERT: A 1228 ASN cc_start: 0.8981 (m110) cc_final: 0.8750 (m-40) REVERT: A 1230 GLU cc_start: 0.7361 (pm20) cc_final: 0.7140 (mp0) REVERT: A 1238 HIS cc_start: 0.8113 (p90) cc_final: 0.7701 (p-80) REVERT: A 1254 GLU cc_start: 0.8533 (tt0) cc_final: 0.8018 (tt0) REVERT: B 7 GLU cc_start: 0.7386 (pt0) cc_final: 0.6807 (pm20) REVERT: B 22 LEU cc_start: 0.7999 (tp) cc_final: 0.7721 (tp) REVERT: B 55 ASN cc_start: 0.8330 (m110) cc_final: 0.7985 (m110) REVERT: B 98 LEU cc_start: 0.8590 (tp) cc_final: 0.7508 (tp) REVERT: B 106 HIS cc_start: 0.6861 (m90) cc_final: 0.6585 (m170) REVERT: B 144 LYS cc_start: 0.7235 (tptp) cc_final: 0.6948 (tptp) REVERT: B 150 MET cc_start: 0.7585 (ptp) cc_final: 0.6882 (ppp) REVERT: B 151 CYS cc_start: 0.7892 (t) cc_final: 0.7515 (t) REVERT: B 152 LEU cc_start: 0.9073 (mt) cc_final: 0.8814 (mt) REVERT: B 156 ASN cc_start: 0.8325 (p0) cc_final: 0.7955 (p0) REVERT: B 184 ASP cc_start: 0.7191 (t0) cc_final: 0.6974 (t0) REVERT: B 207 GLU cc_start: 0.7240 (mp0) cc_final: 0.7007 (mp0) REVERT: B 238 LEU cc_start: 0.7808 (tt) cc_final: 0.7605 (tp) REVERT: B 239 TYR cc_start: 0.7691 (p90) cc_final: 0.7378 (p90) REVERT: B 328 TRP cc_start: 0.7999 (m-10) cc_final: 0.6943 (m100) REVERT: B 377 GLU cc_start: 0.8024 (tt0) cc_final: 0.6958 (tt0) REVERT: B 435 GLN cc_start: 0.8699 (pp30) cc_final: 0.8405 (pp30) REVERT: B 447 ILE cc_start: 0.7706 (mm) cc_final: 0.7371 (mm) REVERT: B 473 ASN cc_start: 0.8631 (t0) cc_final: 0.8338 (t0) REVERT: B 474 PHE cc_start: 0.8258 (t80) cc_final: 0.7991 (t80) REVERT: B 478 THR cc_start: 0.6529 (t) cc_final: 0.6287 (t) REVERT: B 559 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 586 CYS cc_start: 0.8308 (p) cc_final: 0.8093 (p) REVERT: B 612 PHE cc_start: 0.7963 (t80) cc_final: 0.7458 (t80) REVERT: B 618 THR cc_start: 0.6959 (m) cc_final: 0.6716 (m) REVERT: B 619 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7288 (tp-100) REVERT: B 625 ASN cc_start: 0.8508 (t0) cc_final: 0.7565 (t0) REVERT: B 627 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7576 (mmmt) REVERT: B 628 PHE cc_start: 0.7243 (m-80) cc_final: 0.6559 (m-80) REVERT: B 636 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: B 638 TRP cc_start: 0.7820 (p-90) cc_final: 0.7429 (p-90) REVERT: B 641 TRP cc_start: 0.7431 (m100) cc_final: 0.6622 (m100) REVERT: B 684 PHE cc_start: 0.7255 (p90) cc_final: 0.6883 (p90) REVERT: B 748 LYS cc_start: 0.8428 (tptt) cc_final: 0.7925 (tptt) REVERT: B 788 LYS cc_start: 0.8250 (tptp) cc_final: 0.7490 (tptp) REVERT: B 789 ASN cc_start: 0.8544 (t0) cc_final: 0.7870 (t0) REVERT: B 816 VAL cc_start: 0.8592 (t) cc_final: 0.8306 (m) REVERT: B 817 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7945 (mtmt) REVERT: C 17 LEU cc_start: 0.8954 (mt) cc_final: 0.8524 (mt) REVERT: C 28 GLU cc_start: 0.8625 (tt0) cc_final: 0.7938 (tt0) REVERT: C 31 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 32 GLN cc_start: 0.7536 (mp10) cc_final: 0.7318 (mp10) REVERT: C 40 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8282 (mmtt) REVERT: C 60 ILE cc_start: 0.8068 (mt) cc_final: 0.7865 (mt) REVERT: C 87 ILE cc_start: 0.8264 (mm) cc_final: 0.8014 (mm) REVERT: C 154 GLN cc_start: 0.7813 (tt0) cc_final: 0.7004 (tt0) REVERT: C 167 PHE cc_start: 0.8082 (m-80) cc_final: 0.7738 (m-80) REVERT: C 199 ASN cc_start: 0.7711 (t0) cc_final: 0.7261 (t0) REVERT: C 203 GLU cc_start: 0.8075 (tt0) cc_final: 0.7681 (tt0) REVERT: C 219 THR cc_start: 0.7434 (p) cc_final: 0.7149 (p) REVERT: C 223 ARG cc_start: 0.7789 (ptm160) cc_final: 0.7363 (ptm-80) REVERT: C 235 MET cc_start: 0.7069 (mmm) cc_final: 0.6834 (mmm) REVERT: C 300 GLN cc_start: 0.8553 (pp30) cc_final: 0.8163 (pp30) REVERT: C 318 TYR cc_start: 0.7613 (m-80) cc_final: 0.7409 (m-80) REVERT: C 340 TYR cc_start: 0.8161 (m-10) cc_final: 0.7716 (m-10) REVERT: C 382 ASN cc_start: 0.8218 (p0) cc_final: 0.8017 (t0) REVERT: C 411 ILE cc_start: 0.8715 (tt) cc_final: 0.8397 (mm) REVERT: C 414 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8155 (mmtm) REVERT: C 426 ASP cc_start: 0.7996 (p0) cc_final: 0.7754 (p0) REVERT: C 428 VAL cc_start: 0.8565 (t) cc_final: 0.8306 (m) REVERT: C 434 GLU cc_start: 0.7638 (mp0) cc_final: 0.6999 (mp0) REVERT: C 444 GLN cc_start: 0.8522 (mp10) cc_final: 0.8030 (mp10) REVERT: C 445 ASP cc_start: 0.7670 (m-30) cc_final: 0.7308 (m-30) REVERT: C 459 GLU cc_start: 0.7770 (pm20) cc_final: 0.7162 (pm20) REVERT: C 464 GLU cc_start: 0.8516 (mp0) cc_final: 0.7778 (pm20) REVERT: C 474 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 497 PHE cc_start: 0.7615 (m-80) cc_final: 0.6991 (m-80) REVERT: C 507 ARG cc_start: 0.8239 (tmm-80) cc_final: 0.7934 (tmm-80) REVERT: C 508 ILE cc_start: 0.8529 (tp) cc_final: 0.8145 (tp) REVERT: C 518 ILE cc_start: 0.8775 (mt) cc_final: 0.8524 (mt) REVERT: C 529 TYR cc_start: 0.8082 (t80) cc_final: 0.7605 (t80) REVERT: C 532 LYS cc_start: 0.8476 (mttp) cc_final: 0.8047 (mttp) REVERT: C 535 TYR cc_start: 0.8358 (m-80) cc_final: 0.7750 (m-80) REVERT: C 538 GLN cc_start: 0.8116 (tt0) cc_final: 0.7723 (tt0) REVERT: C 542 MET cc_start: 0.6794 (tpp) cc_final: 0.6579 (tpp) REVERT: C 543 VAL cc_start: 0.8701 (p) cc_final: 0.7720 (t) REVERT: E 939 TYR cc_start: 0.7318 (m-10) cc_final: 0.7047 (m-10) REVERT: E 985 TYR cc_start: 0.7845 (t80) cc_final: 0.7131 (t80) REVERT: E 992 TYR cc_start: 0.7525 (t80) cc_final: 0.7159 (t80) REVERT: E 997 MET cc_start: 0.7544 (mmt) cc_final: 0.6953 (mmt) REVERT: E 1059 GLN cc_start: 0.8233 (mm110) cc_final: 0.7827 (mm110) REVERT: E 1064 ASP cc_start: 0.7492 (p0) cc_final: 0.7186 (t0) REVERT: E 1095 LEU cc_start: 0.8483 (mt) cc_final: 0.8216 (mt) REVERT: E 1103 ASP cc_start: 0.8068 (m-30) cc_final: 0.7789 (m-30) REVERT: E 1115 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8512 (tm-30) REVERT: E 1230 GLU cc_start: 0.8699 (mp0) cc_final: 0.8421 (pm20) REVERT: E 1241 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8319 (mmtm) REVERT: E 1264 GLN cc_start: 0.7605 (mp-120) cc_final: 0.7342 (tp40) outliers start: 1 outliers final: 0 residues processed: 790 average time/residue: 0.3727 time to fit residues: 441.2452 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 : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 205 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 422 HIS A 530 HIS A 721 HIS A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 282 HIS ** B 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 196 HIS C 291 ASN C 380 HIS E1015 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097287 restraints weight = 43837.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101198 restraints weight = 22036.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103293 restraints weight = 11957.839| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23074 Z= 0.158 Angle : 0.698 27.192 31629 Z= 0.343 Chirality : 0.046 0.315 3593 Planarity : 0.005 0.056 3753 Dihedral : 14.367 79.682 3988 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2567 helix: 0.28 (0.19), residues: 765 sheet: -1.35 (0.20), residues: 621 loop : -1.90 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 117 HIS 0.011 0.001 HIS A1238 PHE 0.032 0.002 PHE B 450 TYR 0.020 0.002 TYR E1120 ARG 0.012 0.001 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 855) hydrogen bonds : angle 5.45473 ( 2328) metal coordination : bond 0.01555 ( 3) metal coordination : angle 14.32899 ( 9) covalent geometry : bond 0.00326 (23071) covalent geometry : angle 0.65448 (31620) *********************** 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 779 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 777 time to evaluate : 2.387 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: 0.7283 (ttp-170) cc_final: 0.6876 (ptt-90) REVERT: A 34 LEU cc_start: 0.8311 (mt) cc_final: 0.8054 (mm) REVERT: A 43 GLU cc_start: 0.7506 (tt0) cc_final: 0.7261 (tp30) REVERT: A 52 LYS cc_start: 0.9105 (mmpt) cc_final: 0.8845 (mmtm) REVERT: A 80 GLN cc_start: 0.8583 (mt0) cc_final: 0.8285 (mt0) REVERT: A 121 GLN cc_start: 0.8276 (mp10) cc_final: 0.7861 (mp10) REVERT: A 122 GLU cc_start: 0.7801 (tp30) cc_final: 0.7561 (tp30) REVERT: A 136 MET cc_start: 0.7876 (pmm) cc_final: 0.7342 (pmm) REVERT: A 189 LEU cc_start: 0.8813 (tp) cc_final: 0.8439 (tp) REVERT: A 193 ASP cc_start: 0.8345 (t0) cc_final: 0.8050 (m-30) REVERT: A 205 GLN cc_start: 0.8116 (mt0) cc_final: 0.7911 (mt0) REVERT: A 257 GLN cc_start: 0.8845 (tt0) cc_final: 0.8600 (tt0) REVERT: A 259 LYS cc_start: 0.8547 (tppt) cc_final: 0.8196 (tppt) REVERT: A 274 LEU cc_start: 0.8864 (pp) cc_final: 0.8651 (tp) REVERT: A 286 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7779 (tt0) REVERT: A 327 ASN cc_start: 0.8453 (m-40) cc_final: 0.8189 (m-40) REVERT: A 337 SER cc_start: 0.7553 (m) cc_final: 0.7252 (t) REVERT: A 377 THR cc_start: 0.8114 (p) cc_final: 0.7828 (p) REVERT: A 378 ASP cc_start: 0.7504 (m-30) cc_final: 0.7127 (m-30) REVERT: A 414 CYS cc_start: 0.7734 (p) cc_final: 0.7527 (p) REVERT: A 443 ASP cc_start: 0.7742 (t0) cc_final: 0.7493 (t0) REVERT: A 452 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8140 (tppp) REVERT: A 474 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8062 (mmtt) REVERT: A 476 CYS cc_start: 0.7545 (m) cc_final: 0.7249 (t) REVERT: A 487 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7986 (mmtt) REVERT: A 489 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7959 (tp-100) REVERT: A 573 LEU cc_start: 0.8073 (tp) cc_final: 0.7721 (mp) REVERT: A 580 LYS cc_start: 0.8329 (tmmt) cc_final: 0.7827 (tmmt) REVERT: A 622 LEU cc_start: 0.8442 (mp) cc_final: 0.8223 (mt) REVERT: A 660 CYS cc_start: 0.8445 (t) cc_final: 0.7712 (p) REVERT: A 661 GLN cc_start: 0.8492 (pm20) cc_final: 0.7896 (pm20) REVERT: A 677 LEU cc_start: 0.8688 (tp) cc_final: 0.8323 (tp) REVERT: A 689 ARG cc_start: 0.7707 (tmt-80) cc_final: 0.7078 (tmt-80) REVERT: A 725 VAL cc_start: 0.8680 (t) cc_final: 0.8471 (t) REVERT: A 728 GLN cc_start: 0.8361 (tp40) cc_final: 0.8005 (tp40) REVERT: A 731 LYS cc_start: 0.8835 (mmpt) cc_final: 0.8125 (tptp) REVERT: A 737 MET cc_start: 0.6476 (pmm) cc_final: 0.5998 (pmm) REVERT: A 739 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8245 (ptmm) REVERT: A 740 GLU cc_start: 0.8360 (mp0) cc_final: 0.7486 (mp0) REVERT: A 744 CYS cc_start: 0.8107 (t) cc_final: 0.7734 (p) REVERT: A 745 MET cc_start: 0.8468 (ttp) cc_final: 0.8113 (ttp) REVERT: A 753 ASN cc_start: 0.8633 (m-40) cc_final: 0.8359 (m-40) REVERT: A 767 VAL cc_start: 0.8664 (m) cc_final: 0.8168 (t) REVERT: A 771 ILE cc_start: 0.8985 (mm) cc_final: 0.8777 (mm) REVERT: A 834 LYS cc_start: 0.7320 (mttm) cc_final: 0.6834 (mttm) REVERT: A 882 LEU cc_start: 0.8845 (mt) cc_final: 0.8473 (tt) REVERT: A 909 LYS cc_start: 0.8378 (mppt) cc_final: 0.7994 (mmtm) REVERT: A 913 ASP cc_start: 0.8300 (t0) cc_final: 0.7874 (t0) REVERT: A 922 ASN cc_start: 0.8654 (m110) cc_final: 0.8304 (m110) REVERT: A 924 LEU cc_start: 0.8867 (mp) cc_final: 0.8562 (mt) REVERT: A 973 GLU cc_start: 0.8494 (mp0) cc_final: 0.8115 (mp0) REVERT: A 985 TYR cc_start: 0.7431 (t80) cc_final: 0.7098 (t80) REVERT: A 1001 MET cc_start: 0.6397 (mmp) cc_final: 0.6078 (mmp) REVERT: A 1008 MET cc_start: 0.7344 (ppp) cc_final: 0.6900 (ppp) REVERT: A 1029 LYS cc_start: 0.7727 (mptt) cc_final: 0.7460 (mmmm) REVERT: A 1121 MET cc_start: 0.8432 (mmp) cc_final: 0.7730 (mmt) REVERT: A 1125 ASP cc_start: 0.7825 (t0) cc_final: 0.7596 (m-30) REVERT: A 1228 ASN cc_start: 0.9013 (m110) cc_final: 0.8795 (m-40) REVERT: A 1235 GLU cc_start: 0.8464 (mp0) cc_final: 0.8108 (mp0) REVERT: A 1254 GLU cc_start: 0.8582 (tt0) cc_final: 0.8269 (tm-30) REVERT: B 7 GLU cc_start: 0.7833 (pt0) cc_final: 0.7049 (pm20) REVERT: B 98 LEU cc_start: 0.8144 (tp) cc_final: 0.7914 (tp) REVERT: B 144 LYS cc_start: 0.7168 (tptp) cc_final: 0.6847 (tptp) REVERT: B 150 MET cc_start: 0.7776 (ptp) cc_final: 0.6833 (ppp) REVERT: B 151 CYS cc_start: 0.7837 (t) cc_final: 0.7445 (t) REVERT: B 152 LEU cc_start: 0.9070 (mt) cc_final: 0.8777 (mt) REVERT: B 156 ASN cc_start: 0.8372 (p0) cc_final: 0.8059 (p0) REVERT: B 184 ASP cc_start: 0.7306 (t0) cc_final: 0.7001 (t0) REVERT: B 237 LYS cc_start: 0.6447 (ttpt) cc_final: 0.5889 (ttpt) REVERT: B 239 TYR cc_start: 0.7724 (p90) cc_final: 0.7394 (p90) REVERT: B 316 MET cc_start: 0.6888 (mtp) cc_final: 0.6487 (mtp) REVERT: B 328 TRP cc_start: 0.8120 (m-10) cc_final: 0.7024 (m100) REVERT: B 367 LEU cc_start: 0.7955 (tp) cc_final: 0.7624 (tp) REVERT: B 377 GLU cc_start: 0.8008 (tt0) cc_final: 0.6965 (tt0) REVERT: B 381 GLU cc_start: 0.7821 (tp30) cc_final: 0.7536 (tp30) REVERT: B 433 ARG cc_start: 0.8260 (ptp-110) cc_final: 0.7913 (ptp-110) REVERT: B 462 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6832 (mtt90) REVERT: B 473 ASN cc_start: 0.8677 (t0) cc_final: 0.8379 (t0) REVERT: B 474 PHE cc_start: 0.8262 (t80) cc_final: 0.7995 (t80) REVERT: B 597 ILE cc_start: 0.8007 (mt) cc_final: 0.7718 (mp) REVERT: B 612 PHE cc_start: 0.7986 (t80) cc_final: 0.7548 (t80) REVERT: B 618 THR cc_start: 0.6860 (m) cc_final: 0.6631 (m) REVERT: B 619 GLN cc_start: 0.7428 (tp-100) cc_final: 0.7212 (tp-100) REVERT: B 625 ASN cc_start: 0.8433 (t0) cc_final: 0.7973 (t0) REVERT: B 628 PHE cc_start: 0.7301 (m-80) cc_final: 0.6682 (m-80) REVERT: B 632 VAL cc_start: 0.7259 (m) cc_final: 0.7057 (m) REVERT: B 638 TRP cc_start: 0.7828 (p-90) cc_final: 0.7372 (p-90) REVERT: B 691 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7539 (ptpt) REVERT: B 742 VAL cc_start: 0.8405 (t) cc_final: 0.7985 (p) REVERT: B 817 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7828 (mtpp) REVERT: C 17 LEU cc_start: 0.8935 (mt) cc_final: 0.8432 (mt) REVERT: C 25 GLN cc_start: 0.8758 (mt0) cc_final: 0.8516 (mt0) REVERT: C 28 GLU cc_start: 0.8615 (tt0) cc_final: 0.7098 (tm-30) REVERT: C 32 GLN cc_start: 0.7521 (mp10) cc_final: 0.7080 (mp10) REVERT: C 40 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8282 (mmtt) REVERT: C 59 ASP cc_start: 0.8378 (m-30) cc_final: 0.8089 (m-30) REVERT: C 69 ARG cc_start: 0.8088 (ptp-170) cc_final: 0.7158 (ptp-170) REVERT: C 87 ILE cc_start: 0.8249 (mm) cc_final: 0.7983 (mp) REVERT: C 98 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7575 (tpp80) REVERT: C 153 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6495 (tm-30) REVERT: C 154 GLN cc_start: 0.7673 (tt0) cc_final: 0.6891 (tt0) REVERT: C 170 MET cc_start: 0.7372 (mmp) cc_final: 0.7155 (mmp) REVERT: C 219 THR cc_start: 0.7345 (p) cc_final: 0.7135 (m) REVERT: C 244 GLU cc_start: 0.7221 (mp0) cc_final: 0.6892 (mp0) REVERT: C 259 ASN cc_start: 0.8995 (t0) cc_final: 0.8794 (t0) REVERT: C 285 MET cc_start: 0.8115 (mmm) cc_final: 0.7667 (mmm) REVERT: C 295 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 297 ASP cc_start: 0.8103 (m-30) cc_final: 0.7652 (m-30) REVERT: C 300 GLN cc_start: 0.8636 (pp30) cc_final: 0.8195 (pp30) REVERT: C 330 GLU cc_start: 0.8585 (mp0) cc_final: 0.8165 (mp0) REVERT: C 348 LEU cc_start: 0.8694 (mp) cc_final: 0.8475 (mp) REVERT: C 368 ASP cc_start: 0.7740 (m-30) cc_final: 0.7527 (m-30) REVERT: C 402 ARG cc_start: 0.8152 (tpt-90) cc_final: 0.7850 (tpt-90) REVERT: C 421 GLU cc_start: 0.7019 (mp0) cc_final: 0.6807 (mp0) REVERT: C 428 VAL cc_start: 0.8504 (t) cc_final: 0.8241 (m) REVERT: C 434 GLU cc_start: 0.7713 (mp0) cc_final: 0.7078 (mp0) REVERT: C 440 GLU cc_start: 0.6925 (pm20) cc_final: 0.6436 (pm20) REVERT: C 444 GLN cc_start: 0.8503 (mp10) cc_final: 0.8228 (mp10) REVERT: C 445 ASP cc_start: 0.7740 (m-30) cc_final: 0.7469 (m-30) REVERT: C 459 GLU cc_start: 0.7771 (pm20) cc_final: 0.7192 (pm20) REVERT: C 464 GLU cc_start: 0.8454 (mp0) cc_final: 0.7766 (mp0) REVERT: C 507 ARG cc_start: 0.8268 (tmm-80) cc_final: 0.8057 (tmm-80) REVERT: C 508 ILE cc_start: 0.8505 (tp) cc_final: 0.8294 (tp) REVERT: C 512 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7064 (mt-10) REVERT: C 518 ILE cc_start: 0.8629 (mt) cc_final: 0.8386 (mt) REVERT: C 529 TYR cc_start: 0.8096 (t80) cc_final: 0.7633 (t80) REVERT: C 532 LYS cc_start: 0.8486 (mttp) cc_final: 0.8160 (mttp) REVERT: C 535 TYR cc_start: 0.8375 (m-80) cc_final: 0.7757 (m-80) REVERT: C 538 GLN cc_start: 0.7966 (tt0) cc_final: 0.7584 (tt0) REVERT: C 542 MET cc_start: 0.6875 (tpp) cc_final: 0.6504 (tpp) REVERT: C 543 VAL cc_start: 0.8597 (p) cc_final: 0.7627 (t) REVERT: E 935 THR cc_start: 0.5005 (p) cc_final: 0.4732 (p) REVERT: E 939 TYR cc_start: 0.7424 (m-10) cc_final: 0.7124 (m-10) REVERT: E 983 GLN cc_start: 0.6594 (pp30) cc_final: 0.6147 (pp30) REVERT: E 985 TYR cc_start: 0.7854 (t80) cc_final: 0.7180 (t80) REVERT: E 992 TYR cc_start: 0.7613 (t80) cc_final: 0.6934 (t80) REVERT: E 1008 MET cc_start: 0.7898 (mmp) cc_final: 0.6891 (mmp) REVERT: E 1055 LYS cc_start: 0.8933 (tppt) cc_final: 0.8702 (tppt) REVERT: E 1059 GLN cc_start: 0.8185 (mm110) cc_final: 0.7880 (mm110) REVERT: E 1064 ASP cc_start: 0.7369 (p0) cc_final: 0.7169 (t0) REVERT: E 1106 GLU cc_start: 0.8285 (pt0) cc_final: 0.8042 (pt0) REVERT: E 1110 LYS cc_start: 0.8863 (tttt) cc_final: 0.8417 (tptt) REVERT: E 1115 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8545 (tm-30) REVERT: E 1120 TYR cc_start: 0.8333 (t80) cc_final: 0.7923 (t80) REVERT: E 1241 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8358 (mmtm) outliers start: 2 outliers final: 0 residues processed: 778 average time/residue: 0.3823 time to fit residues: 446.4428 Evaluate side-chains 705 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 185 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 221 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 321 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 529 HIS ** A 703 GLN ** 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 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN B 776 GLN C 125 GLN C 291 ASN E1100 ASN E1264 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.123339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097052 restraints weight = 44158.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101611 restraints weight = 22213.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103536 restraints weight = 11720.294| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23074 Z= 0.138 Angle : 0.684 24.019 31629 Z= 0.336 Chirality : 0.045 0.230 3593 Planarity : 0.004 0.049 3753 Dihedral : 14.193 79.193 3988 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2567 helix: 0.34 (0.19), residues: 766 sheet: -1.20 (0.20), residues: 603 loop : -1.85 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 24 HIS 0.009 0.001 HIS B 57 PHE 0.027 0.002 PHE A1009 TYR 0.025 0.001 TYR A 917 ARG 0.007 0.001 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 855) hydrogen bonds : angle 5.28424 ( 2328) metal coordination : bond 0.01230 ( 3) metal coordination : angle 13.54055 ( 9) covalent geometry : bond 0.00294 (23071) covalent geometry : angle 0.64488 (31620) *********************** 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 764 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 764 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7293 (ttp-170) cc_final: 0.6883 (ptt-90) REVERT: A 43 GLU cc_start: 0.7525 (tt0) cc_final: 0.7234 (tp30) REVERT: A 52 LYS cc_start: 0.9083 (mmpt) cc_final: 0.8855 (mmtm) REVERT: A 114 VAL cc_start: 0.7456 (p) cc_final: 0.7207 (t) REVERT: A 121 GLN cc_start: 0.8355 (mp10) cc_final: 0.7804 (mp10) REVERT: A 122 GLU cc_start: 0.7745 (tp30) cc_final: 0.7365 (tp30) REVERT: A 131 GLN cc_start: 0.8428 (mp10) cc_final: 0.8174 (mp10) REVERT: A 135 MET cc_start: 0.7153 (tpt) cc_final: 0.6904 (tpt) REVERT: A 136 MET cc_start: 0.7855 (pmm) cc_final: 0.7443 (pmm) REVERT: A 189 LEU cc_start: 0.8748 (tp) cc_final: 0.8289 (tp) REVERT: A 285 ASP cc_start: 0.8344 (t0) cc_final: 0.8087 (t0) REVERT: A 286 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7797 (tt0) REVERT: A 337 SER cc_start: 0.7527 (m) cc_final: 0.7225 (t) REVERT: A 377 THR cc_start: 0.8124 (p) cc_final: 0.7800 (p) REVERT: A 378 ASP cc_start: 0.7538 (m-30) cc_final: 0.7134 (m-30) REVERT: A 427 VAL cc_start: 0.7903 (p) cc_final: 0.7440 (t) REVERT: A 443 ASP cc_start: 0.7700 (t0) cc_final: 0.7471 (t0) REVERT: A 474 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8052 (mmtt) REVERT: A 476 CYS cc_start: 0.7646 (m) cc_final: 0.7331 (t) REVERT: A 487 LYS cc_start: 0.8245 (mmmt) cc_final: 0.8012 (mmtt) REVERT: A 573 LEU cc_start: 0.8032 (tp) cc_final: 0.7717 (mp) REVERT: A 580 LYS cc_start: 0.8293 (tmmt) cc_final: 0.7803 (tmmt) REVERT: A 622 LEU cc_start: 0.8528 (mp) cc_final: 0.8216 (mt) REVERT: A 660 CYS cc_start: 0.8341 (t) cc_final: 0.7622 (p) REVERT: A 661 GLN cc_start: 0.8440 (pm20) cc_final: 0.7907 (pm20) REVERT: A 677 LEU cc_start: 0.8623 (tp) cc_final: 0.8349 (tp) REVERT: A 689 ARG cc_start: 0.7612 (tmt-80) cc_final: 0.6992 (tmt-80) REVERT: A 725 VAL cc_start: 0.8587 (t) cc_final: 0.8385 (t) REVERT: A 728 GLN cc_start: 0.8290 (tp40) cc_final: 0.7985 (tp40) REVERT: A 731 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8096 (tptp) REVERT: A 737 MET cc_start: 0.6218 (pmm) cc_final: 0.5890 (pmm) REVERT: A 739 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8420 (ptmm) REVERT: A 740 GLU cc_start: 0.8308 (mp0) cc_final: 0.7669 (mp0) REVERT: A 745 MET cc_start: 0.8423 (ttp) cc_final: 0.8092 (ttp) REVERT: A 753 ASN cc_start: 0.8745 (m-40) cc_final: 0.8346 (m-40) REVERT: A 767 VAL cc_start: 0.8686 (m) cc_final: 0.8174 (t) REVERT: A 794 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8452 (mmtt) REVERT: A 823 MET cc_start: 0.8415 (ptm) cc_final: 0.8143 (ptm) REVERT: A 827 MET cc_start: 0.8785 (ppp) cc_final: 0.8316 (ppp) REVERT: A 833 HIS cc_start: 0.7663 (m90) cc_final: 0.7340 (m90) REVERT: A 834 LYS cc_start: 0.7406 (mttm) cc_final: 0.6931 (mttm) REVERT: A 850 GLU cc_start: 0.8159 (mp0) cc_final: 0.7728 (mp0) REVERT: A 860 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 882 LEU cc_start: 0.8859 (mt) cc_final: 0.8453 (tt) REVERT: A 893 HIS cc_start: 0.8290 (m90) cc_final: 0.7976 (m90) REVERT: A 913 ASP cc_start: 0.8283 (t0) cc_final: 0.7898 (t0) REVERT: A 924 LEU cc_start: 0.8809 (mp) cc_final: 0.8536 (mt) REVERT: A 985 TYR cc_start: 0.7459 (t80) cc_final: 0.7150 (t80) REVERT: A 1008 MET cc_start: 0.7550 (ppp) cc_final: 0.7157 (ppp) REVERT: A 1089 TRP cc_start: 0.7583 (m100) cc_final: 0.7380 (m100) REVERT: A 1112 SER cc_start: 0.8706 (m) cc_final: 0.8503 (p) REVERT: A 1121 MET cc_start: 0.8461 (mmp) cc_final: 0.7754 (mmt) REVERT: A 1125 ASP cc_start: 0.7868 (t0) cc_final: 0.7619 (m-30) REVERT: A 1228 ASN cc_start: 0.9043 (m110) cc_final: 0.8725 (m-40) REVERT: A 1254 GLU cc_start: 0.8618 (tt0) cc_final: 0.8292 (tm-30) REVERT: B 32 LEU cc_start: 0.7197 (mt) cc_final: 0.6780 (mt) REVERT: B 55 ASN cc_start: 0.8175 (m110) cc_final: 0.7909 (m110) REVERT: B 91 GLU cc_start: 0.7349 (pt0) cc_final: 0.6835 (pt0) REVERT: B 98 LEU cc_start: 0.8388 (tp) cc_final: 0.7831 (tp) REVERT: B 144 LYS cc_start: 0.7195 (tptp) cc_final: 0.6887 (tptp) REVERT: B 150 MET cc_start: 0.7759 (ptp) cc_final: 0.6907 (ppp) REVERT: B 151 CYS cc_start: 0.7872 (t) cc_final: 0.7404 (t) REVERT: B 152 LEU cc_start: 0.9064 (mt) cc_final: 0.8740 (mt) REVERT: B 156 ASN cc_start: 0.8407 (p0) cc_final: 0.8096 (p0) REVERT: B 184 ASP cc_start: 0.7301 (t0) cc_final: 0.6757 (t0) REVERT: B 237 LYS cc_start: 0.6478 (ttpt) cc_final: 0.5925 (ttpt) REVERT: B 239 TYR cc_start: 0.7707 (p90) cc_final: 0.7331 (p90) REVERT: B 292 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7377 (tp-100) REVERT: B 316 MET cc_start: 0.6806 (mtp) cc_final: 0.6266 (mtp) REVERT: B 328 TRP cc_start: 0.8152 (m-10) cc_final: 0.7009 (m100) REVERT: B 377 GLU cc_start: 0.8007 (tt0) cc_final: 0.7034 (tt0) REVERT: B 381 GLU cc_start: 0.7830 (tp30) cc_final: 0.7505 (tp30) REVERT: B 382 ILE cc_start: 0.8357 (mp) cc_final: 0.8128 (mp) REVERT: B 393 ASP cc_start: 0.7655 (m-30) cc_final: 0.7258 (m-30) REVERT: B 415 PHE cc_start: 0.6428 (m-80) cc_final: 0.6180 (m-80) REVERT: B 430 GLU cc_start: 0.8198 (pm20) cc_final: 0.7461 (pm20) REVERT: B 433 ARG cc_start: 0.8180 (ptp-110) cc_final: 0.7819 (ptp-170) REVERT: B 435 GLN cc_start: 0.8744 (pp30) cc_final: 0.8485 (pp30) REVERT: B 450 PHE cc_start: 0.8591 (m-10) cc_final: 0.8273 (m-10) REVERT: B 462 ARG cc_start: 0.7284 (mtt90) cc_final: 0.6807 (mtt90) REVERT: B 473 ASN cc_start: 0.8705 (t0) cc_final: 0.8445 (t0) REVERT: B 474 PHE cc_start: 0.8277 (t80) cc_final: 0.7974 (t80) REVERT: B 586 CYS cc_start: 0.8219 (p) cc_final: 0.7978 (p) REVERT: B 612 PHE cc_start: 0.7894 (t80) cc_final: 0.7582 (t80) REVERT: B 625 ASN cc_start: 0.8420 (t0) cc_final: 0.7919 (t0) REVERT: B 638 TRP cc_start: 0.7838 (p-90) cc_final: 0.7430 (p-90) REVERT: B 691 LYS cc_start: 0.8137 (ptpp) cc_final: 0.7555 (ptpt) REVERT: B 742 VAL cc_start: 0.8425 (t) cc_final: 0.8018 (p) REVERT: B 812 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 817 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7811 (mtpp) REVERT: C 17 LEU cc_start: 0.8934 (mt) cc_final: 0.8422 (mt) REVERT: C 25 GLN cc_start: 0.8795 (mt0) cc_final: 0.8515 (mt0) REVERT: C 28 GLU cc_start: 0.8622 (tt0) cc_final: 0.7735 (tt0) REVERT: C 31 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7853 (mt-10) REVERT: C 32 GLN cc_start: 0.7489 (mp10) cc_final: 0.7288 (mp10) REVERT: C 40 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8315 (mmtt) REVERT: C 58 VAL cc_start: 0.8381 (t) cc_final: 0.8069 (p) REVERT: C 59 ASP cc_start: 0.8411 (m-30) cc_final: 0.7908 (m-30) REVERT: C 69 ARG cc_start: 0.8091 (ptp-170) cc_final: 0.7179 (ptp-170) REVERT: C 143 ASP cc_start: 0.7734 (t0) cc_final: 0.7487 (t70) REVERT: C 150 HIS cc_start: 0.7088 (t70) cc_final: 0.6879 (t70) REVERT: C 153 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6622 (tm-30) REVERT: C 154 GLN cc_start: 0.7834 (tt0) cc_final: 0.6924 (tt0) REVERT: C 170 MET cc_start: 0.7310 (mmp) cc_final: 0.7065 (mmp) REVERT: C 235 MET cc_start: 0.7070 (mmm) cc_final: 0.6645 (mmm) REVERT: C 244 GLU cc_start: 0.7126 (mp0) cc_final: 0.6849 (mp0) REVERT: C 259 ASN cc_start: 0.9008 (t0) cc_final: 0.8797 (t0) REVERT: C 285 MET cc_start: 0.7980 (mmm) cc_final: 0.7581 (mmm) REVERT: C 294 LEU cc_start: 0.8084 (mp) cc_final: 0.7681 (mp) REVERT: C 297 ASP cc_start: 0.8004 (m-30) cc_final: 0.7574 (m-30) REVERT: C 300 GLN cc_start: 0.8520 (pp30) cc_final: 0.8048 (pp30) REVERT: C 330 GLU cc_start: 0.8561 (mp0) cc_final: 0.8154 (mp0) REVERT: C 347 GLU cc_start: 0.8119 (mp0) cc_final: 0.7837 (mp0) REVERT: C 348 LEU cc_start: 0.8684 (mp) cc_final: 0.8437 (mp) REVERT: C 368 ASP cc_start: 0.7828 (m-30) cc_final: 0.7577 (m-30) REVERT: C 391 MET cc_start: 0.7219 (ppp) cc_final: 0.6869 (ppp) REVERT: C 402 ARG cc_start: 0.8077 (tpt-90) cc_final: 0.7799 (tpt-90) REVERT: C 428 VAL cc_start: 0.8512 (t) cc_final: 0.8273 (m) REVERT: C 434 GLU cc_start: 0.7734 (mp0) cc_final: 0.7028 (mp0) REVERT: C 440 GLU cc_start: 0.7031 (pm20) cc_final: 0.6405 (pm20) REVERT: C 441 ASP cc_start: 0.6885 (t0) cc_final: 0.6574 (t0) REVERT: C 444 GLN cc_start: 0.8448 (mp10) cc_final: 0.7383 (mp10) REVERT: C 445 ASP cc_start: 0.7878 (m-30) cc_final: 0.7407 (m-30) REVERT: C 459 GLU cc_start: 0.7825 (pm20) cc_final: 0.7575 (pm20) REVERT: C 504 GLU cc_start: 0.8124 (tp30) cc_final: 0.7433 (tp30) REVERT: C 507 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7906 (tmm-80) REVERT: C 512 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6957 (mt-10) REVERT: C 518 ILE cc_start: 0.8540 (mt) cc_final: 0.8339 (mt) REVERT: C 529 TYR cc_start: 0.8016 (t80) cc_final: 0.7646 (t80) REVERT: C 532 LYS cc_start: 0.8453 (mttp) cc_final: 0.8128 (mttp) REVERT: C 535 TYR cc_start: 0.8362 (m-80) cc_final: 0.7504 (m-10) REVERT: C 538 GLN cc_start: 0.8025 (tt0) cc_final: 0.7576 (tt0) REVERT: C 542 MET cc_start: 0.6945 (tpp) cc_final: 0.6525 (tpp) REVERT: C 543 VAL cc_start: 0.8562 (p) cc_final: 0.7643 (t) REVERT: E 939 TYR cc_start: 0.7469 (m-10) cc_final: 0.7185 (m-10) REVERT: E 983 GLN cc_start: 0.6824 (pp30) cc_final: 0.6417 (pp30) REVERT: E 985 TYR cc_start: 0.7865 (t80) cc_final: 0.7168 (t80) REVERT: E 992 TYR cc_start: 0.7688 (t80) cc_final: 0.6980 (t80) REVERT: E 997 MET cc_start: 0.7112 (mmt) cc_final: 0.6829 (mmt) REVERT: E 1056 LEU cc_start: 0.8590 (mt) cc_final: 0.8389 (mt) REVERT: E 1094 ARG cc_start: 0.8045 (pmt-80) cc_final: 0.7420 (pmt-80) REVERT: E 1095 LEU cc_start: 0.8431 (mt) cc_final: 0.8167 (mt) REVERT: E 1110 LYS cc_start: 0.8906 (tttt) cc_final: 0.8508 (tptt) REVERT: E 1115 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8521 (pp20) REVERT: E 1241 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8298 (mmtm) REVERT: E 1264 GLN cc_start: 0.7442 (mp-120) cc_final: 0.7152 (tp40) outliers start: 0 outliers final: 0 residues processed: 764 average time/residue: 0.3765 time to fit residues: 428.9463 Evaluate side-chains 694 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 202 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A 932 GLN A 969 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 776 GLN B 822 ASN C 147 GLN C 190 HIS C 291 ASN E1030 GLN ** E1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097210 restraints weight = 44094.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101835 restraints weight = 21895.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103738 restraints weight = 11478.456| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23074 Z= 0.140 Angle : 0.682 23.032 31629 Z= 0.336 Chirality : 0.045 0.226 3593 Planarity : 0.004 0.047 3753 Dihedral : 14.075 79.197 3988 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2567 helix: 0.26 (0.18), residues: 789 sheet: -1.06 (0.20), residues: 613 loop : -1.90 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 142 HIS 0.009 0.001 HIS B 57 PHE 0.032 0.002 PHE A1009 TYR 0.027 0.001 TYR A 917 ARG 0.010 0.001 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 855) hydrogen bonds : angle 5.16650 ( 2328) metal coordination : bond 0.01123 ( 3) metal coordination : angle 13.28043 ( 9) covalent geometry : bond 0.00302 (23071) covalent geometry : angle 0.64403 (31620) *********************** 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 776 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 775 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6970 (ttp80) REVERT: A 43 GLU cc_start: 0.7627 (tt0) cc_final: 0.7141 (tp30) REVERT: A 50 GLU cc_start: 0.6743 (mp0) cc_final: 0.6540 (mp0) REVERT: A 52 LYS cc_start: 0.9112 (mmpt) cc_final: 0.8650 (tmtt) REVERT: A 75 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 80 GLN cc_start: 0.8586 (mt0) cc_final: 0.8349 (mt0) REVERT: A 114 VAL cc_start: 0.7475 (p) cc_final: 0.7240 (t) REVERT: A 121 GLN cc_start: 0.8295 (mp10) cc_final: 0.7837 (mp10) REVERT: A 122 GLU cc_start: 0.7788 (tp30) cc_final: 0.7498 (tp30) REVERT: A 128 THR cc_start: 0.9105 (p) cc_final: 0.8764 (p) REVERT: A 131 GLN cc_start: 0.8497 (mp10) cc_final: 0.8247 (mp10) REVERT: A 136 MET cc_start: 0.7857 (pmm) cc_final: 0.7472 (pmm) REVERT: A 189 LEU cc_start: 0.8730 (tp) cc_final: 0.8244 (tp) REVERT: A 205 GLN cc_start: 0.8180 (mt0) cc_final: 0.7956 (mt0) REVERT: A 257 GLN cc_start: 0.8726 (tt0) cc_final: 0.8498 (tt0) REVERT: A 261 ASN cc_start: 0.7773 (m110) cc_final: 0.7388 (t0) REVERT: A 285 ASP cc_start: 0.8313 (t0) cc_final: 0.8015 (t0) REVERT: A 286 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7761 (tt0) REVERT: A 337 SER cc_start: 0.7531 (m) cc_final: 0.7220 (t) REVERT: A 377 THR cc_start: 0.8107 (p) cc_final: 0.7869 (p) REVERT: A 378 ASP cc_start: 0.7506 (m-30) cc_final: 0.7183 (m-30) REVERT: A 427 VAL cc_start: 0.7863 (p) cc_final: 0.7408 (t) REVERT: A 443 ASP cc_start: 0.7776 (t0) cc_final: 0.7385 (t0) REVERT: A 446 ASN cc_start: 0.8706 (m110) cc_final: 0.8490 (m110) REVERT: A 474 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8115 (mmtt) REVERT: A 561 CYS cc_start: 0.8469 (t) cc_final: 0.7871 (m) REVERT: A 573 LEU cc_start: 0.8075 (tp) cc_final: 0.7724 (mp) REVERT: A 580 LYS cc_start: 0.8286 (tmmt) cc_final: 0.7779 (tmmt) REVERT: A 610 THR cc_start: 0.8428 (p) cc_final: 0.7531 (p) REVERT: A 622 LEU cc_start: 0.8518 (mp) cc_final: 0.8211 (mt) REVERT: A 660 CYS cc_start: 0.8398 (t) cc_final: 0.7461 (p) REVERT: A 661 GLN cc_start: 0.8452 (pm20) cc_final: 0.7632 (pm20) REVERT: A 664 CYS cc_start: 0.8252 (t) cc_final: 0.7028 (t) REVERT: A 689 ARG cc_start: 0.7619 (tmt-80) cc_final: 0.7060 (ttt90) REVERT: A 696 ARG cc_start: 0.7400 (mtm180) cc_final: 0.7151 (mtp180) REVERT: A 731 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8142 (tptp) REVERT: A 739 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8309 (ttpt) REVERT: A 740 GLU cc_start: 0.8078 (mp0) cc_final: 0.7705 (mp0) REVERT: A 743 GLU cc_start: 0.8308 (pt0) cc_final: 0.8107 (pt0) REVERT: A 745 MET cc_start: 0.8429 (ttp) cc_final: 0.8156 (ttm) REVERT: A 753 ASN cc_start: 0.8762 (m-40) cc_final: 0.8436 (m-40) REVERT: A 767 VAL cc_start: 0.8671 (m) cc_final: 0.8148 (t) REVERT: A 827 MET cc_start: 0.8768 (ppp) cc_final: 0.8299 (ppp) REVERT: A 833 HIS cc_start: 0.7626 (m90) cc_final: 0.7352 (m90) REVERT: A 834 LYS cc_start: 0.7431 (mttm) cc_final: 0.6970 (mttm) REVERT: A 850 GLU cc_start: 0.7971 (mp0) cc_final: 0.7394 (mp0) REVERT: A 882 LEU cc_start: 0.8863 (mt) cc_final: 0.8594 (mt) REVERT: A 893 HIS cc_start: 0.8277 (m90) cc_final: 0.7988 (m90) REVERT: A 909 LYS cc_start: 0.8385 (mppt) cc_final: 0.7989 (mmtm) REVERT: A 913 ASP cc_start: 0.8323 (t0) cc_final: 0.7962 (t0) REVERT: A 920 PHE cc_start: 0.7957 (t80) cc_final: 0.7717 (t80) REVERT: A 924 LEU cc_start: 0.8965 (mp) cc_final: 0.8709 (mt) REVERT: A 985 TYR cc_start: 0.7429 (t80) cc_final: 0.7145 (t80) REVERT: A 1008 MET cc_start: 0.7607 (ppp) cc_final: 0.7305 (ppp) REVERT: A 1112 SER cc_start: 0.8694 (m) cc_final: 0.8224 (p) REVERT: A 1121 MET cc_start: 0.8479 (mmp) cc_final: 0.7834 (mmt) REVERT: A 1125 ASP cc_start: 0.7889 (t0) cc_final: 0.7641 (m-30) REVERT: A 1135 LYS cc_start: 0.7473 (pttp) cc_final: 0.7236 (pttp) REVERT: A 1228 ASN cc_start: 0.9071 (m110) cc_final: 0.8838 (m-40) REVERT: A 1239 ILE cc_start: 0.9105 (mm) cc_final: 0.8884 (mm) REVERT: A 1254 GLU cc_start: 0.8661 (tt0) cc_final: 0.8335 (tm-30) REVERT: A 1266 MET cc_start: 0.8064 (mpp) cc_final: 0.7840 (mpp) REVERT: B 32 LEU cc_start: 0.7605 (mt) cc_final: 0.7390 (mt) REVERT: B 55 ASN cc_start: 0.8137 (m110) cc_final: 0.7799 (m110) REVERT: B 91 GLU cc_start: 0.7634 (pt0) cc_final: 0.6973 (pt0) REVERT: B 98 LEU cc_start: 0.8325 (tp) cc_final: 0.8104 (tp) REVERT: B 144 LYS cc_start: 0.7199 (tptp) cc_final: 0.6903 (tptp) REVERT: B 150 MET cc_start: 0.7749 (ptp) cc_final: 0.7072 (ppp) REVERT: B 152 LEU cc_start: 0.8925 (mt) cc_final: 0.8570 (mt) REVERT: B 156 ASN cc_start: 0.8440 (p0) cc_final: 0.8145 (p0) REVERT: B 184 ASP cc_start: 0.7357 (t0) cc_final: 0.6874 (t0) REVERT: B 237 LYS cc_start: 0.6423 (ttpt) cc_final: 0.5833 (ttpt) REVERT: B 239 TYR cc_start: 0.7677 (p90) cc_final: 0.7298 (p90) REVERT: B 328 TRP cc_start: 0.8117 (m-10) cc_final: 0.6992 (m100) REVERT: B 377 GLU cc_start: 0.8063 (tt0) cc_final: 0.7040 (tt0) REVERT: B 393 ASP cc_start: 0.7617 (m-30) cc_final: 0.7316 (m-30) REVERT: B 415 PHE cc_start: 0.6437 (m-80) cc_final: 0.6147 (m-80) REVERT: B 430 GLU cc_start: 0.8168 (pm20) cc_final: 0.7541 (pm20) REVERT: B 433 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7621 (ptp-110) REVERT: B 462 ARG cc_start: 0.7315 (mtt90) cc_final: 0.6941 (mtt90) REVERT: B 473 ASN cc_start: 0.8726 (t0) cc_final: 0.8476 (t0) REVERT: B 474 PHE cc_start: 0.8290 (t80) cc_final: 0.7901 (t80) REVERT: B 566 HIS cc_start: 0.7381 (m90) cc_final: 0.7019 (m90) REVERT: B 586 CYS cc_start: 0.8223 (p) cc_final: 0.7965 (p) REVERT: B 612 PHE cc_start: 0.7898 (t80) cc_final: 0.7496 (t80) REVERT: B 619 GLN cc_start: 0.7273 (tp-100) cc_final: 0.7045 (tp-100) REVERT: B 625 ASN cc_start: 0.8423 (t0) cc_final: 0.7899 (t0) REVERT: B 636 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7517 (mtm-85) REVERT: B 638 TRP cc_start: 0.7846 (p-90) cc_final: 0.7437 (p-90) REVERT: B 691 LYS cc_start: 0.8201 (ptpp) cc_final: 0.7600 (ptpt) REVERT: B 742 VAL cc_start: 0.8465 (t) cc_final: 0.8037 (p) REVERT: B 788 LYS cc_start: 0.8543 (tptp) cc_final: 0.7934 (tppt) REVERT: B 817 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7649 (mtpp) REVERT: C 17 LEU cc_start: 0.8946 (mt) cc_final: 0.8479 (mt) REVERT: C 25 GLN cc_start: 0.8794 (mt0) cc_final: 0.8490 (mt0) REVERT: C 28 GLU cc_start: 0.8647 (tt0) cc_final: 0.7027 (tm-30) REVERT: C 31 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7849 (mt-10) REVERT: C 32 GLN cc_start: 0.7478 (mp10) cc_final: 0.6832 (mp10) REVERT: C 40 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8285 (mmtt) REVERT: C 69 ARG cc_start: 0.8090 (ptp-170) cc_final: 0.7211 (ptp-170) REVERT: C 77 LYS cc_start: 0.8420 (ptpt) cc_final: 0.8205 (ptpt) REVERT: C 153 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6584 (tm-30) REVERT: C 154 GLN cc_start: 0.7791 (tt0) cc_final: 0.6884 (tt0) REVERT: C 168 ILE cc_start: 0.8599 (tp) cc_final: 0.8313 (tp) REVERT: C 173 THR cc_start: 0.7677 (m) cc_final: 0.7466 (p) REVERT: C 235 MET cc_start: 0.6949 (mmm) cc_final: 0.6474 (mmm) REVERT: C 285 MET cc_start: 0.7990 (mmm) cc_final: 0.7609 (mmm) REVERT: C 294 LEU cc_start: 0.8075 (mp) cc_final: 0.7667 (mp) REVERT: C 295 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7389 (mt-10) REVERT: C 297 ASP cc_start: 0.8032 (m-30) cc_final: 0.7676 (m-30) REVERT: C 300 GLN cc_start: 0.8577 (pp30) cc_final: 0.8021 (pp30) REVERT: C 340 TYR cc_start: 0.8202 (m-10) cc_final: 0.7813 (m-10) REVERT: C 344 ASP cc_start: 0.8461 (m-30) cc_final: 0.8243 (m-30) REVERT: C 368 ASP cc_start: 0.7862 (m-30) cc_final: 0.7617 (m-30) REVERT: C 391 MET cc_start: 0.7049 (ppp) cc_final: 0.6566 (ppp) REVERT: C 402 ARG cc_start: 0.8075 (tpt-90) cc_final: 0.7837 (tpt-90) REVERT: C 416 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8067 (mmm-85) REVERT: C 440 GLU cc_start: 0.6981 (pm20) cc_final: 0.6476 (pm20) REVERT: C 441 ASP cc_start: 0.6962 (t0) cc_final: 0.6592 (t0) REVERT: C 444 GLN cc_start: 0.8446 (mp10) cc_final: 0.7351 (mp10) REVERT: C 445 ASP cc_start: 0.7826 (m-30) cc_final: 0.7466 (m-30) REVERT: C 459 GLU cc_start: 0.7877 (pm20) cc_final: 0.7462 (pm20) REVERT: C 464 GLU cc_start: 0.8469 (mp0) cc_final: 0.7876 (pm20) REVERT: C 504 GLU cc_start: 0.8139 (tp30) cc_final: 0.7812 (tp30) REVERT: C 507 ARG cc_start: 0.8285 (tmm-80) cc_final: 0.8049 (tmm-80) REVERT: C 508 ILE cc_start: 0.8428 (tp) cc_final: 0.8166 (tp) REVERT: C 533 ILE cc_start: 0.9118 (mp) cc_final: 0.8811 (tp) REVERT: C 535 TYR cc_start: 0.8331 (m-80) cc_final: 0.7708 (m-10) REVERT: C 538 GLN cc_start: 0.8047 (tt0) cc_final: 0.7495 (tt0) REVERT: C 542 MET cc_start: 0.6977 (tpp) cc_final: 0.6643 (tpp) REVERT: C 543 VAL cc_start: 0.8581 (p) cc_final: 0.7672 (t) REVERT: E 935 THR cc_start: 0.5070 (p) cc_final: 0.4773 (p) REVERT: E 939 TYR cc_start: 0.7519 (m-10) cc_final: 0.7249 (m-10) REVERT: E 983 GLN cc_start: 0.6966 (pp30) cc_final: 0.6522 (pp30) REVERT: E 985 TYR cc_start: 0.7927 (t80) cc_final: 0.7213 (t80) REVERT: E 992 TYR cc_start: 0.7669 (t80) cc_final: 0.6963 (t80) REVERT: E 996 LEU cc_start: 0.8083 (mm) cc_final: 0.7880 (mm) REVERT: E 997 MET cc_start: 0.7135 (mmt) cc_final: 0.6879 (mmt) REVERT: E 1008 MET cc_start: 0.8025 (mmp) cc_final: 0.7142 (mmp) REVERT: E 1094 ARG cc_start: 0.8096 (pmt-80) cc_final: 0.7547 (pmt-80) REVERT: E 1095 LEU cc_start: 0.8218 (mt) cc_final: 0.7988 (mt) REVERT: E 1110 LYS cc_start: 0.8914 (tttt) cc_final: 0.8604 (tptt) REVERT: E 1115 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8505 (pp20) REVERT: E 1120 TYR cc_start: 0.8456 (t80) cc_final: 0.7816 (t80) REVERT: E 1241 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8324 (mmtm) outliers start: 1 outliers final: 0 residues processed: 776 average time/residue: 0.3723 time to fit residues: 432.3811 Evaluate side-chains 699 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 699 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 142 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN C 291 ASN E 949 HIS E 969 ASN E1100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.095058 restraints weight = 43864.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099566 restraints weight = 22454.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101493 restraints weight = 11732.429| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23074 Z= 0.185 Angle : 0.722 22.691 31629 Z= 0.362 Chirality : 0.046 0.259 3593 Planarity : 0.005 0.050 3753 Dihedral : 14.053 79.710 3988 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2567 helix: 0.27 (0.18), residues: 775 sheet: -1.00 (0.21), residues: 608 loop : -1.92 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 433 HIS 0.005 0.001 HIS A 658 PHE 0.028 0.002 PHE A1009 TYR 0.022 0.002 TYR C 439 ARG 0.009 0.001 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 855) hydrogen bonds : angle 5.26513 ( 2328) metal coordination : bond 0.01330 ( 3) metal coordination : angle 12.72699 ( 9) covalent geometry : bond 0.00398 (23071) covalent geometry : angle 0.68981 (31620) *********************** 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 776 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 2.291 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: 0.7301 (ttp-170) cc_final: 0.6978 (ptt-90) REVERT: A 43 GLU cc_start: 0.7678 (tt0) cc_final: 0.7212 (tp30) REVERT: A 50 GLU cc_start: 0.6547 (mp0) cc_final: 0.6311 (mp0) REVERT: A 52 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8902 (mmtm) REVERT: A 75 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 80 GLN cc_start: 0.8686 (mt0) cc_final: 0.8363 (mt0) REVERT: A 121 GLN cc_start: 0.8353 (mp10) cc_final: 0.7816 (mp10) REVERT: A 122 GLU cc_start: 0.7765 (tp30) cc_final: 0.7364 (tp30) REVERT: A 131 GLN cc_start: 0.8530 (mp10) cc_final: 0.8283 (mp10) REVERT: A 135 MET cc_start: 0.7215 (tpt) cc_final: 0.6896 (tpt) REVERT: A 136 MET cc_start: 0.7894 (pmm) cc_final: 0.7502 (pmm) REVERT: A 189 LEU cc_start: 0.8706 (tp) cc_final: 0.8153 (tp) REVERT: A 205 GLN cc_start: 0.8234 (mt0) cc_final: 0.8007 (mt0) REVERT: A 224 TRP cc_start: 0.7511 (m100) cc_final: 0.7056 (m100) REVERT: A 230 LEU cc_start: 0.8507 (pt) cc_final: 0.8135 (pt) REVERT: A 258 ASP cc_start: 0.7836 (t70) cc_final: 0.7587 (t0) REVERT: A 261 ASN cc_start: 0.8008 (m110) cc_final: 0.7569 (t0) REVERT: A 285 ASP cc_start: 0.8254 (t0) cc_final: 0.7942 (t0) REVERT: A 286 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7801 (tt0) REVERT: A 377 THR cc_start: 0.8022 (p) cc_final: 0.7716 (p) REVERT: A 378 ASP cc_start: 0.7565 (m-30) cc_final: 0.7107 (m-30) REVERT: A 414 CYS cc_start: 0.7816 (p) cc_final: 0.7515 (p) REVERT: A 443 ASP cc_start: 0.7646 (t0) cc_final: 0.7317 (t0) REVERT: A 474 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8082 (mmtt) REVERT: A 487 LYS cc_start: 0.8525 (tppt) cc_final: 0.8142 (mmmt) REVERT: A 529 HIS cc_start: 0.8265 (m90) cc_final: 0.7907 (m90) REVERT: A 573 LEU cc_start: 0.8075 (tp) cc_final: 0.7689 (mp) REVERT: A 580 LYS cc_start: 0.8282 (tmmt) cc_final: 0.7773 (tmmt) REVERT: A 619 GLU cc_start: 0.7961 (mp0) cc_final: 0.7696 (mp0) REVERT: A 622 LEU cc_start: 0.8563 (mp) cc_final: 0.8266 (mt) REVERT: A 660 CYS cc_start: 0.8324 (t) cc_final: 0.7433 (p) REVERT: A 661 GLN cc_start: 0.8448 (pm20) cc_final: 0.7691 (pm20) REVERT: A 689 ARG cc_start: 0.7589 (tmt-80) cc_final: 0.7148 (tpt90) REVERT: A 696 ARG cc_start: 0.7520 (mtm180) cc_final: 0.7110 (mtp180) REVERT: A 728 GLN cc_start: 0.8364 (tp40) cc_final: 0.8080 (tp40) REVERT: A 731 LYS cc_start: 0.8781 (mmpt) cc_final: 0.8107 (tptp) REVERT: A 739 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8313 (ttpt) REVERT: A 740 GLU cc_start: 0.8098 (mp0) cc_final: 0.7624 (mp0) REVERT: A 743 GLU cc_start: 0.8287 (pt0) cc_final: 0.8075 (pt0) REVERT: A 744 CYS cc_start: 0.7910 (p) cc_final: 0.7662 (p) REVERT: A 745 MET cc_start: 0.8444 (ttp) cc_final: 0.7558 (mmm) REVERT: A 753 ASN cc_start: 0.8809 (m-40) cc_final: 0.8435 (m-40) REVERT: A 767 VAL cc_start: 0.8702 (m) cc_final: 0.8191 (t) REVERT: A 834 LYS cc_start: 0.7587 (mttm) cc_final: 0.7087 (mttm) REVERT: A 846 LYS cc_start: 0.8088 (tptp) cc_final: 0.7710 (tptt) REVERT: A 850 GLU cc_start: 0.7810 (mp0) cc_final: 0.7307 (mp0) REVERT: A 860 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 882 LEU cc_start: 0.8857 (mt) cc_final: 0.8651 (mt) REVERT: A 893 HIS cc_start: 0.8243 (m90) cc_final: 0.7923 (m90) REVERT: A 909 LYS cc_start: 0.8366 (mppt) cc_final: 0.7877 (mmtm) REVERT: A 911 GLN cc_start: 0.7837 (tt0) cc_final: 0.7536 (tp40) REVERT: A 916 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7553 (tp30) REVERT: A 918 LEU cc_start: 0.7569 (tp) cc_final: 0.7276 (tp) REVERT: A 922 ASN cc_start: 0.8626 (m110) cc_final: 0.8411 (m-40) REVERT: A 924 LEU cc_start: 0.8952 (mp) cc_final: 0.8599 (mt) REVERT: A 985 TYR cc_start: 0.7475 (t80) cc_final: 0.7194 (t80) REVERT: A 1008 MET cc_start: 0.7652 (ppp) cc_final: 0.7225 (ppp) REVERT: A 1112 SER cc_start: 0.8526 (m) cc_final: 0.8235 (p) REVERT: A 1121 MET cc_start: 0.8483 (mmp) cc_final: 0.7725 (mmt) REVERT: A 1125 ASP cc_start: 0.7935 (t0) cc_final: 0.7710 (m-30) REVERT: A 1228 ASN cc_start: 0.9049 (m110) cc_final: 0.8758 (m-40) REVERT: A 1237 TYR cc_start: 0.8137 (t80) cc_final: 0.7747 (t80) REVERT: A 1239 ILE cc_start: 0.9065 (mm) cc_final: 0.8840 (mm) REVERT: A 1266 MET cc_start: 0.8031 (mpp) cc_final: 0.7798 (mpp) REVERT: B 32 LEU cc_start: 0.7754 (mt) cc_final: 0.7310 (mt) REVERT: B 55 ASN cc_start: 0.8140 (m110) cc_final: 0.7218 (m110) REVERT: B 92 ILE cc_start: 0.8561 (mm) cc_final: 0.8266 (mm) REVERT: B 98 LEU cc_start: 0.8294 (tp) cc_final: 0.8022 (tp) REVERT: B 144 LYS cc_start: 0.7195 (tptp) cc_final: 0.6907 (tptp) REVERT: B 150 MET cc_start: 0.7683 (ptp) cc_final: 0.6802 (ppp) REVERT: B 152 LEU cc_start: 0.9020 (mt) cc_final: 0.8707 (mt) REVERT: B 156 ASN cc_start: 0.8370 (p0) cc_final: 0.8088 (p0) REVERT: B 184 ASP cc_start: 0.7338 (t0) cc_final: 0.6960 (t0) REVERT: B 239 TYR cc_start: 0.7528 (p90) cc_final: 0.7280 (p90) REVERT: B 377 GLU cc_start: 0.8052 (tt0) cc_final: 0.7084 (tt0) REVERT: B 393 ASP cc_start: 0.7681 (m-30) cc_final: 0.7425 (m-30) REVERT: B 433 ARG cc_start: 0.8160 (ptp-110) cc_final: 0.7821 (ptp-170) REVERT: B 442 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7580 (mtpp) REVERT: B 447 ILE cc_start: 0.7648 (mm) cc_final: 0.7433 (mm) REVERT: B 450 PHE cc_start: 0.8667 (m-10) cc_final: 0.8164 (m-10) REVERT: B 462 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6910 (mtt90) REVERT: B 473 ASN cc_start: 0.8732 (t0) cc_final: 0.8502 (t0) REVERT: B 474 PHE cc_start: 0.8296 (t80) cc_final: 0.7876 (t80) REVERT: B 566 HIS cc_start: 0.7376 (m90) cc_final: 0.6979 (m90) REVERT: B 570 ILE cc_start: 0.8323 (tp) cc_final: 0.8016 (tp) REVERT: B 586 CYS cc_start: 0.8317 (p) cc_final: 0.8044 (p) REVERT: B 612 PHE cc_start: 0.7975 (t80) cc_final: 0.7597 (t80) REVERT: B 625 ASN cc_start: 0.8453 (t0) cc_final: 0.7921 (t0) REVERT: B 638 TRP cc_start: 0.7849 (p-90) cc_final: 0.7404 (p-90) REVERT: B 680 ASP cc_start: 0.8022 (t0) cc_final: 0.7300 (t70) REVERT: B 691 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7642 (ptpt) REVERT: B 742 VAL cc_start: 0.8540 (t) cc_final: 0.8095 (p) REVERT: B 774 GLN cc_start: 0.8468 (tp40) cc_final: 0.7572 (tm-30) REVERT: B 788 LYS cc_start: 0.8710 (tptp) cc_final: 0.8007 (tppt) REVERT: B 789 ASN cc_start: 0.8796 (t0) cc_final: 0.8051 (t0) REVERT: B 817 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7882 (mtpp) REVERT: C 25 GLN cc_start: 0.8790 (mt0) cc_final: 0.8513 (mt0) REVERT: C 28 GLU cc_start: 0.8625 (tt0) cc_final: 0.7500 (tm-30) REVERT: C 31 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 40 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8314 (mmtt) REVERT: C 59 ASP cc_start: 0.8438 (m-30) cc_final: 0.8019 (m-30) REVERT: C 69 ARG cc_start: 0.8110 (ptp-170) cc_final: 0.7331 (ptp-170) REVERT: C 77 LYS cc_start: 0.8436 (ptpt) cc_final: 0.8222 (ptpt) REVERT: C 94 CYS cc_start: 0.8754 (t) cc_final: 0.8511 (t) REVERT: C 153 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6645 (tm-30) REVERT: C 154 GLN cc_start: 0.7760 (tt0) cc_final: 0.6881 (tt0) REVERT: C 198 SER cc_start: 0.7331 (p) cc_final: 0.6648 (t) REVERT: C 199 ASN cc_start: 0.7486 (t0) cc_final: 0.6445 (t0) REVERT: C 203 GLU cc_start: 0.7688 (tt0) cc_final: 0.6885 (tt0) REVERT: C 234 ASP cc_start: 0.7497 (t0) cc_final: 0.6978 (t0) REVERT: C 235 MET cc_start: 0.7082 (mmm) cc_final: 0.6568 (mmm) REVERT: C 238 TYR cc_start: 0.8150 (m-10) cc_final: 0.7888 (m-10) REVERT: C 240 CYS cc_start: 0.8191 (m) cc_final: 0.7753 (m) REVERT: C 244 GLU cc_start: 0.6987 (mp0) cc_final: 0.6650 (mp0) REVERT: C 279 PHE cc_start: 0.8219 (m-10) cc_final: 0.7914 (m-10) REVERT: C 280 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7382 (mmmt) REVERT: C 285 MET cc_start: 0.7979 (mmm) cc_final: 0.7644 (mmm) REVERT: C 288 ASP cc_start: 0.8089 (t0) cc_final: 0.6081 (t70) REVERT: C 294 LEU cc_start: 0.8157 (mp) cc_final: 0.7751 (mm) REVERT: C 295 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7455 (mt-10) REVERT: C 297 ASP cc_start: 0.8091 (m-30) cc_final: 0.7479 (m-30) REVERT: C 300 GLN cc_start: 0.8612 (pp30) cc_final: 0.8342 (pp30) REVERT: C 340 TYR cc_start: 0.8264 (m-10) cc_final: 0.7674 (m-10) REVERT: C 347 GLU cc_start: 0.8178 (mp0) cc_final: 0.7836 (pm20) REVERT: C 352 ILE cc_start: 0.9106 (mt) cc_final: 0.8902 (mm) REVERT: C 368 ASP cc_start: 0.7868 (m-30) cc_final: 0.7624 (m-30) REVERT: C 416 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8242 (mmm-85) REVERT: C 426 ASP cc_start: 0.7868 (p0) cc_final: 0.7659 (p0) REVERT: C 428 VAL cc_start: 0.8501 (t) cc_final: 0.8219 (m) REVERT: C 440 GLU cc_start: 0.7027 (pm20) cc_final: 0.6438 (pm20) REVERT: C 444 GLN cc_start: 0.8473 (mp10) cc_final: 0.7847 (mp10) REVERT: C 445 ASP cc_start: 0.7814 (m-30) cc_final: 0.7494 (m-30) REVERT: C 464 GLU cc_start: 0.8440 (mp0) cc_final: 0.7783 (pm20) REVERT: C 474 GLU cc_start: 0.7663 (tp30) cc_final: 0.7323 (tp30) REVERT: C 503 GLU cc_start: 0.7496 (pp20) cc_final: 0.7074 (tm-30) REVERT: C 504 GLU cc_start: 0.8227 (tp30) cc_final: 0.7608 (tp30) REVERT: C 507 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.7935 (tmm-80) REVERT: C 512 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7054 (mt-10) REVERT: C 526 THR cc_start: 0.8188 (p) cc_final: 0.7963 (p) REVERT: C 535 TYR cc_start: 0.8452 (m-80) cc_final: 0.7748 (m-10) REVERT: C 538 GLN cc_start: 0.8049 (tt0) cc_final: 0.7423 (tt0) REVERT: C 542 MET cc_start: 0.7075 (tpp) cc_final: 0.6696 (tpp) REVERT: C 543 VAL cc_start: 0.8633 (p) cc_final: 0.7771 (t) REVERT: E 939 TYR cc_start: 0.7543 (m-10) cc_final: 0.7304 (m-10) REVERT: E 983 GLN cc_start: 0.7062 (pp30) cc_final: 0.6597 (pp30) REVERT: E 985 TYR cc_start: 0.7926 (t80) cc_final: 0.7248 (t80) REVERT: E 992 TYR cc_start: 0.7622 (t80) cc_final: 0.7009 (t80) REVERT: E 997 MET cc_start: 0.7249 (mmt) cc_final: 0.6929 (mmt) REVERT: E 1008 MET cc_start: 0.8079 (mmp) cc_final: 0.7290 (mmp) REVERT: E 1056 LEU cc_start: 0.8388 (tp) cc_final: 0.8060 (pp) REVERT: E 1095 LEU cc_start: 0.8441 (mt) cc_final: 0.8120 (mt) REVERT: E 1097 TYR cc_start: 0.7473 (m-80) cc_final: 0.7242 (m-80) REVERT: E 1110 LYS cc_start: 0.8923 (tttt) cc_final: 0.8662 (tptt) REVERT: E 1115 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8493 (pp20) REVERT: E 1120 TYR cc_start: 0.8449 (t80) cc_final: 0.7764 (t80) REVERT: E 1124 LEU cc_start: 0.8578 (mp) cc_final: 0.8374 (mp) REVERT: E 1241 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8375 (mmtm) outliers start: 0 outliers final: 0 residues processed: 776 average time/residue: 0.3684 time to fit residues: 429.3623 Evaluate side-chains 707 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 192 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 561 GLN B 819 HIS C 97 HIS C 190 HIS C 291 ASN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092429 restraints weight = 44294.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097017 restraints weight = 22928.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098734 restraints weight = 12142.419| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23074 Z= 0.266 Angle : 0.793 23.548 31629 Z= 0.405 Chirality : 0.049 0.224 3593 Planarity : 0.006 0.092 3753 Dihedral : 14.124 80.391 3988 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 2567 helix: 0.08 (0.18), residues: 780 sheet: -1.03 (0.21), residues: 600 loop : -2.19 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP A 117 HIS 0.010 0.002 HIS C 196 PHE 0.034 0.002 PHE A 784 TYR 0.021 0.002 TYR B 296 ARG 0.008 0.001 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.06042 ( 855) hydrogen bonds : angle 5.42268 ( 2328) metal coordination : bond 0.01632 ( 3) metal coordination : angle 12.33164 ( 9) covalent geometry : bond 0.00563 (23071) covalent geometry : angle 0.76507 (31620) *********************** 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 792 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 792 time to evaluate : 2.157 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: 0.7290 (ttp-170) cc_final: 0.6844 (ptt-90) REVERT: A 43 GLU cc_start: 0.7674 (tt0) cc_final: 0.7277 (tp30) REVERT: A 75 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 80 GLN cc_start: 0.8687 (mt0) cc_final: 0.8372 (mt0) REVERT: A 121 GLN cc_start: 0.8323 (mp10) cc_final: 0.7797 (mp10) REVERT: A 122 GLU cc_start: 0.7879 (tp30) cc_final: 0.7503 (tp30) REVERT: A 131 GLN cc_start: 0.8593 (mp10) cc_final: 0.8146 (mp10) REVERT: A 135 MET cc_start: 0.7339 (tpt) cc_final: 0.7025 (tpt) REVERT: A 136 MET cc_start: 0.7815 (pmm) cc_final: 0.7473 (pmm) REVERT: A 203 ASP cc_start: 0.7964 (p0) cc_final: 0.7671 (p0) REVERT: A 205 GLN cc_start: 0.8453 (mt0) cc_final: 0.8216 (mt0) REVERT: A 258 ASP cc_start: 0.7730 (t70) cc_final: 0.7503 (t0) REVERT: A 261 ASN cc_start: 0.8210 (m110) cc_final: 0.7630 (t0) REVERT: A 285 ASP cc_start: 0.8222 (t0) cc_final: 0.7859 (t0) REVERT: A 377 THR cc_start: 0.8007 (p) cc_final: 0.7714 (p) REVERT: A 378 ASP cc_start: 0.7700 (m-30) cc_final: 0.7214 (m-30) REVERT: A 414 CYS cc_start: 0.7740 (p) cc_final: 0.7485 (p) REVERT: A 443 ASP cc_start: 0.7722 (t0) cc_final: 0.6649 (p0) REVERT: A 476 CYS cc_start: 0.8026 (m) cc_final: 0.7556 (t) REVERT: A 512 ASP cc_start: 0.8220 (p0) cc_final: 0.7977 (p0) REVERT: A 573 LEU cc_start: 0.8134 (tp) cc_final: 0.7676 (mp) REVERT: A 580 LYS cc_start: 0.8305 (tmmt) cc_final: 0.7821 (tmmt) REVERT: A 614 MET cc_start: 0.8507 (tpt) cc_final: 0.8076 (tpt) REVERT: A 620 CYS cc_start: 0.8404 (p) cc_final: 0.8197 (p) REVERT: A 622 LEU cc_start: 0.8548 (mp) cc_final: 0.8216 (mt) REVERT: A 631 PHE cc_start: 0.7695 (m-80) cc_final: 0.7371 (m-80) REVERT: A 639 SER cc_start: 0.7949 (p) cc_final: 0.7705 (p) REVERT: A 660 CYS cc_start: 0.8333 (t) cc_final: 0.7513 (p) REVERT: A 661 GLN cc_start: 0.8471 (pm20) cc_final: 0.7853 (pm20) REVERT: A 689 ARG cc_start: 0.7606 (tmt-80) cc_final: 0.7096 (ttt90) REVERT: A 692 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6608 (mm-30) REVERT: A 696 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7278 (mtm180) REVERT: A 728 GLN cc_start: 0.8378 (tp40) cc_final: 0.8084 (tp40) REVERT: A 731 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8172 (tptp) REVERT: A 739 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8486 (ttpp) REVERT: A 745 MET cc_start: 0.8518 (ttp) cc_final: 0.8235 (ttp) REVERT: A 753 ASN cc_start: 0.8857 (m110) cc_final: 0.8527 (m-40) REVERT: A 767 VAL cc_start: 0.8725 (m) cc_final: 0.8251 (t) REVERT: A 794 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8430 (mmtt) REVERT: A 823 MET cc_start: 0.8598 (ptm) cc_final: 0.8246 (ptp) REVERT: A 827 MET cc_start: 0.8786 (ppp) cc_final: 0.8532 (ppp) REVERT: A 834 LYS cc_start: 0.7634 (mttm) cc_final: 0.7290 (mttm) REVERT: A 846 LYS cc_start: 0.8110 (tptp) cc_final: 0.7780 (tptp) REVERT: A 850 GLU cc_start: 0.7793 (mp0) cc_final: 0.7364 (mp0) REVERT: A 878 LEU cc_start: 0.8789 (tp) cc_final: 0.8492 (tp) REVERT: A 882 LEU cc_start: 0.8900 (mt) cc_final: 0.8627 (mt) REVERT: A 893 HIS cc_start: 0.8314 (m90) cc_final: 0.7939 (m90) REVERT: A 909 LYS cc_start: 0.8300 (mppt) cc_final: 0.7741 (mmtm) REVERT: A 911 GLN cc_start: 0.8024 (tt0) cc_final: 0.7811 (tp40) REVERT: A 913 ASP cc_start: 0.8338 (t0) cc_final: 0.8014 (t0) REVERT: A 918 LEU cc_start: 0.7658 (tp) cc_final: 0.7379 (tp) REVERT: A 922 ASN cc_start: 0.8566 (m110) cc_final: 0.8314 (m-40) REVERT: A 924 LEU cc_start: 0.8967 (mp) cc_final: 0.8640 (mt) REVERT: A 947 ILE cc_start: 0.7973 (mm) cc_final: 0.7754 (mm) REVERT: A 985 TYR cc_start: 0.7495 (t80) cc_final: 0.7239 (t80) REVERT: A 1008 MET cc_start: 0.7400 (ppp) cc_final: 0.6956 (ppp) REVERT: A 1009 PHE cc_start: 0.7183 (m-10) cc_final: 0.6938 (m-10) REVERT: A 1058 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 1112 SER cc_start: 0.8586 (m) cc_final: 0.8348 (p) REVERT: A 1121 MET cc_start: 0.8238 (mmp) cc_final: 0.7938 (mmp) REVERT: A 1125 ASP cc_start: 0.8012 (t0) cc_final: 0.7794 (m-30) REVERT: A 1135 LYS cc_start: 0.7662 (pttp) cc_final: 0.7392 (pttp) REVERT: A 1228 ASN cc_start: 0.8985 (m110) cc_final: 0.8729 (m-40) REVERT: A 1238 HIS cc_start: 0.8102 (p-80) cc_final: 0.7845 (p-80) REVERT: B 44 ASP cc_start: 0.8937 (p0) cc_final: 0.8611 (p0) REVERT: B 55 ASN cc_start: 0.8069 (m110) cc_final: 0.7061 (m110) REVERT: B 144 LYS cc_start: 0.7396 (tptp) cc_final: 0.6985 (tptp) REVERT: B 150 MET cc_start: 0.7713 (ptp) cc_final: 0.7037 (ppp) REVERT: B 152 LEU cc_start: 0.9059 (mt) cc_final: 0.8741 (mt) REVERT: B 156 ASN cc_start: 0.8516 (p0) cc_final: 0.8304 (p0) REVERT: B 184 ASP cc_start: 0.7483 (t0) cc_final: 0.7228 (t0) REVERT: B 239 TYR cc_start: 0.7637 (p90) cc_final: 0.7323 (p90) REVERT: B 314 LYS cc_start: 0.6582 (mmtt) cc_final: 0.6342 (mmtt) REVERT: B 377 GLU cc_start: 0.7863 (tt0) cc_final: 0.6870 (tt0) REVERT: B 381 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6547 (tm-30) REVERT: B 382 ILE cc_start: 0.8224 (mp) cc_final: 0.7827 (mp) REVERT: B 388 PHE cc_start: 0.7540 (p90) cc_final: 0.7338 (p90) REVERT: B 393 ASP cc_start: 0.7745 (m-30) cc_final: 0.7540 (m-30) REVERT: B 430 GLU cc_start: 0.8233 (pm20) cc_final: 0.8027 (pm20) REVERT: B 433 ARG cc_start: 0.8110 (ptp-110) cc_final: 0.7754 (ptp-170) REVERT: B 442 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7668 (mtpp) REVERT: B 473 ASN cc_start: 0.8783 (t0) cc_final: 0.8513 (t0) REVERT: B 474 PHE cc_start: 0.8271 (t80) cc_final: 0.8022 (t80) REVERT: B 554 ASN cc_start: 0.7202 (t0) cc_final: 0.6469 (t0) REVERT: B 566 HIS cc_start: 0.7386 (m90) cc_final: 0.6969 (m90) REVERT: B 569 GLU cc_start: 0.7806 (pm20) cc_final: 0.7464 (pm20) REVERT: B 586 CYS cc_start: 0.8307 (p) cc_final: 0.8076 (p) REVERT: B 612 PHE cc_start: 0.8049 (t80) cc_final: 0.7788 (t80) REVERT: B 625 ASN cc_start: 0.8524 (t0) cc_final: 0.7841 (t0) REVERT: B 636 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7469 (mtm-85) REVERT: B 638 TRP cc_start: 0.7859 (p-90) cc_final: 0.7401 (p-90) REVERT: B 642 LYS cc_start: 0.8252 (tptt) cc_final: 0.8037 (tptp) REVERT: B 674 SER cc_start: 0.8692 (t) cc_final: 0.8160 (p) REVERT: B 691 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7714 (ptpt) REVERT: B 742 VAL cc_start: 0.8522 (t) cc_final: 0.8115 (p) REVERT: B 774 GLN cc_start: 0.8498 (tp40) cc_final: 0.7590 (tm-30) REVERT: B 783 ARG cc_start: 0.8458 (mmt180) cc_final: 0.8031 (mmt90) REVERT: B 788 LYS cc_start: 0.8732 (tptp) cc_final: 0.8156 (tppt) REVERT: B 817 LYS cc_start: 0.8513 (mtmt) cc_final: 0.7840 (mtpp) REVERT: C 25 GLN cc_start: 0.8834 (mt0) cc_final: 0.8523 (mt0) REVERT: C 28 GLU cc_start: 0.8613 (tt0) cc_final: 0.7017 (tm-30) REVERT: C 31 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 32 GLN cc_start: 0.7520 (mp10) cc_final: 0.6961 (mp10) REVERT: C 42 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8282 (mtpp) REVERT: C 59 ASP cc_start: 0.8421 (m-30) cc_final: 0.8117 (m-30) REVERT: C 94 CYS cc_start: 0.8776 (t) cc_final: 0.8486 (t) REVERT: C 143 ASP cc_start: 0.7991 (t0) cc_final: 0.7749 (t0) REVERT: C 153 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6754 (tm-30) REVERT: C 154 GLN cc_start: 0.7797 (tt0) cc_final: 0.6855 (tt0) REVERT: C 166 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6759 (tm-30) REVERT: C 167 PHE cc_start: 0.8147 (m-10) cc_final: 0.7555 (m-10) REVERT: C 198 SER cc_start: 0.7407 (p) cc_final: 0.6743 (t) REVERT: C 199 ASN cc_start: 0.7671 (t0) cc_final: 0.6636 (t0) REVERT: C 203 GLU cc_start: 0.7835 (tt0) cc_final: 0.7142 (tt0) REVERT: C 235 MET cc_start: 0.6981 (mmm) cc_final: 0.6406 (mmm) REVERT: C 240 CYS cc_start: 0.8297 (m) cc_final: 0.7828 (m) REVERT: C 244 GLU cc_start: 0.6967 (mp0) cc_final: 0.6745 (mp0) REVERT: C 285 MET cc_start: 0.8011 (mmm) cc_final: 0.7734 (mmm) REVERT: C 288 ASP cc_start: 0.7983 (t0) cc_final: 0.5961 (t70) REVERT: C 291 ASN cc_start: 0.8566 (m-40) cc_final: 0.8312 (m110) REVERT: C 294 LEU cc_start: 0.8283 (mp) cc_final: 0.7927 (mm) REVERT: C 295 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 296 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7939 (mtp85) REVERT: C 297 ASP cc_start: 0.8103 (m-30) cc_final: 0.7613 (m-30) REVERT: C 300 GLN cc_start: 0.8678 (pp30) cc_final: 0.8296 (pp30) REVERT: C 318 TYR cc_start: 0.7909 (m-10) cc_final: 0.7342 (m-10) REVERT: C 340 TYR cc_start: 0.8301 (m-10) cc_final: 0.7680 (m-10) REVERT: C 343 SER cc_start: 0.8264 (p) cc_final: 0.6665 (t) REVERT: C 347 GLU cc_start: 0.8098 (mp0) cc_final: 0.7669 (mp0) REVERT: C 368 ASP cc_start: 0.7860 (m-30) cc_final: 0.7625 (m-30) REVERT: C 402 ARG cc_start: 0.8273 (tpt-90) cc_final: 0.8000 (tpt-90) REVERT: C 426 ASP cc_start: 0.7967 (p0) cc_final: 0.7652 (p0) REVERT: C 440 GLU cc_start: 0.7036 (pm20) cc_final: 0.6632 (pm20) REVERT: C 444 GLN cc_start: 0.8502 (mp10) cc_final: 0.7919 (mp10) REVERT: C 445 ASP cc_start: 0.7835 (m-30) cc_final: 0.7443 (m-30) REVERT: C 446 ILE cc_start: 0.8012 (tt) cc_final: 0.7740 (tt) REVERT: C 474 GLU cc_start: 0.7749 (tp30) cc_final: 0.7348 (tp30) REVERT: C 503 GLU cc_start: 0.7576 (pp20) cc_final: 0.7019 (tm-30) REVERT: C 504 GLU cc_start: 0.8245 (tp30) cc_final: 0.7949 (tp30) REVERT: C 507 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7925 (tmm-80) REVERT: C 512 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 526 THR cc_start: 0.8237 (p) cc_final: 0.8018 (p) REVERT: C 533 ILE cc_start: 0.9223 (mp) cc_final: 0.8826 (tp) REVERT: C 535 TYR cc_start: 0.8438 (m-80) cc_final: 0.7951 (m-80) REVERT: C 538 GLN cc_start: 0.7995 (tt0) cc_final: 0.7466 (tt0) REVERT: C 542 MET cc_start: 0.6949 (tpp) cc_final: 0.6634 (tpp) REVERT: C 543 VAL cc_start: 0.8640 (p) cc_final: 0.7753 (t) REVERT: E 939 TYR cc_start: 0.7529 (m-10) cc_final: 0.7320 (m-10) REVERT: E 983 GLN cc_start: 0.7256 (pp30) cc_final: 0.6629 (pp30) REVERT: E 985 TYR cc_start: 0.7988 (t80) cc_final: 0.7345 (t80) REVERT: E 992 TYR cc_start: 0.7626 (t80) cc_final: 0.7044 (t80) REVERT: E 997 MET cc_start: 0.7294 (mmt) cc_final: 0.6971 (mmt) REVERT: E 1008 MET cc_start: 0.8107 (mmp) cc_final: 0.7564 (mmp) REVERT: E 1094 ARG cc_start: 0.8177 (pmt170) cc_final: 0.7808 (pmt170) REVERT: E 1095 LEU cc_start: 0.8451 (mt) cc_final: 0.8044 (mt) REVERT: E 1097 TYR cc_start: 0.7361 (m-80) cc_final: 0.7159 (m-80) REVERT: E 1101 ARG cc_start: 0.6291 (mpt180) cc_final: 0.5820 (mpp-170) REVERT: E 1110 LYS cc_start: 0.8972 (tttt) cc_final: 0.8621 (tptt) REVERT: E 1115 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8582 (tm-30) REVERT: E 1120 TYR cc_start: 0.8438 (t80) cc_final: 0.7737 (t80) REVERT: E 1124 LEU cc_start: 0.8593 (mp) cc_final: 0.8346 (mp) REVERT: E 1241 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8429 (mmtm) outliers start: 0 outliers final: 0 residues processed: 792 average time/residue: 0.3588 time to fit residues: 427.1223 Evaluate side-chains 733 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 733 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 203 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 251 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A 932 GLN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 GLN C 495 GLN C 513 HIS C 528 ASN E1015 HIS E1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095032 restraints weight = 44217.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099307 restraints weight = 22877.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101203 restraints weight = 12403.724| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23074 Z= 0.158 Angle : 0.729 22.143 31629 Z= 0.366 Chirality : 0.047 0.232 3593 Planarity : 0.005 0.066 3753 Dihedral : 14.021 78.666 3988 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2567 helix: 0.22 (0.18), residues: 782 sheet: -0.83 (0.21), residues: 594 loop : -2.12 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 378 HIS 0.007 0.001 HIS C 513 PHE 0.023 0.002 PHE B 684 TYR 0.020 0.002 TYR A 917 ARG 0.007 0.001 ARG B 462 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 855) hydrogen bonds : angle 5.17727 ( 2328) metal coordination : bond 0.01116 ( 3) metal coordination : angle 11.73477 ( 9) covalent geometry : bond 0.00342 (23071) covalent geometry : angle 0.70137 (31620) *********************** 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 781 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 781 time to evaluate : 2.360 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: 0.7334 (ttp-170) cc_final: 0.6913 (ptt-90) REVERT: A 43 GLU cc_start: 0.7665 (tt0) cc_final: 0.7312 (tp30) REVERT: A 52 LYS cc_start: 0.9191 (mmpt) cc_final: 0.8687 (tmtt) REVERT: A 75 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 80 GLN cc_start: 0.8710 (mt0) cc_final: 0.8259 (mm110) REVERT: A 121 GLN cc_start: 0.8362 (mp10) cc_final: 0.7738 (mp10) REVERT: A 122 GLU cc_start: 0.7835 (tp30) cc_final: 0.7438 (tp30) REVERT: A 135 MET cc_start: 0.7343 (tpt) cc_final: 0.6996 (tpt) REVERT: A 136 MET cc_start: 0.7934 (pmm) cc_final: 0.7552 (pmm) REVERT: A 203 ASP cc_start: 0.7840 (p0) cc_final: 0.7600 (p0) REVERT: A 205 GLN cc_start: 0.8383 (mt0) cc_final: 0.8148 (mt0) REVERT: A 257 GLN cc_start: 0.8625 (tt0) cc_final: 0.8205 (tp-100) REVERT: A 261 ASN cc_start: 0.8211 (m110) cc_final: 0.7590 (t0) REVERT: A 271 ASN cc_start: 0.8192 (t0) cc_final: 0.7988 (t0) REVERT: A 285 ASP cc_start: 0.8089 (t0) cc_final: 0.7712 (t0) REVERT: A 304 TRP cc_start: 0.7420 (t60) cc_final: 0.7146 (t60) REVERT: A 337 SER cc_start: 0.7440 (m) cc_final: 0.7125 (t) REVERT: A 377 THR cc_start: 0.8046 (p) cc_final: 0.7781 (p) REVERT: A 378 ASP cc_start: 0.7623 (m-30) cc_final: 0.7136 (m-30) REVERT: A 414 CYS cc_start: 0.7539 (p) cc_final: 0.7296 (p) REVERT: A 415 THR cc_start: 0.8283 (m) cc_final: 0.7993 (t) REVERT: A 443 ASP cc_start: 0.7660 (t0) cc_final: 0.7330 (t0) REVERT: A 487 LYS cc_start: 0.8611 (tppt) cc_final: 0.8153 (mmmt) REVERT: A 529 HIS cc_start: 0.8210 (m-70) cc_final: 0.7917 (m90) REVERT: A 567 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8548 (mtmm) REVERT: A 573 LEU cc_start: 0.8089 (tp) cc_final: 0.7663 (mp) REVERT: A 580 LYS cc_start: 0.8322 (tmmt) cc_final: 0.7801 (tmmt) REVERT: A 620 CYS cc_start: 0.8412 (p) cc_final: 0.8189 (p) REVERT: A 622 LEU cc_start: 0.8573 (mp) cc_final: 0.8226 (mt) REVERT: A 631 PHE cc_start: 0.7689 (m-80) cc_final: 0.7350 (m-80) REVERT: A 660 CYS cc_start: 0.8276 (t) cc_final: 0.7546 (p) REVERT: A 661 GLN cc_start: 0.8428 (pm20) cc_final: 0.7881 (pm20) REVERT: A 696 ARG cc_start: 0.7475 (mtm180) cc_final: 0.7194 (mtp180) REVERT: A 731 LYS cc_start: 0.8804 (mmpt) cc_final: 0.8161 (tptp) REVERT: A 737 MET cc_start: 0.5948 (pmm) cc_final: 0.5694 (pmm) REVERT: A 739 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8442 (ttpp) REVERT: A 744 CYS cc_start: 0.7908 (p) cc_final: 0.7697 (p) REVERT: A 745 MET cc_start: 0.8517 (ttp) cc_final: 0.8245 (ttp) REVERT: A 753 ASN cc_start: 0.8843 (m110) cc_final: 0.8465 (m-40) REVERT: A 767 VAL cc_start: 0.8690 (m) cc_final: 0.8175 (t) REVERT: A 794 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8432 (mmtt) REVERT: A 827 MET cc_start: 0.8749 (ppp) cc_final: 0.8470 (ppp) REVERT: A 834 LYS cc_start: 0.7752 (mttm) cc_final: 0.7427 (mttm) REVERT: A 846 LYS cc_start: 0.8113 (tptp) cc_final: 0.7793 (tptp) REVERT: A 850 GLU cc_start: 0.7764 (mp0) cc_final: 0.7330 (mp0) REVERT: A 856 GLN cc_start: 0.8160 (tp40) cc_final: 0.7862 (tp40) REVERT: A 860 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 878 LEU cc_start: 0.8753 (tp) cc_final: 0.8422 (tp) REVERT: A 882 LEU cc_start: 0.8875 (mt) cc_final: 0.8602 (mt) REVERT: A 893 HIS cc_start: 0.8307 (m90) cc_final: 0.7984 (m90) REVERT: A 909 LYS cc_start: 0.8309 (mppt) cc_final: 0.7729 (mmtm) REVERT: A 913 ASP cc_start: 0.8293 (t0) cc_final: 0.8042 (t0) REVERT: A 924 LEU cc_start: 0.8896 (mp) cc_final: 0.8465 (mt) REVERT: A 947 ILE cc_start: 0.7954 (mm) cc_final: 0.7723 (mm) REVERT: A 985 TYR cc_start: 0.7421 (t80) cc_final: 0.7141 (t80) REVERT: A 1008 MET cc_start: 0.7451 (ppp) cc_final: 0.7009 (ppp) REVERT: A 1009 PHE cc_start: 0.7106 (m-10) cc_final: 0.6828 (m-10) REVERT: A 1058 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 1112 SER cc_start: 0.8587 (m) cc_final: 0.8350 (p) REVERT: A 1125 ASP cc_start: 0.7987 (t0) cc_final: 0.7766 (m-30) REVERT: A 1228 ASN cc_start: 0.8961 (m110) cc_final: 0.8700 (m-40) REVERT: A 1237 TYR cc_start: 0.8220 (t80) cc_final: 0.7920 (t80) REVERT: A 1266 MET cc_start: 0.8093 (mmp) cc_final: 0.7865 (mmp) REVERT: B 32 LEU cc_start: 0.7711 (mt) cc_final: 0.7442 (mt) REVERT: B 55 ASN cc_start: 0.7839 (m110) cc_final: 0.7583 (m110) REVERT: B 92 ILE cc_start: 0.8535 (mm) cc_final: 0.8194 (mm) REVERT: B 150 MET cc_start: 0.7644 (ptp) cc_final: 0.6969 (ppp) REVERT: B 152 LEU cc_start: 0.9078 (mt) cc_final: 0.8721 (mt) REVERT: B 163 LEU cc_start: 0.8378 (mp) cc_final: 0.7951 (mm) REVERT: B 184 ASP cc_start: 0.7490 (t0) cc_final: 0.7173 (t0) REVERT: B 256 LYS cc_start: 0.8582 (tppp) cc_final: 0.8285 (tmtt) REVERT: B 367 LEU cc_start: 0.8030 (tp) cc_final: 0.7564 (tp) REVERT: B 377 GLU cc_start: 0.7841 (tt0) cc_final: 0.6901 (tt0) REVERT: B 381 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6569 (tm-30) REVERT: B 382 ILE cc_start: 0.8236 (mp) cc_final: 0.7808 (mp) REVERT: B 403 ILE cc_start: 0.8475 (mm) cc_final: 0.8174 (tp) REVERT: B 430 GLU cc_start: 0.8168 (pm20) cc_final: 0.7871 (pm20) REVERT: B 433 ARG cc_start: 0.8177 (ptp-110) cc_final: 0.7646 (ptp-110) REVERT: B 442 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7689 (mtpp) REVERT: B 447 ILE cc_start: 0.7903 (mm) cc_final: 0.7446 (mm) REVERT: B 473 ASN cc_start: 0.8727 (t0) cc_final: 0.8431 (t0) REVERT: B 474 PHE cc_start: 0.8142 (t80) cc_final: 0.7933 (t80) REVERT: B 554 ASN cc_start: 0.7158 (t0) cc_final: 0.6426 (t0) REVERT: B 566 HIS cc_start: 0.7278 (m90) cc_final: 0.6640 (m90) REVERT: B 569 GLU cc_start: 0.7762 (pm20) cc_final: 0.7307 (mp0) REVERT: B 570 ILE cc_start: 0.8381 (tp) cc_final: 0.7993 (tp) REVERT: B 584 SER cc_start: 0.8200 (m) cc_final: 0.7720 (p) REVERT: B 612 PHE cc_start: 0.7972 (t80) cc_final: 0.7502 (t80) REVERT: B 625 ASN cc_start: 0.8496 (t0) cc_final: 0.7825 (t0) REVERT: B 638 TRP cc_start: 0.7864 (p-90) cc_final: 0.7415 (p-90) REVERT: B 674 SER cc_start: 0.8678 (t) cc_final: 0.8138 (p) REVERT: B 675 CYS cc_start: 0.8057 (p) cc_final: 0.7840 (p) REVERT: B 680 ASP cc_start: 0.8113 (t0) cc_final: 0.7382 (t70) REVERT: B 691 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7624 (ptpt) REVERT: B 742 VAL cc_start: 0.8512 (t) cc_final: 0.8083 (p) REVERT: B 774 GLN cc_start: 0.8475 (tp40) cc_final: 0.8272 (tp-100) REVERT: B 783 ARG cc_start: 0.8395 (mmt180) cc_final: 0.7909 (mmt90) REVERT: B 788 LYS cc_start: 0.8751 (tptp) cc_final: 0.8134 (tppt) REVERT: B 817 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7859 (mtpp) REVERT: C 25 GLN cc_start: 0.8835 (mt0) cc_final: 0.8506 (mt0) REVERT: C 31 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 42 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8209 (mtpp) REVERT: C 69 ARG cc_start: 0.8086 (ptp-170) cc_final: 0.7329 (ptp-170) REVERT: C 77 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8147 (ptpt) REVERT: C 94 CYS cc_start: 0.8789 (t) cc_final: 0.8483 (t) REVERT: C 143 ASP cc_start: 0.7842 (t0) cc_final: 0.7407 (t0) REVERT: C 153 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6641 (tm-30) REVERT: C 154 GLN cc_start: 0.7768 (tt0) cc_final: 0.6836 (tt0) REVERT: C 166 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6660 (tm-30) REVERT: C 167 PHE cc_start: 0.8075 (m-10) cc_final: 0.7520 (m-10) REVERT: C 198 SER cc_start: 0.7333 (p) cc_final: 0.6715 (t) REVERT: C 199 ASN cc_start: 0.7600 (t0) cc_final: 0.6648 (t0) REVERT: C 200 ASN cc_start: 0.9083 (p0) cc_final: 0.8830 (p0) REVERT: C 203 GLU cc_start: 0.7675 (tt0) cc_final: 0.6890 (tt0) REVERT: C 235 MET cc_start: 0.7094 (mmm) cc_final: 0.6511 (mmm) REVERT: C 238 TYR cc_start: 0.8086 (m-10) cc_final: 0.7826 (m-10) REVERT: C 244 GLU cc_start: 0.7058 (mp0) cc_final: 0.6755 (mp0) REVERT: C 280 LYS cc_start: 0.7922 (mmpt) cc_final: 0.7316 (mmpt) REVERT: C 285 MET cc_start: 0.7859 (mmm) cc_final: 0.7573 (mmm) REVERT: C 288 ASP cc_start: 0.8057 (t0) cc_final: 0.6379 (t70) REVERT: C 291 ASN cc_start: 0.8598 (m-40) cc_final: 0.8376 (m-40) REVERT: C 294 LEU cc_start: 0.8134 (mp) cc_final: 0.7785 (mm) REVERT: C 295 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7226 (mt-10) REVERT: C 296 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7909 (mtp85) REVERT: C 297 ASP cc_start: 0.8081 (m-30) cc_final: 0.7549 (m-30) REVERT: C 300 GLN cc_start: 0.8648 (pp30) cc_final: 0.8256 (pp30) REVERT: C 340 TYR cc_start: 0.8268 (m-10) cc_final: 0.7735 (m-10) REVERT: C 343 SER cc_start: 0.8184 (p) cc_final: 0.7742 (t) REVERT: C 367 ARG cc_start: 0.7431 (tpp-160) cc_final: 0.7126 (tpp80) REVERT: C 368 ASP cc_start: 0.7845 (m-30) cc_final: 0.7513 (m-30) REVERT: C 402 ARG cc_start: 0.8218 (tpt-90) cc_final: 0.7980 (tpt-90) REVERT: C 414 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8070 (mmtm) REVERT: C 433 TRP cc_start: 0.8380 (t60) cc_final: 0.8151 (t60) REVERT: C 440 GLU cc_start: 0.7183 (pm20) cc_final: 0.6604 (pm20) REVERT: C 441 ASP cc_start: 0.7242 (t0) cc_final: 0.6490 (t0) REVERT: C 444 GLN cc_start: 0.8448 (mp10) cc_final: 0.7214 (mp10) REVERT: C 445 ASP cc_start: 0.7887 (m-30) cc_final: 0.7537 (m-30) REVERT: C 446 ILE cc_start: 0.7952 (tt) cc_final: 0.7695 (tt) REVERT: C 448 ILE cc_start: 0.8162 (pt) cc_final: 0.7821 (pt) REVERT: C 473 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7548 (ttm170) REVERT: C 497 PHE cc_start: 0.7940 (m-80) cc_final: 0.7738 (m-80) REVERT: C 503 GLU cc_start: 0.7491 (pp20) cc_final: 0.7206 (tm-30) REVERT: C 504 GLU cc_start: 0.8202 (tp30) cc_final: 0.7871 (tp30) REVERT: C 507 ARG cc_start: 0.8288 (tmm-80) cc_final: 0.8084 (tmm-80) REVERT: C 512 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7149 (mt-10) REVERT: C 533 ILE cc_start: 0.9172 (mp) cc_final: 0.8832 (tp) REVERT: C 535 TYR cc_start: 0.8407 (m-80) cc_final: 0.7888 (m-10) REVERT: C 538 GLN cc_start: 0.7964 (tt0) cc_final: 0.7352 (tt0) REVERT: C 542 MET cc_start: 0.6934 (tpp) cc_final: 0.6649 (tpp) REVERT: C 543 VAL cc_start: 0.8578 (p) cc_final: 0.7856 (t) REVERT: E 939 TYR cc_start: 0.7552 (m-10) cc_final: 0.7307 (m-10) REVERT: E 983 GLN cc_start: 0.7206 (pp30) cc_final: 0.6604 (pp30) REVERT: E 985 TYR cc_start: 0.7968 (t80) cc_final: 0.7273 (t80) REVERT: E 992 TYR cc_start: 0.7721 (t80) cc_final: 0.7096 (t80) REVERT: E 997 MET cc_start: 0.7308 (mmt) cc_final: 0.6957 (mmt) REVERT: E 1007 LEU cc_start: 0.7851 (tt) cc_final: 0.7616 (tt) REVERT: E 1008 MET cc_start: 0.8121 (mmp) cc_final: 0.7602 (mmp) REVERT: E 1094 ARG cc_start: 0.8124 (pmt170) cc_final: 0.7806 (pmt170) REVERT: E 1095 LEU cc_start: 0.8335 (mt) cc_final: 0.8045 (mt) REVERT: E 1097 TYR cc_start: 0.7352 (m-80) cc_final: 0.7144 (m-80) REVERT: E 1110 LYS cc_start: 0.8931 (tttt) cc_final: 0.8671 (tptt) REVERT: E 1115 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8486 (pp20) REVERT: E 1120 TYR cc_start: 0.8510 (t80) cc_final: 0.7750 (t80) REVERT: E 1121 MET cc_start: 0.7172 (mtt) cc_final: 0.6966 (mmt) REVERT: E 1124 LEU cc_start: 0.8563 (mp) cc_final: 0.8324 (mp) REVERT: E 1241 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8401 (mmtm) REVERT: E 1255 LEU cc_start: 0.8632 (tp) cc_final: 0.8328 (tp) REVERT: C 604 MET cc_start: 0.7216 (pmm) cc_final: 0.6922 (pmm) outliers start: 0 outliers final: 0 residues processed: 781 average time/residue: 0.3680 time to fit residues: 432.9662 Evaluate side-chains 709 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 202 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 147 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 21 optimal weight: 0.0010 chunk 38 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 overall best weight: 0.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 GLN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 125 GLN C 190 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095743 restraints weight = 43669.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100708 restraints weight = 22423.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102627 restraints weight = 11213.853| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23074 Z= 0.141 Angle : 0.725 21.375 31629 Z= 0.363 Chirality : 0.046 0.250 3593 Planarity : 0.005 0.061 3753 Dihedral : 13.923 78.181 3988 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2567 helix: 0.23 (0.18), residues: 789 sheet: -0.70 (0.21), residues: 585 loop : -2.09 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 117 HIS 0.012 0.001 HIS B 57 PHE 0.022 0.002 PHE B 684 TYR 0.033 0.002 TYR B 117 ARG 0.007 0.001 ARG B 462 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 855) hydrogen bonds : angle 5.10742 ( 2328) metal coordination : bond 0.01022 ( 3) metal coordination : angle 11.53434 ( 9) covalent geometry : bond 0.00309 (23071) covalent geometry : angle 0.69860 (31620) *********************** 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 763 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 763 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.6914 (ptt-90) REVERT: A 29 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 43 GLU cc_start: 0.7690 (tt0) cc_final: 0.7336 (tp30) REVERT: A 45 ASP cc_start: 0.8175 (t0) cc_final: 0.7868 (t70) REVERT: A 52 LYS cc_start: 0.9167 (mmpt) cc_final: 0.8712 (tmtt) REVERT: A 75 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 121 GLN cc_start: 0.8306 (mp10) cc_final: 0.7734 (mp10) REVERT: A 122 GLU cc_start: 0.7824 (tp30) cc_final: 0.7451 (tp30) REVERT: A 135 MET cc_start: 0.7278 (tpt) cc_final: 0.6993 (tpt) REVERT: A 136 MET cc_start: 0.7976 (pmm) cc_final: 0.7659 (pmm) REVERT: A 189 LEU cc_start: 0.8862 (tp) cc_final: 0.8400 (tp) REVERT: A 257 GLN cc_start: 0.8602 (tt0) cc_final: 0.8346 (tp-100) REVERT: A 261 ASN cc_start: 0.8205 (m110) cc_final: 0.7585 (t0) REVERT: A 285 ASP cc_start: 0.8087 (t0) cc_final: 0.7665 (t0) REVERT: A 333 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8591 (mmtt) REVERT: A 378 ASP cc_start: 0.7479 (m-30) cc_final: 0.6955 (m-30) REVERT: A 414 CYS cc_start: 0.7441 (p) cc_final: 0.7197 (p) REVERT: A 415 THR cc_start: 0.8200 (m) cc_final: 0.7928 (t) REVERT: A 443 ASP cc_start: 0.7598 (t0) cc_final: 0.7281 (t0) REVERT: A 487 LYS cc_start: 0.8629 (tppt) cc_final: 0.8052 (mmmt) REVERT: A 529 HIS cc_start: 0.8211 (m-70) cc_final: 0.7919 (m90) REVERT: A 567 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8577 (mtmm) REVERT: A 573 LEU cc_start: 0.8045 (tp) cc_final: 0.7665 (mp) REVERT: A 580 LYS cc_start: 0.8273 (tmmt) cc_final: 0.7782 (tmmt) REVERT: A 583 TRP cc_start: 0.8413 (p-90) cc_final: 0.8153 (p-90) REVERT: A 614 MET cc_start: 0.8745 (tpt) cc_final: 0.8351 (tpt) REVERT: A 660 CYS cc_start: 0.8190 (t) cc_final: 0.7559 (p) REVERT: A 661 GLN cc_start: 0.8446 (pm20) cc_final: 0.7886 (pm20) REVERT: A 696 ARG cc_start: 0.7458 (mtm180) cc_final: 0.7161 (mtp180) REVERT: A 731 LYS cc_start: 0.8798 (mmpt) cc_final: 0.8125 (tptp) REVERT: A 737 MET cc_start: 0.6144 (pmm) cc_final: 0.5907 (pmm) REVERT: A 739 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8418 (ttpp) REVERT: A 744 CYS cc_start: 0.7853 (p) cc_final: 0.7575 (p) REVERT: A 753 ASN cc_start: 0.8839 (m110) cc_final: 0.8413 (m-40) REVERT: A 767 VAL cc_start: 0.8652 (m) cc_final: 0.8156 (t) REVERT: A 794 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8442 (mmtt) REVERT: A 827 MET cc_start: 0.8797 (ppp) cc_final: 0.8398 (ppp) REVERT: A 834 LYS cc_start: 0.7657 (mttm) cc_final: 0.7166 (mttm) REVERT: A 846 LYS cc_start: 0.8120 (tptp) cc_final: 0.7813 (tptp) REVERT: A 850 GLU cc_start: 0.7712 (mp0) cc_final: 0.7283 (mp0) REVERT: A 856 GLN cc_start: 0.8092 (tp40) cc_final: 0.7782 (tp40) REVERT: A 860 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 878 LEU cc_start: 0.8792 (tp) cc_final: 0.8418 (tp) REVERT: A 882 LEU cc_start: 0.8874 (mt) cc_final: 0.8593 (mt) REVERT: A 893 HIS cc_start: 0.8291 (m90) cc_final: 0.7992 (m90) REVERT: A 898 TYR cc_start: 0.6012 (t80) cc_final: 0.5798 (t80) REVERT: A 909 LYS cc_start: 0.8261 (mppt) cc_final: 0.7715 (mmtm) REVERT: A 913 ASP cc_start: 0.8267 (t0) cc_final: 0.7883 (t0) REVERT: A 924 LEU cc_start: 0.8815 (mp) cc_final: 0.8496 (mt) REVERT: A 933 ARG cc_start: 0.6697 (tpp-160) cc_final: 0.6285 (mmt180) REVERT: A 985 TYR cc_start: 0.7395 (t80) cc_final: 0.7193 (t80) REVERT: A 1008 MET cc_start: 0.7415 (ppp) cc_final: 0.6976 (ppp) REVERT: A 1009 PHE cc_start: 0.7044 (m-10) cc_final: 0.6746 (m-10) REVERT: A 1032 LEU cc_start: 0.8014 (tp) cc_final: 0.7790 (tp) REVERT: A 1058 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 1112 SER cc_start: 0.8572 (m) cc_final: 0.8313 (p) REVERT: A 1135 LYS cc_start: 0.7699 (pttp) cc_final: 0.7439 (pttp) REVERT: A 1228 ASN cc_start: 0.8917 (m110) cc_final: 0.8647 (m-40) REVERT: A 1237 TYR cc_start: 0.8240 (t80) cc_final: 0.7775 (t80) REVERT: A 1238 HIS cc_start: 0.8221 (p-80) cc_final: 0.7809 (p-80) REVERT: A 1239 ILE cc_start: 0.8995 (mm) cc_final: 0.8699 (mm) REVERT: B 32 LEU cc_start: 0.7785 (mt) cc_final: 0.7552 (mt) REVERT: B 55 ASN cc_start: 0.7849 (m110) cc_final: 0.7556 (m110) REVERT: B 99 LYS cc_start: 0.8549 (pttm) cc_final: 0.8286 (ptpp) REVERT: B 150 MET cc_start: 0.7642 (ptp) cc_final: 0.6967 (ppp) REVERT: B 152 LEU cc_start: 0.9065 (mt) cc_final: 0.8719 (mt) REVERT: B 163 LEU cc_start: 0.8385 (mp) cc_final: 0.7967 (mm) REVERT: B 184 ASP cc_start: 0.7469 (t0) cc_final: 0.7035 (t0) REVERT: B 193 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 256 LYS cc_start: 0.8546 (tppp) cc_final: 0.8260 (tmtt) REVERT: B 377 GLU cc_start: 0.7961 (tt0) cc_final: 0.7015 (tt0) REVERT: B 430 GLU cc_start: 0.8132 (pm20) cc_final: 0.7912 (pm20) REVERT: B 433 ARG cc_start: 0.8136 (ptp-110) cc_final: 0.7850 (ptp-170) REVERT: B 442 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7684 (mtpp) REVERT: B 443 CYS cc_start: 0.6669 (m) cc_final: 0.6391 (m) REVERT: B 473 ASN cc_start: 0.8740 (t0) cc_final: 0.8454 (t0) REVERT: B 474 PHE cc_start: 0.8152 (t80) cc_final: 0.7912 (t80) REVERT: B 554 ASN cc_start: 0.7119 (t0) cc_final: 0.6392 (t0) REVERT: B 566 HIS cc_start: 0.7221 (m90) cc_final: 0.6563 (m90) REVERT: B 569 GLU cc_start: 0.7755 (pm20) cc_final: 0.7352 (mp0) REVERT: B 584 SER cc_start: 0.8160 (m) cc_final: 0.7640 (p) REVERT: B 612 PHE cc_start: 0.7961 (t80) cc_final: 0.7519 (t80) REVERT: B 625 ASN cc_start: 0.8469 (t0) cc_final: 0.7831 (t0) REVERT: B 638 TRP cc_start: 0.7835 (p-90) cc_final: 0.7410 (p-90) REVERT: B 643 LYS cc_start: 0.8398 (tmmt) cc_final: 0.8070 (tppt) REVERT: B 674 SER cc_start: 0.8661 (t) cc_final: 0.8072 (p) REVERT: B 691 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7584 (ptpt) REVERT: B 742 VAL cc_start: 0.8477 (t) cc_final: 0.8053 (p) REVERT: B 774 GLN cc_start: 0.8440 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 788 LYS cc_start: 0.8722 (tptp) cc_final: 0.8110 (tppt) REVERT: B 817 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7816 (mtpp) REVERT: C 25 GLN cc_start: 0.8814 (mt0) cc_final: 0.8481 (mt0) REVERT: C 31 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7839 (mt-10) REVERT: C 42 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8206 (mtpp) REVERT: C 69 ARG cc_start: 0.8064 (ptp-170) cc_final: 0.7294 (ptp-170) REVERT: C 77 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8128 (ptpt) REVERT: C 94 CYS cc_start: 0.8748 (t) cc_final: 0.8533 (t) REVERT: C 143 ASP cc_start: 0.7735 (t0) cc_final: 0.7331 (t0) REVERT: C 153 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6627 (tm-30) REVERT: C 154 GLN cc_start: 0.7791 (tt0) cc_final: 0.6846 (tt0) REVERT: C 166 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6642 (tm-30) REVERT: C 167 PHE cc_start: 0.7981 (m-10) cc_final: 0.7424 (m-10) REVERT: C 199 ASN cc_start: 0.7753 (t0) cc_final: 0.7546 (t0) REVERT: C 200 ASN cc_start: 0.9066 (p0) cc_final: 0.7564 (p0) REVERT: C 235 MET cc_start: 0.7231 (mmm) cc_final: 0.6763 (mmm) REVERT: C 238 TYR cc_start: 0.8005 (m-10) cc_final: 0.7755 (m-10) REVERT: C 244 GLU cc_start: 0.7030 (mp0) cc_final: 0.6752 (mp0) REVERT: C 285 MET cc_start: 0.7844 (mmm) cc_final: 0.7552 (mmm) REVERT: C 288 ASP cc_start: 0.8076 (t0) cc_final: 0.6332 (t70) REVERT: C 295 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 296 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7950 (mtp85) REVERT: C 297 ASP cc_start: 0.8016 (m-30) cc_final: 0.7456 (m-30) REVERT: C 300 GLN cc_start: 0.8610 (pp30) cc_final: 0.8181 (pp30) REVERT: C 318 TYR cc_start: 0.7677 (m-10) cc_final: 0.7234 (m-10) REVERT: C 336 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7655 (mtp-110) REVERT: C 340 TYR cc_start: 0.8308 (m-10) cc_final: 0.7758 (m-10) REVERT: C 347 GLU cc_start: 0.8128 (mp0) cc_final: 0.7685 (mp0) REVERT: C 348 LEU cc_start: 0.8678 (mp) cc_final: 0.8461 (mp) REVERT: C 368 ASP cc_start: 0.7842 (m-30) cc_final: 0.7568 (m-30) REVERT: C 414 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8042 (mmtm) REVERT: C 426 ASP cc_start: 0.7903 (p0) cc_final: 0.7660 (p0) REVERT: C 433 TRP cc_start: 0.8331 (t60) cc_final: 0.8088 (t60) REVERT: C 440 GLU cc_start: 0.7147 (pm20) cc_final: 0.6553 (pm20) REVERT: C 441 ASP cc_start: 0.7233 (t0) cc_final: 0.6546 (t0) REVERT: C 444 GLN cc_start: 0.8447 (mp10) cc_final: 0.7209 (mp10) REVERT: C 445 ASP cc_start: 0.7889 (m-30) cc_final: 0.7559 (m-30) REVERT: C 446 ILE cc_start: 0.7907 (tt) cc_final: 0.7666 (tt) REVERT: C 448 ILE cc_start: 0.8120 (pt) cc_final: 0.7798 (pt) REVERT: C 503 GLU cc_start: 0.7438 (pp20) cc_final: 0.7161 (tm-30) REVERT: C 504 GLU cc_start: 0.8191 (tp30) cc_final: 0.7847 (tp30) REVERT: C 508 ILE cc_start: 0.8260 (tp) cc_final: 0.8053 (tp) REVERT: C 512 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 528 ASN cc_start: 0.8622 (m-40) cc_final: 0.8398 (m-40) REVERT: C 533 ILE cc_start: 0.9144 (mp) cc_final: 0.8832 (tp) REVERT: C 535 TYR cc_start: 0.8405 (m-80) cc_final: 0.7880 (m-10) REVERT: C 538 GLN cc_start: 0.7944 (tt0) cc_final: 0.7368 (tt0) REVERT: C 542 MET cc_start: 0.6816 (tpp) cc_final: 0.6583 (tpp) REVERT: C 543 VAL cc_start: 0.8533 (p) cc_final: 0.7852 (t) REVERT: E 939 TYR cc_start: 0.7554 (m-10) cc_final: 0.7300 (m-10) REVERT: E 976 LYS cc_start: 0.8456 (ptpp) cc_final: 0.8243 (pttm) REVERT: E 983 GLN cc_start: 0.7241 (pp30) cc_final: 0.6607 (pp30) REVERT: E 985 TYR cc_start: 0.7961 (t80) cc_final: 0.7255 (t80) REVERT: E 992 TYR cc_start: 0.7659 (t80) cc_final: 0.7056 (t80) REVERT: E 997 MET cc_start: 0.7311 (mmt) cc_final: 0.6963 (mmt) REVERT: E 1007 LEU cc_start: 0.7845 (tt) cc_final: 0.7569 (tt) REVERT: E 1008 MET cc_start: 0.8107 (mmp) cc_final: 0.7547 (mmp) REVERT: E 1095 LEU cc_start: 0.8261 (mt) cc_final: 0.8012 (mt) REVERT: E 1110 LYS cc_start: 0.8933 (tttt) cc_final: 0.8664 (tptt) REVERT: E 1115 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8517 (pp20) REVERT: E 1120 TYR cc_start: 0.8468 (t80) cc_final: 0.8146 (t80) REVERT: E 1121 MET cc_start: 0.7091 (mtt) cc_final: 0.6883 (mmt) REVERT: E 1241 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8398 (mmtm) REVERT: E 1255 LEU cc_start: 0.8632 (tp) cc_final: 0.8222 (tp) REVERT: C 604 MET cc_start: 0.7239 (pmm) cc_final: 0.6790 (pmm) outliers start: 0 outliers final: 0 residues processed: 763 average time/residue: 0.3646 time to fit residues: 419.9369 Evaluate side-chains 708 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 708 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 87 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 94 optimal weight: 0.3980 chunk 82 optimal weight: 0.0970 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 321 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN A 721 HIS A 922 ASN ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 104 GLN C 513 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097085 restraints weight = 43845.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102117 restraints weight = 22472.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103945 restraints weight = 11708.789| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23074 Z= 0.126 Angle : 0.716 21.313 31629 Z= 0.356 Chirality : 0.045 0.202 3593 Planarity : 0.005 0.081 3753 Dihedral : 13.849 77.578 3988 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2567 helix: 0.25 (0.19), residues: 785 sheet: -0.54 (0.22), residues: 574 loop : -2.04 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 304 HIS 0.010 0.001 HIS B 57 PHE 0.022 0.001 PHE B 684 TYR 0.028 0.001 TYR C 184 ARG 0.009 0.001 ARG E1101 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 855) hydrogen bonds : angle 5.01007 ( 2328) metal coordination : bond 0.00724 ( 3) metal coordination : angle 11.73853 ( 9) covalent geometry : bond 0.00278 (23071) covalent geometry : angle 0.68822 (31620) ********************** 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 779 residues out of total 2297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 779 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7286 (ttp-170) cc_final: 0.6850 (ttp-170) REVERT: A 43 GLU cc_start: 0.7695 (tt0) cc_final: 0.7363 (tp30) REVERT: A 52 LYS cc_start: 0.9191 (mmpt) cc_final: 0.8726 (tmtt) REVERT: A 75 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 121 GLN cc_start: 0.8312 (mp10) cc_final: 0.7704 (mp10) REVERT: A 122 GLU cc_start: 0.7800 (tp30) cc_final: 0.7384 (tp30) REVERT: A 131 GLN cc_start: 0.8520 (mp10) cc_final: 0.8241 (mp10) REVERT: A 136 MET cc_start: 0.8046 (pmm) cc_final: 0.7729 (pmm) REVERT: A 189 LEU cc_start: 0.8676 (tp) cc_final: 0.8253 (tp) REVERT: A 220 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8427 (mtpp) REVERT: A 261 ASN cc_start: 0.8207 (m110) cc_final: 0.7640 (t0) REVERT: A 262 GLN cc_start: 0.8325 (pm20) cc_final: 0.8072 (pm20) REVERT: A 285 ASP cc_start: 0.8080 (t0) cc_final: 0.7667 (t0) REVERT: A 337 SER cc_start: 0.7443 (m) cc_final: 0.7156 (t) REVERT: A 378 ASP cc_start: 0.7447 (m-30) cc_final: 0.6954 (m-30) REVERT: A 380 SER cc_start: 0.9100 (t) cc_final: 0.8894 (t) REVERT: A 415 THR cc_start: 0.8178 (m) cc_final: 0.7916 (t) REVERT: A 443 ASP cc_start: 0.7599 (t0) cc_final: 0.7260 (t0) REVERT: A 487 LYS cc_start: 0.8644 (tppt) cc_final: 0.8035 (mmmt) REVERT: A 529 HIS cc_start: 0.8173 (m-70) cc_final: 0.7894 (m90) REVERT: A 567 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8492 (mtmm) REVERT: A 573 LEU cc_start: 0.7975 (tp) cc_final: 0.7729 (mp) REVERT: A 580 LYS cc_start: 0.8250 (tmmt) cc_final: 0.7848 (tmmt) REVERT: A 581 TYR cc_start: 0.8103 (t80) cc_final: 0.7871 (t80) REVERT: A 590 ILE cc_start: 0.8247 (tp) cc_final: 0.8039 (pt) REVERT: A 629 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7719 (mtp-110) REVERT: A 660 CYS cc_start: 0.8136 (t) cc_final: 0.7495 (p) REVERT: A 661 GLN cc_start: 0.8386 (pm20) cc_final: 0.7768 (pm20) REVERT: A 696 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7120 (mtp180) REVERT: A 731 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8083 (tptp) REVERT: A 737 MET cc_start: 0.6088 (pmm) cc_final: 0.5845 (pmm) REVERT: A 739 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8381 (ttpp) REVERT: A 744 CYS cc_start: 0.7865 (p) cc_final: 0.7550 (p) REVERT: A 753 ASN cc_start: 0.8797 (m110) cc_final: 0.8320 (m-40) REVERT: A 767 VAL cc_start: 0.8610 (m) cc_final: 0.8116 (t) REVERT: A 834 LYS cc_start: 0.7706 (mttm) cc_final: 0.7250 (mttm) REVERT: A 846 LYS cc_start: 0.8119 (tptp) cc_final: 0.7871 (tptp) REVERT: A 850 GLU cc_start: 0.7652 (mp0) cc_final: 0.7269 (pm20) REVERT: A 856 GLN cc_start: 0.8062 (tp40) cc_final: 0.7751 (tp40) REVERT: A 860 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 893 HIS cc_start: 0.8262 (m90) cc_final: 0.7967 (m90) REVERT: A 898 TYR cc_start: 0.5902 (t80) cc_final: 0.5352 (t80) REVERT: A 909 LYS cc_start: 0.8225 (mppt) cc_final: 0.7954 (mttp) REVERT: A 920 PHE cc_start: 0.7707 (t80) cc_final: 0.7291 (t80) REVERT: A 924 LEU cc_start: 0.8795 (mp) cc_final: 0.8462 (mp) REVERT: A 933 ARG cc_start: 0.6561 (tpp-160) cc_final: 0.6143 (mmt180) REVERT: A 947 ILE cc_start: 0.7880 (mm) cc_final: 0.7655 (mm) REVERT: A 1008 MET cc_start: 0.7439 (ppp) cc_final: 0.6992 (ppp) REVERT: A 1009 PHE cc_start: 0.7009 (m-10) cc_final: 0.6759 (m-10) REVERT: A 1032 LEU cc_start: 0.7974 (tp) cc_final: 0.7771 (tp) REVERT: A 1112 SER cc_start: 0.8564 (m) cc_final: 0.8351 (p) REVERT: A 1135 LYS cc_start: 0.7699 (pttp) cc_final: 0.7426 (pttp) REVERT: A 1228 ASN cc_start: 0.8887 (m110) cc_final: 0.8637 (m-40) REVERT: A 1237 TYR cc_start: 0.8221 (t80) cc_final: 0.7855 (t80) REVERT: A 1238 HIS cc_start: 0.8077 (p-80) cc_final: 0.7855 (p-80) REVERT: B 55 ASN cc_start: 0.7869 (m110) cc_final: 0.7607 (m110) REVERT: B 99 LYS cc_start: 0.8535 (pttm) cc_final: 0.8311 (ptpp) REVERT: B 148 GLU cc_start: 0.7284 (tm-30) cc_final: 0.7016 (tm-30) REVERT: B 150 MET cc_start: 0.7623 (ptp) cc_final: 0.7021 (ppp) REVERT: B 152 LEU cc_start: 0.9033 (mt) cc_final: 0.8647 (mt) REVERT: B 163 LEU cc_start: 0.8364 (mp) cc_final: 0.7966 (mm) REVERT: B 184 ASP cc_start: 0.7475 (t0) cc_final: 0.6994 (t0) REVERT: B 193 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 238 LEU cc_start: 0.7673 (tp) cc_final: 0.7471 (tp) REVERT: B 256 LYS cc_start: 0.8528 (tppp) cc_final: 0.8196 (tmtt) REVERT: B 367 LEU cc_start: 0.7941 (tp) cc_final: 0.7351 (tp) REVERT: B 377 GLU cc_start: 0.7971 (tt0) cc_final: 0.7082 (tt0) REVERT: B 381 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6367 (tm-30) REVERT: B 382 ILE cc_start: 0.8287 (mp) cc_final: 0.7756 (mp) REVERT: B 393 ASP cc_start: 0.7727 (m-30) cc_final: 0.7431 (m-30) REVERT: B 433 ARG cc_start: 0.8149 (ptp-110) cc_final: 0.7888 (ptp-170) REVERT: B 442 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7704 (mtpp) REVERT: B 447 ILE cc_start: 0.7768 (mm) cc_final: 0.7470 (mm) REVERT: B 473 ASN cc_start: 0.8742 (t0) cc_final: 0.8473 (t0) REVERT: B 474 PHE cc_start: 0.8096 (t80) cc_final: 0.7889 (t80) REVERT: B 554 ASN cc_start: 0.7073 (t0) cc_final: 0.6333 (t0) REVERT: B 566 HIS cc_start: 0.7152 (m90) cc_final: 0.6417 (m90) REVERT: B 569 GLU cc_start: 0.7771 (pm20) cc_final: 0.7373 (mp0) REVERT: B 584 SER cc_start: 0.8122 (m) cc_final: 0.7527 (p) REVERT: B 612 PHE cc_start: 0.7934 (t80) cc_final: 0.7604 (t80) REVERT: B 620 MET cc_start: 0.6970 (mmp) cc_final: 0.6674 (mmp) REVERT: B 625 ASN cc_start: 0.8448 (t0) cc_final: 0.7832 (t0) REVERT: B 628 PHE cc_start: 0.7343 (m-80) cc_final: 0.6849 (m-80) REVERT: B 638 TRP cc_start: 0.7812 (p-90) cc_final: 0.7410 (p-90) REVERT: B 643 LYS cc_start: 0.8383 (tmmt) cc_final: 0.8068 (tppt) REVERT: B 668 HIS cc_start: 0.7178 (m-70) cc_final: 0.6976 (m-70) REVERT: B 680 ASP cc_start: 0.8129 (t0) cc_final: 0.7541 (t70) REVERT: B 691 LYS cc_start: 0.8151 (ptpp) cc_final: 0.7578 (ptpt) REVERT: B 742 VAL cc_start: 0.8473 (t) cc_final: 0.8034 (p) REVERT: B 745 GLU cc_start: 0.7070 (tt0) cc_final: 0.6696 (tm-30) REVERT: B 774 GLN cc_start: 0.8435 (tp40) cc_final: 0.8171 (tp-100) REVERT: B 784 LYS cc_start: 0.8221 (tptp) cc_final: 0.7582 (tptp) REVERT: B 788 LYS cc_start: 0.8741 (tptp) cc_final: 0.8097 (tppt) REVERT: B 817 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7779 (mtpp) REVERT: C 25 GLN cc_start: 0.8815 (mt0) cc_final: 0.8458 (mt0) REVERT: C 31 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7830 (mt-10) REVERT: C 42 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8202 (mtpp) REVERT: C 69 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7216 (ptp-170) REVERT: C 77 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8141 (ptpt) REVERT: C 94 CYS cc_start: 0.8765 (t) cc_final: 0.8497 (t) REVERT: C 143 ASP cc_start: 0.7693 (t0) cc_final: 0.7266 (t0) REVERT: C 153 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6558 (tm-30) REVERT: C 154 GLN cc_start: 0.7735 (tt0) cc_final: 0.6823 (tt0) REVERT: C 166 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6617 (tm-30) REVERT: C 167 PHE cc_start: 0.7905 (m-10) cc_final: 0.7230 (m-10) REVERT: C 168 ILE cc_start: 0.8608 (tp) cc_final: 0.8391 (tp) REVERT: C 170 MET cc_start: 0.7336 (mmp) cc_final: 0.7134 (mmp) REVERT: C 200 ASN cc_start: 0.8921 (p0) cc_final: 0.8292 (p0) REVERT: C 235 MET cc_start: 0.7191 (mmm) cc_final: 0.6697 (mmm) REVERT: C 238 TYR cc_start: 0.7950 (m-10) cc_final: 0.7687 (m-10) REVERT: C 244 GLU cc_start: 0.6998 (mp0) cc_final: 0.6743 (mp0) REVERT: C 285 MET cc_start: 0.7803 (mmm) cc_final: 0.7451 (mmm) REVERT: C 288 ASP cc_start: 0.8059 (t0) cc_final: 0.6302 (t70) REVERT: C 291 ASN cc_start: 0.8635 (m-40) cc_final: 0.8416 (m110) REVERT: C 295 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7348 (mt-10) REVERT: C 297 ASP cc_start: 0.7998 (m-30) cc_final: 0.7471 (m-30) REVERT: C 300 GLN cc_start: 0.8578 (pp30) cc_final: 0.8156 (pp30) REVERT: C 340 TYR cc_start: 0.8252 (m-10) cc_final: 0.7719 (m-10) REVERT: C 347 GLU cc_start: 0.8209 (mp0) cc_final: 0.7700 (mp0) REVERT: C 367 ARG cc_start: 0.7554 (tpp-160) cc_final: 0.7220 (tpp80) REVERT: C 368 ASP cc_start: 0.7928 (m-30) cc_final: 0.7600 (m-30) REVERT: C 402 ARG cc_start: 0.8119 (tpt-90) cc_final: 0.7814 (tpt-90) REVERT: C 440 GLU cc_start: 0.7198 (pm20) cc_final: 0.6523 (pm20) REVERT: C 445 ASP cc_start: 0.7891 (m-30) cc_final: 0.7628 (m-30) REVERT: C 448 ILE cc_start: 0.8131 (pt) cc_final: 0.7774 (pt) REVERT: C 497 PHE cc_start: 0.7702 (m-80) cc_final: 0.7501 (m-80) REVERT: C 503 GLU cc_start: 0.7461 (pp20) cc_final: 0.6634 (tm-30) REVERT: C 504 GLU cc_start: 0.8178 (tp30) cc_final: 0.7819 (tp30) REVERT: C 507 ARG cc_start: 0.8248 (tmm-80) cc_final: 0.8002 (tmm-80) REVERT: C 508 ILE cc_start: 0.8326 (tp) cc_final: 0.8087 (tp) REVERT: C 512 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7053 (mt-10) REVERT: C 533 ILE cc_start: 0.9141 (mp) cc_final: 0.8808 (tp) REVERT: C 535 TYR cc_start: 0.8408 (m-80) cc_final: 0.7894 (m-80) REVERT: C 538 GLN cc_start: 0.7935 (tt0) cc_final: 0.7329 (tt0) REVERT: C 542 MET cc_start: 0.6871 (tpp) cc_final: 0.6593 (tpp) REVERT: C 543 VAL cc_start: 0.8518 (p) cc_final: 0.7841 (t) REVERT: E 939 TYR cc_start: 0.7570 (m-10) cc_final: 0.7321 (m-10) REVERT: E 983 GLN cc_start: 0.7277 (pp30) cc_final: 0.6665 (pp30) REVERT: E 985 TYR cc_start: 0.7923 (t80) cc_final: 0.7214 (t80) REVERT: E 992 TYR cc_start: 0.7674 (t80) cc_final: 0.7078 (t80) REVERT: E 997 MET cc_start: 0.7360 (mmt) cc_final: 0.7014 (mmt) REVERT: E 1007 LEU cc_start: 0.7836 (tt) cc_final: 0.7560 (tt) REVERT: E 1008 MET cc_start: 0.8097 (mmp) cc_final: 0.7542 (mmp) REVERT: E 1033 CYS cc_start: 0.8162 (m) cc_final: 0.7935 (m) REVERT: E 1095 LEU cc_start: 0.8206 (mt) cc_final: 0.7988 (mt) REVERT: E 1110 LYS cc_start: 0.8912 (tttt) cc_final: 0.8643 (tptt) REVERT: E 1115 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8517 (pp20) REVERT: E 1121 MET cc_start: 0.7026 (mtt) cc_final: 0.6809 (mmm) REVERT: E 1241 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8378 (mmtm) REVERT: C 604 MET cc_start: 0.7179 (pmm) cc_final: 0.6884 (pmm) outliers start: 0 outliers final: 0 residues processed: 779 average time/residue: 0.3658 time to fit residues: 430.9008 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 : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 54 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.0020 chunk 229 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 0.0570 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 321 GLN A 572 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 366 GLN C 495 GLN E1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097146 restraints weight = 43399.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102184 restraints weight = 22374.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104004 restraints weight = 11435.610| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23074 Z= 0.127 Angle : 0.711 20.613 31629 Z= 0.353 Chirality : 0.045 0.235 3593 Planarity : 0.005 0.061 3753 Dihedral : 13.773 77.580 3988 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.16), residues: 2567 helix: 0.28 (0.19), residues: 781 sheet: -0.52 (0.22), residues: 578 loop : -2.04 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 304 HIS 0.013 0.001 HIS B 10 PHE 0.022 0.001 PHE B 684 TYR 0.022 0.001 TYR A 917 ARG 0.012 0.001 ARG C 399 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 855) hydrogen bonds : angle 4.96882 ( 2328) metal coordination : bond 0.00840 ( 3) metal coordination : angle 11.53383 ( 9) covalent geometry : bond 0.00280 (23071) covalent geometry : angle 0.68352 (31620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9542.10 seconds wall clock time: 165 minutes 30.08 seconds (9930.08 seconds total)