Starting phenix.real_space_refine on Sun Jul 5 06:44:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i24_35131/07_2026/8i24_35131.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 110 5.49 5 Mg 1 5.21 5 S 79 5.16 5 C 16294 2.51 5 N 4589 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26321 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1753 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "C" Number of atoms: 9121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9121 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1109} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 8969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 8969 Classifications: {'peptide': 1152} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 47, 'TRANS': 1104} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 497 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1940 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain: "O" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1199 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "P" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1064 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18879 SG CYS D 817 110.155 61.027 85.810 1.00 36.83 S ATOM 19449 SG CYS D 891 106.876 60.711 87.594 1.00 31.90 S ATOM 19503 SG CYS D 898 107.208 62.776 84.361 1.00 29.86 S ATOM 19523 SG CYS D 901 107.184 59.036 84.210 1.00 29.57 S ATOM 13083 SG CYS D 83 79.097 103.867 128.741 1.00 65.67 S ATOM 13099 SG CYS D 85 77.379 104.629 131.900 1.00 67.09 S ATOM 13209 SG CYS D 98 81.230 104.240 132.156 1.00 67.73 S ATOM 13234 SG CYS D 101 79.622 101.325 131.245 1.00 62.68 S Time building chain proxies: 5.74, per 1000 atoms: 0.22 Number of scatterers: 26321 At special positions: 0 Unit cell: (135.2, 167.44, 177.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 79 16.00 P 110 15.00 Mg 1 11.99 O 5246 8.00 N 4589 7.00 C 16294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 817 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 901 " pdb=" ZN D1202 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 101 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 83 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 98 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 85 " Number of angles added : 12 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5678 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 44 sheets defined 40.8% alpha, 15.8% beta 24 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.880A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.590A pdb=" N ILE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.532A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.728A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 205 through 226 removed outlier: 3.961A pdb=" N SER A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 50 removed outlier: 3.684A pdb=" N LYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.007A pdb=" N LEU C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.670A pdb=" N LEU C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.877A pdb=" N GLY C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.581A pdb=" N ILE C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 377 through 393 removed outlier: 3.903A pdb=" N ILE C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.801A pdb=" N ILE C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 403 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 456 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.578A pdb=" N LEU C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 470 " --> pdb=" O PRO C 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 465 through 470' Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.782A pdb=" N TYR C 532 " --> pdb=" O HIS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 655 through 666 Processing helix chain 'C' and resid 684 through 693 removed outlier: 4.001A pdb=" N GLY C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 798 Processing helix chain 'C' and resid 831 through 835 removed outlier: 3.527A pdb=" N ALA C 834 " --> pdb=" O SER C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 879 Processing helix chain 'C' and resid 974 through 979 removed outlier: 4.201A pdb=" N SER C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 979 " --> pdb=" O GLY C 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 974 through 979' Processing helix chain 'C' and resid 982 through 998 Processing helix chain 'C' and resid 1010 through 1021 Processing helix chain 'C' and resid 1057 through 1061 removed outlier: 3.787A pdb=" N ASP C1060 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1101 Processing helix chain 'C' and resid 1102 through 1112 removed outlier: 3.663A pdb=" N LEU C1106 " --> pdb=" O ALA C1102 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C1107 " --> pdb=" O ALA C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1130 removed outlier: 3.870A pdb=" N VAL C1121 " --> pdb=" O VAL C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1152 removed outlier: 3.769A pdb=" N LYS C1143 " --> pdb=" O PRO C1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.748A pdb=" N VAL D 110 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 112 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 130 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 194 through 203 removed outlier: 3.556A pdb=" N VAL D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 removed outlier: 3.544A pdb=" N LEU D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 241 removed outlier: 4.105A pdb=" N VAL D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 275 through 297 removed outlier: 3.668A pdb=" N ASP D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 320 Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 382 through 389 Processing helix chain 'D' and resid 389 through 401 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.831A pdb=" N ALA D 409 " --> pdb=" O ASN D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 420 through 428 removed outlier: 3.571A pdb=" N LEU D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 541 through 551 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 616 through 630 Processing helix chain 'D' and resid 633 through 654 removed outlier: 3.634A pdb=" N ILE D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 662 removed outlier: 3.666A pdb=" N MET D 662 " --> pdb=" O ILE D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 685 Processing helix chain 'D' and resid 692 through 719 removed outlier: 3.673A pdb=" N LEU D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 736 through 745 removed outlier: 3.987A pdb=" N GLN D 742 " --> pdb=" O ASN D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 807 removed outlier: 3.982A pdb=" N HIS D 780 " --> pdb=" O PHE D 776 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 782 " --> pdb=" O SER D 778 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 790 " --> pdb=" O LEU D 786 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 842 removed outlier: 3.679A pdb=" N ILE D 842 " --> pdb=" O SER D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 879 Processing helix chain 'D' and resid 887 through 891 removed outlier: 3.811A pdb=" N CYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 917 through 928 removed outlier: 3.706A pdb=" N ILE D 921 " --> pdb=" O ALA D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 931 No H-bonds generated for 'chain 'D' and resid 929 through 931' Processing helix chain 'D' and resid 951 through 961 Processing helix chain 'D' and resid 1028 through 1036 removed outlier: 3.544A pdb=" N ILE D1032 " --> pdb=" O ASN D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1056 removed outlier: 3.608A pdb=" N VAL D1046 " --> pdb=" O GLN D1042 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D1056 " --> pdb=" O VAL D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1072 removed outlier: 4.024A pdb=" N ILE D1065 " --> pdb=" O ASN D1061 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D1067 " --> pdb=" O LYS D1063 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D1068 " --> pdb=" O HIS D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1107 removed outlier: 3.575A pdb=" N GLU D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1127 Processing helix chain 'D' and resid 1130 through 1138 removed outlier: 3.691A pdb=" N ALA D1134 " --> pdb=" O SER D1130 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN D1138 " --> pdb=" O ALA D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1151 removed outlier: 3.818A pdb=" N VAL D1143 " --> pdb=" O GLU D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1166 removed outlier: 3.700A pdb=" N ASN D1162 " --> pdb=" O GLY D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1171 through 1174 Processing helix chain 'D' and resid 1175 through 1180 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.502A pdb=" N GLU E 21 " --> pdb=" O ASN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.859A pdb=" N VAL E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 65 Processing helix chain 'F' and resid 15 through 28 removed outlier: 4.120A pdb=" N ILE F 19 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 53 removed outlier: 4.470A pdb=" N GLU F 35 " --> pdb=" O ASP F 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Proline residue: F 43 - end of helix Processing helix chain 'F' and resid 62 through 79 removed outlier: 3.979A pdb=" N SER F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 107 removed outlier: 4.110A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 122 through 129 removed outlier: 3.710A pdb=" N GLU F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 157 removed outlier: 4.289A pdb=" N SER F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 167 Processing helix chain 'F' and resid 171 through 189 removed outlier: 4.171A pdb=" N LEU F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 189 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 214 through 232 removed outlier: 5.106A pdb=" N LYS F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 245 removed outlier: 4.120A pdb=" N LYS F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.708A pdb=" N LYS B 22 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N CYS B 14 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR B 20 " --> pdb=" O CYS B 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 21 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS B 193 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 180 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 195 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR B 178 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU B 197 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL B 176 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP B 199 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.666A pdb=" N ALA B 101 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 136 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE B 58 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE B 56 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.961A pdb=" N ASN B 88 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.594A pdb=" N ALA B 128 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'A' and resid 10 through 14 removed outlier: 5.700A pdb=" N CYS A 11 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 24 " --> pdb=" O CYS A 11 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 13 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 21 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 175 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 101 removed outlier: 6.038A pdb=" N GLU A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 56 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 52 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.793A pdb=" N ASN A 88 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 108 removed outlier: 7.189A pdb=" N VAL A 107 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.714A pdb=" N MET C 13 " --> pdb=" O ALA C1002 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 68 removed outlier: 3.831A pdb=" N ILE C 61 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 65 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS C 94 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR C 67 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS C 92 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY C 113 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 93 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE C 111 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N VAL C 95 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU C 109 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 97 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU C 107 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB4, first strand: chain 'C' and resid 428 through 431 removed outlier: 3.563A pdb=" N SER C 135 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 149 removed outlier: 3.569A pdb=" N ALA C 146 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 173 removed outlier: 3.583A pdb=" N GLU C 170 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.693A pdb=" N ILE C 288 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 341 through 342 removed outlier: 3.550A pdb=" N LYS C 362 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 557 through 558 removed outlier: 6.691A pdb=" N ILE C 564 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 586 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR C 566 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 584 " --> pdb=" O THR C 566 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR C 568 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 582 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 570 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AC2, first strand: chain 'C' and resid 614 through 618 removed outlier: 4.107A pdb=" N VAL C 614 " --> pdb=" O VAL C 625 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 625 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 623 " --> pdb=" O CYS C 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 696 through 697 removed outlier: 7.289A pdb=" N ILE C 696 " --> pdb=" O ILE C 756 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 756 " --> pdb=" O ILE C 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 703 through 707 removed outlier: 7.027A pdb=" N ILE C 713 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL C 707 " --> pdb=" O GLU C 711 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 728 through 731 Processing sheet with id=AC6, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC7, first strand: chain 'C' and resid 939 through 940 removed outlier: 4.898A pdb=" N THR C1045 " --> pdb=" O PHE C 777 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 773 " --> pdb=" O MET C1049 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE C 969 " --> pdb=" O ASN C 772 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU C 774 " --> pdb=" O ILE C 969 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU C 971 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY C 776 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 790 " --> pdb=" O VAL C 970 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE C 789 " --> pdb=" O ARG C 951 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU C 953 " --> pdb=" O ILE C 789 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 791 " --> pdb=" O LEU C 953 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 939 through 940 Processing sheet with id=AC9, first strand: chain 'C' and resid 819 through 820 removed outlier: 3.527A pdb=" N THR C 816 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 921 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 815 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 919 " --> pdb=" O ASP C 815 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP C 903 " --> pdb=" O TYR C 926 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA C 928 " --> pdb=" O VAL C 901 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL C 901 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYS C 930 " --> pdb=" O GLY C 899 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N GLY C 899 " --> pdb=" O LYS C 930 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 855 through 857 removed outlier: 7.173A pdb=" N LEU C 891 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 860 through 862 Processing sheet with id=AD3, first strand: chain 'C' and resid 1063 through 1065 removed outlier: 7.454A pdb=" N LEU D 459 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 366 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU D 461 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 368 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1087 through 1089 removed outlier: 3.785A pdb=" N GLN C1087 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1154 through 1157 Processing sheet with id=AD6, first strand: chain 'D' and resid 47 through 50 removed outlier: 7.578A pdb=" N HIS D 117 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU D 50 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLU D 119 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N LEU D 120 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N ALA D 122 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL D 253 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 57 through 58 removed outlier: 4.276A pdb=" N LYS D 63 " --> pdb=" O ASN D 58 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 172 through 173 removed outlier: 7.220A pdb=" N ARG D 190 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 264 through 266 removed outlier: 6.438A pdb=" N PHE D 272 " --> pdb=" O TYR F 113 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 538 through 539 removed outlier: 3.677A pdb=" N VAL D 562 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 575 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 566 " --> pdb=" O LYS D 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 812 through 814 Processing sheet with id=AE3, first strand: chain 'D' and resid 823 through 825 removed outlier: 4.148A pdb=" N VAL D 883 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 828 through 829 removed outlier: 6.976A pdb=" N ILE D 828 " --> pdb=" O ILE D 835 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 851 through 852 removed outlier: 7.238A pdb=" N ILE D 851 " --> pdb=" O ILE D 860 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 980 through 981 removed outlier: 3.857A pdb=" N GLU D 987 " --> pdb=" O ILE D1002 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1091 through 1093 removed outlier: 7.216A pdb=" N VAL D1113 " --> pdb=" O GLU D1079 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1183 through 1184 removed outlier: 3.688A pdb=" N THR E 69 " --> pdb=" O SER D1184 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 6.95 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4287 1.30 - 1.43: 6672 1.43 - 1.56: 15662 1.56 - 1.68: 215 1.68 - 1.81: 136 Bond restraints: 26972 Sorted by residual: bond pdb=" CA GLU F 218 " pdb=" C GLU F 218 " ideal model delta sigma weight residual 1.524 1.438 0.087 1.24e-02 6.50e+03 4.87e+01 bond pdb=" C ILE F 217 " pdb=" N GLU F 218 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.23e-02 6.61e+03 3.85e+01 bond pdb=" C ARG F 215 " pdb=" O ARG F 215 " ideal model delta sigma weight residual 1.236 1.308 -0.073 1.28e-02 6.10e+03 3.21e+01 bond pdb=" CA ILE F 217 " pdb=" C ILE F 217 " ideal model delta sigma weight residual 1.523 1.443 0.080 1.42e-02 4.96e+03 3.14e+01 bond pdb=" N GLU F 218 " pdb=" CA GLU F 218 " ideal model delta sigma weight residual 1.459 1.397 0.062 1.17e-02 7.31e+03 2.78e+01 ... (remaining 26967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 36426 2.28 - 4.56: 398 4.56 - 6.84: 46 6.84 - 9.12: 11 9.12 - 11.40: 6 Bond angle restraints: 36887 Sorted by residual: angle pdb=" N LYS C 353 " pdb=" CA LYS C 353 " pdb=" C LYS C 353 " ideal model delta sigma weight residual 111.28 122.68 -11.40 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 111.36 120.89 -9.53 1.09e+00 8.42e-01 7.64e+01 angle pdb=" N PRO C 352 " pdb=" CA PRO C 352 " pdb=" C PRO C 352 " ideal model delta sigma weight residual 114.80 104.87 9.93 1.42e+00 4.96e-01 4.89e+01 angle pdb=" C ASP C 351 " pdb=" N PRO C 352 " pdb=" CA PRO C 352 " ideal model delta sigma weight residual 120.89 113.08 7.81 1.21e+00 6.83e-01 4.16e+01 angle pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" C ASP E 24 " ideal model delta sigma weight residual 110.56 121.27 -10.71 1.94e+00 2.66e-01 3.05e+01 ... (remaining 36882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 14302 21.55 - 43.11: 1490 43.11 - 64.66: 475 64.66 - 86.21: 38 86.21 - 107.76: 6 Dihedral angle restraints: 16311 sinusoidal: 7479 harmonic: 8832 Sorted by residual: dihedral pdb=" CA SER C1114 " pdb=" C SER C1114 " pdb=" N ASP C1115 " pdb=" CA ASP C1115 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN D 717 " pdb=" C ASN D 717 " pdb=" N ASN D 718 " pdb=" CA ASN D 718 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ALA C 870 " pdb=" C ALA C 870 " pdb=" N GLU C 871 " pdb=" CA GLU C 871 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 16308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4108 0.111 - 0.223: 95 0.223 - 0.334: 8 0.334 - 0.446: 3 0.446 - 0.557: 1 Chirality restraints: 4215 Sorted by residual: chirality pdb=" C3' DT O 55 " pdb=" C4' DT O 55 " pdb=" O3' DT O 55 " pdb=" C2' DT O 55 " both_signs ideal model delta sigma weight residual False -2.73 -2.17 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA ASN D 28 " pdb=" N ASN D 28 " pdb=" C ASN D 28 " pdb=" CB ASN D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 4212 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 601 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO D 602 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO D 602 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 602 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 819 " -0.062 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO C 820 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 820 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 820 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 351 " 0.049 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO C 352 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " 0.045 5.00e-02 4.00e+02 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 230 2.60 - 3.18: 21028 3.18 - 3.75: 40543 3.75 - 4.33: 56967 4.33 - 4.90: 91811 Nonbonded interactions: 210579 Sorted by model distance: nonbonded pdb=" OD1 ASP D 474 " pdb="MG MG D1203 " model vdw 2.029 2.170 nonbonded pdb=" OD2 ASP D 474 " pdb="MG MG D1203 " model vdw 2.068 2.170 nonbonded pdb=" OG1 THR A 189 " pdb=" OE2 GLU D 455 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP C 718 " pdb=" NZ LYS C 720 " model vdw 2.203 3.120 nonbonded pdb=" O SER C 140 " pdb=" OH TYR C 144 " model vdw 2.209 3.040 ... (remaining 210574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 4 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 32.490 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.004 0.087 26980 Z= 0.234 Angle : 0.615 13.377 36899 Z= 0.373 Chirality : 0.049 0.557 4215 Planarity : 0.004 0.117 4386 Dihedral : 18.263 107.764 10633 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.91 % Allowed : 0.76 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3054 helix: 0.35 (0.16), residues: 1113 sheet: 0.24 (0.31), residues: 311 loop : -0.84 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 55 TYR 0.013 0.001 TYR D 649 PHE 0.012 0.001 PHE C 491 TRP 0.013 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.23 (26972) covalent geometry : angle 0.60230 / 0.37 (36887) hydrogen bonds : bond 0.19046 / 12.37 ( 992) hydrogen bonds : angle 7.03443 / 4.94 ( 2796) metal coordination : bond 0.00748 / 0.36 ( 8) metal coordination : angle 7.01700 / 3.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 575 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7770 (m-30) cc_final: 0.7397 (m-30) REVERT: A 17 ASP cc_start: 0.7489 (t0) cc_final: 0.7250 (t0) REVERT: C 362 LYS cc_start: 0.7061 (mmpt) cc_final: 0.6722 (mmpt) REVERT: C 963 ASP cc_start: 0.8131 (p0) cc_final: 0.7916 (p0) REVERT: D 412 MET cc_start: 0.8238 (mtp) cc_final: 0.7943 (mtp) REVERT: D 706 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6268 (mm-30) REVERT: D 788 ASP cc_start: 0.7428 (m-30) cc_final: 0.7054 (m-30) REVERT: F 26 ILE cc_start: 0.7811 (mm) cc_final: 0.7499 (mm) REVERT: F 110 LYS cc_start: 0.8610 (mmpt) cc_final: 0.8292 (mmmt) REVERT: F 219 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.4934 (ptp90) outliers start: 24 outliers final: 5 residues processed: 595 average time/residue: 0.2028 time to fit residues: 184.6068 Evaluate side-chains 514 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 508 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN C 784 ASN C 929 GLN D 736 ASN E 45 ASN F 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.145366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.102006 restraints weight = 31857.785| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.59 r_work: 0.2799 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26980 Z= 0.172 Angle : 0.585 10.164 36899 Z= 0.314 Chirality : 0.046 0.246 4215 Planarity : 0.005 0.077 4386 Dihedral : 18.428 94.739 4590 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.67 % Allowed : 8.90 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3054 helix: 0.46 (0.16), residues: 1134 sheet: 0.29 (0.30), residues: 318 loop : -0.91 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 55 TYR 0.016 0.001 TYR D 895 PHE 0.016 0.001 PHE C 491 TRP 0.015 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (26972) covalent geometry : angle 0.57893 / 0.31 (36887) hydrogen bonds : bond 0.05411 / 3.69 ( 992) hydrogen bonds : angle 5.04561 / 3.60 ( 2796) metal coordination : bond 0.00727 / 0.37 ( 8) metal coordination : angle 4.59691 / 2.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 525 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: B 46 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 88 ASN cc_start: 0.8864 (p0) cc_final: 0.8594 (p0) REVERT: B 205 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8398 (mptt) REVERT: B 226 ASP cc_start: 0.7758 (m-30) cc_final: 0.7372 (m-30) REVERT: A 17 ASP cc_start: 0.8088 (t0) cc_final: 0.7734 (t0) REVERT: C 112 MET cc_start: 0.8284 (mtt) cc_final: 0.7933 (mtt) REVERT: C 362 LYS cc_start: 0.7263 (mmpt) cc_final: 0.7020 (mmpt) REVERT: C 367 MET cc_start: 0.6834 (mmp) cc_final: 0.6508 (mmp) REVERT: C 703 VAL cc_start: 0.8254 (t) cc_final: 0.8027 (p) REVERT: D 137 MET cc_start: 0.8831 (mtm) cc_final: 0.8618 (mtm) REVERT: D 287 ARG cc_start: 0.8047 (tpm170) cc_final: 0.7833 (tpm170) REVERT: D 412 MET cc_start: 0.8475 (mtp) cc_final: 0.8242 (mtp) REVERT: D 671 TYR cc_start: 0.6848 (m-10) cc_final: 0.6455 (m-10) REVERT: D 706 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6804 (mm-30) REVERT: D 788 ASP cc_start: 0.7977 (m-30) cc_final: 0.7550 (m-30) REVERT: D 866 MET cc_start: 0.8687 (tpp) cc_final: 0.7966 (tpp) REVERT: E 51 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: F 110 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8442 (mmmt) outliers start: 44 outliers final: 30 residues processed: 553 average time/residue: 0.1966 time to fit residues: 165.9402 Evaluate side-chains 541 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 509 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 0 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 138 optimal weight: 0.0870 chunk 307 optimal weight: 9.9990 chunk 209 optimal weight: 0.0970 chunk 215 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 639 GLN D 399 ASN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.099553 restraints weight = 31934.520| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.61 r_work: 0.2776 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26980 Z= 0.182 Angle : 0.572 9.323 36899 Z= 0.308 Chirality : 0.045 0.217 4215 Planarity : 0.004 0.069 4386 Dihedral : 18.389 92.452 4587 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.28 % Allowed : 11.83 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3054 helix: 0.43 (0.16), residues: 1138 sheet: 0.19 (0.30), residues: 329 loop : -0.97 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 608 TYR 0.016 0.001 TYR D 649 PHE 0.019 0.001 PHE F 72 TRP 0.018 0.002 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (26972) covalent geometry : angle 0.56646 / 0.31 (36887) hydrogen bonds : bond 0.04921 / 3.35 ( 992) hydrogen bonds : angle 4.75204 / 3.38 ( 2796) metal coordination : bond 0.00759 / 0.39 ( 8) metal coordination : angle 4.54926 / 2.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 531 time to evaluate : 1.022 Fit side-chains REVERT: B 6 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8151 (tppt) REVERT: B 88 ASN cc_start: 0.8852 (p0) cc_final: 0.8590 (p0) REVERT: B 191 TYR cc_start: 0.6213 (p90) cc_final: 0.5001 (p90) REVERT: A 17 ASP cc_start: 0.8076 (t0) cc_final: 0.7694 (t0) REVERT: C 79 GLU cc_start: 0.7670 (pm20) cc_final: 0.7460 (mp0) REVERT: C 112 MET cc_start: 0.8239 (mtt) cc_final: 0.7869 (mtt) REVERT: C 362 LYS cc_start: 0.7239 (mmpt) cc_final: 0.6948 (mmpt) REVERT: C 367 MET cc_start: 0.7037 (mmp) cc_final: 0.6645 (mmp) REVERT: D 153 TYR cc_start: 0.7951 (m-10) cc_final: 0.7558 (m-10) REVERT: D 412 MET cc_start: 0.8544 (mtp) cc_final: 0.8290 (mtp) REVERT: D 671 TYR cc_start: 0.6911 (m-10) cc_final: 0.6552 (m-10) REVERT: D 706 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6779 (mm-30) REVERT: D 788 ASP cc_start: 0.7992 (m-30) cc_final: 0.7550 (m-30) REVERT: D 866 MET cc_start: 0.8674 (tpp) cc_final: 0.8008 (tpp) REVERT: F 127 ARG cc_start: 0.5870 (mtt-85) cc_final: 0.5667 (mtt-85) outliers start: 60 outliers final: 43 residues processed: 569 average time/residue: 0.2033 time to fit residues: 176.7533 Evaluate side-chains 556 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 513 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 120 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.139723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.096472 restraints weight = 31831.910| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.60 r_work: 0.2724 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 26980 Z= 0.295 Angle : 0.677 11.094 36899 Z= 0.357 Chirality : 0.049 0.202 4215 Planarity : 0.005 0.072 4386 Dihedral : 18.500 97.262 4587 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.74 % Allowed : 14.98 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3054 helix: 0.06 (0.15), residues: 1142 sheet: 0.01 (0.29), residues: 342 loop : -1.19 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 139 TYR 0.018 0.002 TYR D 649 PHE 0.021 0.002 PHE F 72 TRP 0.025 0.002 TRP C 999 HIS 0.007 0.001 HIS C 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.29 (26972) covalent geometry : angle 0.66755 / 0.36 (36887) hydrogen bonds : bond 0.05950 / 4.03 ( 992) hydrogen bonds : angle 4.86387 / 3.47 ( 2796) metal coordination : bond 0.01169 / 0.59 ( 8) metal coordination : angle 6.42265 / 3.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 496 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 191 TYR cc_start: 0.6352 (p90) cc_final: 0.5077 (p90) REVERT: A 17 ASP cc_start: 0.8147 (t0) cc_final: 0.7707 (t0) REVERT: A 140 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7056 (mmp) REVERT: C 112 MET cc_start: 0.8137 (mtt) cc_final: 0.7781 (mtt) REVERT: C 149 ILE cc_start: 0.7428 (mt) cc_final: 0.7145 (mm) REVERT: C 362 LYS cc_start: 0.7270 (mmpt) cc_final: 0.6953 (mmpt) REVERT: C 367 MET cc_start: 0.6977 (mmp) cc_final: 0.6581 (mmp) REVERT: D 153 TYR cc_start: 0.7980 (m-10) cc_final: 0.7593 (m-10) REVERT: D 193 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7896 (ttp) REVERT: D 287 ARG cc_start: 0.8212 (tpm170) cc_final: 0.7888 (tpm170) REVERT: D 426 GLU cc_start: 0.8418 (mp0) cc_final: 0.7896 (mp0) REVERT: D 561 LYS cc_start: 0.8406 (mmtp) cc_final: 0.7939 (mppt) REVERT: D 671 TYR cc_start: 0.7213 (m-10) cc_final: 0.6710 (m-10) REVERT: D 706 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6844 (mm-30) REVERT: D 788 ASP cc_start: 0.8063 (m-30) cc_final: 0.7592 (m-30) outliers start: 72 outliers final: 54 residues processed: 541 average time/residue: 0.2017 time to fit residues: 166.2784 Evaluate side-chains 546 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 490 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 140 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 639 GLN D 399 ASN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.143358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.099962 restraints weight = 31843.099| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.61 r_work: 0.2787 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26980 Z= 0.127 Angle : 0.541 11.068 36899 Z= 0.293 Chirality : 0.044 0.214 4215 Planarity : 0.004 0.067 4386 Dihedral : 18.324 97.046 4587 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.28 % Allowed : 16.62 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 3054 helix: 0.41 (0.16), residues: 1133 sheet: 0.06 (0.29), residues: 348 loop : -1.01 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 608 TYR 0.015 0.001 TYR D 649 PHE 0.023 0.001 PHE F 72 TRP 0.011 0.001 TRP C 999 HIS 0.006 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (26972) covalent geometry : angle 0.53728 / 0.29 (36887) hydrogen bonds : bond 0.04208 / 2.84 ( 992) hydrogen bonds : angle 4.56856 / 3.25 ( 2796) metal coordination : bond 0.00595 / 0.32 ( 8) metal coordination : angle 3.66490 / 1.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 536 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8895 (p0) cc_final: 0.8638 (p0) REVERT: A 17 ASP cc_start: 0.8114 (t0) cc_final: 0.7681 (t0) REVERT: C 59 ASN cc_start: 0.6978 (p0) cc_final: 0.5054 (t0) REVERT: C 149 ILE cc_start: 0.7359 (mt) cc_final: 0.7081 (mm) REVERT: C 362 LYS cc_start: 0.7229 (mmpt) cc_final: 0.6957 (mmpt) REVERT: C 367 MET cc_start: 0.6990 (mmp) cc_final: 0.6605 (mmp) REVERT: C 608 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7949 (mtp-110) REVERT: D 561 LYS cc_start: 0.8397 (mmtp) cc_final: 0.7948 (mppt) REVERT: D 671 TYR cc_start: 0.6994 (m-10) cc_final: 0.6573 (m-10) REVERT: D 706 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6708 (mm-30) REVERT: D 788 ASP cc_start: 0.7982 (m-30) cc_final: 0.7528 (m-30) REVERT: D 1056 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8100 (mm-40) REVERT: D 1099 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6726 (pt0) REVERT: E 51 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6327 (pm20) outliers start: 60 outliers final: 39 residues processed: 576 average time/residue: 0.1967 time to fit residues: 173.5595 Evaluate side-chains 559 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 518 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 250 optimal weight: 0.0010 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 259 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.145125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.102089 restraints weight = 31726.294| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.59 r_work: 0.2812 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26980 Z= 0.110 Angle : 0.520 11.819 36899 Z= 0.280 Chirality : 0.043 0.210 4215 Planarity : 0.004 0.064 4386 Dihedral : 18.194 94.862 4587 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.05 % Allowed : 18.06 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3054 helix: 0.63 (0.16), residues: 1135 sheet: 0.17 (0.29), residues: 348 loop : -0.89 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 608 TYR 0.016 0.001 TYR D 649 PHE 0.024 0.001 PHE F 72 TRP 0.008 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (26972) covalent geometry : angle 0.51696 / 0.28 (36887) hydrogen bonds : bond 0.03740 / 2.55 ( 992) hydrogen bonds : angle 4.39996 / 3.11 ( 2796) metal coordination : bond 0.00497 / 0.27 ( 8) metal coordination : angle 3.14011 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 554 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8501 (tppt) cc_final: 0.8277 (tppt) REVERT: B 88 ASN cc_start: 0.8828 (p0) cc_final: 0.8554 (p0) REVERT: B 205 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8368 (mptt) REVERT: B 226 ASP cc_start: 0.7453 (m-30) cc_final: 0.7144 (m-30) REVERT: A 17 ASP cc_start: 0.8143 (t0) cc_final: 0.7704 (t0) REVERT: C 37 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8216 (tp40) REVERT: C 59 ASN cc_start: 0.6861 (p0) cc_final: 0.5366 (t0) REVERT: C 79 GLU cc_start: 0.7596 (pm20) cc_final: 0.7309 (mp0) REVERT: C 149 ILE cc_start: 0.7317 (mt) cc_final: 0.7008 (mm) REVERT: C 194 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7051 (tt) REVERT: C 362 LYS cc_start: 0.7225 (mmpt) cc_final: 0.6953 (mmtt) REVERT: C 367 MET cc_start: 0.7039 (mmp) cc_final: 0.6639 (mmp) REVERT: C 799 ASP cc_start: 0.7981 (p0) cc_final: 0.7696 (p0) REVERT: D 149 GLU cc_start: 0.8680 (tt0) cc_final: 0.8465 (tt0) REVERT: D 426 GLU cc_start: 0.8419 (mp0) cc_final: 0.7912 (mp0) REVERT: D 551 ASN cc_start: 0.8512 (m-40) cc_final: 0.8157 (m-40) REVERT: D 561 LYS cc_start: 0.8428 (mmtp) cc_final: 0.7947 (mppt) REVERT: D 671 TYR cc_start: 0.6965 (m-10) cc_final: 0.6544 (m-10) REVERT: D 706 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6691 (mm-30) REVERT: D 788 ASP cc_start: 0.7956 (m-30) cc_final: 0.7490 (m-30) REVERT: D 1099 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6670 (pt0) REVERT: E 51 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6274 (pm20) REVERT: F 126 GLU cc_start: 0.6907 (mp0) cc_final: 0.6390 (mp0) outliers start: 54 outliers final: 39 residues processed: 585 average time/residue: 0.1925 time to fit residues: 172.8620 Evaluate side-chains 570 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 528 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 150 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 784 ASN C1076 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.140506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.097232 restraints weight = 31844.636| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.60 r_work: 0.2743 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 26980 Z= 0.247 Angle : 0.627 10.807 36899 Z= 0.329 Chirality : 0.047 0.187 4215 Planarity : 0.005 0.068 4386 Dihedral : 18.315 96.959 4587 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.74 % Allowed : 18.56 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3054 helix: 0.28 (0.15), residues: 1154 sheet: 0.11 (0.29), residues: 343 loop : -1.05 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 139 TYR 0.017 0.002 TYR D 649 PHE 0.027 0.002 PHE F 72 TRP 0.020 0.002 TRP C 999 HIS 0.006 0.001 HIS C 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (26972) covalent geometry : angle 0.61897 / 0.33 (36887) hydrogen bonds : bond 0.05174 / 3.52 ( 992) hydrogen bonds : angle 4.64306 / 3.31 ( 2796) metal coordination : bond 0.00999 / 0.51 ( 8) metal coordination : angle 5.52682 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 507 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8934 (p0) cc_final: 0.8660 (p0) REVERT: A 17 ASP cc_start: 0.8144 (t0) cc_final: 0.7680 (t0) REVERT: A 140 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7064 (mmp) REVERT: C 59 ASN cc_start: 0.6761 (p0) cc_final: 0.6499 (p0) REVERT: C 149 ILE cc_start: 0.7413 (mt) cc_final: 0.7129 (mm) REVERT: C 194 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7201 (mp) REVERT: C 362 LYS cc_start: 0.7297 (mmpt) cc_final: 0.7024 (mmtt) REVERT: C 367 MET cc_start: 0.6989 (mmp) cc_final: 0.6617 (mmp) REVERT: D 426 GLU cc_start: 0.8446 (mp0) cc_final: 0.7907 (mp0) REVERT: D 671 TYR cc_start: 0.7025 (m-10) cc_final: 0.6555 (m-10) REVERT: D 706 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6767 (mm-30) REVERT: D 788 ASP cc_start: 0.8026 (m-30) cc_final: 0.7542 (m-30) REVERT: D 935 MET cc_start: 0.5358 (ptp) cc_final: 0.4958 (tpp) REVERT: D 1099 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: E 51 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6370 (pm20) outliers start: 72 outliers final: 59 residues processed: 558 average time/residue: 0.1881 time to fit residues: 161.4455 Evaluate side-chains 559 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 496 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1073 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 226 optimal weight: 0.0060 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.142378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.099406 restraints weight = 31741.847| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.58 r_work: 0.2763 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26980 Z= 0.178 Angle : 0.574 12.196 36899 Z= 0.305 Chirality : 0.045 0.215 4215 Planarity : 0.004 0.066 4386 Dihedral : 18.288 98.124 4587 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 19.09 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3054 helix: 0.33 (0.15), residues: 1149 sheet: 0.03 (0.29), residues: 348 loop : -1.02 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 608 TYR 0.016 0.001 TYR D 649 PHE 0.026 0.001 PHE F 72 TRP 0.016 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (26972) covalent geometry : angle 0.56847 / 0.31 (36887) hydrogen bonds : bond 0.04563 / 3.09 ( 992) hydrogen bonds : angle 4.57361 / 3.25 ( 2796) metal coordination : bond 0.00788 / 0.41 ( 8) metal coordination : angle 4.42107 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 516 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8928 (p0) cc_final: 0.8655 (p0) REVERT: B 205 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8417 (mptt) REVERT: A 17 ASP cc_start: 0.8164 (t0) cc_final: 0.7705 (t0) REVERT: A 140 MET cc_start: 0.7735 (mmp) cc_final: 0.7034 (mtp) REVERT: C 59 ASN cc_start: 0.6917 (p0) cc_final: 0.5588 (t0) REVERT: C 79 GLU cc_start: 0.7645 (pm20) cc_final: 0.7361 (mp0) REVERT: C 149 ILE cc_start: 0.7424 (mt) cc_final: 0.7162 (mm) REVERT: C 362 LYS cc_start: 0.7278 (mmpt) cc_final: 0.7010 (mmtt) REVERT: C 367 MET cc_start: 0.6985 (mmp) cc_final: 0.6588 (mmp) REVERT: C 447 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7659 (mtt180) REVERT: C 608 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7941 (mtp-110) REVERT: C 745 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8372 (mmtm) REVERT: D 426 GLU cc_start: 0.8401 (mp0) cc_final: 0.7852 (mp0) REVERT: D 561 LYS cc_start: 0.8449 (mmtp) cc_final: 0.7874 (mmmt) REVERT: D 671 TYR cc_start: 0.7010 (m-10) cc_final: 0.6549 (m-10) REVERT: D 706 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6708 (mm-30) REVERT: D 788 ASP cc_start: 0.8043 (m-30) cc_final: 0.7569 (m-30) REVERT: D 1099 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: E 51 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6331 (pm20) outliers start: 63 outliers final: 54 residues processed: 560 average time/residue: 0.1937 time to fit residues: 166.0902 Evaluate side-chains 566 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 510 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 242 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 639 GLN C 784 ASN C1076 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.143519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.100363 restraints weight = 31874.009| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.61 r_work: 0.2787 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26980 Z= 0.127 Angle : 0.537 11.260 36899 Z= 0.288 Chirality : 0.043 0.194 4215 Planarity : 0.004 0.065 4386 Dihedral : 18.216 97.948 4587 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.32 % Allowed : 19.32 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3054 helix: 0.49 (0.16), residues: 1149 sheet: 0.10 (0.29), residues: 348 loop : -0.92 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 608 TYR 0.016 0.001 TYR D 649 PHE 0.026 0.001 PHE F 72 TRP 0.011 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (26972) covalent geometry : angle 0.53370 / 0.29 (36887) hydrogen bonds : bond 0.03942 / 2.67 ( 992) hydrogen bonds : angle 4.45206 / 3.15 ( 2796) metal coordination : bond 0.00581 / 0.32 ( 8) metal coordination : angle 3.52527 / 1.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 535 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8438 (tppt) cc_final: 0.8235 (tppt) REVERT: B 88 ASN cc_start: 0.8870 (p0) cc_final: 0.8602 (p0) REVERT: A 17 ASP cc_start: 0.8146 (t0) cc_final: 0.7692 (t0) REVERT: A 140 MET cc_start: 0.7695 (mmp) cc_final: 0.7251 (mtp) REVERT: C 37 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8272 (tp40) REVERT: C 59 ASN cc_start: 0.7014 (p0) cc_final: 0.5655 (t0) REVERT: C 79 GLU cc_start: 0.7585 (pm20) cc_final: 0.7337 (mp0) REVERT: C 149 ILE cc_start: 0.7391 (mt) cc_final: 0.7128 (mm) REVERT: C 189 LEU cc_start: 0.7405 (tp) cc_final: 0.7143 (tt) REVERT: C 362 LYS cc_start: 0.7276 (mmpt) cc_final: 0.7013 (mmtt) REVERT: C 367 MET cc_start: 0.6980 (mmp) cc_final: 0.6593 (mmp) REVERT: C 447 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7513 (mtt180) REVERT: C 608 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7890 (mtp-110) REVERT: C 745 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8361 (mmtm) REVERT: D 561 LYS cc_start: 0.8474 (mmtp) cc_final: 0.7922 (mmmt) REVERT: D 671 TYR cc_start: 0.6992 (m-10) cc_final: 0.6538 (m-10) REVERT: D 706 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6688 (mm-30) REVERT: D 730 GLN cc_start: 0.8266 (mp10) cc_final: 0.8043 (mp10) REVERT: D 788 ASP cc_start: 0.8019 (m-30) cc_final: 0.7556 (m-30) REVERT: D 866 MET cc_start: 0.8810 (tpp) cc_final: 0.8501 (tpp) REVERT: D 1099 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6679 (pt0) REVERT: E 51 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6234 (pm20) outliers start: 61 outliers final: 52 residues processed: 576 average time/residue: 0.1971 time to fit residues: 173.6086 Evaluate side-chains 584 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 530 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 52 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 313 optimal weight: 30.0000 chunk 201 optimal weight: 4.9990 chunk 171 optimal weight: 0.4980 chunk 173 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 233 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 639 GLN C 784 ASN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.142442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.099661 restraints weight = 31509.364| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.58 r_work: 0.2767 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26980 Z= 0.183 Angle : 0.581 11.924 36899 Z= 0.308 Chirality : 0.045 0.199 4215 Planarity : 0.004 0.066 4386 Dihedral : 18.236 98.313 4587 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 19.54 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3054 helix: 0.40 (0.16), residues: 1155 sheet: 0.10 (0.29), residues: 347 loop : -0.99 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 608 TYR 0.017 0.001 TYR D 649 PHE 0.028 0.001 PHE F 72 TRP 0.015 0.002 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (26972) covalent geometry : angle 0.57508 / 0.31 (36887) hydrogen bonds : bond 0.04519 / 3.07 ( 992) hydrogen bonds : angle 4.54168 / 3.23 ( 2796) metal coordination : bond 0.00783 / 0.41 ( 8) metal coordination : angle 4.49658 / 2.38 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 519 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8897 (p0) cc_final: 0.8620 (p0) REVERT: A 17 ASP cc_start: 0.8125 (t0) cc_final: 0.7669 (t0) REVERT: A 30 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8361 (ttp-170) REVERT: A 113 LYS cc_start: 0.6824 (mmtm) cc_final: 0.6591 (mmtt) REVERT: A 140 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7436 (mmm) REVERT: C 59 ASN cc_start: 0.6922 (p0) cc_final: 0.6650 (p0) REVERT: C 79 GLU cc_start: 0.7618 (pm20) cc_final: 0.7358 (mp0) REVERT: C 149 ILE cc_start: 0.7419 (mt) cc_final: 0.7150 (mm) REVERT: C 189 LEU cc_start: 0.7395 (tp) cc_final: 0.7180 (tt) REVERT: C 362 LYS cc_start: 0.7302 (mmpt) cc_final: 0.7033 (mmtt) REVERT: C 367 MET cc_start: 0.6963 (mmp) cc_final: 0.6581 (mmp) REVERT: C 447 ARG cc_start: 0.7857 (mmt90) cc_final: 0.7619 (mtt180) REVERT: C 608 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7898 (mtp-110) REVERT: C 745 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8427 (mmtm) REVERT: D 561 LYS cc_start: 0.8481 (mmtp) cc_final: 0.7918 (mmmt) REVERT: D 671 TYR cc_start: 0.7011 (m-10) cc_final: 0.6490 (m-10) REVERT: D 706 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6719 (mm-30) REVERT: D 730 GLN cc_start: 0.8250 (mp10) cc_final: 0.7988 (mp10) REVERT: D 788 ASP cc_start: 0.8049 (m-30) cc_final: 0.7588 (m-30) REVERT: D 866 MET cc_start: 0.8775 (tpp) cc_final: 0.8281 (tpp) REVERT: D 1099 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6724 (pt0) REVERT: E 51 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6347 (pm20) outliers start: 61 outliers final: 55 residues processed: 558 average time/residue: 0.1958 time to fit residues: 166.7461 Evaluate side-chains 573 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 515 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1073 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 173 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 252 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN C 639 GLN C1076 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.143736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.100973 restraints weight = 31568.722| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.58 r_work: 0.2792 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26980 Z= 0.123 Angle : 0.539 12.224 36899 Z= 0.288 Chirality : 0.043 0.189 4215 Planarity : 0.004 0.065 4386 Dihedral : 18.174 98.061 4587 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.24 % Allowed : 19.62 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3054 helix: 0.53 (0.16), residues: 1150 sheet: 0.14 (0.29), residues: 348 loop : -0.89 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 608 TYR 0.016 0.001 TYR D 649 PHE 0.027 0.001 PHE F 72 TRP 0.010 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (26972) covalent geometry : angle 0.53540 / 0.29 (36887) hydrogen bonds : bond 0.03900 / 2.64 ( 992) hydrogen bonds : angle 4.44161 / 3.15 ( 2796) metal coordination : bond 0.00526 / 0.28 ( 8) metal coordination : angle 3.42481 / 1.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7620.00 seconds wall clock time: 130 minutes 58.33 seconds (7858.33 seconds total)