Starting phenix.real_space_refine on Mon Aug 25 07:33:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i24_35131/08_2025/8i24_35131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i24_35131/08_2025/8i24_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_35131/08_2025/8i24_35131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i24_35131/08_2025/8i24_35131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i24_35131/08_2025/8i24_35131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i24_35131/08_2025/8i24_35131.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.85, 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: 2.19 Conformation dependent library (CDL) restraints added in 990.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.02 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: 6.42 Time building geometry restraints manager: 2.93 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: 36398 2.28 - 4.56: 425 4.56 - 6.84: 47 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 - 0.097: 3967 0.097 - 0.195: 230 0.195 - 0.292: 12 0.292 - 0.390: 2 0.390 - 0.487: 4 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 -2.66 -2.17 -0.49 2.00e-01 2.50e+01 5.93e+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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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= 0.196 Angle : 0.618 13.377 36899 Z= 0.349 Chirality : 0.048 0.487 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 aren 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 covalent geometry : bond 0.00359 (26972) covalent geometry : angle 0.60523 (36887) hydrogen bonds : bond 0.19046 ( 992) hydrogen bonds : angle 7.03443 ( 2796) metal coordination : bond 0.00748 ( 8) metal coordination : angle 7.01700 ( 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 : 1.006 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: 0.5956 (OUTLIER) cc_final: 0.4934 (ptp90) outliers start: 24 outliers final: 5 residues processed: 595 average time/residue: 0.1968 time to fit residues: 178.0848 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 : 1.051 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 18 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN C 784 ASN C 929 GLN D 399 ASN D 736 ASN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.144822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.101592 restraints weight = 31833.749| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.58 r_work: 0.2792 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26980 Z= 0.175 Angle : 0.570 10.012 36899 Z= 0.305 Chirality : 0.044 0.205 4215 Planarity : 0.004 0.075 4386 Dihedral : 18.358 95.468 4590 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.90 % Allowed : 9.28 % Favored : 88.82 % 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 aren not related in a simple way. whole: -0.38 (0.15), residues: 3054 helix: 0.50 (0.16), residues: 1128 sheet: 0.31 (0.30), residues: 324 loop : -0.90 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 139 TYR 0.015 0.001 TYR D 649 PHE 0.020 0.001 PHE C 491 TRP 0.018 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00401 (26972) covalent geometry : angle 0.56454 (36887) hydrogen bonds : bond 0.04755 ( 992) hydrogen bonds : angle 4.84242 ( 2796) metal coordination : bond 0.00760 ( 8) metal coordination : angle 4.50658 ( 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 583 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 533 time to evaluate : 1.081 Fit side-chains REVERT: B 191 TYR cc_start: 0.6199 (p90) cc_final: 0.4999 (p90) REVERT: B 226 ASP cc_start: 0.7733 (m-30) cc_final: 0.7377 (m-30) REVERT: A 17 ASP cc_start: 0.8107 (t0) cc_final: 0.7735 (t0) REVERT: A 140 MET cc_start: 0.7695 (mmp) cc_final: 0.7233 (mmm) REVERT: C 112 MET cc_start: 0.8189 (mtt) cc_final: 0.7839 (mtt) REVERT: C 362 LYS cc_start: 0.7291 (mmpt) cc_final: 0.7006 (mmpt) REVERT: C 367 MET cc_start: 0.6976 (mmp) cc_final: 0.6536 (mmp) REVERT: C 920 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: D 137 MET cc_start: 0.8804 (mtm) cc_final: 0.8573 (mtm) REVERT: D 412 MET cc_start: 0.8532 (mtp) cc_final: 0.8296 (mtp) REVERT: D 671 TYR cc_start: 0.6977 (m-10) cc_final: 0.6584 (m-10) REVERT: D 706 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6836 (mm-30) REVERT: D 788 ASP cc_start: 0.8028 (m-30) cc_final: 0.7606 (m-30) REVERT: E 51 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6389 (pm20) REVERT: F 110 LYS cc_start: 0.8790 (mmpt) cc_final: 0.8410 (mmmt) outliers start: 50 outliers final: 32 residues processed: 563 average time/residue: 0.2169 time to fit residues: 184.6287 Evaluate side-chains 546 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 512 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 449 GLU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL 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 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 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 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1115 LYS 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: 3.9990 chunk 197 optimal weight: 4.9990 chunk 138 optimal weight: 0.0870 chunk 307 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.101966 restraints weight = 31876.897| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.60 r_work: 0.2807 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26980 Z= 0.130 Angle : 0.515 9.700 36899 Z= 0.276 Chirality : 0.042 0.166 4215 Planarity : 0.004 0.065 4386 Dihedral : 18.124 94.504 4587 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.79 % Allowed : 12.24 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.15), residues: 3054 helix: 0.63 (0.16), residues: 1140 sheet: 0.36 (0.30), residues: 325 loop : -0.85 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 608 TYR 0.015 0.001 TYR D 649 PHE 0.021 0.001 PHE F 72 TRP 0.013 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00303 (26972) covalent geometry : angle 0.51028 (36887) hydrogen bonds : bond 0.04033 ( 992) hydrogen bonds : angle 4.54440 ( 2796) metal coordination : bond 0.00572 ( 8) metal coordination : angle 3.76233 ( 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 598 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 551 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8765 (p0) cc_final: 0.8516 (p0) REVERT: B 226 ASP cc_start: 0.7593 (m-30) cc_final: 0.7261 (m-30) REVERT: A 17 ASP cc_start: 0.8117 (t0) cc_final: 0.7740 (t0) REVERT: C 79 GLU cc_start: 0.7602 (pm20) cc_final: 0.7384 (mp0) REVERT: C 362 LYS cc_start: 0.7236 (mmpt) cc_final: 0.6952 (mmpt) REVERT: C 367 MET cc_start: 0.7043 (mmp) cc_final: 0.6637 (mmp) REVERT: C 799 ASP cc_start: 0.7914 (p0) cc_final: 0.7606 (p0) REVERT: D 307 GLU cc_start: 0.8236 (tp30) cc_final: 0.7840 (mm-30) REVERT: D 412 MET cc_start: 0.8484 (mtp) cc_final: 0.8227 (mtp) REVERT: D 561 LYS cc_start: 0.8428 (mmtp) cc_final: 0.7881 (mppt) REVERT: D 671 TYR cc_start: 0.6917 (m-10) cc_final: 0.6566 (m-10) REVERT: D 706 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6762 (mm-30) REVERT: D 768 GLU cc_start: 0.8315 (pt0) cc_final: 0.8031 (pt0) REVERT: D 788 ASP cc_start: 0.7992 (m-30) cc_final: 0.7543 (m-30) REVERT: D 1099 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6581 (pt0) REVERT: F 110 LYS cc_start: 0.8792 (mmpt) cc_final: 0.8417 (mmmt) outliers start: 47 outliers final: 34 residues processed: 578 average time/residue: 0.1909 time to fit residues: 168.1427 Evaluate side-chains 556 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 522 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 A residue 141 THR 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 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 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 422 ASP Chi-restraints excluded: chain D residue 567 VAL 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 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL 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: 3.9990 chunk 222 optimal weight: 0.5980 chunk 232 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 113 optimal weight: 0.0470 chunk 279 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 196 optimal weight: 2.9990 chunk 274 optimal weight: 0.4980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.145173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.101586 restraints weight = 31786.985| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.62 r_work: 0.2807 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1488 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= 0.126 Angle : 0.507 9.459 36899 Z= 0.271 Chirality : 0.042 0.166 4215 Planarity : 0.004 0.063 4386 Dihedral : 17.976 91.750 4587 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.13 % Allowed : 14.14 % Favored : 83.73 % 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 aren not related in a simple way. whole: -0.18 (0.15), residues: 3054 helix: 0.72 (0.16), residues: 1140 sheet: 0.37 (0.30), residues: 325 loop : -0.82 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 608 TYR 0.016 0.001 TYR D 649 PHE 0.024 0.001 PHE F 72 TRP 0.013 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00293 (26972) covalent geometry : angle 0.50279 (36887) hydrogen bonds : bond 0.03827 ( 992) hydrogen bonds : angle 4.38367 ( 2796) metal coordination : bond 0.00553 ( 8) metal coordination : angle 3.52745 ( 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 608 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 552 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 18 ASN cc_start: 0.8648 (m-40) cc_final: 0.8311 (m-40) REVERT: B 88 ASN cc_start: 0.8748 (p0) cc_final: 0.8503 (p0) REVERT: B 205 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8416 (tppt) REVERT: B 226 ASP cc_start: 0.7585 (m-30) cc_final: 0.7265 (m-30) REVERT: A 17 ASP cc_start: 0.8119 (t0) cc_final: 0.7735 (t0) REVERT: C 37 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8243 (tp40) REVERT: C 59 ASN cc_start: 0.6977 (p0) cc_final: 0.5229 (t0) REVERT: C 362 LYS cc_start: 0.7215 (mmpt) cc_final: 0.6920 (mmtt) REVERT: C 367 MET cc_start: 0.7086 (mmp) cc_final: 0.6681 (mmp) REVERT: C 608 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7757 (mtp-110) REVERT: C 799 ASP cc_start: 0.7937 (p0) cc_final: 0.7698 (p0) REVERT: D 412 MET cc_start: 0.8477 (mtp) cc_final: 0.8200 (mtp) REVERT: D 551 ASN cc_start: 0.8506 (m-40) cc_final: 0.8151 (m-40) REVERT: D 561 LYS cc_start: 0.8389 (mmtp) cc_final: 0.7918 (mppt) REVERT: D 671 TYR cc_start: 0.6930 (m-10) cc_final: 0.6513 (m-10) REVERT: D 706 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6739 (mm-30) REVERT: D 768 GLU cc_start: 0.8295 (pt0) cc_final: 0.8058 (pt0) REVERT: D 788 ASP cc_start: 0.8027 (m-30) cc_final: 0.7587 (m-30) REVERT: D 866 MET cc_start: 0.8756 (tpp) cc_final: 0.8394 (tpp) REVERT: D 1099 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6653 (pt0) REVERT: F 110 LYS cc_start: 0.8870 (mmpt) cc_final: 0.8429 (mmmt) outliers start: 56 outliers final: 41 residues processed: 585 average time/residue: 0.1937 time to fit residues: 172.3080 Evaluate side-chains 570 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 529 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 860 VAL 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 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 280 LEU 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 667 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL 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: 2.9990 chunk 207 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 0.0370 chunk 222 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.104511 restraints weight = 31755.245| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.59 r_work: 0.2834 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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= 0.106 Angle : 0.486 8.758 36899 Z= 0.261 Chirality : 0.041 0.188 4215 Planarity : 0.004 0.061 4386 Dihedral : 17.886 91.600 4587 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.13 % Allowed : 15.44 % Favored : 82.43 % 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 aren not related in a simple way. whole: -0.05 (0.15), residues: 3054 helix: 0.84 (0.16), residues: 1145 sheet: 0.38 (0.30), residues: 336 loop : -0.75 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 139 TYR 0.017 0.001 TYR D 895 PHE 0.021 0.001 PHE F 72 TRP 0.010 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00240 (26972) covalent geometry : angle 0.48370 (36887) hydrogen bonds : bond 0.03400 ( 992) hydrogen bonds : angle 4.27172 ( 2796) metal coordination : bond 0.00431 ( 8) metal coordination : angle 2.89141 ( 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 627 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 571 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7575 (m-30) cc_final: 0.7225 (m-30) REVERT: A 17 ASP cc_start: 0.8097 (t0) cc_final: 0.7742 (t0) REVERT: A 140 MET cc_start: 0.7731 (mmp) cc_final: 0.7332 (mmm) REVERT: C 37 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8234 (tp40) REVERT: C 59 ASN cc_start: 0.6945 (p0) cc_final: 0.4990 (t0) REVERT: C 60 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5661 (tp) REVERT: C 189 LEU cc_start: 0.7437 (tp) cc_final: 0.7198 (tt) REVERT: C 362 LYS cc_start: 0.7217 (mmpt) cc_final: 0.6922 (mmtt) REVERT: C 367 MET cc_start: 0.7063 (mmp) cc_final: 0.6664 (mmp) REVERT: C 647 MET cc_start: 0.8934 (mtt) cc_final: 0.8668 (mmm) REVERT: C 799 ASP cc_start: 0.7907 (p0) cc_final: 0.7540 (p0) REVERT: D 412 MET cc_start: 0.8425 (mtp) cc_final: 0.8127 (mtp) REVERT: D 561 LYS cc_start: 0.8382 (mmtp) cc_final: 0.7896 (mppt) REVERT: D 671 TYR cc_start: 0.6928 (m-10) cc_final: 0.6504 (m-10) REVERT: D 706 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6678 (mm-30) REVERT: D 768 GLU cc_start: 0.8229 (pt0) cc_final: 0.7973 (pt0) REVERT: D 788 ASP cc_start: 0.7930 (m-30) cc_final: 0.7471 (m-30) REVERT: D 1099 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6596 (pt0) REVERT: F 110 LYS cc_start: 0.8869 (mmpt) cc_final: 0.8423 (mmmt) outliers start: 56 outliers final: 40 residues processed: 602 average time/residue: 0.2030 time to fit residues: 185.7012 Evaluate side-chains 586 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 545 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 LEU 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 60 LEU 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 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 580 THR Chi-restraints excluded: chain C residue 708 THR 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 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 422 ASP Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 716 ILE 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 E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 250 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 784 ASN C1076 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.142985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.099974 restraints weight = 31655.588| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.58 r_work: 0.2768 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26980 Z= 0.195 Angle : 0.566 8.981 36899 Z= 0.298 Chirality : 0.044 0.171 4215 Planarity : 0.004 0.064 4386 Dihedral : 18.013 96.102 4583 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.40 % Allowed : 16.58 % Favored : 81.03 % 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 aren not related in a simple way. whole: -0.32 (0.15), residues: 3054 helix: 0.53 (0.16), residues: 1158 sheet: 0.19 (0.29), residues: 350 loop : -0.84 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 139 TYR 0.017 0.001 TYR D 649 PHE 0.020 0.002 PHE F 72 TRP 0.019 0.002 TRP C 999 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00463 (26972) covalent geometry : angle 0.55999 (36887) hydrogen bonds : bond 0.04607 ( 992) hydrogen bonds : angle 4.48455 ( 2796) metal coordination : bond 0.00818 ( 8) metal coordination : angle 4.50332 ( 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 593 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 530 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8868 (p0) cc_final: 0.8595 (p0) REVERT: A 17 ASP cc_start: 0.8120 (t0) cc_final: 0.7708 (t0) REVERT: A 113 LYS cc_start: 0.6781 (mmtm) cc_final: 0.6485 (mmtt) REVERT: C 59 ASN cc_start: 0.7039 (p0) cc_final: 0.6667 (p0) REVERT: C 149 ILE cc_start: 0.7255 (mt) cc_final: 0.6923 (mm) REVERT: C 362 LYS cc_start: 0.7257 (mmpt) cc_final: 0.6963 (mmtt) REVERT: C 367 MET cc_start: 0.7079 (mmp) cc_final: 0.6652 (mmp) REVERT: D 153 TYR cc_start: 0.7923 (m-10) cc_final: 0.7493 (m-10) REVERT: D 561 LYS cc_start: 0.8419 (mmtp) cc_final: 0.7981 (mppt) REVERT: D 671 TYR cc_start: 0.7014 (m-10) cc_final: 0.6549 (m-10) REVERT: D 706 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6766 (mm-30) REVERT: D 788 ASP cc_start: 0.7970 (m-30) cc_final: 0.7505 (m-30) REVERT: D 866 MET cc_start: 0.8762 (tpp) cc_final: 0.8262 (tpp) REVERT: D 1099 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6718 (pt0) REVERT: F 219 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5701 (mmt-90) outliers start: 63 outliers final: 49 residues processed: 574 average time/residue: 0.1813 time to fit residues: 159.5109 Evaluate side-chains 565 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 515 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ILE 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 485 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 708 THR 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 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 1112 VAL 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 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 423 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 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 219 ARG Chi-restraints excluded: chain F residue 241 TYR 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: 6.9990 chunk 309 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** 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 = 0.3428 r_free = 0.3428 target = 0.140551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.097836 restraints weight = 31725.741| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.57 r_work: 0.2740 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26980 Z= 0.250 Angle : 0.626 10.392 36899 Z= 0.328 Chirality : 0.046 0.182 4215 Planarity : 0.005 0.065 4386 Dihedral : 18.145 102.493 4583 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.66 % Allowed : 17.38 % Favored : 79.96 % 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 aren not related in a simple way. whole: -0.69 (0.15), residues: 3054 helix: 0.20 (0.15), residues: 1158 sheet: 0.04 (0.28), residues: 353 loop : -1.05 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 219 TYR 0.016 0.002 TYR D 649 PHE 0.023 0.002 PHE F 72 TRP 0.022 0.002 TRP C 999 HIS 0.006 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00595 (26972) covalent geometry : angle 0.61827 (36887) hydrogen bonds : bond 0.05235 ( 992) hydrogen bonds : angle 4.66714 ( 2796) metal coordination : bond 0.01043 ( 8) metal coordination : angle 5.47093 ( 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 568 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 498 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 205 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8432 (mptt) REVERT: A 17 ASP cc_start: 0.8114 (t0) cc_final: 0.7650 (t0) REVERT: A 113 LYS cc_start: 0.6845 (mmtm) cc_final: 0.6398 (mmtt) REVERT: C 59 ASN cc_start: 0.6971 (p0) cc_final: 0.6624 (p0) REVERT: C 149 ILE cc_start: 0.7466 (mt) cc_final: 0.7203 (mm) REVERT: C 188 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7423 (mttt) REVERT: C 362 LYS cc_start: 0.7308 (mmpt) cc_final: 0.7023 (mmtt) REVERT: C 367 MET cc_start: 0.7069 (mmp) cc_final: 0.6636 (mmp) REVERT: C 447 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7655 (mtt180) REVERT: C 487 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 193 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7855 (ttp) REVERT: D 426 GLU cc_start: 0.8416 (mp0) cc_final: 0.7822 (mp0) REVERT: D 561 LYS cc_start: 0.8394 (mmtp) cc_final: 0.7924 (mppt) REVERT: D 671 TYR cc_start: 0.7172 (m-10) cc_final: 0.6682 (m-10) REVERT: D 706 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6740 (mm-30) REVERT: D 788 ASP cc_start: 0.8017 (m-30) cc_final: 0.7539 (m-30) REVERT: D 866 MET cc_start: 0.8698 (tpp) cc_final: 0.8315 (tpp) REVERT: F 35 GLU cc_start: 0.7349 (mp0) cc_final: 0.7098 (mp0) outliers start: 70 outliers final: 53 residues processed: 548 average time/residue: 0.1881 time to fit residues: 156.2567 Evaluate side-chains 542 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 488 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ILE Chi-restraints excluded: chain C residue 192 THR 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 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 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 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1072 LEU 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 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 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 241 TYR 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: 0.2980 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 295 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN C 639 GLN C1076 GLN D 243 GLN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.143813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.100633 restraints weight = 31879.663| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.60 r_work: 0.2792 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26980 Z= 0.124 Angle : 0.530 10.411 36899 Z= 0.281 Chirality : 0.042 0.181 4215 Planarity : 0.004 0.063 4386 Dihedral : 17.992 100.646 4583 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 18.25 % Favored : 79.62 % 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 aren not related in a simple way. whole: -0.40 (0.15), residues: 3054 helix: 0.49 (0.16), residues: 1155 sheet: 0.09 (0.29), residues: 349 loop : -0.89 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 219 TYR 0.016 0.001 TYR D 649 PHE 0.024 0.001 PHE F 72 TRP 0.010 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00289 (26972) covalent geometry : angle 0.52624 (36887) hydrogen bonds : bond 0.03813 ( 992) hydrogen bonds : angle 4.42180 ( 2796) metal coordination : bond 0.00548 ( 8) metal coordination : angle 3.46806 ( 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 595 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 539 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: B 205 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8405 (mptt) REVERT: B 226 ASP cc_start: 0.7450 (m-30) cc_final: 0.7139 (m-30) REVERT: A 17 ASP cc_start: 0.8143 (t0) cc_final: 0.7705 (t0) REVERT: A 113 LYS cc_start: 0.6765 (mmtm) cc_final: 0.6322 (mmtt) REVERT: C 59 ASN cc_start: 0.6920 (p0) cc_final: 0.5663 (t0) REVERT: C 149 ILE cc_start: 0.7344 (mt) cc_final: 0.7037 (mm) REVERT: C 188 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7142 (mttt) REVERT: C 362 LYS cc_start: 0.7304 (mmpt) cc_final: 0.7010 (mmtt) REVERT: C 367 MET cc_start: 0.7059 (mmp) cc_final: 0.6623 (mmp) REVERT: C 608 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7743 (mtp-110) REVERT: D 243 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: D 412 MET cc_start: 0.8521 (mtp) cc_final: 0.8250 (mtp) REVERT: D 426 GLU cc_start: 0.8440 (mp0) cc_final: 0.8187 (mp0) REVERT: D 561 LYS cc_start: 0.8416 (mmtp) cc_final: 0.7968 (mppt) REVERT: D 671 TYR cc_start: 0.6966 (m-10) cc_final: 0.6476 (m-10) REVERT: D 706 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6720 (mm-30) REVERT: D 788 ASP cc_start: 0.8010 (m-30) cc_final: 0.7546 (m-30) REVERT: D 866 MET cc_start: 0.8656 (tpp) cc_final: 0.8283 (tpp) REVERT: D 1099 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6661 (pt0) outliers start: 56 outliers final: 49 residues processed: 574 average time/residue: 0.1941 time to fit residues: 169.0119 Evaluate side-chains 568 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 518 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 217 LEU 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 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 580 THR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 708 THR 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 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1072 LEU 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 243 GLN 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 550 ASP Chi-restraints excluded: chain D residue 567 VAL 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 E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 129 LEU 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: 0.0270 chunk 67 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 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 = 0.3475 r_free = 0.3475 target = 0.144510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.101755 restraints weight = 31845.137| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.58 r_work: 0.2794 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26980 Z= 0.131 Angle : 0.535 12.905 36899 Z= 0.282 Chirality : 0.042 0.180 4215 Planarity : 0.004 0.064 4386 Dihedral : 17.945 99.927 4583 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.09 % Allowed : 18.94 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 3054 helix: 0.58 (0.16), residues: 1155 sheet: 0.12 (0.29), residues: 349 loop : -0.85 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.018 0.001 TYR D 895 PHE 0.027 0.001 PHE F 72 TRP 0.011 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00305 (26972) covalent geometry : angle 0.53111 (36887) hydrogen bonds : bond 0.03835 ( 992) hydrogen bonds : angle 4.37389 ( 2796) metal coordination : bond 0.00573 ( 8) metal coordination : angle 3.42731 ( 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 584 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 529 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7486 (m-30) cc_final: 0.7165 (m-30) REVERT: A 17 ASP cc_start: 0.8126 (t0) cc_final: 0.7683 (t0) REVERT: A 113 LYS cc_start: 0.6790 (mmtm) cc_final: 0.6330 (mmtt) REVERT: C 37 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8241 (tp40) REVERT: C 59 ASN cc_start: 0.6925 (p0) cc_final: 0.5765 (t0) REVERT: C 188 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7180 (mttt) REVERT: C 362 LYS cc_start: 0.7354 (mmpt) cc_final: 0.7064 (mmtt) REVERT: C 367 MET cc_start: 0.7028 (mmp) cc_final: 0.6608 (mmp) REVERT: C 608 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7708 (mtp-110) REVERT: C 799 ASP cc_start: 0.7972 (p0) cc_final: 0.7771 (p0) REVERT: D 412 MET cc_start: 0.8455 (mtp) cc_final: 0.8171 (mtp) REVERT: D 561 LYS cc_start: 0.8425 (mmtp) cc_final: 0.7978 (mppt) REVERT: D 671 TYR cc_start: 0.6988 (m-10) cc_final: 0.6505 (m-10) REVERT: D 706 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6717 (mm-30) REVERT: D 788 ASP cc_start: 0.8009 (m-30) cc_final: 0.7556 (m-30) REVERT: D 866 MET cc_start: 0.8691 (tpp) cc_final: 0.8308 (tpp) REVERT: D 1099 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6642 (pt0) outliers start: 55 outliers final: 49 residues processed: 562 average time/residue: 0.2075 time to fit residues: 176.8731 Evaluate side-chains 573 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 524 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ILE 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 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 708 THR 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 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 550 ASP Chi-restraints excluded: chain D residue 567 VAL 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 E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 129 LEU 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: 0.0970 chunk 261 optimal weight: 2.9990 chunk 313 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN C 51 ASN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 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 = 0.3492 r_free = 0.3492 target = 0.145979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.102837 restraints weight = 31758.896| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.60 r_work: 0.2822 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26980 Z= 0.112 Angle : 0.515 12.640 36899 Z= 0.272 Chirality : 0.042 0.198 4215 Planarity : 0.004 0.063 4386 Dihedral : 17.852 98.074 4583 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.83 % Allowed : 19.13 % Favored : 79.05 % 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 aren not related in a simple way. whole: -0.13 (0.15), residues: 3054 helix: 0.72 (0.16), residues: 1152 sheet: 0.27 (0.29), residues: 345 loop : -0.75 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 55 TYR 0.019 0.001 TYR D 895 PHE 0.030 0.001 PHE F 72 TRP 0.009 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00258 (26972) covalent geometry : angle 0.51288 (36887) hydrogen bonds : bond 0.03412 ( 992) hydrogen bonds : angle 4.26639 ( 2796) metal coordination : bond 0.00454 ( 8) metal coordination : angle 2.86370 ( 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 599 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 551 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7453 (m-30) cc_final: 0.7120 (m-30) REVERT: A 17 ASP cc_start: 0.8098 (t0) cc_final: 0.7728 (t0) REVERT: A 113 LYS cc_start: 0.6770 (mmtm) cc_final: 0.6312 (mmtt) REVERT: C 37 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8254 (tp40) REVERT: C 59 ASN cc_start: 0.6916 (p0) cc_final: 0.5903 (t0) REVERT: C 139 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7870 (ttt90) REVERT: C 343 ASP cc_start: 0.7318 (p0) cc_final: 0.7064 (p0) REVERT: C 362 LYS cc_start: 0.7280 (mmpt) cc_final: 0.6970 (mmtt) REVERT: C 367 MET cc_start: 0.6900 (mmp) cc_final: 0.6512 (mmp) REVERT: C 647 MET cc_start: 0.8921 (mtt) cc_final: 0.8648 (mmm) REVERT: C 799 ASP cc_start: 0.7963 (p0) cc_final: 0.7752 (p0) REVERT: D 412 MET cc_start: 0.8495 (mtp) cc_final: 0.8211 (mtp) REVERT: D 561 LYS cc_start: 0.8443 (mmtp) cc_final: 0.7959 (mppt) REVERT: D 671 TYR cc_start: 0.6891 (m-10) cc_final: 0.6488 (m-10) REVERT: D 706 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6647 (mm-30) REVERT: D 788 ASP cc_start: 0.7964 (m-30) cc_final: 0.7496 (m-30) REVERT: D 1095 PHE cc_start: 0.6646 (t80) cc_final: 0.6256 (t80) REVERT: D 1099 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6584 (pt0) outliers start: 48 outliers final: 43 residues processed: 581 average time/residue: 0.2182 time to fit residues: 194.7426 Evaluate side-chains 578 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 535 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 580 THR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 708 THR 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 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 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 567 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 E residue 28 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 129 LEU 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS ** F 86 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 = 0.3468 r_free = 0.3468 target = 0.143962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.101136 restraints weight = 31689.734| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.58 r_work: 0.2790 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26980 Z= 0.148 Angle : 0.551 12.219 36899 Z= 0.288 Chirality : 0.043 0.209 4215 Planarity : 0.004 0.064 4386 Dihedral : 17.914 98.829 4583 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.94 % Allowed : 19.43 % Favored : 78.63 % 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 aren not related in a simple way. whole: -0.25 (0.15), residues: 3054 helix: 0.59 (0.16), residues: 1156 sheet: 0.25 (0.29), residues: 344 loop : -0.81 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 55 TYR 0.016 0.001 TYR D 649 PHE 0.024 0.001 PHE F 72 TRP 0.018 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00353 (26972) covalent geometry : angle 0.54694 (36887) hydrogen bonds : bond 0.03999 ( 992) hydrogen bonds : angle 4.35712 ( 2796) metal coordination : bond 0.00685 ( 8) metal coordination : angle 3.73261 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7590.46 seconds wall clock time: 130 minutes 23.84 seconds (7823.84 seconds total)