Starting phenix.real_space_refine on Sun Jun 22 17:55:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i24_35131/06_2025/8i24_35131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i24_35131/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i24_35131/06_2025/8i24_35131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i24_35131/06_2025/8i24_35131.map" model { file = "/net/cci-nas-00/data/ceres_data/8i24_35131/06_2025/8i24_35131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i24_35131/06_2025/8i24_35131.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, '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: 15.35, per 1000 atoms: 0.58 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: 6.65 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 817 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 901 " pdb=" ZN D1202 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 101 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 83 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 98 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 85 " Number of angles added : 12 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5678 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 44 sheets defined 40.8% alpha, 15.8% beta 24 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 9.87 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: 12.83 Time building geometry restraints manager: 7.88 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 74.070 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.930 ------------------------------------------------------------------------------- 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 : 7.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.012 0.001 PHE C 491 TYR 0.013 0.001 TYR D 649 ARG 0.009 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.19046 ( 992) hydrogen bonds : angle 7.03443 ( 2796) metal coordination : bond 0.00748 ( 8) metal coordination : angle 7.01700 ( 12) covalent geometry : bond 0.00359 (26972) covalent geometry : angle 0.60523 (36887) *********************** 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 : 3.066 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: 0.4244 time to fit residues: 384.1635 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 : 2.946 ------------------------------------------------------------------------------- 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 265 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 0.0370 chunk 95 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.144183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.100809 restraints weight = 31769.162| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.58 r_work: 0.2788 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26980 Z= 0.186 Angle : 0.578 9.974 36899 Z= 0.308 Chirality : 0.044 0.215 4215 Planarity : 0.005 0.076 4386 Dihedral : 18.376 97.448 4590 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.83 % Allowed : 9.20 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3054 helix: 0.43 (0.16), residues: 1134 sheet: 0.30 (0.30), residues: 324 loop : -0.93 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.020 0.001 PHE C 491 TYR 0.015 0.001 TYR D 649 ARG 0.006 0.001 ARG C 363 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 992) hydrogen bonds : angle 4.90419 ( 2796) metal coordination : bond 0.00834 ( 8) metal coordination : angle 4.79689 ( 12) covalent geometry : bond 0.00437 (26972) covalent geometry : angle 0.57201 (36887) *********************** 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 577 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 529 time to evaluate : 2.879 Fit side-chains REVERT: B 88 ASN cc_start: 0.8850 (p0) cc_final: 0.8600 (p0) REVERT: B 191 TYR cc_start: 0.6213 (p90) cc_final: 0.5032 (p90) REVERT: B 205 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8409 (mptt) REVERT: B 226 ASP cc_start: 0.7748 (m-30) cc_final: 0.7397 (m-30) REVERT: A 17 ASP cc_start: 0.8049 (t0) cc_final: 0.7689 (t0) REVERT: C 112 MET cc_start: 0.8200 (mtt) cc_final: 0.7823 (mtt) REVERT: C 362 LYS cc_start: 0.7270 (mmpt) cc_final: 0.6986 (mmpt) REVERT: C 367 MET cc_start: 0.6947 (mmp) cc_final: 0.6521 (mmp) REVERT: C 703 VAL cc_start: 0.8259 (t) cc_final: 0.8058 (p) REVERT: C 920 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8183 (m-40) REVERT: D 137 MET cc_start: 0.8806 (mtm) cc_final: 0.8571 (mtm) REVERT: D 287 ARG cc_start: 0.8111 (tpm170) cc_final: 0.7881 (tpm170) REVERT: D 412 MET cc_start: 0.8541 (mtp) cc_final: 0.8303 (mtp) REVERT: D 671 TYR cc_start: 0.6989 (m-10) cc_final: 0.6596 (m-10) REVERT: D 706 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6799 (mm-30) REVERT: D 788 ASP cc_start: 0.8026 (m-30) cc_final: 0.7601 (m-30) REVERT: E 51 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: F 110 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8413 (mmmt) outliers start: 48 outliers final: 32 residues processed: 558 average time/residue: 0.4323 time to fit residues: 367.4227 Evaluate side-chains 536 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 502 time to evaluate : 3.630 ------------------------------------------------------------------------------- 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 20 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 246 optimal weight: 0.0770 chunk 226 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 210 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- 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 D 399 ASN ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN 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 = 0.143712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.100440 restraints weight = 31614.843| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.59 r_work: 0.2788 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26980 Z= 0.160 Angle : 0.542 9.670 36899 Z= 0.290 Chirality : 0.043 0.167 4215 Planarity : 0.004 0.066 4386 Dihedral : 18.200 96.253 4587 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.17 % Allowed : 12.32 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3054 helix: 0.52 (0.16), residues: 1140 sheet: 0.32 (0.30), residues: 332 loop : -0.94 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.022 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.005 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 992) hydrogen bonds : angle 4.62266 ( 2796) metal coordination : bond 0.00697 ( 8) metal coordination : angle 4.30459 ( 12) covalent geometry : bond 0.00376 (26972) covalent geometry : angle 0.53657 (36887) *********************** 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 601 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 544 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8813 (p0) cc_final: 0.8562 (p0) REVERT: B 226 ASP cc_start: 0.7782 (m-30) cc_final: 0.7477 (m-30) REVERT: A 17 ASP cc_start: 0.8123 (t0) cc_final: 0.7724 (t0) REVERT: A 108 LYS cc_start: 0.7738 (tppt) cc_final: 0.7512 (tppt) REVERT: C 79 GLU cc_start: 0.7708 (pm20) cc_final: 0.7491 (mp0) REVERT: C 362 LYS cc_start: 0.7221 (mmpt) cc_final: 0.6937 (mmpt) REVERT: C 367 MET cc_start: 0.6996 (mmp) cc_final: 0.6622 (mmp) REVERT: D 153 TYR cc_start: 0.7958 (m-10) cc_final: 0.7569 (m-10) REVERT: D 412 MET cc_start: 0.8499 (mtp) cc_final: 0.8227 (mtp) REVERT: D 561 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7889 (mppt) REVERT: D 671 TYR cc_start: 0.6942 (m-10) cc_final: 0.6527 (m-10) REVERT: D 706 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6742 (mm-30) REVERT: D 788 ASP cc_start: 0.8058 (m-30) cc_final: 0.7619 (m-30) REVERT: D 1099 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6637 (pt0) outliers start: 57 outliers final: 40 residues processed: 578 average time/residue: 0.4356 time to fit residues: 383.5059 Evaluate side-chains 552 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 512 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 115 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** 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 = 0.3449 r_free = 0.3449 target = 0.142240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.099347 restraints weight = 32093.810| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.78 r_work: 0.2750 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26980 Z= 0.189 Angle : 0.567 9.438 36899 Z= 0.301 Chirality : 0.044 0.169 4215 Planarity : 0.004 0.067 4386 Dihedral : 18.148 97.077 4587 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.40 % Allowed : 14.56 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3054 helix: 0.35 (0.15), residues: 1153 sheet: 0.17 (0.29), residues: 348 loop : -0.94 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.023 0.001 PHE F 72 TYR 0.017 0.001 TYR D 649 ARG 0.008 0.000 ARG C 608 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 992) hydrogen bonds : angle 4.58727 ( 2796) metal coordination : bond 0.00838 ( 8) metal coordination : angle 4.77421 ( 12) covalent geometry : bond 0.00448 (26972) covalent geometry : angle 0.56034 (36887) *********************** 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 585 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 522 time to evaluate : 4.847 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8870 (p0) cc_final: 0.8604 (p0) REVERT: A 17 ASP cc_start: 0.8153 (t0) cc_final: 0.7727 (t0) REVERT: A 108 LYS cc_start: 0.7677 (tppt) cc_final: 0.7441 (tppt) REVERT: C 59 ASN cc_start: 0.7006 (p0) cc_final: 0.6735 (p0) REVERT: C 79 GLU cc_start: 0.7668 (pm20) cc_final: 0.7448 (mp0) REVERT: C 112 MET cc_start: 0.8230 (mtt) cc_final: 0.7855 (mtt) REVERT: C 149 ILE cc_start: 0.7282 (mt) cc_final: 0.6960 (mm) REVERT: C 188 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7227 (mttt) REVERT: C 362 LYS cc_start: 0.7282 (mmpt) cc_final: 0.6971 (mmpt) REVERT: C 367 MET cc_start: 0.7075 (mmp) cc_final: 0.6648 (mmp) REVERT: C 608 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7799 (mtp-110) REVERT: D 137 MET cc_start: 0.8789 (mtm) cc_final: 0.8584 (mtm) REVERT: D 307 GLU cc_start: 0.8352 (tp30) cc_final: 0.8038 (mm-30) REVERT: D 426 GLU cc_start: 0.8477 (mp0) cc_final: 0.7874 (mp0) REVERT: D 561 LYS cc_start: 0.8390 (mmtp) cc_final: 0.7903 (mppt) REVERT: D 671 TYR cc_start: 0.6986 (m-10) cc_final: 0.6504 (m-10) REVERT: D 706 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6754 (mm-30) REVERT: D 788 ASP cc_start: 0.8040 (m-30) cc_final: 0.7595 (m-30) REVERT: D 866 MET cc_start: 0.8664 (tpp) cc_final: 0.8277 (tpp) REVERT: D 1056 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8257 (mm-40) REVERT: D 1099 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6675 (pt0) outliers start: 63 outliers final: 48 residues processed: 562 average time/residue: 0.4617 time to fit residues: 399.4545 Evaluate side-chains 561 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 513 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 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 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 303 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 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 15 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 126 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 243 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN ** D 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 HIS ** 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 = 0.3448 r_free = 0.3448 target = 0.142159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.099259 restraints weight = 31669.658| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.58 r_work: 0.2759 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26980 Z= 0.193 Angle : 0.565 9.675 36899 Z= 0.300 Chirality : 0.044 0.168 4215 Planarity : 0.004 0.066 4386 Dihedral : 18.135 100.005 4587 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.81 % Allowed : 16.54 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3054 helix: 0.33 (0.15), residues: 1153 sheet: 0.10 (0.29), residues: 348 loop : -0.98 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.024 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.007 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 992) hydrogen bonds : angle 4.57326 ( 2796) metal coordination : bond 0.00817 ( 8) metal coordination : angle 4.72853 ( 12) covalent geometry : bond 0.00459 (26972) covalent geometry : angle 0.55890 (36887) *********************** 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 593 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 519 time to evaluate : 2.830 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8897 (p0) cc_final: 0.8628 (p0) REVERT: A 17 ASP cc_start: 0.8123 (t0) cc_final: 0.7676 (t0) REVERT: A 108 LYS cc_start: 0.7743 (tppt) cc_final: 0.7503 (tppt) REVERT: C 59 ASN cc_start: 0.7052 (p0) cc_final: 0.6533 (p0) REVERT: C 149 ILE cc_start: 0.7321 (mt) cc_final: 0.7020 (mm) REVERT: C 188 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7262 (mttt) REVERT: C 362 LYS cc_start: 0.7294 (mmpt) cc_final: 0.7014 (mmpt) REVERT: C 367 MET cc_start: 0.7050 (mmp) cc_final: 0.6611 (mmp) REVERT: D 153 TYR cc_start: 0.8018 (m-10) cc_final: 0.7659 (m-10) REVERT: D 561 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7973 (mppt) REVERT: D 671 TYR cc_start: 0.7017 (m-10) cc_final: 0.6551 (m-10) REVERT: D 706 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6733 (mm-30) REVERT: D 730 GLN cc_start: 0.8140 (mp10) cc_final: 0.7827 (mm-40) REVERT: D 788 ASP cc_start: 0.7997 (m-30) cc_final: 0.7534 (m-30) REVERT: D 895 TYR cc_start: 0.7678 (m-80) cc_final: 0.7462 (m-80) REVERT: D 1056 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8228 (mm-40) outliers start: 74 outliers final: 57 residues processed: 571 average time/residue: 0.5070 time to fit residues: 445.3014 Evaluate side-chains 560 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 503 time to evaluate : 8.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 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 838 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 934 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 15 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 246 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 252 optimal weight: 0.5980 chunk 301 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.143571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.100744 restraints weight = 31619.699| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.58 r_work: 0.2788 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26980 Z= 0.132 Angle : 0.522 9.988 36899 Z= 0.278 Chirality : 0.042 0.169 4215 Planarity : 0.004 0.064 4386 Dihedral : 18.078 99.106 4587 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.59 % Allowed : 17.60 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3054 helix: 0.51 (0.16), residues: 1154 sheet: 0.14 (0.29), residues: 348 loop : -0.90 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.023 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.007 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 992) hydrogen bonds : angle 4.40264 ( 2796) metal coordination : bond 0.00579 ( 8) metal coordination : angle 3.58846 ( 12) covalent geometry : bond 0.00308 (26972) covalent geometry : angle 0.51763 (36887) *********************** 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 613 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 545 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: B 205 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8418 (mptt) REVERT: A 17 ASP cc_start: 0.8109 (t0) cc_final: 0.7659 (t0) REVERT: A 108 LYS cc_start: 0.7663 (tppt) cc_final: 0.7419 (tppt) REVERT: C 59 ASN cc_start: 0.6875 (p0) cc_final: 0.5319 (t0) REVERT: C 149 ILE cc_start: 0.7282 (mt) cc_final: 0.6981 (mm) REVERT: C 188 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7154 (mttt) REVERT: C 362 LYS cc_start: 0.7305 (mmpt) cc_final: 0.7017 (mmtt) REVERT: C 367 MET cc_start: 0.7045 (mmp) cc_final: 0.6606 (mmp) REVERT: D 149 GLU cc_start: 0.8742 (tt0) cc_final: 0.8524 (tt0) REVERT: D 412 MET cc_start: 0.8475 (mtp) cc_final: 0.8207 (mtp) REVERT: D 561 LYS cc_start: 0.8426 (mmtp) cc_final: 0.7987 (mppt) REVERT: D 671 TYR cc_start: 0.6998 (m-10) cc_final: 0.6565 (m-10) REVERT: D 706 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6720 (mm-30) REVERT: D 730 GLN cc_start: 0.8133 (mp10) cc_final: 0.7886 (mp10) REVERT: D 788 ASP cc_start: 0.8008 (m-30) cc_final: 0.7544 (m-30) REVERT: D 1056 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8248 (mm-40) REVERT: D 1099 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6588 (pt0) outliers start: 68 outliers final: 51 residues processed: 589 average time/residue: 0.4230 time to fit residues: 381.3540 Evaluate side-chains 575 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 524 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain 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 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 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 838 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1073 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 916 GLU 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 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 72 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN D 224 GLN ** 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 = 0.3453 r_free = 0.3453 target = 0.142705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.099881 restraints weight = 31731.974| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.57 r_work: 0.2773 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26980 Z= 0.164 Angle : 0.548 10.031 36899 Z= 0.290 Chirality : 0.043 0.167 4215 Planarity : 0.004 0.065 4386 Dihedral : 18.082 100.019 4583 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.62 % Allowed : 18.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3054 helix: 0.44 (0.16), residues: 1154 sheet: 0.13 (0.29), residues: 348 loop : -0.92 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 999 HIS 0.005 0.001 HIS F 84 PHE 0.025 0.001 PHE F 72 TYR 0.020 0.001 TYR D 895 ARG 0.007 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 992) hydrogen bonds : angle 4.45301 ( 2796) metal coordination : bond 0.00705 ( 8) metal coordination : angle 4.12399 ( 12) covalent geometry : bond 0.00388 (26972) covalent geometry : angle 0.54276 (36887) *********************** 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 605 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 536 time to evaluate : 2.930 Fit side-chains revert: symmetry clash REVERT: B 205 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8415 (mptt) REVERT: A 17 ASP cc_start: 0.8096 (t0) cc_final: 0.7655 (t0) REVERT: A 108 LYS cc_start: 0.7623 (tppt) cc_final: 0.7390 (tppt) REVERT: C 59 ASN cc_start: 0.7003 (p0) cc_final: 0.5650 (t0) REVERT: C 149 ILE cc_start: 0.7371 (mt) cc_final: 0.7101 (mm) REVERT: C 188 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7271 (mttt) REVERT: C 362 LYS cc_start: 0.7302 (mmpt) cc_final: 0.7002 (mmtt) REVERT: C 367 MET cc_start: 0.7041 (mmp) cc_final: 0.6612 (mmp) REVERT: D 149 GLU cc_start: 0.8764 (tt0) cc_final: 0.8501 (tt0) REVERT: D 412 MET cc_start: 0.8478 (mtp) cc_final: 0.8226 (mtp) REVERT: D 561 LYS cc_start: 0.8426 (mmtp) cc_final: 0.7978 (mppt) REVERT: D 671 TYR cc_start: 0.7027 (m-10) cc_final: 0.6540 (m-10) REVERT: D 706 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6713 (mm-30) REVERT: D 730 GLN cc_start: 0.8089 (mp10) cc_final: 0.7843 (mm-40) REVERT: D 788 ASP cc_start: 0.8035 (m-30) cc_final: 0.7582 (m-30) REVERT: D 1099 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6606 (pt0) REVERT: E 51 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6657 (pm20) REVERT: F 58 GLU cc_start: 0.7325 (mp0) cc_final: 0.7097 (mp0) outliers start: 69 outliers final: 56 residues processed: 579 average time/residue: 0.4186 time to fit residues: 369.6290 Evaluate side-chains 584 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 526 time to evaluate : 2.710 ------------------------------------------------------------------------------- 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 130 LEU 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 141 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 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 838 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER Chi-restraints excluded: chain C residue 1073 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 393 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 934 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 31 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 0.0970 chunk 233 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ** D 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.144806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.101628 restraints weight = 31996.685| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.60 r_work: 0.2812 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26980 Z= 0.115 Angle : 0.511 9.531 36899 Z= 0.272 Chirality : 0.042 0.175 4215 Planarity : 0.004 0.063 4386 Dihedral : 17.993 98.544 4583 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.94 % Allowed : 19.05 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3054 helix: 0.67 (0.16), residues: 1146 sheet: 0.28 (0.29), residues: 344 loop : -0.82 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.026 0.001 PHE F 72 TYR 0.019 0.001 TYR D 895 ARG 0.009 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 992) hydrogen bonds : angle 4.31587 ( 2796) metal coordination : bond 0.00468 ( 8) metal coordination : angle 3.08711 ( 12) covalent geometry : bond 0.00265 (26972) covalent geometry : angle 0.50755 (36887) *********************** 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 602 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 551 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8768 (p0) cc_final: 0.8492 (p0) REVERT: A 17 ASP cc_start: 0.8115 (t0) cc_final: 0.7725 (t0) REVERT: A 108 LYS cc_start: 0.7619 (tppt) cc_final: 0.7408 (tppt) REVERT: A 113 LYS cc_start: 0.6888 (mmtm) cc_final: 0.6622 (mmtt) REVERT: C 37 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8266 (tp40) REVERT: C 59 ASN cc_start: 0.6970 (p0) cc_final: 0.5678 (t0) REVERT: C 362 LYS cc_start: 0.7243 (mmpt) cc_final: 0.6936 (mmtt) REVERT: C 367 MET cc_start: 0.7059 (mmp) cc_final: 0.6647 (mmp) REVERT: D 412 MET cc_start: 0.8429 (mtp) cc_final: 0.8149 (mtp) REVERT: D 561 LYS cc_start: 0.8419 (mmtp) cc_final: 0.7966 (mppt) REVERT: D 671 TYR cc_start: 0.6916 (m-10) cc_final: 0.6494 (m-10) REVERT: D 706 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6675 (mm-30) REVERT: D 730 GLN cc_start: 0.8123 (mp10) cc_final: 0.7909 (mm-40) REVERT: D 788 ASP cc_start: 0.7966 (m-30) cc_final: 0.7498 (m-30) REVERT: D 1099 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6568 (pt0) REVERT: F 232 ARG cc_start: 0.5381 (mtm180) cc_final: 0.4874 (ptp90) outliers start: 51 outliers final: 39 residues processed: 583 average time/residue: 0.4153 time to fit residues: 371.4112 Evaluate side-chains 574 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 534 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 130 LEU 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 24 MET 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 322 VAL 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 1073 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 72 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 300 optimal weight: 8.9990 chunk 111 optimal weight: 0.5980 chunk 6 optimal weight: 0.0170 chunk 101 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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** F 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.100372 restraints weight = 31806.039| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.59 r_work: 0.2786 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26980 Z= 0.147 Angle : 0.536 10.651 36899 Z= 0.283 Chirality : 0.042 0.167 4215 Planarity : 0.004 0.064 4386 Dihedral : 18.003 99.076 4583 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.28 % Allowed : 19.20 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3054 helix: 0.57 (0.16), residues: 1156 sheet: 0.16 (0.29), residues: 355 loop : -0.83 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.027 0.001 PHE F 72 TYR 0.016 0.001 TYR D 649 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 992) hydrogen bonds : angle 4.36639 ( 2796) metal coordination : bond 0.00630 ( 8) metal coordination : angle 3.68426 ( 12) covalent geometry : bond 0.00349 (26972) covalent geometry : angle 0.53188 (36887) *********************** 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 586 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 526 time to evaluate : 3.034 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8102 (t0) cc_final: 0.7713 (t0) REVERT: A 113 LYS cc_start: 0.6866 (mmtm) cc_final: 0.6574 (mmtt) REVERT: C 37 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8266 (tp40) REVERT: C 59 ASN cc_start: 0.6927 (p0) cc_final: 0.5689 (t0) REVERT: C 149 ILE cc_start: 0.7355 (mt) cc_final: 0.7076 (mm) REVERT: C 188 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7131 (mttt) REVERT: C 362 LYS cc_start: 0.7327 (mmpt) cc_final: 0.7024 (mmtt) REVERT: C 367 MET cc_start: 0.7049 (mmp) cc_final: 0.6619 (mmp) REVERT: C 799 ASP cc_start: 0.7964 (p0) cc_final: 0.7762 (p0) REVERT: D 412 MET cc_start: 0.8447 (mtp) cc_final: 0.8175 (mtp) REVERT: D 561 LYS cc_start: 0.8407 (mmtp) cc_final: 0.7962 (mppt) REVERT: D 671 TYR cc_start: 0.6950 (m-10) cc_final: 0.6478 (m-10) REVERT: D 706 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6707 (mm-30) REVERT: D 730 GLN cc_start: 0.8130 (mp10) cc_final: 0.7920 (mm-40) REVERT: D 788 ASP cc_start: 0.8030 (m-30) cc_final: 0.7572 (m-30) REVERT: D 1099 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: E 51 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6185 (pm20) REVERT: F 232 ARG cc_start: 0.5503 (mtm180) cc_final: 0.4888 (ptp90) outliers start: 60 outliers final: 52 residues processed: 567 average time/residue: 0.4180 time to fit residues: 361.7699 Evaluate side-chains 570 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 516 time to evaluate : 2.886 ------------------------------------------------------------------------------- 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 130 LEU 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 56 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain C residue 24 MET 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 322 VAL 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 838 LEU 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 1073 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 310 MET 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 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1128 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain F residue 112 VAL 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 94 optimal weight: 0.0770 chunk 247 optimal weight: 0.4980 chunk 6 optimal weight: 0.0070 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 305 optimal weight: 7.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.146268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.103481 restraints weight = 31788.943| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.58 r_work: 0.2832 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26980 Z= 0.106 Angle : 0.505 12.285 36899 Z= 0.267 Chirality : 0.041 0.197 4215 Planarity : 0.004 0.064 4386 Dihedral : 17.903 97.489 4583 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.98 % Allowed : 19.47 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3054 helix: 0.72 (0.16), residues: 1160 sheet: 0.33 (0.29), residues: 341 loop : -0.77 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.029 0.001 PHE F 72 TYR 0.015 0.001 TYR D 895 ARG 0.009 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 992) hydrogen bonds : angle 4.23576 ( 2796) metal coordination : bond 0.00421 ( 8) metal coordination : angle 2.86358 ( 12) covalent geometry : bond 0.00240 (26972) covalent geometry : angle 0.50269 (36887) ********************** 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 614 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 562 time to evaluate : 3.947 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8062 (t0) cc_final: 0.7687 (t0) REVERT: A 113 LYS cc_start: 0.6799 (mmtm) cc_final: 0.6530 (mmtt) REVERT: C 37 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8277 (tp40) REVERT: C 59 ASN cc_start: 0.6994 (p0) cc_final: 0.5944 (t0) REVERT: C 189 LEU cc_start: 0.7517 (tp) cc_final: 0.7138 (tt) REVERT: C 343 ASP cc_start: 0.7368 (p0) cc_final: 0.7115 (p0) REVERT: C 362 LYS cc_start: 0.7228 (mmpt) cc_final: 0.6932 (mmtt) REVERT: C 367 MET cc_start: 0.7050 (mmp) cc_final: 0.6661 (mmp) REVERT: C 608 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7650 (mtp-110) REVERT: C 647 MET cc_start: 0.8916 (mtt) cc_final: 0.8662 (mmm) REVERT: C 722 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: C 799 ASP cc_start: 0.7977 (p0) cc_final: 0.7777 (p0) REVERT: D 412 MET cc_start: 0.8416 (mtp) cc_final: 0.8125 (mtp) REVERT: D 561 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7976 (mppt) REVERT: D 671 TYR cc_start: 0.6882 (m-10) cc_final: 0.6413 (m-10) REVERT: D 706 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6650 (mm-30) REVERT: D 730 GLN cc_start: 0.8114 (mp10) cc_final: 0.7911 (mm-40) REVERT: D 788 ASP cc_start: 0.7947 (m-30) cc_final: 0.7483 (m-30) REVERT: D 1095 PHE cc_start: 0.6585 (t80) cc_final: 0.6205 (t80) REVERT: D 1099 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6576 (pt0) REVERT: E 51 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: F 232 ARG cc_start: 0.5534 (mtm180) cc_final: 0.4985 (ptp90) outliers start: 52 outliers final: 41 residues processed: 596 average time/residue: 0.5394 time to fit residues: 502.6633 Evaluate side-chains 580 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 536 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 130 LEU 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 322 VAL 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 722 ASP Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1071 SER 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 222 THR Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 990 VAL Chi-restraints excluded: chain D residue 1099 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain F residue 112 VAL 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 125 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 197 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 272 optimal weight: 0.5980 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.099478 restraints weight = 31901.210| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.59 r_work: 0.2763 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26980 Z= 0.199 Angle : 0.583 12.491 36899 Z= 0.304 Chirality : 0.044 0.206 4215 Planarity : 0.004 0.065 4386 Dihedral : 18.026 99.671 4582 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.05 % Allowed : 19.89 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3054 helix: 0.47 (0.16), residues: 1158 sheet: 0.19 (0.29), residues: 354 loop : -0.86 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 999 HIS 0.004 0.001 HIS F 84 PHE 0.026 0.002 PHE F 72 TYR 0.017 0.001 TYR D 649 ARG 0.012 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 992) hydrogen bonds : angle 4.45380 ( 2796) metal coordination : bond 0.00768 ( 8) metal coordination : angle 4.40896 ( 12) covalent geometry : bond 0.00478 (26972) covalent geometry : angle 0.57795 (36887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17342.36 seconds wall clock time: 302 minutes 49.56 seconds (18169.56 seconds total)