Starting phenix.real_space_refine on Mon Jul 6 00:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji3_61493/07_2026/9ji3_61493.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji3_61493/07_2026/9ji3_61493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ji3_61493/07_2026/9ji3_61493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji3_61493/07_2026/9ji3_61493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ji3_61493/07_2026/9ji3_61493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji3_61493/07_2026/9ji3_61493.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1881 atoms to isotropic. 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 106 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 17783 2.51 5 N 5143 2.21 5 O 5740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28870 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1708 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8551 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9877 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1207} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1078 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1108 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "F" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 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 19073 SG CYS D 891 76.166 119.128 84.370 1.00 78.47 S ATOM 19640 SG CYS D 968 77.738 115.786 86.157 1.00 62.26 S ATOM 19700 SG CYS D 978 79.152 117.677 83.055 1.00 57.27 S ATOM 12521 SG CYS D 60 56.333 64.314 119.751 1.00110.28 S ATOM 12674 SG CYS D 78 58.793 66.845 122.496 1.00106.07 S Time building chain proxies: 5.34, per 1000 atoms: 0.18 Number of scatterers: 28870 At special positions: 0 Unit cell: (159.6, 148.8, 190.8, 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 95 16.00 P 106 15.00 Mg 1 11.99 O 5740 8.00 N 5143 7.00 C 17783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 926.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6346 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 43 sheets defined 43.5% alpha, 14.9% beta 29 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.276A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.995A pdb=" N LEU A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.286A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.079A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.981A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.670A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.165A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.501A pdb=" N ILE C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.585A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.607A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.532A pdb=" N TYR C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.242A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.578A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.987A pdb=" N ARG C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 469 through 474' Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.679A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 removed outlier: 4.041A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 538' Processing helix chain 'C' and resid 572 through 576 removed outlier: 3.828A pdb=" N GLU C 575 " --> pdb=" O PRO C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.666A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.031A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 removed outlier: 3.645A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.663A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.537A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.547A pdb=" N GLY C1080 " --> pdb=" O MET C1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.896A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.736A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.915A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 124 Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 147 through 185 Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.735A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.569A pdb=" N ARG D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.757A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.968A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.521A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.970A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.708A pdb=" N LEU D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 removed outlier: 4.098A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.623A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 728 removed outlier: 3.919A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.691A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.630A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.680A pdb=" N THR D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.738A pdb=" N THR D 967 " --> pdb=" O SER D 964 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 964 through 968' Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1144 Proline residue: D1127 - end of helix removed outlier: 3.901A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1163 removed outlier: 4.229A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.539A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.571A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.905A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 3.603A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 307 removed outlier: 3.893A pdb=" N ARG F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N MET F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 311 removed outlier: 3.710A pdb=" N THR F 311 " --> pdb=" O LYS F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 308 through 311' Processing helix chain 'F' and resid 316 through 335 removed outlier: 4.017A pdb=" N GLU F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS F 334 " --> pdb=" O ARG F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.611A pdb=" N LYS F 339 " --> pdb=" O ASP F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.827A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 363 " --> pdb=" O MET F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 4.356A pdb=" N VAL F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN F 388 " --> pdb=" O ARG F 384 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 417 removed outlier: 3.552A pdb=" N VAL F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 439 removed outlier: 3.678A pdb=" N ILE F 439 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 467 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.737A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 188 Processing helix chain 'J' and resid 194 through 202 Processing helix chain 'J' and resid 211 through 225 removed outlier: 3.889A pdb=" N GLU J 215 " --> pdb=" O VAL J 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 194 through 202 Processing helix chain 'K' and resid 211 through 225 removed outlier: 3.798A pdb=" N GLU K 215 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.082A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.706A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 50 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.567A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 3.662A pdb=" N GLN B 20 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.841A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.103A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.582A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.054A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.522A pdb=" N VAL C 180 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 187 through 191 removed outlier: 5.013A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB7, first strand: chain 'C' and resid 505 through 506 removed outlier: 7.310A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AB9, first strand: chain 'C' and resid 561 through 562 Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.441A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.915A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC4, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.203A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.050A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASN C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C 854 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS C 876 " --> pdb=" O SER C 844 " (cutoff:3.500A) removed outlier: 9.873A pdb=" N SER C 844 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.916A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AC9, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.495A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD2, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD3, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.159A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.094A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.166A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 removed outlier: 3.613A pdb=" N ARG D 636 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.765A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 929 through 930 removed outlier: 6.970A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1075 through 1081 removed outlier: 3.721A pdb=" N ILE D1064 " --> pdb=" O TYR D1077 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AE3, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE4, first strand: chain 'J' and resid 151 through 153 removed outlier: 3.790A pdb=" N VAL J 165 " --> pdb=" O VAL J 172 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 192 through 193 Processing sheet with id=AE6, first strand: chain 'K' and resid 151 through 153 removed outlier: 4.195A pdb=" N VAL K 165 " --> pdb=" O VAL K 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 233 through 236 1179 hydrogen bonds defined for protein. 3315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8869 1.33 - 1.46: 4713 1.46 - 1.58: 15625 1.58 - 1.70: 210 1.70 - 1.82: 168 Bond restraints: 29585 Sorted by residual: bond pdb=" C3' DA G 49 " pdb=" C2' DA G 49 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C1' DT H 44 " pdb=" N1 DT H 44 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.22e+01 bond pdb=" C3' DC H 53 " pdb=" C2' DC H 53 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC H 29 " pdb=" C2' DC H 29 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DA G 21 " pdb=" C2' DA G 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 29580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 40004 2.49 - 4.98: 477 4.98 - 7.47: 51 7.47 - 9.96: 14 9.96 - 12.45: 3 Bond angle restraints: 40549 Sorted by residual: angle pdb=" O4' DG G 12 " pdb=" C4' DG G 12 " pdb=" C3' DG G 12 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" CA ARG D 206 " pdb=" CB ARG D 206 " pdb=" CG ARG D 206 " ideal model delta sigma weight residual 114.10 123.70 -9.60 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA ARG D 478 " pdb=" CB ARG D 478 " pdb=" CG ARG D 478 " ideal model delta sigma weight residual 114.10 122.79 -8.69 2.00e+00 2.50e-01 1.89e+01 angle pdb=" N3 DT H 21 " pdb=" C4 DT H 21 " pdb=" O4 DT H 21 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" C ARG C 830 " pdb=" N GLU C 831 " pdb=" CA GLU C 831 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 ... (remaining 40544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 16736 35.82 - 71.64: 955 71.64 - 107.46: 58 107.46 - 143.27: 3 143.27 - 179.09: 7 Dihedral angle restraints: 17759 sinusoidal: 7894 harmonic: 9865 Sorted by residual: dihedral pdb=" CA VAL D 110 " pdb=" C VAL D 110 " pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N ASP B 188 " pdb=" CA ASP B 188 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLN D 657 " pdb=" C GLN D 657 " pdb=" N PRO D 658 " pdb=" CA PRO D 658 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 17756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3342 0.043 - 0.086: 958 0.086 - 0.129: 297 0.129 - 0.172: 27 0.172 - 0.216: 6 Chirality restraints: 4630 Sorted by residual: chirality pdb=" P DC H 3 " pdb=" OP1 DC H 3 " pdb=" OP2 DC H 3 " pdb=" O5' DC H 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.55 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE C 773 " pdb=" CA ILE C 773 " pdb=" CG1 ILE C 773 " pdb=" CG2 ILE C 773 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU K 233 " pdb=" N LEU K 233 " pdb=" C LEU K 233 " pdb=" CB LEU K 233 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4627 not shown) Planarity restraints: 4944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 326 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO C 327 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 363 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO C 364 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 364 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 364 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO D 434 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.027 5.00e-02 4.00e+02 ... (remaining 4941 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 482 2.64 - 3.20: 27078 3.20 - 3.77: 47340 3.77 - 4.33: 61453 4.33 - 4.90: 98739 Nonbonded interactions: 235092 Sorted by model distance: nonbonded pdb=" NH2 ARG D 77 " pdb="ZN ZN D2001 " model vdw 2.075 2.310 nonbonded pdb=" N TYR D 61 " pdb="ZN ZN D2001 " model vdw 2.187 2.310 nonbonded pdb=" O LEU C 308 " pdb=" OG SER C 331 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU D 376 " pdb=" OG SER F 227 " model vdw 2.203 3.040 nonbonded pdb=" O SER C 182 " pdb=" OH TYR C 186 " model vdw 2.206 3.040 ... (remaining 235087 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' and (resid 3 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 3 through 226) } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.920 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 0.062 29590 Z= 0.247 Angle : 0.695 12.448 40549 Z= 0.426 Chirality : 0.044 0.216 4630 Planarity : 0.005 0.096 4944 Dihedral : 20.449 179.092 11413 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 0.31 % Allowed : 30.05 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3423 helix: 0.71 (0.15), residues: 1321 sheet: -0.88 (0.29), residues: 343 loop : -1.04 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1191 TYR 0.023 0.001 TYR F 526 PHE 0.024 0.002 PHE D1061 TRP 0.031 0.002 TRP J 166 HIS 0.010 0.001 HIS J 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.25 (29585) covalent geometry : angle 0.69490 / 0.43 (40549) hydrogen bonds : bond 0.14868 / 10.30 ( 1248) hydrogen bonds : angle 6.23685 / 4.33 ( 3465) metal coordination : bond 0.02412 / 1.22 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 370 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.7987 (tp30) cc_final: 0.7475 (tp30) REVERT: C 275 LEU cc_start: 0.9066 (pp) cc_final: 0.8781 (mt) REVERT: C 756 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: C 835 THR cc_start: 0.8803 (p) cc_final: 0.8541 (p) REVERT: D 86 LYS cc_start: 0.8567 (pttm) cc_final: 0.8180 (pttp) REVERT: D 147 GLU cc_start: 0.9074 (tp30) cc_final: 0.8859 (tp30) REVERT: D 1112 MET cc_start: 0.8191 (tpp) cc_final: 0.7975 (tpp) REVERT: D 1142 TYR cc_start: 0.7797 (t80) cc_final: 0.7120 (t80) REVERT: F 359 MET cc_start: 0.8709 (tpp) cc_final: 0.8457 (mtp) REVERT: J 188 ASN cc_start: 0.7359 (m-40) cc_final: 0.7108 (m-40) outliers start: 9 outliers final: 3 residues processed: 376 average time/residue: 0.1887 time to fit residues: 112.0087 Evaluate side-chains 328 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 324 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0060 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN C 442 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 HIS D 304 GLN D 854 HIS D1001 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090454 restraints weight = 59854.165| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.58 r_work: 0.3101 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29590 Z= 0.150 Angle : 0.630 9.716 40549 Z= 0.333 Chirality : 0.045 0.259 4630 Planarity : 0.005 0.062 4944 Dihedral : 18.527 172.733 4936 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.53 % Allowed : 27.28 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3423 helix: 0.83 (0.14), residues: 1341 sheet: -0.66 (0.30), residues: 326 loop : -1.06 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 515 TYR 0.025 0.001 TYR K 220 PHE 0.017 0.002 PHE J 179 TRP 0.017 0.001 TRP J 166 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (29585) covalent geometry : angle 0.62979 / 0.33 (40549) hydrogen bonds : bond 0.04711 / 3.28 ( 1248) hydrogen bonds : angle 5.11033 / 3.56 ( 3465) metal coordination : bond 0.00636 / 0.37 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 355 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8990 (mm) REVERT: B 57 ASP cc_start: 0.8023 (p0) cc_final: 0.7712 (t0) REVERT: B 75 GLU cc_start: 0.8421 (tp30) cc_final: 0.7766 (tp30) REVERT: B 189 PHE cc_start: 0.7813 (m-10) cc_final: 0.7449 (m-80) REVERT: C 103 MET cc_start: 0.8363 (ppp) cc_final: 0.7776 (ppp) REVERT: C 261 THR cc_start: 0.8777 (m) cc_final: 0.8450 (p) REVERT: C 275 LEU cc_start: 0.9136 (pp) cc_final: 0.8772 (mt) REVERT: C 306 TYR cc_start: 0.8495 (t80) cc_final: 0.8275 (t80) REVERT: C 513 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 756 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 818 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 1076 MET cc_start: 0.9121 (tpp) cc_final: 0.8817 (tpp) REVERT: D 86 LYS cc_start: 0.8780 (pttm) cc_final: 0.8353 (pttp) REVERT: D 497 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8514 (mt) REVERT: D 706 MET cc_start: 0.8182 (tpt) cc_final: 0.7926 (mtt) REVERT: D 1142 TYR cc_start: 0.7982 (t80) cc_final: 0.6886 (t80) REVERT: F 359 MET cc_start: 0.9212 (tpp) cc_final: 0.8920 (mtp) REVERT: F 374 GLU cc_start: 0.9093 (tt0) cc_final: 0.8819 (mt-10) REVERT: F 465 ASP cc_start: 0.7601 (m-30) cc_final: 0.7389 (m-30) REVERT: F 524 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5970 (tpp-160) outliers start: 101 outliers final: 48 residues processed: 426 average time/residue: 0.1863 time to fit residues: 126.4168 Evaluate side-chains 387 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 335 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 524 ARG Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 241 TYR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 84 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 854 HIS ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN F 377 ASN ** J 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.132754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091040 restraints weight = 59381.784| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.30 r_work: 0.3118 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29590 Z= 0.136 Angle : 0.596 9.098 40549 Z= 0.316 Chirality : 0.044 0.253 4630 Planarity : 0.005 0.057 4944 Dihedral : 18.462 173.056 4930 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.53 % Allowed : 27.32 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3423 helix: 0.91 (0.14), residues: 1336 sheet: -0.69 (0.29), residues: 333 loop : -0.99 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1204 TYR 0.019 0.001 TYR K 220 PHE 0.012 0.001 PHE B 219 TRP 0.015 0.001 TRP J 166 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (29585) covalent geometry : angle 0.59649 / 0.32 (40549) hydrogen bonds : bond 0.04208 / 2.93 ( 1248) hydrogen bonds : angle 4.89047 / 3.40 ( 3465) metal coordination : bond 0.00619 / 0.35 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 356 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8396 (pm20) cc_final: 0.8175 (pm20) REVERT: A 89 GLU cc_start: 0.8110 (pm20) cc_final: 0.7768 (pm20) REVERT: B 57 ASP cc_start: 0.8055 (p0) cc_final: 0.7738 (t0) REVERT: B 75 GLU cc_start: 0.8468 (tp30) cc_final: 0.7782 (tp30) REVERT: B 124 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.8268 (t-90) REVERT: B 189 PHE cc_start: 0.7810 (m-10) cc_final: 0.7201 (m-80) REVERT: B 197 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: C 103 MET cc_start: 0.8357 (ppp) cc_final: 0.8112 (ppp) REVERT: C 258 MET cc_start: 0.8524 (ttt) cc_final: 0.8319 (ttm) REVERT: C 261 THR cc_start: 0.8869 (m) cc_final: 0.8519 (p) REVERT: C 275 LEU cc_start: 0.9127 (pp) cc_final: 0.8780 (mt) REVERT: C 293 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7401 (tp-100) REVERT: C 440 MET cc_start: 0.8479 (ttt) cc_final: 0.8059 (ttm) REVERT: C 513 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: C 763 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8631 (ptmt) REVERT: C 818 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7554 (mt-10) REVERT: C 1076 MET cc_start: 0.9089 (tpp) cc_final: 0.8880 (tpp) REVERT: D 67 ARG cc_start: 0.8666 (mmt180) cc_final: 0.8456 (mmt180) REVERT: D 86 LYS cc_start: 0.8827 (pttm) cc_final: 0.8455 (pttp) REVERT: D 147 GLU cc_start: 0.9203 (tp30) cc_final: 0.8960 (tp30) REVERT: D 400 LYS cc_start: 0.9330 (tttm) cc_final: 0.9017 (tttm) REVERT: D 497 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8468 (mt) REVERT: D 706 MET cc_start: 0.8190 (tpt) cc_final: 0.7910 (mtt) REVERT: D 791 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7096 (pp20) REVERT: D 1142 TYR cc_start: 0.7927 (t80) cc_final: 0.6929 (t80) REVERT: E 70 GLN cc_start: 0.8284 (mm110) cc_final: 0.8048 (mm110) REVERT: F 359 MET cc_start: 0.9194 (tpp) cc_final: 0.8884 (mtp) REVERT: F 465 ASP cc_start: 0.7567 (m-30) cc_final: 0.7319 (m-30) outliers start: 101 outliers final: 59 residues processed: 432 average time/residue: 0.1669 time to fit residues: 117.4375 Evaluate side-chains 402 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 338 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 333 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085904 restraints weight = 59642.539| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.24 r_work: 0.3023 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 29590 Z= 0.282 Angle : 0.701 9.937 40549 Z= 0.368 Chirality : 0.047 0.274 4630 Planarity : 0.005 0.058 4944 Dihedral : 18.511 173.303 4930 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.77 % Allowed : 26.76 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3423 helix: 0.84 (0.14), residues: 1323 sheet: -1.16 (0.28), residues: 337 loop : -1.06 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 77 TYR 0.033 0.002 TYR D 36 PHE 0.022 0.002 PHE D 452 TRP 0.017 0.002 TRP C 955 HIS 0.007 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.28 (29585) covalent geometry : angle 0.70082 / 0.37 (40549) hydrogen bonds : bond 0.04780 / 3.31 ( 1248) hydrogen bonds : angle 4.96576 / 3.47 ( 3465) metal coordination : bond 0.01461 / 0.86 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 321 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8487 (pm20) cc_final: 0.8191 (pm20) REVERT: A 38 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8987 (mm) REVERT: B 57 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7592 (p0) REVERT: B 75 GLU cc_start: 0.8562 (tp30) cc_final: 0.7837 (tp30) REVERT: B 124 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8027 (t-90) REVERT: C 103 MET cc_start: 0.8448 (ppp) cc_final: 0.8220 (ppp) REVERT: C 266 ASN cc_start: 0.8581 (m-40) cc_final: 0.8211 (m110) REVERT: C 275 LEU cc_start: 0.9175 (pp) cc_final: 0.8838 (mt) REVERT: C 306 TYR cc_start: 0.8567 (t80) cc_final: 0.8338 (t80) REVERT: C 513 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: C 819 ARG cc_start: 0.8374 (mmt90) cc_final: 0.8138 (mmt90) REVERT: C 1076 MET cc_start: 0.9205 (tpp) cc_final: 0.8984 (tpp) REVERT: C 1125 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8591 (mp) REVERT: D 67 ARG cc_start: 0.8681 (mmt180) cc_final: 0.8479 (mmt180) REVERT: D 497 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8484 (mt) REVERT: D 608 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: D 675 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8927 (tp30) REVERT: D 706 MET cc_start: 0.8267 (tpt) cc_final: 0.7977 (mtt) REVERT: D 791 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6984 (pp20) REVERT: D 904 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6812 (tpp-160) REVERT: D 1142 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7031 (t80) REVERT: E 98 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8434 (mt-10) outliers start: 165 outliers final: 100 residues processed: 449 average time/residue: 0.1699 time to fit residues: 123.5724 Evaluate side-chains 413 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 303 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 186 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 311 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 854 HIS ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN F 457 GLN J 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087765 restraints weight = 59307.828| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.25 r_work: 0.3071 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29590 Z= 0.149 Angle : 0.616 9.341 40549 Z= 0.324 Chirality : 0.044 0.254 4630 Planarity : 0.005 0.065 4944 Dihedral : 18.440 174.318 4930 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.55 % Allowed : 27.81 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3423 helix: 0.91 (0.14), residues: 1341 sheet: -0.75 (0.29), residues: 336 loop : -1.06 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.018 0.001 TYR D 36 PHE 0.017 0.001 PHE J 179 TRP 0.012 0.001 TRP J 166 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (29585) covalent geometry : angle 0.61582 / 0.32 (40549) hydrogen bonds : bond 0.04124 / 2.87 ( 1248) hydrogen bonds : angle 4.75101 / 3.29 ( 3465) metal coordination : bond 0.00798 / 0.44 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 333 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8399 (pm20) cc_final: 0.8136 (pm20) REVERT: A 38 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8987 (mm) REVERT: A 89 GLU cc_start: 0.8281 (pm20) cc_final: 0.7961 (pm20) REVERT: A 135 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7826 (tp30) REVERT: B 75 GLU cc_start: 0.8446 (tp30) cc_final: 0.7745 (tp30) REVERT: B 133 LYS cc_start: 0.7946 (tppt) cc_final: 0.7568 (tppp) REVERT: B 189 PHE cc_start: 0.8055 (m-10) cc_final: 0.7547 (m-80) REVERT: B 197 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: C 103 MET cc_start: 0.8489 (ppp) cc_final: 0.7890 (ppp) REVERT: C 165 THR cc_start: 0.9316 (p) cc_final: 0.9095 (t) REVERT: C 201 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.8017 (p) REVERT: C 266 ASN cc_start: 0.8557 (m-40) cc_final: 0.8185 (m110) REVERT: C 275 LEU cc_start: 0.9144 (pp) cc_final: 0.8837 (mt) REVERT: C 293 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7263 (tp-100) REVERT: C 306 TYR cc_start: 0.8537 (t80) cc_final: 0.8249 (t80) REVERT: C 513 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: C 527 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8637 (tm-30) REVERT: C 819 ARG cc_start: 0.8259 (mmt90) cc_final: 0.8000 (mmt90) REVERT: D 67 ARG cc_start: 0.8747 (mmt180) cc_final: 0.8522 (mmt180) REVERT: D 497 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8511 (mt) REVERT: D 608 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: D 706 MET cc_start: 0.8192 (tpt) cc_final: 0.7962 (mtt) REVERT: D 791 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6927 (pp20) REVERT: D 1142 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6933 (t80) REVERT: E 98 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8404 (mt-10) outliers start: 130 outliers final: 87 residues processed: 435 average time/residue: 0.1649 time to fit residues: 115.9902 Evaluate side-chains 413 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 317 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 214 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 291 optimal weight: 40.0000 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 336 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS D1110 GLN D1125 GLN J 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.128934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087133 restraints weight = 59186.246| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.25 r_work: 0.3053 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29590 Z= 0.180 Angle : 0.628 10.064 40549 Z= 0.329 Chirality : 0.045 0.266 4630 Planarity : 0.005 0.067 4944 Dihedral : 18.379 174.958 4930 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.97 % Allowed : 28.02 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3423 helix: 0.91 (0.14), residues: 1342 sheet: -0.76 (0.29), residues: 336 loop : -1.06 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 925 TYR 0.019 0.001 TYR D 36 PHE 0.019 0.002 PHE K 185 TRP 0.018 0.001 TRP C1074 HIS 0.005 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (29585) covalent geometry : angle 0.62816 / 0.33 (40549) hydrogen bonds : bond 0.04125 / 2.85 ( 1248) hydrogen bonds : angle 4.70548 / 3.26 ( 3465) metal coordination : bond 0.00877 / 0.50 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 325 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8465 (pm20) cc_final: 0.8158 (pm20) REVERT: A 38 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8983 (mm) REVERT: A 89 GLU cc_start: 0.8251 (pm20) cc_final: 0.7973 (pm20) REVERT: A 135 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: A 151 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8297 (mp10) REVERT: A 186 ARG cc_start: 0.6458 (OUTLIER) cc_final: 0.5640 (ppt170) REVERT: B 75 GLU cc_start: 0.8480 (tp30) cc_final: 0.7767 (tp30) REVERT: B 188 ASP cc_start: 0.5710 (t0) cc_final: 0.5452 (t0) REVERT: B 197 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: C 96 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6748 (pp) REVERT: C 103 MET cc_start: 0.8323 (ppp) cc_final: 0.7708 (ppp) REVERT: C 201 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (p) REVERT: C 266 ASN cc_start: 0.8574 (m-40) cc_final: 0.8275 (m-40) REVERT: C 275 LEU cc_start: 0.9161 (pp) cc_final: 0.8834 (mt) REVERT: C 293 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7250 (tp-100) REVERT: C 306 TYR cc_start: 0.8630 (t80) cc_final: 0.8239 (t80) REVERT: C 465 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7128 (ptp-170) REVERT: C 509 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 513 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: C 527 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 763 LYS cc_start: 0.9094 (mtmm) cc_final: 0.8460 (ptmt) REVERT: C 815 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6446 (p) REVERT: C 819 ARG cc_start: 0.8245 (mmt90) cc_final: 0.7951 (mmt90) REVERT: D 36 TYR cc_start: 0.8862 (p90) cc_final: 0.8631 (p90) REVERT: D 67 ARG cc_start: 0.8752 (mmt180) cc_final: 0.8517 (mmt180) REVERT: D 497 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8493 (mt) REVERT: D 608 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 706 MET cc_start: 0.8220 (tpt) cc_final: 0.7965 (mtt) REVERT: D 791 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: D 1142 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6897 (t80) REVERT: E 98 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8413 (mt-10) outliers start: 142 outliers final: 96 residues processed: 438 average time/residue: 0.1812 time to fit residues: 128.8866 Evaluate side-chains 420 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 310 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 242 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 283 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 288 optimal weight: 0.0270 chunk 61 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 chunk 70 optimal weight: 0.0010 chunk 211 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.9246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN C 603 ASN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS F 377 ASN J 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.089386 restraints weight = 58930.523| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.25 r_work: 0.3092 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29590 Z= 0.126 Angle : 0.614 11.640 40549 Z= 0.321 Chirality : 0.044 0.266 4630 Planarity : 0.005 0.099 4944 Dihedral : 18.296 175.750 4930 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.30 % Allowed : 28.61 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3423 helix: 0.93 (0.14), residues: 1342 sheet: -0.68 (0.29), residues: 326 loop : -1.01 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1191 TYR 0.018 0.001 TYR F 337 PHE 0.015 0.001 PHE K 185 TRP 0.023 0.001 TRP F 283 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (29585) covalent geometry : angle 0.61418 / 0.32 (40549) hydrogen bonds : bond 0.03837 / 2.66 ( 1248) hydrogen bonds : angle 4.63235 / 3.20 ( 3465) metal coordination : bond 0.00443 / 0.24 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 336 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8402 (pm20) cc_final: 0.8143 (pm20) REVERT: A 38 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8980 (mm) REVERT: A 89 GLU cc_start: 0.8135 (pm20) cc_final: 0.7866 (pm20) REVERT: A 135 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: A 151 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8293 (mp10) REVERT: A 186 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5643 (ppt170) REVERT: B 75 GLU cc_start: 0.8470 (tp30) cc_final: 0.7749 (tp30) REVERT: B 189 PHE cc_start: 0.8134 (m-10) cc_final: 0.7606 (m-80) REVERT: B 197 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: C 96 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6826 (pp) REVERT: C 103 MET cc_start: 0.8362 (ppp) cc_final: 0.7746 (ppp) REVERT: C 266 ASN cc_start: 0.8566 (m-40) cc_final: 0.8267 (m-40) REVERT: C 275 LEU cc_start: 0.9117 (pp) cc_final: 0.8817 (mt) REVERT: C 293 GLN cc_start: 0.7601 (tp-100) cc_final: 0.7185 (tp-100) REVERT: C 306 TYR cc_start: 0.8515 (t80) cc_final: 0.8080 (t80) REVERT: C 348 LEU cc_start: 0.9324 (tp) cc_final: 0.9036 (tp) REVERT: C 509 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7883 (t80) REVERT: C 513 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: C 527 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8616 (tm-30) REVERT: C 538 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8503 (mtm110) REVERT: C 601 ASP cc_start: 0.8522 (t0) cc_final: 0.8054 (t0) REVERT: C 763 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8511 (ptmt) REVERT: C 819 ARG cc_start: 0.8155 (mmt90) cc_final: 0.7848 (mmt90) REVERT: D 36 TYR cc_start: 0.8810 (p90) cc_final: 0.8592 (p90) REVERT: D 67 ARG cc_start: 0.8750 (mmt180) cc_final: 0.8511 (mmt180) REVERT: D 312 MET cc_start: 0.9321 (mmm) cc_final: 0.8440 (mmt) REVERT: D 477 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8157 (mm-30) REVERT: D 497 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8490 (mt) REVERT: D 608 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: D 706 MET cc_start: 0.8159 (tpt) cc_final: 0.7896 (mtt) REVERT: D 791 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6892 (pp20) REVERT: D 1142 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6803 (t80) REVERT: D 1191 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7730 (mtm110) REVERT: E 98 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8387 (mt-10) REVERT: F 465 ASP cc_start: 0.7488 (m-30) cc_final: 0.7207 (p0) outliers start: 123 outliers final: 90 residues processed: 429 average time/residue: 0.1640 time to fit residues: 115.2672 Evaluate side-chains 424 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 323 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 827 GLU Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 204 ARG Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 274 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.085880 restraints weight = 59573.103| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.25 r_work: 0.3030 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 29590 Z= 0.230 Angle : 0.660 12.993 40549 Z= 0.345 Chirality : 0.045 0.265 4630 Planarity : 0.005 0.074 4944 Dihedral : 18.287 176.077 4930 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.11 % Allowed : 27.95 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3423 helix: 0.90 (0.15), residues: 1335 sheet: -0.91 (0.29), residues: 330 loop : -1.04 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 206 TYR 0.018 0.002 TYR F 337 PHE 0.015 0.002 PHE D 452 TRP 0.013 0.002 TRP D 223 HIS 0.006 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (29585) covalent geometry : angle 0.65985 / 0.35 (40549) hydrogen bonds : bond 0.04278 / 2.96 ( 1248) hydrogen bonds : angle 4.72194 / 3.28 ( 3465) metal coordination : bond 0.00750 / 0.46 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 316 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8997 (mm) REVERT: A 89 GLU cc_start: 0.8282 (pm20) cc_final: 0.8068 (pm20) REVERT: A 135 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: A 151 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8352 (mp10) REVERT: A 186 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5707 (ppt170) REVERT: B 75 GLU cc_start: 0.8567 (tp30) cc_final: 0.7867 (tp30) REVERT: B 133 LYS cc_start: 0.7866 (tppt) cc_final: 0.7536 (tppp) REVERT: C 96 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6732 (pp) REVERT: C 103 MET cc_start: 0.8364 (ppp) cc_final: 0.7776 (ppp) REVERT: C 127 MET cc_start: 0.8957 (ptm) cc_final: 0.8687 (ptm) REVERT: C 266 ASN cc_start: 0.8525 (m-40) cc_final: 0.8213 (m-40) REVERT: C 275 LEU cc_start: 0.9150 (pp) cc_final: 0.8852 (mt) REVERT: C 293 GLN cc_start: 0.7572 (tp-100) cc_final: 0.7145 (tp-100) REVERT: C 306 TYR cc_start: 0.8697 (t80) cc_final: 0.8214 (t80) REVERT: C 465 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7289 (ptp-170) REVERT: C 509 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 513 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: C 527 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 904 MET cc_start: 0.9391 (mmp) cc_final: 0.9000 (mmp) REVERT: C 1125 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 36 TYR cc_start: 0.8884 (p90) cc_final: 0.8664 (p90) REVERT: D 67 ARG cc_start: 0.8765 (mmt180) cc_final: 0.8531 (mmt180) REVERT: D 400 LYS cc_start: 0.9377 (tttm) cc_final: 0.9100 (tttm) REVERT: D 497 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8523 (mt) REVERT: D 608 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: D 791 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: D 1142 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6966 (t80) REVERT: E 98 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8409 (mt-10) REVERT: J 188 ASN cc_start: 0.7398 (m-40) cc_final: 0.7112 (m-40) outliers start: 146 outliers final: 106 residues processed: 434 average time/residue: 0.1666 time to fit residues: 117.8432 Evaluate side-chains 427 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 309 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 917 LEU Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 204 ARG Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 39 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 306 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS F 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089090 restraints weight = 59086.174| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.26 r_work: 0.3083 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29590 Z= 0.128 Angle : 0.624 12.965 40549 Z= 0.325 Chirality : 0.043 0.275 4630 Planarity : 0.005 0.069 4944 Dihedral : 18.230 176.925 4930 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.09 % Allowed : 28.79 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3423 helix: 0.93 (0.15), residues: 1337 sheet: -0.66 (0.30), residues: 323 loop : -0.99 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1191 TYR 0.020 0.001 TYR F 337 PHE 0.028 0.001 PHE J 179 TRP 0.021 0.001 TRP F 283 HIS 0.004 0.001 HIS C 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (29585) covalent geometry : angle 0.62403 / 0.33 (40549) hydrogen bonds : bond 0.03834 / 2.67 ( 1248) hydrogen bonds : angle 4.59421 / 3.17 ( 3465) metal coordination : bond 0.00408 / 0.22 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 332 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8957 (mm) REVERT: A 135 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: A 151 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8376 (mp10) REVERT: B 75 GLU cc_start: 0.8387 (tp30) cc_final: 0.7728 (tp30) REVERT: B 189 PHE cc_start: 0.8235 (m-10) cc_final: 0.7672 (m-80) REVERT: C 96 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6783 (pp) REVERT: C 103 MET cc_start: 0.8409 (ppp) cc_final: 0.7829 (ppp) REVERT: C 127 MET cc_start: 0.8900 (ptm) cc_final: 0.8631 (ptm) REVERT: C 258 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8178 (ppp) REVERT: C 266 ASN cc_start: 0.8564 (m-40) cc_final: 0.8256 (m-40) REVERT: C 275 LEU cc_start: 0.9134 (pp) cc_final: 0.8807 (mt) REVERT: C 293 GLN cc_start: 0.7601 (tp-100) cc_final: 0.7158 (tp-100) REVERT: C 306 TYR cc_start: 0.8522 (t80) cc_final: 0.8020 (t80) REVERT: C 348 LEU cc_start: 0.9322 (tp) cc_final: 0.9080 (tp) REVERT: C 509 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7869 (t80) REVERT: C 513 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: C 527 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8618 (tm-30) REVERT: C 538 ARG cc_start: 0.8968 (mtm110) cc_final: 0.8528 (mtm110) REVERT: C 813 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 36 TYR cc_start: 0.8851 (p90) cc_final: 0.8621 (p90) REVERT: D 312 MET cc_start: 0.9405 (mmm) cc_final: 0.9093 (mmt) REVERT: D 400 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9076 (tttm) REVERT: D 497 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8573 (mt) REVERT: D 608 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 706 MET cc_start: 0.8179 (tpt) cc_final: 0.7930 (mtt) REVERT: D 791 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6871 (pp20) REVERT: D 1112 MET cc_start: 0.8154 (tpp) cc_final: 0.7879 (tpp) REVERT: D 1142 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6838 (t80) REVERT: F 465 ASP cc_start: 0.7517 (m-30) cc_final: 0.7190 (p0) REVERT: J 188 ASN cc_start: 0.7350 (m-40) cc_final: 0.7108 (m-40) outliers start: 117 outliers final: 91 residues processed: 421 average time/residue: 0.1638 time to fit residues: 111.6853 Evaluate side-chains 424 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 322 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 204 ARG Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 89 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 312 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.129675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088377 restraints weight = 58957.515| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.23 r_work: 0.3071 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29590 Z= 0.154 Angle : 0.629 11.159 40549 Z= 0.327 Chirality : 0.044 0.273 4630 Planarity : 0.005 0.123 4944 Dihedral : 18.199 177.189 4930 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.85 % Allowed : 29.14 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3423 helix: 0.94 (0.15), residues: 1336 sheet: -0.64 (0.29), residues: 330 loop : -1.01 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1191 TYR 0.019 0.001 TYR F 337 PHE 0.021 0.001 PHE J 179 TRP 0.019 0.001 TRP F 283 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (29585) covalent geometry : angle 0.62853 / 0.33 (40549) hydrogen bonds : bond 0.03868 / 2.69 ( 1248) hydrogen bonds : angle 4.60383 / 3.18 ( 3465) metal coordination : bond 0.00543 / 0.32 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 323 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8972 (mm) REVERT: A 135 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: A 151 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8386 (mp10) REVERT: B 75 GLU cc_start: 0.8459 (tp30) cc_final: 0.7738 (tp30) REVERT: B 189 PHE cc_start: 0.8175 (m-10) cc_final: 0.7649 (m-80) REVERT: C 96 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6798 (pp) REVERT: C 103 MET cc_start: 0.8434 (ppp) cc_final: 0.7814 (ppp) REVERT: C 127 MET cc_start: 0.8881 (ptm) cc_final: 0.8605 (ptm) REVERT: C 188 ASP cc_start: 0.8455 (p0) cc_final: 0.8195 (p0) REVERT: C 201 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7886 (p) REVERT: C 266 ASN cc_start: 0.8514 (m-40) cc_final: 0.8203 (m-40) REVERT: C 275 LEU cc_start: 0.9099 (pp) cc_final: 0.8838 (mt) REVERT: C 293 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7381 (tp-100) REVERT: C 306 TYR cc_start: 0.8600 (t80) cc_final: 0.8080 (t80) REVERT: C 348 LEU cc_start: 0.9315 (tp) cc_final: 0.9030 (tp) REVERT: C 509 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7901 (t80) REVERT: C 513 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: C 527 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 538 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8526 (mtm110) REVERT: C 813 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8634 (tm-30) REVERT: D 36 TYR cc_start: 0.8842 (p90) cc_final: 0.8615 (p90) REVERT: D 400 LYS cc_start: 0.9344 (tttm) cc_final: 0.9060 (tttm) REVERT: D 497 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8566 (mt) REVERT: D 608 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: D 706 MET cc_start: 0.8170 (tpt) cc_final: 0.7898 (mtt) REVERT: D 791 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6935 (pp20) REVERT: D 1112 MET cc_start: 0.8132 (tpp) cc_final: 0.7842 (tpp) REVERT: D 1142 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6871 (t80) REVERT: E 41 ASP cc_start: 0.8528 (m-30) cc_final: 0.8326 (m-30) REVERT: E 98 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8383 (mt-10) REVERT: F 465 ASP cc_start: 0.7550 (m-30) cc_final: 0.7204 (p0) REVERT: J 188 ASN cc_start: 0.7495 (m-40) cc_final: 0.7175 (m110) outliers start: 110 outliers final: 89 residues processed: 408 average time/residue: 0.1567 time to fit residues: 103.9623 Evaluate side-chains 417 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 318 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 827 GLU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 608 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1142 TYR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1219 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 204 ARG Chi-restraints excluded: chain K residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 269 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 298 optimal weight: 40.0000 chunk 75 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 325 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS F 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.131304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090059 restraints weight = 59213.359| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.26 r_work: 0.3098 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29590 Z= 0.124 Angle : 0.628 12.999 40549 Z= 0.327 Chirality : 0.044 0.278 4630 Planarity : 0.005 0.097 4944 Dihedral : 18.158 177.735 4930 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.81 % Allowed : 29.03 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3423 helix: 0.94 (0.15), residues: 1331 sheet: -0.73 (0.29), residues: 343 loop : -0.98 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 211 TYR 0.018 0.001 TYR F 337 PHE 0.022 0.001 PHE J 179 TRP 0.020 0.001 TRP F 283 HIS 0.006 0.001 HIS J 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (29585) covalent geometry : angle 0.62831 / 0.33 (40549) hydrogen bonds : bond 0.03727 / 2.59 ( 1248) hydrogen bonds : angle 4.57566 / 3.15 ( 3465) metal coordination : bond 0.00407 / 0.22 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7220.91 seconds wall clock time: 124 minutes 8.64 seconds (7448.64 seconds total)