Starting phenix.real_space_refine on Sun Jul 5 05:52:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eos_28466/07_2026/8eos_28466_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eos_28466/07_2026/8eos_28466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eos_28466/07_2026/8eos_28466_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eos_28466/07_2026/8eos_28466_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eos_28466/07_2026/8eos_28466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eos_28466/07_2026/8eos_28466.map" } resolution = 3.1 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= 0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 90 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 15759 2.51 5 N 4564 2.21 5 O 5102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25606 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} 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: 8686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8686 Classifications: {'peptide': 1123} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1061} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 9982 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1215} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "G" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 968 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 774 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "R" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 288 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2TM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19226 SG CYS D 891 75.984 23.919 87.353 1.00 56.97 S ATOM 19793 SG CYS D 968 74.786 27.253 88.760 1.00 44.72 S ATOM 19835 SG CYS D 975 76.375 27.133 85.308 1.00 45.87 S ATOM 19853 SG CYS D 978 72.979 25.745 85.784 1.00 57.84 S ATOM 12664 SG CYS D 60 108.078 79.295 116.139 1.00121.58 S ATOM 12682 SG CYS D 62 109.245 82.270 118.193 1.00128.23 S ATOM 12791 SG CYS D 75 110.252 78.449 118.868 1.00127.60 S ATOM 12817 SG CYS D 78 106.692 80.099 119.556 1.00132.10 S Time building chain proxies: 5.31, per 1000 atoms: 0.21 Number of scatterers: 25606 At special positions: 0 Unit cell: (125.28, 138.33, 200.97, 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 87 16.00 P 90 15.00 Mg 2 11.99 O 5102 8.00 N 4564 7.00 C 15759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 910.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb=" ZN D2004 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 75 " Number of angles added : 12 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 44 sheets defined 38.1% alpha, 16.7% beta 33 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.693A pdb=" N GLY A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 183 through 187 removed outlier: 4.149A pdb=" N ARG A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 187 " --> pdb=" O GLU A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 187' Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.627A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 221 No H-bonds generated for 'chain 'A' and resid 220 through 221' Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.614A pdb=" N GLY B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 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 212 Processing helix chain 'B' and resid 215 through 224 removed outlier: 4.347A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.405A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.629A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.932A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.779A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.838A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.670A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.616A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.517A pdb=" N GLY C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.762A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.915A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.755A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 630 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.542A pdb=" N ASP C 903 " --> pdb=" O PRO C 900 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 900 through 904' Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.650A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.587A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.628A pdb=" N LYS C1040 " --> pdb=" O VAL C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.795A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1109 removed outlier: 3.730A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.966A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.592A pdb=" N PHE D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.906A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.661A pdb=" N LEU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 185 removed outlier: 4.093A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 228 removed outlier: 3.949A pdb=" N ASP D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.788A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.633A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.784A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.961A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 360 removed outlier: 3.539A pdb=" N TYR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.753A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (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 Processing helix chain 'D' and resid 468 through 479 removed outlier: 3.742A pdb=" N ALA D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.625A pdb=" N ILE D 491 " --> pdb=" O LEU D 487 " (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 removed outlier: 3.743A pdb=" N PHE D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 625 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.676A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 removed outlier: 3.589A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.961A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.989A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 851 Processing helix chain 'D' and resid 853 through 864 removed outlier: 3.517A pdb=" N ARG D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 881 removed outlier: 3.534A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1012 removed outlier: 3.849A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) Proline residue: D1006 - end of helix Processing helix chain 'D' and resid 1024 through 1036 Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1146 removed outlier: 3.853A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.999A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.077A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.664A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 removed outlier: 3.765A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1263 removed outlier: 3.528A pdb=" N GLY D1263 " --> pdb=" O ALA D1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1260 through 1263' Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.583A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.915A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.591A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 45 Processing helix chain 'G' and resid 58 through 74 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'G' and resid 143 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.689A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.763A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 9 removed outlier: 7.027A pdb=" N GLN B 20 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL B 13 " --> pdb=" O GLN B 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.222A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.688A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.785A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.836A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.603A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.297A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.503A pdb=" N VAL C 363 " --> pdb=" O MET C 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.043A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC2, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.609A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 667 through 671 removed outlier: 5.986A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.519A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.624A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.666A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.604A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.775A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (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 1066 through 1068 removed outlier: 3.897A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.768A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.299A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.943A 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: 7.353A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD7, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 899 Processing sheet with id=AD9, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE1, first strand: chain 'D' and resid 930 through 931 removed outlier: 3.959A pdb=" N ASN D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1051 through 1052 Processing sheet with id=AE3, first strand: chain 'D' and resid 1061 through 1064 removed outlier: 6.594A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.674A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.627A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 81 through 83 removed outlier: 3.719A pdb=" N GLN G 81 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY G 131 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 86 through 93 942 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4290 1.31 - 1.45: 6946 1.45 - 1.59: 14663 1.59 - 1.72: 173 1.72 - 1.86: 155 Bond restraints: 26227 Sorted by residual: bond pdb=" C2' 2TM C1201 " pdb=" C3' 2TM C1201 " ideal model delta sigma weight residual 1.543 1.296 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C4' 2TM C1201 " pdb=" O4' 2TM C1201 " ideal model delta sigma weight residual 1.442 1.296 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C5 2TM C1201 " pdb=" C6 2TM C1201 " ideal model delta sigma weight residual 1.352 1.495 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C1' 2TM C1201 " pdb=" N1 2TM C1201 " ideal model delta sigma weight residual 1.480 1.339 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C1' 2TM C1201 " pdb=" O4' 2TM C1201 " ideal model delta sigma weight residual 1.409 1.538 -0.129 2.00e-02 2.50e+03 4.17e+01 ... (remaining 26222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 35651 2.60 - 5.20: 261 5.20 - 7.80: 9 7.80 - 10.40: 2 10.40 - 13.00: 1 Bond angle restraints: 35924 Sorted by residual: angle pdb=" O4' DC T 17 " pdb=" C4' DC T 17 " pdb=" C3' DC T 17 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" C GLU C1149 " pdb=" CA GLU C1149 " pdb=" CB GLU C1149 " ideal model delta sigma weight residual 115.89 109.99 5.90 1.32e+00 5.74e-01 1.99e+01 angle pdb=" O4' DA T 16 " pdb=" C4' DA T 16 " pdb=" C3' DA T 16 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" PA 2TM C1201 " pdb=" C1 2TM C1201 " pdb=" PB 2TM C1201 " ideal model delta sigma weight residual 120.85 107.85 13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 35919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 15239 33.49 - 66.98: 581 66.98 - 100.48: 9 100.48 - 133.97: 1 133.97 - 167.46: 2 Dihedral angle restraints: 15832 sinusoidal: 7055 harmonic: 8777 Sorted by residual: dihedral pdb=" O4' G R 20 " pdb=" C1' G R 20 " pdb=" N9 G R 20 " pdb=" C4 G R 20 " ideal model delta sinusoidal sigma weight residual 254.00 177.91 76.09 1 1.70e+01 3.46e-03 2.52e+01 dihedral pdb=" CA GLY D 63 " pdb=" C GLY D 63 " pdb=" N LYS D 64 " pdb=" CA LYS D 64 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" O1A 2TM C1201 " pdb=" C1 2TM C1201 " pdb=" PA 2TM C1201 " pdb=" PB 2TM C1201 " ideal model delta sinusoidal sigma weight residual 45.47 -164.12 -150.41 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 15829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3761 0.081 - 0.162: 336 0.162 - 0.243: 0 0.243 - 0.325: 0 0.325 - 0.406: 1 Chirality restraints: 4098 Sorted by residual: chirality pdb=" C2' 2TM C1201 " pdb=" C1' 2TM C1201 " pdb=" C3' 2TM C1201 " pdb=" O2' 2TM C1201 " both_signs ideal model delta sigma weight residual False -2.76 -2.35 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ILE D1149 " pdb=" N ILE D1149 " pdb=" C ILE D1149 " pdb=" CB ILE D1149 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 4095 not shown) Planarity restraints: 4418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 576 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO D 577 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 32 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO C 33 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 33 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 33 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO D 434 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.021 5.00e-02 4.00e+02 ... (remaining 4415 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 102 2.45 - 3.06: 17144 3.06 - 3.68: 35487 3.68 - 4.29: 53074 4.29 - 4.90: 92194 Nonbonded interactions: 198001 Sorted by model distance: nonbonded pdb=" O3G 2TM C1201 " pdb="MG MG D2002 " model vdw 1.840 2.170 nonbonded pdb=" OE2 GLU D1036 " pdb=" OG1 THR D1211 " model vdw 1.848 3.040 nonbonded pdb=" O1B 2TM C1201 " pdb="MG MG D2002 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR C 165 " pdb=" OE2 GLU C 172 " model vdw 1.964 3.040 nonbonded pdb=" NZ LYS D 123 " pdb=" OP2 DT N 36 " model vdw 1.970 3.120 ... (remaining 197996 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 1 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 1 through 226) } 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 : 0.006 0.247 26235 Z= 0.300 Angle : 0.618 12.996 35936 Z= 0.387 Chirality : 0.044 0.406 4098 Planarity : 0.004 0.063 4418 Dihedral : 15.362 167.460 10192 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 3.59 % Allowed : 8.54 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.81 (0.15), residues: 3053 helix: 0.92 (0.17), residues: 1058 sheet: 0.29 (0.27), residues: 393 loop : -1.85 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1163 TYR 0.012 0.001 TYR C 129 PHE 0.019 0.001 PHE C 906 TRP 0.010 0.001 TRP D 778 HIS 0.005 0.001 HIS C 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.30 (26227) covalent geometry : angle 0.61166 / 0.39 (35924) hydrogen bonds : bond 0.16539 / 11.45 ( 1027) hydrogen bonds : angle 5.66265 / 4.00 ( 2818) metal coordination : bond 0.00632 / 0.31 ( 8) metal coordination : angle 4.93624 / 2.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 188 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping revert: symmetry clash REVERT: A 185 GLN cc_start: 0.8633 (mp10) cc_final: 0.8392 (mp10) REVERT: B 120 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8466 (p0) REVERT: C 1028 MET cc_start: 0.8874 (ttt) cc_final: 0.8672 (ttm) REVERT: D 143 MET cc_start: 0.8618 (mpp) cc_final: 0.8245 (mpp) REVERT: D 707 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8064 (tt) REVERT: D 1112 MET cc_start: 0.8625 (mmm) cc_final: 0.7956 (mmm) REVERT: G 48 ASP cc_start: 0.8504 (m-30) cc_final: 0.8211 (m-30) REVERT: G 124 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8666 (tpp80) REVERT: G 146 ASP cc_start: 0.9250 (m-30) cc_final: 0.8961 (m-30) outliers start: 93 outliers final: 46 residues processed: 271 average time/residue: 0.1735 time to fit residues: 73.0069 Evaluate side-chains 189 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 863 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 106 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 120 ASN C 150 GLN C 178 GLN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN C 479 HIS C 610 ASN C 866 ASN C 889 HIS C1055 GLN D 262 GLN D 341 ASN D 369 ASN D 375 GLN D 410 GLN D 479 GLN D 540 GLN D 552 GLN D 563 ASN D 693 GLN D 787 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.048673 restraints weight = 68177.331| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.30 r_work: 0.2582 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26235 Z= 0.175 Angle : 0.646 13.375 35936 Z= 0.336 Chirality : 0.046 0.316 4098 Planarity : 0.005 0.055 4418 Dihedral : 16.791 167.353 4464 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer: Outliers : 3.24 % Allowed : 10.03 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.73 (0.15), residues: 3053 helix: 0.91 (0.17), residues: 1071 sheet: 0.21 (0.26), residues: 400 loop : -1.73 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 112 TYR 0.013 0.001 TYR C 731 PHE 0.012 0.001 PHE C 153 TRP 0.011 0.001 TRP D1220 HIS 0.006 0.001 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (26227) covalent geometry : angle 0.63320 / 0.34 (35924) hydrogen bonds : bond 0.05024 / 3.37 ( 1027) hydrogen bonds : angle 4.64341 / 3.26 ( 2818) metal coordination : bond 0.00687 / 0.34 ( 8) metal coordination : angle 7.06547 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 156 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 185 GLN cc_start: 0.8744 (mp10) cc_final: 0.8426 (mp10) REVERT: C 323 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7385 (p90) REVERT: C 737 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9216 (mp) REVERT: C 1028 MET cc_start: 0.9148 (ttt) cc_final: 0.8787 (ttm) REVERT: D 143 MET cc_start: 0.8889 (mpp) cc_final: 0.8500 (mpp) REVERT: D 707 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7633 (tt) REVERT: D 1112 MET cc_start: 0.8753 (mmm) cc_final: 0.8009 (mmm) REVERT: E 30 ASP cc_start: 0.8078 (m-30) cc_final: 0.7848 (t0) REVERT: G 48 ASP cc_start: 0.8159 (m-30) cc_final: 0.7954 (m-30) REVERT: G 69 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8195 (ttm-80) outliers start: 84 outliers final: 56 residues processed: 233 average time/residue: 0.1664 time to fit residues: 61.5630 Evaluate side-chains 197 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 125 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 407 GLN C 451 HIS C 891 ASN D 304 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN E 100 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.047600 restraints weight = 68314.590| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.17 r_work: 0.2568 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26235 Z= 0.215 Angle : 0.612 13.333 35936 Z= 0.320 Chirality : 0.045 0.236 4098 Planarity : 0.005 0.065 4418 Dihedral : 16.745 164.536 4446 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.92 % Rotamer: Outliers : 3.16 % Allowed : 11.24 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.67 (0.15), residues: 3053 helix: 1.03 (0.17), residues: 1071 sheet: 0.10 (0.26), residues: 409 loop : -1.71 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 310 TYR 0.013 0.001 TYR C 129 PHE 0.013 0.001 PHE C 906 TRP 0.009 0.001 TRP D1220 HIS 0.005 0.001 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 (26227) covalent geometry : angle 0.59900 / 0.32 (35924) hydrogen bonds : bond 0.05173 / 3.48 ( 1027) hydrogen bonds : angle 4.48430 / 3.14 ( 2818) metal coordination : bond 0.00944 / 0.46 ( 8) metal coordination : angle 6.86173 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 139 time to evaluate : 0.935 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 185 GLN cc_start: 0.8742 (mp10) cc_final: 0.8427 (mp10) REVERT: C 323 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.7559 (p90) REVERT: C 737 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9335 (mp) REVERT: C 763 LYS cc_start: 0.9093 (pptt) cc_final: 0.8844 (pptt) REVERT: D 143 MET cc_start: 0.8926 (mpp) cc_final: 0.8501 (mpp) REVERT: D 707 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7809 (tt) REVERT: D 1112 MET cc_start: 0.9071 (mmm) cc_final: 0.8108 (mmm) REVERT: G 45 LYS cc_start: 0.8758 (tppp) cc_final: 0.8475 (tppt) REVERT: G 48 ASP cc_start: 0.8273 (m-30) cc_final: 0.8051 (m-30) REVERT: G 69 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8134 (ttp80) outliers start: 82 outliers final: 57 residues processed: 215 average time/residue: 0.1610 time to fit residues: 55.8396 Evaluate side-chains 191 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 863 THR Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 126 optimal weight: 0.0000 chunk 224 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 272 optimal weight: 0.7980 chunk 104 optimal weight: 0.0370 chunk 187 optimal weight: 0.0040 chunk 165 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.080907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.049361 restraints weight = 68167.191| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.20 r_work: 0.2629 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26235 Z= 0.110 Angle : 0.553 12.356 35936 Z= 0.288 Chirality : 0.043 0.239 4098 Planarity : 0.004 0.053 4418 Dihedral : 16.617 162.560 4433 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 2.73 % Allowed : 11.59 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.40 (0.15), residues: 3053 helix: 1.28 (0.17), residues: 1061 sheet: 0.22 (0.26), residues: 417 loop : -1.57 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 124 TYR 0.010 0.001 TYR C 129 PHE 0.010 0.001 PHE C 430 TRP 0.008 0.001 TRP G 120 HIS 0.005 0.000 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (26227) covalent geometry : angle 0.53922 / 0.29 (35924) hydrogen bonds : bond 0.03843 / 2.58 ( 1027) hydrogen bonds : angle 4.23253 / 2.97 ( 2818) metal coordination : bond 0.00392 / 0.18 ( 8) metal coordination : angle 6.65865 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 1.590 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 185 GLN cc_start: 0.8749 (mp10) cc_final: 0.8526 (mp10) REVERT: C 103 MET cc_start: 0.9180 (mtm) cc_final: 0.8542 (ptm) REVERT: C 323 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.7675 (p90) REVERT: C 737 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9385 (mp) REVERT: D 143 MET cc_start: 0.8989 (mpp) cc_final: 0.8552 (mpp) REVERT: D 707 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7909 (tt) REVERT: D 1112 MET cc_start: 0.9207 (mmm) cc_final: 0.8265 (mmm) REVERT: E 105 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: G 45 LYS cc_start: 0.8652 (tppp) cc_final: 0.8431 (tppt) REVERT: G 48 ASP cc_start: 0.8329 (m-30) cc_final: 0.8088 (m-30) REVERT: G 69 ARG cc_start: 0.8655 (mtp-110) cc_final: 0.8147 (ttp80) outliers start: 71 outliers final: 46 residues processed: 207 average time/residue: 0.1538 time to fit residues: 52.3098 Evaluate side-chains 188 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 3 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.078193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.046613 restraints weight = 68762.232| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.18 r_work: 0.2551 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 26235 Z= 0.289 Angle : 0.647 18.009 35936 Z= 0.335 Chirality : 0.047 0.237 4098 Planarity : 0.005 0.052 4418 Dihedral : 16.692 162.523 4426 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.57 % Favored : 94.30 % Rotamer: Outliers : 3.36 % Allowed : 12.45 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.61 (0.15), residues: 3053 helix: 1.07 (0.17), residues: 1078 sheet: 0.02 (0.26), residues: 412 loop : -1.65 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 43 TYR 0.018 0.001 TYR D 251 PHE 0.016 0.002 PHE C 906 TRP 0.010 0.001 TRP C 944 HIS 0.005 0.001 HIS D 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.29 (26227) covalent geometry : angle 0.63515 / 0.33 (35924) hydrogen bonds : bond 0.05508 / 3.69 ( 1027) hydrogen bonds : angle 4.40718 / 3.08 ( 2818) metal coordination : bond 0.01240 / 0.61 ( 8) metal coordination : angle 6.80498 / 3.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 135 time to evaluate : 0.981 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 185 GLN cc_start: 0.8774 (mp10) cc_final: 0.8454 (mp10) REVERT: C 103 MET cc_start: 0.9233 (mtm) cc_final: 0.8628 (ptm) REVERT: C 323 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.7747 (p90) REVERT: C 763 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8896 (pptt) REVERT: D 143 MET cc_start: 0.8972 (mpp) cc_final: 0.8523 (mpp) REVERT: D 707 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8069 (tt) REVERT: D 1112 MET cc_start: 0.9189 (mmm) cc_final: 0.8204 (mmm) REVERT: E 105 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: G 48 ASP cc_start: 0.8416 (m-30) cc_final: 0.8164 (m-30) REVERT: G 69 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8176 (ttp80) REVERT: G 88 GLU cc_start: 0.8761 (tp30) cc_final: 0.8555 (tp30) outliers start: 87 outliers final: 64 residues processed: 213 average time/residue: 0.1592 time to fit residues: 55.2119 Evaluate side-chains 197 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 863 THR Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 24 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 179 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 775 ASN D 653 HIS ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.079455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.047596 restraints weight = 67689.151| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.34 r_work: 0.2563 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26235 Z= 0.124 Angle : 0.558 14.401 35936 Z= 0.290 Chirality : 0.043 0.240 4098 Planarity : 0.004 0.052 4418 Dihedral : 16.616 161.793 4424 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 2.81 % Allowed : 13.46 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.34 (0.15), residues: 3053 helix: 1.35 (0.17), residues: 1061 sheet: 0.24 (0.26), residues: 406 loop : -1.51 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 43 TYR 0.015 0.001 TYR D 251 PHE 0.010 0.001 PHE C 906 TRP 0.008 0.001 TRP C 70 HIS 0.003 0.001 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (26227) covalent geometry : angle 0.54472 / 0.29 (35924) hydrogen bonds : bond 0.04184 / 2.80 ( 1027) hydrogen bonds : angle 4.21514 / 2.95 ( 2818) metal coordination : bond 0.00494 / 0.23 ( 8) metal coordination : angle 6.76142 / 3.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 0.996 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 185 GLN cc_start: 0.8741 (mp10) cc_final: 0.8523 (mp10) REVERT: C 103 MET cc_start: 0.9304 (mtm) cc_final: 0.8637 (ptm) REVERT: C 323 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.7575 (p90) REVERT: C 717 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7073 (mptt) REVERT: C 763 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8870 (pptt) REVERT: D 143 MET cc_start: 0.8943 (mpp) cc_final: 0.8520 (mpp) REVERT: D 707 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7675 (tt) REVERT: D 1112 MET cc_start: 0.9030 (mmm) cc_final: 0.8063 (mmm) REVERT: E 105 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: G 69 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8220 (ttp80) outliers start: 73 outliers final: 55 residues processed: 201 average time/residue: 0.1682 time to fit residues: 54.6609 Evaluate side-chains 192 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 717 LYS Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 248 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN C 775 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.047470 restraints weight = 67942.660| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.18 r_work: 0.2581 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26235 Z= 0.176 Angle : 0.569 13.282 35936 Z= 0.296 Chirality : 0.044 0.225 4098 Planarity : 0.004 0.051 4418 Dihedral : 16.600 160.776 4424 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 2.81 % Allowed : 13.58 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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 (0.15), residues: 3053 helix: 1.38 (0.17), residues: 1061 sheet: 0.23 (0.26), residues: 407 loop : -1.52 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 43 TYR 0.016 0.001 TYR E 78 PHE 0.014 0.001 PHE C 252 TRP 0.007 0.001 TRP C 944 HIS 0.003 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (26227) covalent geometry : angle 0.55641 / 0.30 (35924) hydrogen bonds : bond 0.04430 / 2.97 ( 1027) hydrogen bonds : angle 4.20124 / 2.93 ( 2818) metal coordination : bond 0.00713 / 0.35 ( 8) metal coordination : angle 6.65320 / 2.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 134 time to evaluate : 1.039 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 185 GLN cc_start: 0.8794 (mp10) cc_final: 0.8586 (mp10) REVERT: C 103 MET cc_start: 0.9226 (mtm) cc_final: 0.8636 (ptm) REVERT: C 323 HIS cc_start: 0.8813 (OUTLIER) cc_final: 0.7762 (p90) REVERT: C 570 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7973 (t80) REVERT: D 143 MET cc_start: 0.8955 (mpp) cc_final: 0.8503 (mpp) REVERT: D 707 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8004 (tt) REVERT: D 1112 MET cc_start: 0.9182 (mmm) cc_final: 0.8199 (mmm) REVERT: E 105 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: G 69 ARG cc_start: 0.8739 (mtp-110) cc_final: 0.8246 (ttp80) outliers start: 73 outliers final: 56 residues processed: 200 average time/residue: 0.1549 time to fit residues: 50.3416 Evaluate side-chains 190 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 230 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.079675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048162 restraints weight = 68145.447| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.18 r_work: 0.2605 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26235 Z= 0.127 Angle : 0.558 12.529 35936 Z= 0.289 Chirality : 0.043 0.315 4098 Planarity : 0.004 0.051 4418 Dihedral : 16.550 159.859 4421 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 2.61 % Allowed : 13.89 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.23 (0.15), residues: 3053 helix: 1.47 (0.17), residues: 1061 sheet: 0.19 (0.26), residues: 413 loop : -1.45 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 43 TYR 0.014 0.001 TYR D 251 PHE 0.010 0.001 PHE C 906 TRP 0.007 0.001 TRP C 70 HIS 0.002 0.000 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (26227) covalent geometry : angle 0.54451 / 0.29 (35924) hydrogen bonds : bond 0.03973 / 2.66 ( 1027) hydrogen bonds : angle 4.12331 / 2.88 ( 2818) metal coordination : bond 0.00481 / 0.23 ( 8) metal coordination : angle 6.59309 / 2.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 137 time to evaluate : 0.950 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: C 103 MET cc_start: 0.9200 (mtm) cc_final: 0.8644 (ptm) REVERT: C 323 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.7761 (p90) REVERT: C 570 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7985 (t80) REVERT: C 763 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8852 (pptt) REVERT: D 143 MET cc_start: 0.8972 (mpp) cc_final: 0.8421 (mpp) REVERT: D 707 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7990 (tt) REVERT: D 1112 MET cc_start: 0.9233 (mmm) cc_final: 0.8269 (mmm) REVERT: E 70 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7021 (pp30) REVERT: E 105 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6853 (pm20) REVERT: G 69 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8259 (ttp80) outliers start: 68 outliers final: 52 residues processed: 199 average time/residue: 0.1554 time to fit residues: 50.3248 Evaluate side-chains 191 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 261 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN C 775 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.078256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.046663 restraints weight = 69214.188| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.21 r_work: 0.2555 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 26235 Z= 0.270 Angle : 0.622 12.681 35936 Z= 0.323 Chirality : 0.046 0.220 4098 Planarity : 0.004 0.050 4418 Dihedral : 16.599 160.066 4420 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.21 % Favored : 94.66 % Rotamer: Outliers : 2.69 % Allowed : 13.77 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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 (0.15), residues: 3053 helix: 1.33 (0.17), residues: 1067 sheet: 0.12 (0.26), residues: 409 loop : -1.55 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 43 TYR 0.014 0.001 TYR D 251 PHE 0.015 0.001 PHE C 906 TRP 0.010 0.001 TRP C 944 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.27 (26227) covalent geometry : angle 0.61055 / 0.32 (35924) hydrogen bonds : bond 0.04985 / 3.33 ( 1027) hydrogen bonds : angle 4.26539 / 2.98 ( 2818) metal coordination : bond 0.01073 / 0.53 ( 8) metal coordination : angle 6.63852 / 2.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 131 time to evaluate : 1.013 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 1 MET cc_start: 0.8248 (tpp) cc_final: 0.7604 (tmm) REVERT: C 103 MET cc_start: 0.9239 (mtm) cc_final: 0.8639 (ptm) REVERT: C 323 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.7822 (p90) REVERT: C 570 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.8029 (t80) REVERT: C 763 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8899 (pptt) REVERT: D 143 MET cc_start: 0.8841 (mpp) cc_final: 0.8421 (mpp) REVERT: D 707 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8056 (tt) REVERT: D 1112 MET cc_start: 0.9186 (mmm) cc_final: 0.8227 (mmm) REVERT: E 105 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: G 69 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8234 (ttp80) outliers start: 70 outliers final: 59 residues processed: 194 average time/residue: 0.1736 time to fit residues: 54.4535 Evaluate side-chains 194 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 863 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 256 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 0.0570 chunk 240 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 775 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.079674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.048154 restraints weight = 67855.709| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.18 r_work: 0.2604 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26235 Z= 0.119 Angle : 0.559 12.763 35936 Z= 0.289 Chirality : 0.044 0.522 4098 Planarity : 0.004 0.054 4418 Dihedral : 16.546 159.230 4420 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 2.50 % Allowed : 13.97 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.16 (0.15), residues: 3053 helix: 1.53 (0.17), residues: 1056 sheet: 0.24 (0.27), residues: 405 loop : -1.40 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 43 TYR 0.014 0.001 TYR D 251 PHE 0.010 0.001 PHE C 430 TRP 0.009 0.001 TRP G 120 HIS 0.002 0.000 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (26227) covalent geometry : angle 0.54581 / 0.29 (35924) hydrogen bonds : bond 0.03877 / 2.59 ( 1027) hydrogen bonds : angle 4.09619 / 2.86 ( 2818) metal coordination : bond 0.00433 / 0.20 ( 8) metal coordination : angle 6.62656 / 3.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 132 time to evaluate : 0.999 Fit side-chains revert: symmetry clash Corrupt residue: chain: D residue: PRO 1040 >>> skipping REVERT: A 1 MET cc_start: 0.8294 (tpp) cc_final: 0.7750 (tmm) REVERT: C 103 MET cc_start: 0.9234 (mtm) cc_final: 0.8598 (ptm) REVERT: C 172 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8637 (tp30) REVERT: C 323 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.7764 (p90) REVERT: C 570 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8020 (t80) REVERT: C 763 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8889 (pptt) REVERT: D 143 MET cc_start: 0.8847 (mpp) cc_final: 0.8422 (mpp) REVERT: D 707 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7914 (tt) REVERT: D 1112 MET cc_start: 0.9184 (mmm) cc_final: 0.8220 (mmm) REVERT: E 70 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6581 (pp30) REVERT: E 105 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: G 69 ARG cc_start: 0.8760 (mtp-110) cc_final: 0.8248 (ttp80) outliers start: 65 outliers final: 51 residues processed: 191 average time/residue: 0.1692 time to fit residues: 52.6614 Evaluate side-chains 190 residues out of total 2587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 132 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1040 PRO Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 231 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 38 optimal weight: 0.0570 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.079640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048105 restraints weight = 67734.782| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.18 r_work: 0.2607 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 26235 Z= 0.179 Angle : 0.722 59.185 35936 Z= 0.400 Chirality : 0.045 0.855 4098 Planarity : 0.004 0.116 4418 Dihedral : 16.534 159.179 4417 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 2.34 % Allowed : 14.12 % Favored : 83.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.29 % 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: -0.16 (0.15), residues: 3053 helix: 1.53 (0.17), residues: 1056 sheet: 0.25 (0.27), residues: 405 loop : -1.39 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 43 TYR 0.014 0.001 TYR D 251 PHE 0.010 0.001 PHE C 906 TRP 0.008 0.001 TRP G 120 HIS 0.002 0.000 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (26227) covalent geometry : angle 0.71187 / 0.40 (35924) hydrogen bonds : bond 0.03906 / 2.61 ( 1027) hydrogen bonds : angle 4.09574 / 2.86 ( 2818) metal coordination : bond 0.00452 / 0.21 ( 8) metal coordination : angle 6.62677 / 3.02 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6548.75 seconds wall clock time: 112 minutes 51.51 seconds (6771.51 seconds total)