Starting phenix.real_space_refine on Fri Mar 6 19:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ldi_0874/03_2026/6ldi_0874.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ldi_0874/03_2026/6ldi_0874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ldi_0874/03_2026/6ldi_0874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ldi_0874/03_2026/6ldi_0874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ldi_0874/03_2026/6ldi_0874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ldi_0874/03_2026/6ldi_0874.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 723 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ag 1 8.66 5 Zn 2 6.06 5 P 102 5.49 5 Mg 1 5.21 5 S 138 5.16 5 C 20282 2.51 5 N 5808 2.21 5 O 6536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32870 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1784 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1748 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10522 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 10290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10290 Classifications: {'peptide': 1331} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1275} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 14, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3748 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'ARG:plan': 8, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "1" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1035 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "3" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "G" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' AG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14494 SG CYS D 70 110.196 54.007 70.645 1.00 64.88 S ATOM 14508 SG CYS D 72 111.625 55.549 67.687 1.00 65.53 S ATOM 14616 SG CYS D 85 114.190 56.327 70.243 1.00 71.82 S ATOM 14640 SG CYS D 88 111.024 58.220 70.042 1.00 67.67 S ATOM 20321 SG CYS D 814 83.043 74.289 129.783 1.00 57.49 S ATOM 20882 SG CYS D 888 81.168 74.379 126.238 1.00 46.84 S ATOM 20933 SG CYS D 895 82.231 71.241 128.060 1.00 50.89 S ATOM 20954 SG CYS D 898 78.688 73.940 128.863 1.00 45.25 S ATOM 32766 SG CYS H 112 131.031 58.331 12.225 1.00154.01 S Time building chain proxies: 7.39, per 1000 atoms: 0.22 Number of scatterers: 32870 At special positions: 0 Unit cell: (163.375, 162.068, 168.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ag 1 46.95 Zn 2 29.99 S 138 16.00 P 102 15.00 Mg 1 11.99 O 6536 8.00 N 5808 7.00 C 20282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 47 sheets defined 40.2% alpha, 12.3% beta 40 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.560A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.337A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.633A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.892A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.269A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.820A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.806A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.639A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.649A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.550A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 40' Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.522A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.690A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.506A pdb=" N ALA C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.501A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.726A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.291A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.058A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.027A pdb=" N SER C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.853A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.923A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.083A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 614 removed outlier: 3.727A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 677 through 685 removed outlier: 3.549A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 689 removed outlier: 4.029A pdb=" N ALA C 689 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.619A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.211A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 943 through 983 removed outlier: 3.693A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.802A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.943A pdb=" N HIS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.523A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1081 through 1085' Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 4.076A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.690A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 3.840A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG C1147 " --> pdb=" O GLU C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1175 Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.547A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C1196 " --> pdb=" O GLU C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.654A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C1282 " --> pdb=" O LEU C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 Processing helix chain 'C' and resid 1300 through 1311 removed outlier: 4.035A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 removed outlier: 3.634A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.784A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.677A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.666A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.915A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.607A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.607A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.708A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.531A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.616A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.568A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 4.252A pdb=" N ARG D 312 " --> pdb=" O ASN D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.686A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 335 removed outlier: 3.818A pdb=" N GLN D 335 " --> pdb=" O LYS D 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.622A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 4.226A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.529A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 4.429A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.884A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 532 removed outlier: 3.507A pdb=" N GLU D 532 " --> pdb=" O GLY D 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 529 through 532' Processing helix chain 'D' and resid 533 through 539 removed outlier: 3.570A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.713A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.589A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 629 removed outlier: 4.075A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 629 " --> pdb=" O MET D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 634 Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.752A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.692A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET D 698 " --> pdb=" O SER D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 769 through 775 Processing helix chain 'D' and resid 775 through 802 removed outlier: 4.187A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 868 through 875 removed outlier: 3.502A pdb=" N LEU D 872 " --> pdb=" O TRP D 868 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.660A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.308A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.684A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 removed outlier: 3.501A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1223 removed outlier: 3.680A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1228 Processing helix chain 'D' and resid 1229 through 1234 removed outlier: 3.984A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1239 Processing helix chain 'D' and resid 1240 through 1245 removed outlier: 3.616A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.780A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1286 Processing helix chain 'D' and resid 1319 through 1324 removed outlier: 3.530A pdb=" N SER D1324 " --> pdb=" O ILE D1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1335 Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.746A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 4.132A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.801A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.761A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.742A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.838A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.560A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 134 removed outlier: 3.922A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.573A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 221 removed outlier: 3.580A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 235 removed outlier: 4.108A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 262 through 294 removed outlier: 4.632A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.660A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 319 removed outlier: 4.065A pdb=" N ALA F 319 " --> pdb=" O TRP F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.634A pdb=" N VAL F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.664A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.043A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 removed outlier: 3.811A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.814A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 438 " --> pdb=" O TRP F 434 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.635A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 3.757A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.927A pdb=" N LYS F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA F 501 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.580A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 548 removed outlier: 3.671A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.588A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.878A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 600 removed outlier: 3.603A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS F 600 " --> pdb=" O ARG F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 609 removed outlier: 3.527A pdb=" N ARG F 608 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER F 609 " --> pdb=" O VAL F 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 605 through 609' Processing helix chain 'G' and resid 5 through 10 removed outlier: 3.526A pdb=" N THR G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 23 removed outlier: 3.864A pdb=" N ARG G 18 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 57 removed outlier: 3.695A pdb=" N GLN G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 72 removed outlier: 4.242A pdb=" N ASN G 68 " --> pdb=" O GLY G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 107 removed outlier: 3.656A pdb=" N GLU G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 13 through 24 removed outlier: 3.712A pdb=" N GLY H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 56 removed outlier: 4.164A pdb=" N THR H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL H 56 " --> pdb=" O GLN H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.974A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 110 removed outlier: 4.400A pdb=" N LYS H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 removed outlier: 3.638A pdb=" N GLU H 124 " --> pdb=" O CYS H 120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 5.592A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.694A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.564A pdb=" N VAL A 110 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.522A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 18 removed outlier: 6.448A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 104 removed outlier: 3.702A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.806A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.518A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.618A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.515A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.715A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.807A pdb=" N ARG C 233 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.762A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 295 through 296 removed outlier: 4.699A pdb=" N LYS C 295 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.636A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.511A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.969A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.840A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.922A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AC9, first strand: chain 'C' and resid 835 through 841 removed outlier: 3.810A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.170A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.661A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.765A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.645A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.540A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.508A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.386A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 removed outlier: 7.047A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.551A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 704 through 706 Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.959A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.817A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AE7, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AE8, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE9, first strand: chain 'D' and resid 1089 through 1090 removed outlier: 5.824A pdb=" N MET D1095 " --> pdb=" O ILE D1090 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1187 through 1189 removed outlier: 3.725A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D1164 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY D1161 " --> pdb=" O VAL D1204 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 1040 hydrogen bonds defined for protein. 2934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6620 1.33 - 1.45: 7640 1.45 - 1.57: 18871 1.57 - 1.69: 204 1.69 - 1.82: 241 Bond restraints: 33576 Sorted by residual: bond pdb=" CD2 TRP D1020 " pdb=" CE2 TRP D1020 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.88e+01 bond pdb=" CD2 TRP F 315 " pdb=" CE2 TRP F 315 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.87e+01 bond pdb=" O3' DG 2 10 " pdb=" P DA 2 11 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.58e+01 bond pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " ideal model delta sigma weight residual 1.398 1.457 -0.059 1.60e-02 3.91e+03 1.34e+01 bond pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " ideal model delta sigma weight residual 1.398 1.456 -0.058 1.60e-02 3.91e+03 1.30e+01 ... (remaining 33571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 44641 2.16 - 4.32: 1017 4.32 - 6.47: 93 6.47 - 8.63: 22 8.63 - 10.79: 11 Bond angle restraints: 45784 Sorted by residual: angle pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " pdb=" CZ3 TRP D1020 " ideal model delta sigma weight residual 118.60 129.39 -10.79 1.30e+00 5.92e-01 6.89e+01 angle pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " pdb=" CZ3 TRP F 315 " ideal model delta sigma weight residual 118.60 129.37 -10.77 1.30e+00 5.92e-01 6.86e+01 angle pdb=" N ILE C1109 " pdb=" CA ILE C1109 " pdb=" C ILE C1109 " ideal model delta sigma weight residual 112.29 105.83 6.46 9.40e-01 1.13e+00 4.73e+01 angle pdb=" CE2 TRP F 315 " pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " ideal model delta sigma weight residual 118.80 124.87 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CE2 TRP D1020 " pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " ideal model delta sigma weight residual 118.80 124.79 -5.99 1.00e+00 1.00e+00 3.59e+01 ... (remaining 45779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 18992 25.74 - 51.48: 1258 51.48 - 77.23: 180 77.23 - 102.97: 14 102.97 - 128.71: 1 Dihedral angle restraints: 20445 sinusoidal: 9148 harmonic: 11297 Sorted by residual: dihedral pdb=" CA VAL F 582 " pdb=" C VAL F 582 " pdb=" N THR F 583 " pdb=" CA THR F 583 " ideal model delta harmonic sigma weight residual -180.00 -144.08 -35.92 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA GLN F 258 " pdb=" C GLN F 258 " pdb=" N PHE F 259 " pdb=" CA PHE F 259 " ideal model delta harmonic sigma weight residual -180.00 -145.20 -34.80 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" CA LYS D 76 " pdb=" C LYS D 76 " pdb=" N ARG D 77 " pdb=" CA ARG D 77 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 20442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4347 0.066 - 0.132: 791 0.132 - 0.198: 82 0.198 - 0.264: 8 0.264 - 0.330: 3 Chirality restraints: 5231 Sorted by residual: chirality pdb=" CB ILE H 3 " pdb=" CA ILE H 3 " pdb=" CG1 ILE H 3 " pdb=" CG2 ILE H 3 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB VAL F 333 " pdb=" CA VAL F 333 " pdb=" CG1 VAL F 333 " pdb=" CG2 VAL F 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 5228 not shown) Planarity restraints: 5614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.76e+00 pdb=" N PRO C 190 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 615 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO D 616 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 616 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 616 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1061 " -0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO C1062 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C1062 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1062 " -0.036 5.00e-02 4.00e+02 ... (remaining 5611 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.63: 385 2.63 - 3.22: 28157 3.22 - 3.82: 54942 3.82 - 4.41: 68202 4.41 - 5.00: 117313 Nonbonded interactions: 268999 Sorted by model distance: nonbonded pdb=" O3' A 3 5 " pdb="MG MG D1503 " model vdw 2.039 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.114 2.170 nonbonded pdb=" OG1 THR F 583 " pdb=" OP2 DT 1 40 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.145 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.227 2.170 ... (remaining 268994 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 6 through 43 or (resid 44 through 45 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name NE or name CZ )) \ or resid 46 through 70 or (resid 71 and (name N or name CA or name C or name O o \ r name CB )) or resid 72 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 232)) selection = (chain 'B' and (resid 6 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 69 through 151 or (resid 152 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or nam \ e CE2 or name CZ )) or resid 153 through 232)) } ncs_group { reference = (chain 'G' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 52 \ through 114 or (resid 115 through 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 127)) selection = (chain 'H' and resid 1 through 127) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.380 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.007 0.500 33584 Z= 0.287 Angle : 0.854 29.988 45796 Z= 0.458 Chirality : 0.052 0.330 5231 Planarity : 0.006 0.070 5614 Dihedral : 16.285 128.708 13153 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.33 % Allowed : 6.58 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.13 % 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: -4.72 (0.10), residues: 3900 helix: -3.62 (0.08), residues: 1468 sheet: -2.29 (0.25), residues: 356 loop : -2.94 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 180 TYR 0.017 0.002 TYR C 123 PHE 0.024 0.002 PHE C 514 TRP 0.015 0.002 TRP D 115 HIS 0.008 0.001 HIS F 338 Details of bonding type rmsd covalent geometry : bond 0.00585 (33576) covalent geometry : angle 0.79692 (45784) hydrogen bonds : bond 0.20040 ( 1134) hydrogen bonds : angle 7.48670 ( 3138) metal coordination : bond 0.22710 ( 8) metal coordination : angle 18.92643 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 473 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8968 (tttt) cc_final: 0.8744 (tttp) REVERT: A 194 GLN cc_start: 0.7751 (mt0) cc_final: 0.7428 (pm20) REVERT: A 204 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 107 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.6988 (ttm-80) REVERT: C 117 ILE cc_start: 0.8218 (mm) cc_final: 0.7990 (tt) REVERT: C 562 GLU cc_start: 0.8206 (tp30) cc_final: 0.7851 (tp30) REVERT: C 1028 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8499 (mtpp) REVERT: C 1188 ASP cc_start: 0.8109 (t0) cc_final: 0.7702 (t0) REVERT: C 1241 ASP cc_start: 0.7787 (m-30) cc_final: 0.7489 (t0) REVERT: D 29 MET cc_start: 0.7909 (tpp) cc_final: 0.7632 (mmt) REVERT: D 625 MET cc_start: 0.8834 (ttp) cc_final: 0.8127 (tmm) REVERT: D 725 MET cc_start: 0.9061 (mtt) cc_final: 0.8817 (mtt) REVERT: D 806 ASP cc_start: 0.8805 (p0) cc_final: 0.8572 (p0) REVERT: D 867 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6903 (tm-30) REVERT: D 1143 ASP cc_start: 0.7442 (t0) cc_final: 0.7159 (t0) REVERT: D 1256 ILE cc_start: 0.8695 (pt) cc_final: 0.8469 (pt) REVERT: F 137 TYR cc_start: 0.6952 (t80) cc_final: 0.6282 (t80) REVERT: F 276 MET cc_start: 0.7814 (mtp) cc_final: 0.7420 (mtp) REVERT: F 291 CYS cc_start: 0.3526 (p) cc_final: 0.3083 (p) REVERT: F 430 TYR cc_start: 0.9288 (t80) cc_final: 0.8537 (t80) REVERT: F 489 MET cc_start: 0.7877 (mmm) cc_final: 0.7421 (mmm) REVERT: F 538 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7591 (tm-30) REVERT: G 59 ASN cc_start: 0.7514 (p0) cc_final: 0.7131 (p0) REVERT: G 122 ILE cc_start: 0.7589 (mt) cc_final: 0.7106 (pt) REVERT: H 15 LYS cc_start: 0.8206 (tptt) cc_final: 0.7974 (tppt) REVERT: H 19 PHE cc_start: 0.8670 (t80) cc_final: 0.8349 (t80) REVERT: H 52 GLN cc_start: 0.8786 (mm110) cc_final: 0.8345 (mp10) outliers start: 11 outliers final: 6 residues processed: 483 average time/residue: 0.2593 time to fit residues: 189.7183 Evaluate side-chains 344 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 338 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 314 ASN C 673 HIS C 932 GLN C1136 GLN C1313 HIS D 294 ASN D 341 ASN D 419 HIS D 488 ASN D 665 GLN D 875 ASN D 962 ASN D1197 ASN D1235 ASN D1249 ASN E 43 ASN E 72 GLN F 383 ASN F 461 ASN G 68 ASN H 52 GLN H 55 GLN H 110 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.079513 restraints weight = 63731.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.079121 restraints weight = 43194.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079535 restraints weight = 35706.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079855 restraints weight = 31100.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.079975 restraints weight = 25971.032| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33584 Z= 0.191 Angle : 0.599 13.193 45796 Z= 0.321 Chirality : 0.042 0.160 5231 Planarity : 0.005 0.062 5614 Dihedral : 15.149 130.209 5441 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.77 % Allowed : 11.01 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.37 (0.12), residues: 3900 helix: -2.04 (0.11), residues: 1477 sheet: -1.97 (0.24), residues: 413 loop : -2.44 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 322 TYR 0.012 0.001 TYR C 47 PHE 0.014 0.001 PHE C 514 TRP 0.008 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00437 (33576) covalent geometry : angle 0.59249 (45784) hydrogen bonds : bond 0.04174 ( 1134) hydrogen bonds : angle 5.03767 ( 3138) metal coordination : bond 0.00473 ( 8) metal coordination : angle 5.39307 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 355 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8972 (tttt) cc_final: 0.8771 (tttp) REVERT: A 131 CYS cc_start: 0.8537 (m) cc_final: 0.7889 (m) REVERT: A 174 ASP cc_start: 0.8168 (m-30) cc_final: 0.7964 (m-30) REVERT: A 194 GLN cc_start: 0.7816 (mt0) cc_final: 0.7519 (pm20) REVERT: B 93 GLN cc_start: 0.7874 (mm110) cc_final: 0.7549 (mm110) REVERT: C 107 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.6914 (ttm-80) REVERT: C 314 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8679 (t0) REVERT: C 562 GLU cc_start: 0.8380 (tp30) cc_final: 0.8044 (tp30) REVERT: C 1003 THR cc_start: 0.6028 (OUTLIER) cc_final: 0.5680 (m) REVERT: C 1028 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8562 (mtpp) REVERT: C 1188 ASP cc_start: 0.8041 (t0) cc_final: 0.7736 (t0) REVERT: C 1241 ASP cc_start: 0.7974 (m-30) cc_final: 0.7576 (t0) REVERT: D 77 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7547 (ttp-170) REVERT: D 725 MET cc_start: 0.9042 (mtt) cc_final: 0.8596 (mtt) REVERT: D 1025 MET cc_start: 0.8072 (ttm) cc_final: 0.7867 (ttp) REVERT: D 1143 ASP cc_start: 0.7726 (t0) cc_final: 0.7450 (t0) REVERT: E 74 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7628 (mt-10) REVERT: F 489 MET cc_start: 0.7604 (mmm) cc_final: 0.6858 (mmm) REVERT: F 569 THR cc_start: 0.8367 (t) cc_final: 0.8049 (t) REVERT: G 102 ARG cc_start: 0.8497 (ttt180) cc_final: 0.8118 (ptm160) REVERT: H 19 PHE cc_start: 0.8640 (t80) cc_final: 0.8353 (t80) REVERT: H 31 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7769 (tpp80) REVERT: H 36 TYR cc_start: 0.6299 (m-80) cc_final: 0.6058 (m-80) REVERT: H 52 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8211 (mp10) outliers start: 59 outliers final: 37 residues processed: 396 average time/residue: 0.2346 time to fit residues: 146.6843 Evaluate side-chains 363 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 264 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 323 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 chunk 393 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 chunk 281 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 194 GLN C 273 HIS D 489 ASN D1108 GLN D1197 ASN G 99 GLN H 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.078651 restraints weight = 64524.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.078478 restraints weight = 39366.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.078610 restraints weight = 34115.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078877 restraints weight = 31513.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.079077 restraints weight = 27753.669| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33584 Z= 0.201 Angle : 0.589 12.235 45796 Z= 0.312 Chirality : 0.042 0.158 5231 Planarity : 0.004 0.058 5614 Dihedral : 15.086 129.332 5441 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.12 % Allowed : 13.29 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.68 (0.12), residues: 3900 helix: -1.27 (0.13), residues: 1484 sheet: -1.81 (0.24), residues: 431 loop : -2.17 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1123 TYR 0.017 0.001 TYR F 137 PHE 0.018 0.001 PHE H 70 TRP 0.008 0.001 TRP D 580 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00465 (33576) covalent geometry : angle 0.58329 (45784) hydrogen bonds : bond 0.03821 ( 1134) hydrogen bonds : angle 4.66115 ( 3138) metal coordination : bond 0.00572 ( 8) metal coordination : angle 5.13505 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: A 71 LYS cc_start: 0.9003 (tttt) cc_final: 0.8799 (tttp) REVERT: A 194 GLN cc_start: 0.7722 (mt0) cc_final: 0.7434 (pm20) REVERT: B 93 GLN cc_start: 0.7891 (mm110) cc_final: 0.7591 (mm110) REVERT: C 107 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.7012 (ttm-80) REVERT: C 272 ARG cc_start: 0.7073 (tmm160) cc_final: 0.6382 (ttp80) REVERT: C 1003 THR cc_start: 0.6106 (OUTLIER) cc_final: 0.5808 (m) REVERT: C 1028 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8544 (mtpp) REVERT: C 1188 ASP cc_start: 0.8113 (t0) cc_final: 0.7814 (t0) REVERT: C 1241 ASP cc_start: 0.7987 (m-30) cc_final: 0.7583 (t0) REVERT: D 77 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7052 (tmm-80) REVERT: D 301 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 306 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9169 (tp) REVERT: D 725 MET cc_start: 0.9040 (mtt) cc_final: 0.8595 (mtt) REVERT: D 867 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7236 (tm-30) REVERT: D 1143 ASP cc_start: 0.7759 (t0) cc_final: 0.7535 (t0) REVERT: F 291 CYS cc_start: 0.4294 (p) cc_final: 0.3981 (p) REVERT: F 489 MET cc_start: 0.7555 (mmm) cc_final: 0.7087 (mmm) REVERT: F 538 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 15 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7826 (mttt) REVERT: H 19 PHE cc_start: 0.8635 (t80) cc_final: 0.8365 (t80) REVERT: H 31 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7756 (tpp80) REVERT: H 36 TYR cc_start: 0.6121 (m-80) cc_final: 0.5843 (m-80) REVERT: H 52 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8302 (mp10) outliers start: 71 outliers final: 56 residues processed: 379 average time/residue: 0.2235 time to fit residues: 133.7111 Evaluate side-chains 372 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1197 ASN Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 0.0370 chunk 153 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 490 GLN D 157 GLN D1197 ASN G 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080564 restraints weight = 63718.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080506 restraints weight = 43214.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.081001 restraints weight = 32394.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081278 restraints weight = 28524.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.081379 restraints weight = 25722.819| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33584 Z= 0.117 Angle : 0.520 13.397 45796 Z= 0.278 Chirality : 0.040 0.160 5231 Planarity : 0.004 0.055 5614 Dihedral : 14.899 128.397 5441 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.09 % Allowed : 14.96 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.16 (0.13), residues: 3900 helix: -0.74 (0.13), residues: 1483 sheet: -1.45 (0.24), residues: 424 loop : -1.97 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1123 TYR 0.018 0.001 TYR F 137 PHE 0.020 0.001 PHE C1025 TRP 0.008 0.001 TRP D 580 HIS 0.024 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00260 (33576) covalent geometry : angle 0.51636 (45784) hydrogen bonds : bond 0.03107 ( 1134) hydrogen bonds : angle 4.32736 ( 3138) metal coordination : bond 0.00295 ( 8) metal coordination : angle 3.97309 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 346 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 25 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8776 (mttm) REVERT: A 84 ASN cc_start: 0.8744 (m110) cc_final: 0.8333 (m110) REVERT: A 194 GLN cc_start: 0.7571 (mt0) cc_final: 0.7371 (pm20) REVERT: B 93 GLN cc_start: 0.7942 (mm110) cc_final: 0.7610 (mm110) REVERT: C 107 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6988 (ttm-80) REVERT: C 562 GLU cc_start: 0.8313 (tp30) cc_final: 0.8004 (tp30) REVERT: C 984 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7153 (p) REVERT: C 1003 THR cc_start: 0.5906 (OUTLIER) cc_final: 0.5622 (m) REVERT: C 1028 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8539 (mtpp) REVERT: C 1188 ASP cc_start: 0.8034 (t0) cc_final: 0.7655 (t0) REVERT: C 1241 ASP cc_start: 0.7919 (m-30) cc_final: 0.7547 (t0) REVERT: C 1315 MET cc_start: 0.7981 (mmm) cc_final: 0.7738 (mmm) REVERT: D 77 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7153 (tmm-80) REVERT: D 301 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7522 (tm-30) REVERT: D 698 MET cc_start: 0.8384 (tpp) cc_final: 0.8158 (mmt) REVERT: D 725 MET cc_start: 0.8992 (mtt) cc_final: 0.8529 (mtt) REVERT: D 867 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7188 (tm-30) REVERT: D 1108 GLN cc_start: 0.2294 (OUTLIER) cc_final: 0.2040 (mt0) REVERT: D 1143 ASP cc_start: 0.7752 (t0) cc_final: 0.7536 (t0) REVERT: E 74 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7573 (mt-10) REVERT: F 470 MET cc_start: 0.8540 (mmm) cc_final: 0.8321 (mmm) REVERT: F 489 MET cc_start: 0.7494 (mmm) cc_final: 0.7002 (mmm) REVERT: F 538 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7791 (tm-30) REVERT: G 102 ARG cc_start: 0.8362 (ttt180) cc_final: 0.8057 (ptm-80) REVERT: H 19 PHE cc_start: 0.8652 (t80) cc_final: 0.8051 (t80) REVERT: H 36 TYR cc_start: 0.6350 (m-80) cc_final: 0.6061 (m-80) REVERT: H 52 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8326 (mp10) REVERT: H 83 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7426 (mtm-85) outliers start: 70 outliers final: 42 residues processed: 394 average time/residue: 0.2246 time to fit residues: 141.2303 Evaluate side-chains 366 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1108 GLN Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 69 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 359 optimal weight: 0.9990 chunk 382 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078922 restraints weight = 63961.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078773 restraints weight = 44911.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079348 restraints weight = 34342.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.079626 restraints weight = 28317.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079770 restraints weight = 25717.940| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33584 Z= 0.216 Angle : 0.583 11.937 45796 Z= 0.307 Chirality : 0.042 0.164 5231 Planarity : 0.004 0.052 5614 Dihedral : 14.967 128.937 5437 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.81 % Allowed : 15.62 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.04 (0.13), residues: 3900 helix: -0.59 (0.13), residues: 1489 sheet: -1.53 (0.24), residues: 427 loop : -1.91 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 332 TYR 0.018 0.001 TYR H 20 PHE 0.025 0.001 PHE H 70 TRP 0.008 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00502 (33576) covalent geometry : angle 0.57871 (45784) hydrogen bonds : bond 0.03611 ( 1134) hydrogen bonds : angle 4.40890 ( 3138) metal coordination : bond 0.00678 ( 8) metal coordination : angle 4.55990 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 315 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 84 ASN cc_start: 0.8761 (m110) cc_final: 0.8407 (m110) REVERT: B 18 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (tp40) REVERT: C 107 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6974 (ttm-80) REVERT: C 1003 THR cc_start: 0.6010 (OUTLIER) cc_final: 0.5722 (m) REVERT: C 1028 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8541 (mtpp) REVERT: C 1188 ASP cc_start: 0.8142 (t0) cc_final: 0.7864 (t0) REVERT: C 1241 ASP cc_start: 0.7907 (m-30) cc_final: 0.7523 (t0) REVERT: C 1315 MET cc_start: 0.8101 (mmm) cc_final: 0.7781 (mmm) REVERT: C 1324 ASN cc_start: 0.8053 (p0) cc_final: 0.7604 (p0) REVERT: D 77 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7258 (tmm-80) REVERT: D 301 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7667 (tm-30) REVERT: D 725 MET cc_start: 0.9049 (mtt) cc_final: 0.8636 (mtt) REVERT: D 867 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7232 (tm-30) REVERT: E 56 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: F 450 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9226 (mm) REVERT: F 489 MET cc_start: 0.7567 (mmm) cc_final: 0.7085 (mmm) REVERT: F 538 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 15 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7824 (mttt) REVERT: H 19 PHE cc_start: 0.8908 (t80) cc_final: 0.8371 (t80) REVERT: H 52 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8356 (mm-40) REVERT: H 102 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7405 (tmt-80) outliers start: 94 outliers final: 69 residues processed: 381 average time/residue: 0.2124 time to fit residues: 129.1706 Evaluate side-chains 377 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 303 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 120 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 285 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 273 HIS C 447 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.078917 restraints weight = 64055.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078756 restraints weight = 44426.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079416 restraints weight = 33690.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079696 restraints weight = 28079.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.079781 restraints weight = 25303.067| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33584 Z= 0.188 Angle : 0.565 12.338 45796 Z= 0.298 Chirality : 0.042 0.160 5231 Planarity : 0.004 0.050 5614 Dihedral : 14.936 128.119 5437 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.87 % Allowed : 16.46 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.86 (0.13), residues: 3900 helix: -0.41 (0.14), residues: 1484 sheet: -1.46 (0.24), residues: 433 loop : -1.82 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 314 TYR 0.016 0.001 TYR F 137 PHE 0.026 0.001 PHE H 70 TRP 0.007 0.001 TRP D 868 HIS 0.007 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00436 (33576) covalent geometry : angle 0.56128 (45784) hydrogen bonds : bond 0.03418 ( 1134) hydrogen bonds : angle 4.33813 ( 3138) metal coordination : bond 0.00553 ( 8) metal coordination : angle 4.28381 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 317 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: A 84 ASN cc_start: 0.8819 (m110) cc_final: 0.8505 (m110) REVERT: B 18 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7768 (tp40) REVERT: C 107 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6966 (ttm-80) REVERT: C 800 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: C 967 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7896 (tt) REVERT: C 1003 THR cc_start: 0.6021 (OUTLIER) cc_final: 0.5757 (m) REVERT: C 1028 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8556 (mtpp) REVERT: C 1188 ASP cc_start: 0.8124 (t0) cc_final: 0.7727 (t0) REVERT: C 1241 ASP cc_start: 0.7887 (m-30) cc_final: 0.7518 (t0) REVERT: C 1315 MET cc_start: 0.8070 (mmm) cc_final: 0.7816 (mmm) REVERT: C 1324 ASN cc_start: 0.8304 (p0) cc_final: 0.7867 (p0) REVERT: D 77 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7134 (tmm-80) REVERT: D 301 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 698 MET cc_start: 0.8404 (tpp) cc_final: 0.8144 (mmt) REVERT: D 725 MET cc_start: 0.9044 (mtt) cc_final: 0.8637 (mtt) REVERT: D 867 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 1149 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7840 (mtp180) REVERT: E 55 GLU cc_start: 0.8273 (pp20) cc_final: 0.6355 (pp20) REVERT: E 56 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: F 450 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9226 (mm) REVERT: F 489 MET cc_start: 0.7539 (mmm) cc_final: 0.7067 (mmm) REVERT: F 538 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 19 PHE cc_start: 0.8860 (t80) cc_final: 0.8408 (t80) REVERT: H 52 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8366 (mm-40) outliers start: 96 outliers final: 77 residues processed: 386 average time/residue: 0.2115 time to fit residues: 131.3066 Evaluate side-chains 387 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 303 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 26 optimal weight: 3.9990 chunk 195 optimal weight: 0.0470 chunk 190 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 227 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 249 optimal weight: 0.0980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 273 HIS C 447 HIS H 34 ASN H 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.080475 restraints weight = 63523.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080567 restraints weight = 43406.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080631 restraints weight = 34146.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.081089 restraints weight = 30375.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081247 restraints weight = 25675.316| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33584 Z= 0.126 Angle : 0.522 11.704 45796 Z= 0.277 Chirality : 0.040 0.154 5231 Planarity : 0.004 0.049 5614 Dihedral : 14.811 127.904 5437 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.51 % Allowed : 17.35 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.59 (0.13), residues: 3900 helix: -0.20 (0.14), residues: 1494 sheet: -1.27 (0.25), residues: 416 loop : -1.67 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.019 0.001 TYR H 36 PHE 0.030 0.001 PHE H 70 TRP 0.009 0.001 TRP D 868 HIS 0.033 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00286 (33576) covalent geometry : angle 0.51876 (45784) hydrogen bonds : bond 0.03000 ( 1134) hydrogen bonds : angle 4.15755 ( 3138) metal coordination : bond 0.00282 ( 8) metal coordination : angle 3.62978 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 330 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: A 84 ASN cc_start: 0.8772 (m110) cc_final: 0.8418 (m110) REVERT: A 185 TYR cc_start: 0.9062 (p90) cc_final: 0.8772 (p90) REVERT: B 18 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7665 (tp40) REVERT: C 107 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.6966 (ttm-80) REVERT: C 332 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7261 (tpp80) REVERT: C 562 GLU cc_start: 0.8428 (tp30) cc_final: 0.8101 (tp30) REVERT: C 1003 THR cc_start: 0.5945 (OUTLIER) cc_final: 0.5669 (m) REVERT: C 1028 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8546 (mtpp) REVERT: C 1188 ASP cc_start: 0.8021 (t0) cc_final: 0.7558 (t0) REVERT: C 1241 ASP cc_start: 0.7857 (m-30) cc_final: 0.7507 (t0) REVERT: C 1315 MET cc_start: 0.7944 (mmm) cc_final: 0.7670 (mmm) REVERT: C 1324 ASN cc_start: 0.8163 (p0) cc_final: 0.7742 (p0) REVERT: D 77 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7248 (tmm-80) REVERT: D 301 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7607 (tm-30) REVERT: D 725 MET cc_start: 0.8996 (mtt) cc_final: 0.8598 (mtt) REVERT: D 867 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 1149 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7779 (mtp180) REVERT: E 55 GLU cc_start: 0.8207 (pp20) cc_final: 0.6280 (pp20) REVERT: E 56 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: F 288 MET cc_start: 0.4586 (mtt) cc_final: 0.4019 (mtm) REVERT: F 450 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9195 (mm) REVERT: F 489 MET cc_start: 0.7456 (mmm) cc_final: 0.6993 (mmm) REVERT: F 538 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 2 ASN cc_start: 0.7597 (m-40) cc_final: 0.6633 (p0) REVERT: H 19 PHE cc_start: 0.8798 (t80) cc_final: 0.8370 (t80) REVERT: H 52 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8356 (mm-40) REVERT: H 94 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.8140 (t-90) outliers start: 84 outliers final: 64 residues processed: 391 average time/residue: 0.2137 time to fit residues: 134.1138 Evaluate side-chains 383 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 313 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 386 optimal weight: 6.9990 chunk 353 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS C1017 GLN G 99 GLN H 34 ASN H 55 GLN H 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.079139 restraints weight = 64197.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.078215 restraints weight = 47667.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078858 restraints weight = 41294.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.079139 restraints weight = 33124.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.079267 restraints weight = 30009.437| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33584 Z= 0.233 Angle : 0.602 12.758 45796 Z= 0.316 Chirality : 0.043 0.164 5231 Planarity : 0.004 0.049 5614 Dihedral : 14.940 128.665 5437 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.84 % Allowed : 17.47 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.66 (0.13), residues: 3900 helix: -0.24 (0.14), residues: 1495 sheet: -1.35 (0.25), residues: 419 loop : -1.72 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 83 TYR 0.023 0.001 TYR H 36 PHE 0.026 0.001 PHE C1025 TRP 0.008 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00545 (33576) covalent geometry : angle 0.59804 (45784) hydrogen bonds : bond 0.03608 ( 1134) hydrogen bonds : angle 4.34514 ( 3138) metal coordination : bond 0.00741 ( 8) metal coordination : angle 4.46894 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 310 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: B 18 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: C 107 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.6921 (ttm-80) REVERT: C 272 ARG cc_start: 0.6714 (tmm160) cc_final: 0.6146 (ttp80) REVERT: C 276 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8255 (tp-100) REVERT: C 315 MET cc_start: 0.7887 (tpt) cc_final: 0.7631 (tpt) REVERT: C 1003 THR cc_start: 0.5975 (OUTLIER) cc_final: 0.5682 (m) REVERT: C 1028 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8531 (mtpp) REVERT: C 1188 ASP cc_start: 0.8113 (t0) cc_final: 0.7818 (t0) REVERT: C 1241 ASP cc_start: 0.7829 (m-30) cc_final: 0.7497 (t0) REVERT: C 1315 MET cc_start: 0.8053 (mmm) cc_final: 0.7834 (mmm) REVERT: C 1324 ASN cc_start: 0.8067 (p0) cc_final: 0.7562 (p0) REVERT: D 77 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7244 (tmm-80) REVERT: D 301 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7632 (tm-30) REVERT: D 698 MET cc_start: 0.8384 (tpp) cc_final: 0.8145 (mmt) REVERT: D 725 MET cc_start: 0.9011 (mtt) cc_final: 0.8633 (mtt) REVERT: D 867 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7218 (tm-30) REVERT: D 1149 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7754 (mtp180) REVERT: E 55 GLU cc_start: 0.8132 (pp20) cc_final: 0.6328 (pp20) REVERT: E 56 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: F 450 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9206 (mm) REVERT: F 489 MET cc_start: 0.7580 (mmm) cc_final: 0.7139 (mmm) REVERT: H 19 PHE cc_start: 0.8839 (t80) cc_final: 0.8424 (t80) REVERT: H 52 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8303 (mm-40) REVERT: H 94 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8360 (t-90) REVERT: H 105 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6919 (mm) outliers start: 95 outliers final: 72 residues processed: 381 average time/residue: 0.2189 time to fit residues: 133.5199 Evaluate side-chains 384 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 304 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Chi-restraints excluded: chain H residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 211 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 316 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS G 99 GLN H 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.081052 restraints weight = 63078.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.080290 restraints weight = 38861.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080835 restraints weight = 33166.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081107 restraints weight = 29829.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081316 restraints weight = 25790.707| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33584 Z= 0.118 Angle : 0.535 13.970 45796 Z= 0.281 Chirality : 0.040 0.187 5231 Planarity : 0.004 0.049 5614 Dihedral : 14.788 127.847 5437 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.36 % Allowed : 17.92 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.37 (0.13), residues: 3900 helix: -0.00 (0.14), residues: 1494 sheet: -1.10 (0.26), residues: 415 loop : -1.57 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 75 TYR 0.028 0.001 TYR H 36 PHE 0.021 0.001 PHE H 70 TRP 0.027 0.001 TRP D 580 HIS 0.004 0.000 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00265 (33576) covalent geometry : angle 0.53182 (45784) hydrogen bonds : bond 0.02942 ( 1134) hydrogen bonds : angle 4.10157 ( 3138) metal coordination : bond 0.00237 ( 8) metal coordination : angle 3.48254 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 330 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: A 84 ASN cc_start: 0.8853 (m110) cc_final: 0.8553 (m110) REVERT: A 185 TYR cc_start: 0.9040 (p90) cc_final: 0.8813 (p90) REVERT: C 107 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.7041 (ttm-80) REVERT: C 272 ARG cc_start: 0.6885 (tmm160) cc_final: 0.6156 (ttp80) REVERT: C 276 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8402 (tp-100) REVERT: C 315 MET cc_start: 0.7992 (tpt) cc_final: 0.7730 (tpt) REVERT: C 332 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7319 (tpp80) REVERT: C 562 GLU cc_start: 0.8289 (tp30) cc_final: 0.7878 (tp30) REVERT: C 1003 THR cc_start: 0.5954 (OUTLIER) cc_final: 0.5683 (m) REVERT: C 1028 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8547 (mtpp) REVERT: C 1188 ASP cc_start: 0.8012 (t0) cc_final: 0.7573 (t0) REVERT: C 1241 ASP cc_start: 0.7821 (m-30) cc_final: 0.7486 (t0) REVERT: C 1315 MET cc_start: 0.7989 (mmm) cc_final: 0.7754 (mmm) REVERT: C 1324 ASN cc_start: 0.8141 (p0) cc_final: 0.7619 (p0) REVERT: D 77 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7241 (tmm-80) REVERT: D 301 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7598 (tm-30) REVERT: D 698 MET cc_start: 0.8338 (tpp) cc_final: 0.8075 (mmt) REVERT: D 725 MET cc_start: 0.9010 (mtt) cc_final: 0.8624 (mtt) REVERT: D 867 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7172 (tm-30) REVERT: D 1123 ARG cc_start: 0.6251 (pmt170) cc_final: 0.5925 (mmm-85) REVERT: D 1149 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7749 (mtp180) REVERT: E 55 GLU cc_start: 0.8186 (pp20) cc_final: 0.7030 (pp20) REVERT: E 56 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: F 288 MET cc_start: 0.4348 (mtt) cc_final: 0.3844 (mtm) REVERT: F 450 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9192 (mm) REVERT: F 489 MET cc_start: 0.7432 (mmm) cc_final: 0.6854 (mmm) REVERT: F 538 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7840 (tm-30) REVERT: H 2 ASN cc_start: 0.7582 (m-40) cc_final: 0.6581 (p0) REVERT: H 19 PHE cc_start: 0.8746 (t80) cc_final: 0.8334 (t80) REVERT: H 52 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8348 (mm-40) REVERT: H 94 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8409 (t-90) REVERT: H 102 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7456 (ttp80) outliers start: 79 outliers final: 64 residues processed: 387 average time/residue: 0.2131 time to fit residues: 132.4779 Evaluate side-chains 388 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 318 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 109 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 343 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS G 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.079353 restraints weight = 63877.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078728 restraints weight = 39821.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.079327 restraints weight = 33210.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.079630 restraints weight = 29847.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079734 restraints weight = 25445.844| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33584 Z= 0.179 Angle : 0.563 12.531 45796 Z= 0.295 Chirality : 0.042 0.221 5231 Planarity : 0.004 0.055 5614 Dihedral : 14.839 129.077 5437 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.36 % Allowed : 18.19 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.35 (0.13), residues: 3900 helix: 0.02 (0.14), residues: 1499 sheet: -1.08 (0.26), residues: 416 loop : -1.57 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 93 TYR 0.017 0.001 TYR H 20 PHE 0.025 0.001 PHE C1025 TRP 0.024 0.001 TRP D 580 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00417 (33576) covalent geometry : angle 0.55930 (45784) hydrogen bonds : bond 0.03254 ( 1134) hydrogen bonds : angle 4.17226 ( 3138) metal coordination : bond 0.00506 ( 8) metal coordination : angle 3.93944 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 315 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 84 ASN cc_start: 0.8748 (m110) cc_final: 0.8401 (m110) REVERT: A 185 TYR cc_start: 0.9055 (p90) cc_final: 0.8812 (p90) REVERT: B 93 GLN cc_start: 0.7963 (mm110) cc_final: 0.7719 (mm110) REVERT: C 107 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7045 (ttm-80) REVERT: C 272 ARG cc_start: 0.6779 (tmm160) cc_final: 0.5950 (ttp80) REVERT: C 276 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8188 (tp-100) REVERT: C 315 MET cc_start: 0.8171 (tpt) cc_final: 0.7948 (tpt) REVERT: C 332 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7244 (tpp80) REVERT: C 800 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: C 1003 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5698 (m) REVERT: C 1028 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8548 (mtpp) REVERT: C 1188 ASP cc_start: 0.8034 (t0) cc_final: 0.7595 (t0) REVERT: C 1241 ASP cc_start: 0.7850 (m-30) cc_final: 0.7502 (t0) REVERT: C 1315 MET cc_start: 0.8075 (mmm) cc_final: 0.7843 (mmm) REVERT: C 1324 ASN cc_start: 0.8136 (p0) cc_final: 0.7640 (p0) REVERT: D 77 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7122 (tmm-80) REVERT: D 301 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 698 MET cc_start: 0.8370 (tpp) cc_final: 0.8112 (mmt) REVERT: D 725 MET cc_start: 0.9057 (mtt) cc_final: 0.8686 (mtt) REVERT: D 867 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7237 (tm-30) REVERT: D 1123 ARG cc_start: 0.6125 (pmt170) cc_final: 0.5632 (mmm-85) REVERT: D 1149 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7773 (mtp180) REVERT: E 55 GLU cc_start: 0.8215 (pp20) cc_final: 0.6440 (pp20) REVERT: E 56 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: F 450 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9184 (mm) REVERT: F 489 MET cc_start: 0.7486 (mmm) cc_final: 0.7025 (mmm) REVERT: F 538 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7805 (tm-30) REVERT: H 2 ASN cc_start: 0.7593 (m-40) cc_final: 0.6580 (p0) REVERT: H 19 PHE cc_start: 0.8755 (t80) cc_final: 0.8344 (t80) REVERT: H 52 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8341 (mm-40) REVERT: H 94 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8505 (t-90) outliers start: 79 outliers final: 69 residues processed: 371 average time/residue: 0.2108 time to fit residues: 125.5037 Evaluate side-chains 385 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 304 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 283 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 379 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 339 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN C 447 HIS G 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.078953 restraints weight = 63795.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078816 restraints weight = 39144.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.079013 restraints weight = 32773.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079351 restraints weight = 30202.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079515 restraints weight = 26115.639| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33584 Z= 0.210 Angle : 0.582 12.949 45796 Z= 0.303 Chirality : 0.042 0.215 5231 Planarity : 0.004 0.072 5614 Dihedral : 14.851 128.979 5437 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.57 % Allowed : 18.04 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.36 (0.13), residues: 3900 helix: -0.00 (0.14), residues: 1500 sheet: -1.11 (0.26), residues: 406 loop : -1.57 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 83 TYR 0.016 0.001 TYR H 20 PHE 0.013 0.001 PHE C 506 TRP 0.022 0.001 TRP D 580 HIS 0.005 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00491 (33576) covalent geometry : angle 0.57792 (45784) hydrogen bonds : bond 0.03355 ( 1134) hydrogen bonds : angle 4.20105 ( 3138) metal coordination : bond 0.00638 ( 8) metal coordination : angle 4.02417 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5090.06 seconds wall clock time: 88 minutes 54.18 seconds (5334.18 seconds total)