Starting phenix.real_space_refine on Fri Mar 6 00:04:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d7c_30604/03_2026/7d7c_30604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d7c_30604/03_2026/7d7c_30604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d7c_30604/03_2026/7d7c_30604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d7c_30604/03_2026/7d7c_30604.map" model { file = "/net/cci-nas-00/data/ceres_data/7d7c_30604/03_2026/7d7c_30604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d7c_30604/03_2026/7d7c_30604.cif" } resolution = 3.6 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 16335 2.51 5 N 4625 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.03s 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: 26249 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "F" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1128 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 519 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20031 SG CYS D 814 86.451 67.375 129.517 1.00115.32 S ATOM 20596 SG CYS D 888 85.667 67.560 125.979 1.00104.77 S ATOM 20647 SG CYS D 895 84.746 64.207 127.826 1.00105.89 S ATOM 20668 SG CYS D 898 83.177 67.277 128.309 1.00103.24 S Time building chain proxies: 6.08, per 1000 atoms: 0.23 Number of scatterers: 26249 At special positions: 0 Unit cell: (133.314, 160.761, 167.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 48 15.00 Mg 1 11.99 O 5128 8.00 N 4625 7.00 C 16335 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 6 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 46 sheets defined 36.4% alpha, 13.7% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.635A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.957A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.270A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.710A pdb=" N THR B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.581A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.290A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.621A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.869A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.776A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 478 removed outlier: 3.502A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 610 through 614 removed outlier: 3.877A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 687 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.693A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.838A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 980 removed outlier: 4.131A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.621A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.689A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.606A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.859A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.831A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.736A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 removed outlier: 3.524A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.627A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.701A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1290 removed outlier: 3.592A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1321 through 1331 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.884A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.549A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.540A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.637A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.730A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.795A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.757A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 594 removed outlier: 3.641A pdb=" N ASN D 593 " --> pdb=" O TYR D 589 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 589 through 594' Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.829A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.606A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.560A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.629A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.521A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.597A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.911A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.596A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 4.611A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.847A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.299A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.995A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.910A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.749A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.823A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 28 removed outlier: 3.859A pdb=" N LEU F 17 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 55 removed outlier: 3.502A pdb=" N GLY F 44 " --> pdb=" O ASN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.709A pdb=" N GLN F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 125 Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.599A pdb=" N ASP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.073A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 61 removed outlier: 5.448A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.804A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.195A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.686A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (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 104 through 105 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.814A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.626A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB7, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.623A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.073A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.747A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.594A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.594A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.757A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 751 removed outlier: 5.662A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 722 " --> pdb=" O VAL C 777 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.316A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AD1, first strand: chain 'C' and resid 835 through 839 Processing sheet with id=AD2, first strand: chain 'C' and resid 842 through 843 removed outlier: 3.754A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD4, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.305A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD7, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.729A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD9, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.415A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE2, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.885A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.579A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.727A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.852A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 958 through 961 removed outlier: 6.564A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1078 through 1079 removed outlier: 3.653A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 4.294A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.800A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7003 1.33 - 1.45: 4364 1.45 - 1.57: 15096 1.57 - 1.69: 92 1.69 - 1.81: 191 Bond restraints: 26746 Sorted by residual: bond pdb=" N TYR C 47 " pdb=" CA TYR C 47 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.51e+00 bond pdb=" C THR C 563 " pdb=" N PRO C 564 " ideal model delta sigma weight residual 1.335 1.312 0.023 8.70e-03 1.32e+04 7.16e+00 bond pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.59e+00 bond pdb=" N HIS F 126 " pdb=" CA HIS F 126 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.09e+00 ... (remaining 26741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 35862 2.64 - 5.28: 427 5.28 - 7.91: 26 7.91 - 10.55: 3 10.55 - 13.19: 1 Bond angle restraints: 36319 Sorted by residual: angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.52 111.32 10.20 1.74e+00 3.30e-01 3.44e+01 angle pdb=" N GLY C 162 " pdb=" CA GLY C 162 " pdb=" C GLY C 162 " ideal model delta sigma weight residual 111.67 116.59 -4.92 9.20e-01 1.18e+00 2.86e+01 angle pdb=" N VAL D 839 " pdb=" CA VAL D 839 " pdb=" C VAL D 839 " ideal model delta sigma weight residual 113.20 108.29 4.91 9.60e-01 1.09e+00 2.62e+01 angle pdb=" C VAL D 244 " pdb=" N LEU D 245 " pdb=" CA LEU D 245 " ideal model delta sigma weight residual 120.94 128.01 -7.07 1.90e+00 2.77e-01 1.39e+01 angle pdb=" CA ARG D1345 " pdb=" C ARG D1345 " pdb=" O ARG D1345 " ideal model delta sigma weight residual 122.36 118.17 4.19 1.21e+00 6.83e-01 1.20e+01 ... (remaining 36314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 15798 35.04 - 70.09: 473 70.09 - 105.13: 39 105.13 - 140.17: 0 140.17 - 175.22: 1 Dihedral angle restraints: 16311 sinusoidal: 7044 harmonic: 9267 Sorted by residual: dihedral pdb=" CA GLY D 852 " pdb=" C GLY D 852 " pdb=" N THR D 853 " pdb=" CA THR D 853 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG F 132 " pdb=" C ARG F 132 " pdb=" N ASP F 133 " pdb=" CA ASP F 133 " ideal model delta harmonic sigma weight residual 180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA SER B 20 " pdb=" C SER B 20 " pdb=" N SER B 21 " pdb=" CA SER B 21 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 16308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2482 0.037 - 0.074: 1174 0.074 - 0.111: 375 0.111 - 0.147: 90 0.147 - 0.184: 16 Chirality restraints: 4137 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CB ILE C 176 " pdb=" CA ILE C 176 " pdb=" CG1 ILE C 176 " pdb=" CG2 ILE C 176 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE C1079 " pdb=" CA ILE C1079 " pdb=" CG1 ILE C1079 " pdb=" CG2 ILE C1079 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 4134 not shown) Planarity restraints: 4580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 42 " -0.094 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO C 43 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 51 " -0.002 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC N 51 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC N 51 " -0.042 2.00e-02 2.50e+03 pdb=" O2 DC N 51 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DC N 51 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC N 51 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC N 51 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC N 51 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC N 51 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 25 " 0.016 2.00e-02 2.50e+03 1.48e-02 6.55e+00 pdb=" N9 DG N 25 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG N 25 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG N 25 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 25 " 0.020 2.00e-02 2.50e+03 pdb=" O6 DG N 25 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG N 25 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG N 25 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG N 25 " -0.022 2.00e-02 2.50e+03 pdb=" N3 DG N 25 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG N 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 4577 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 337 2.55 - 3.14: 22913 3.14 - 3.73: 39723 3.73 - 4.31: 54469 4.31 - 4.90: 89067 Nonbonded interactions: 206509 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1501 " model vdw 1.967 2.170 nonbonded pdb=" NH1 ARG C 267 " pdb=" O ARG C 268 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR D 816 " pdb=" OE1 GLU D 818 " model vdw 2.198 3.040 nonbonded pdb=" O ALA D 741 " pdb=" ND2 ASN D 762 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP C1214 " pdb=" N GLY C1215 " model vdw 2.202 3.120 ... (remaining 206504 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 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 30.020 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.126 26750 Z= 0.341 Angle : 0.801 16.220 36325 Z= 0.458 Chirality : 0.047 0.184 4137 Planarity : 0.005 0.144 4580 Dihedral : 16.349 175.217 10351 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer: Outliers : 0.29 % Allowed : 9.32 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.12), residues: 3203 helix: -1.89 (0.13), residues: 1073 sheet: -2.61 (0.21), residues: 437 loop : -3.71 (0.12), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 97 TYR 0.020 0.002 TYR A 177 PHE 0.014 0.002 PHE A 231 TRP 0.030 0.002 TRP D 115 HIS 0.011 0.002 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00735 (26746) covalent geometry : angle 0.78906 (36319) hydrogen bonds : bond 0.16394 ( 1014) hydrogen bonds : angle 7.47798 ( 2798) metal coordination : bond 0.07406 ( 4) metal coordination : angle 10.64029 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 315 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LYS cc_start: 0.8852 (tttt) cc_final: 0.8412 (tppt) REVERT: C 267 ARG cc_start: 0.7762 (tpt90) cc_final: 0.7373 (ttp80) REVERT: C 366 ILE cc_start: 0.9148 (mt) cc_final: 0.8918 (mm) REVERT: C 370 MET cc_start: 0.9145 (mmm) cc_final: 0.8584 (mmm) REVERT: C 403 MET cc_start: 0.8670 (tmm) cc_final: 0.8380 (tmm) REVERT: C 503 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8708 (mptt) REVERT: C 951 MET cc_start: 0.8466 (mmt) cc_final: 0.8113 (tpp) REVERT: D 42 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7911 (mm-30) REVERT: D 45 ASN cc_start: 0.8935 (t0) cc_final: 0.8731 (t0) REVERT: D 180 MET cc_start: 0.8226 (ptt) cc_final: 0.7874 (ptt) REVERT: D 301 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7958 (tm-30) REVERT: D 325 LYS cc_start: 0.9347 (mtpt) cc_final: 0.9058 (mtpp) REVERT: D 462 ASP cc_start: 0.8493 (m-30) cc_final: 0.8125 (m-30) REVERT: D 617 THR cc_start: 0.9163 (m) cc_final: 0.8876 (p) REVERT: D 625 MET cc_start: 0.8849 (ttp) cc_final: 0.8582 (ttp) REVERT: D 869 CYS cc_start: 0.8055 (m) cc_final: 0.7723 (m) REVERT: D 1369 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.8456 (ttp80) REVERT: F 52 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8339 (tm-30) REVERT: F 65 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8104 (mm-40) REVERT: F 74 ASP cc_start: 0.8833 (t0) cc_final: 0.8550 (t0) REVERT: F 91 TYR cc_start: 0.8303 (m-80) cc_final: 0.7845 (m-80) outliers start: 8 outliers final: 6 residues processed: 322 average time/residue: 0.2058 time to fit residues: 99.3655 Evaluate side-chains 240 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.0040 chunk 298 optimal weight: 8.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 147 GLN B 117 HIS B 194 GLN C 41 GLN C 65 ASN C 618 GLN C 856 ASN C 955 GLN C1038 GLN C1136 GLN C1157 GLN D 320 ASN D 340 GLN D 365 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 665 GLN D 805 GLN D 921 GLN D 929 GLN F 126 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063306 restraints weight = 79398.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065395 restraints weight = 39465.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066803 restraints weight = 25047.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067661 restraints weight = 18691.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068261 restraints weight = 15632.061| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26750 Z= 0.127 Angle : 0.601 7.318 36325 Z= 0.318 Chirality : 0.043 0.166 4137 Planarity : 0.005 0.077 4580 Dihedral : 13.010 167.643 4065 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.60 % Allowed : 13.76 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3203 helix: -0.01 (0.16), residues: 1092 sheet: -1.93 (0.24), residues: 376 loop : -2.87 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 478 TYR 0.015 0.001 TYR D 144 PHE 0.020 0.001 PHE F 58 TRP 0.023 0.002 TRP D1193 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00281 (26746) covalent geometry : angle 0.59900 (36319) hydrogen bonds : bond 0.04530 ( 1014) hydrogen bonds : angle 5.06520 ( 2798) metal coordination : bond 0.00513 ( 4) metal coordination : angle 3.57042 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8223 (m-80) cc_final: 0.7893 (m-80) REVERT: B 145 LYS cc_start: 0.8646 (tttt) cc_final: 0.8145 (tppt) REVERT: B 182 ARG cc_start: 0.8294 (ttt90) cc_final: 0.7890 (ttt-90) REVERT: B 186 ASN cc_start: 0.8537 (t0) cc_final: 0.8070 (p0) REVERT: C 481 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7423 (tp) REVERT: C 947 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9009 (mt-10) REVERT: C 950 GLU cc_start: 0.9005 (pt0) cc_final: 0.8730 (pt0) REVERT: C 952 GLN cc_start: 0.9466 (tt0) cc_final: 0.9061 (tm-30) REVERT: D 42 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 45 ASN cc_start: 0.8987 (t0) cc_final: 0.8661 (t0) REVERT: D 180 MET cc_start: 0.8282 (ptt) cc_final: 0.7917 (ptt) REVERT: D 237 MET cc_start: 0.8624 (mtm) cc_final: 0.8397 (ttm) REVERT: D 301 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 322 ARG cc_start: 0.8201 (ppt170) cc_final: 0.7972 (pmt-80) REVERT: D 325 LYS cc_start: 0.9308 (mtpt) cc_final: 0.9088 (mtpp) REVERT: D 462 ASP cc_start: 0.8127 (m-30) cc_final: 0.7832 (m-30) REVERT: D 625 MET cc_start: 0.9046 (ttp) cc_final: 0.8803 (ttp) REVERT: D 698 MET cc_start: 0.9320 (tpt) cc_final: 0.8967 (tpp) REVERT: D 795 TYR cc_start: 0.9126 (t80) cc_final: 0.8914 (t80) REVERT: D 822 MET cc_start: 0.8817 (mmp) cc_final: 0.8462 (mmt) REVERT: D 869 CYS cc_start: 0.8131 (m) cc_final: 0.7674 (m) REVERT: D 913 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7427 (tm-30) REVERT: D 1095 MET cc_start: 0.7558 (tpt) cc_final: 0.7287 (tpt) REVERT: D 1144 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9174 (mp) REVERT: D 1215 GLU cc_start: 0.8354 (tp30) cc_final: 0.8105 (mm-30) REVERT: F 18 GLN cc_start: 0.9398 (mm110) cc_final: 0.9168 (mm110) REVERT: F 52 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8317 (tm-30) REVERT: F 65 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7994 (mm-40) REVERT: F 74 ASP cc_start: 0.8874 (t0) cc_final: 0.8485 (t0) REVERT: F 91 TYR cc_start: 0.8268 (m-80) cc_final: 0.7905 (m-80) outliers start: 44 outliers final: 21 residues processed: 322 average time/residue: 0.1782 time to fit residues: 91.0483 Evaluate side-chains 258 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 115 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 23 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN C1013 GLN D 320 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 ASN F 84 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059847 restraints weight = 81510.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061810 restraints weight = 41525.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.063131 restraints weight = 26955.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063936 restraints weight = 20369.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064497 restraints weight = 17209.527| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 26750 Z= 0.293 Angle : 0.694 10.788 36325 Z= 0.365 Chirality : 0.045 0.223 4137 Planarity : 0.005 0.070 4580 Dihedral : 13.046 172.712 4062 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.02 % Allowed : 17.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.14), residues: 3203 helix: 0.21 (0.16), residues: 1092 sheet: -1.89 (0.23), residues: 419 loop : -2.77 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1034 TYR 0.019 0.002 TYR D 772 PHE 0.015 0.002 PHE F 58 TRP 0.016 0.002 TRP D1193 HIS 0.010 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00673 (26746) covalent geometry : angle 0.69327 (36319) hydrogen bonds : bond 0.05250 ( 1014) hydrogen bonds : angle 5.18378 ( 2798) metal coordination : bond 0.01638 ( 4) metal coordination : angle 2.80475 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 240 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8157 (m-80) cc_final: 0.7800 (m-80) REVERT: B 145 LYS cc_start: 0.8641 (tttt) cc_final: 0.8276 (tppt) REVERT: B 186 ASN cc_start: 0.8636 (t0) cc_final: 0.8137 (p0) REVERT: C 46 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7936 (mm-40) REVERT: C 84 GLU cc_start: 0.8824 (mp0) cc_final: 0.8613 (pm20) REVERT: C 403 MET cc_start: 0.8745 (tmm) cc_final: 0.8337 (tmm) REVERT: C 481 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7460 (tp) REVERT: C 951 MET cc_start: 0.8490 (mmt) cc_final: 0.7960 (tpt) REVERT: D 45 ASN cc_start: 0.8962 (t0) cc_final: 0.8663 (t0) REVERT: D 180 MET cc_start: 0.8314 (ptt) cc_final: 0.7620 (ptt) REVERT: D 237 MET cc_start: 0.8566 (mtm) cc_final: 0.8343 (ttm) REVERT: D 301 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 322 ARG cc_start: 0.8217 (ppt170) cc_final: 0.7775 (ppt170) REVERT: D 325 LYS cc_start: 0.9345 (mtpt) cc_final: 0.9142 (mtpp) REVERT: D 462 ASP cc_start: 0.8406 (m-30) cc_final: 0.7925 (m-30) REVERT: D 587 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9057 (mp) REVERT: D 617 THR cc_start: 0.9088 (m) cc_final: 0.8857 (p) REVERT: D 625 MET cc_start: 0.8995 (ttp) cc_final: 0.8691 (ttp) REVERT: D 795 TYR cc_start: 0.8971 (t80) cc_final: 0.8736 (t80) REVERT: D 822 MET cc_start: 0.8745 (mmp) cc_final: 0.8421 (mmt) REVERT: D 869 CYS cc_start: 0.8197 (m) cc_final: 0.7644 (m) REVERT: D 1189 MET cc_start: 0.7979 (tpp) cc_final: 0.7678 (tpp) REVERT: D 1215 GLU cc_start: 0.8410 (tp30) cc_final: 0.8119 (mm-30) REVERT: F 15 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8452 (tm-30) REVERT: F 18 GLN cc_start: 0.9417 (mm110) cc_final: 0.9161 (mm110) REVERT: F 52 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8359 (tm-30) REVERT: F 65 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8041 (mm-40) REVERT: F 74 ASP cc_start: 0.8809 (t0) cc_final: 0.8415 (t0) REVERT: F 91 TYR cc_start: 0.8214 (m-80) cc_final: 0.7874 (m-80) outliers start: 83 outliers final: 53 residues processed: 303 average time/residue: 0.1592 time to fit residues: 79.3831 Evaluate side-chains 284 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 204 optimal weight: 0.6980 chunk 283 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 153 optimal weight: 0.8980 chunk 266 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.088022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063695 restraints weight = 79198.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065778 restraints weight = 39260.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067169 restraints weight = 24920.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068029 restraints weight = 18626.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068640 restraints weight = 15576.180| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26750 Z= 0.113 Angle : 0.570 9.482 36325 Z= 0.299 Chirality : 0.042 0.219 4137 Planarity : 0.004 0.053 4580 Dihedral : 12.735 173.081 4062 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.37 % Allowed : 19.65 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3203 helix: 0.70 (0.16), residues: 1100 sheet: -1.40 (0.25), residues: 388 loop : -2.41 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1246 TYR 0.012 0.001 TYR C1229 PHE 0.011 0.001 PHE F 58 TRP 0.021 0.001 TRP D1193 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00254 (26746) covalent geometry : angle 0.56973 (36319) hydrogen bonds : bond 0.03870 ( 1014) hydrogen bonds : angle 4.59052 ( 2798) metal coordination : bond 0.00385 ( 4) metal coordination : angle 2.05849 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7647 (t0) cc_final: 0.7368 (t0) REVERT: B 68 TYR cc_start: 0.8266 (m-80) cc_final: 0.7839 (m-80) REVERT: B 145 LYS cc_start: 0.8573 (tttt) cc_final: 0.8192 (tppt) REVERT: B 182 ARG cc_start: 0.8268 (ttt90) cc_final: 0.7965 (ttt-90) REVERT: B 186 ASN cc_start: 0.8377 (t0) cc_final: 0.8083 (p0) REVERT: C 46 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7917 (mm-40) REVERT: C 200 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8249 (mmm-85) REVERT: C 403 MET cc_start: 0.8657 (tmm) cc_final: 0.8209 (tmm) REVERT: C 481 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7359 (tp) REVERT: C 492 MET cc_start: 0.7657 (mmt) cc_final: 0.7425 (tpt) REVERT: C 711 ASP cc_start: 0.7915 (m-30) cc_final: 0.7611 (m-30) REVERT: C 1059 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6466 (ptm-80) REVERT: C 1270 PHE cc_start: 0.8656 (t80) cc_final: 0.8279 (t80) REVERT: C 1304 MET cc_start: 0.8247 (tpt) cc_final: 0.7832 (tpp) REVERT: D 42 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7569 (mm-30) REVERT: D 45 ASN cc_start: 0.8939 (t0) cc_final: 0.8662 (t0) REVERT: D 180 MET cc_start: 0.8273 (ptt) cc_final: 0.7865 (ptt) REVERT: D 237 MET cc_start: 0.8483 (mtm) cc_final: 0.8261 (ttm) REVERT: D 301 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7851 (tm-30) REVERT: D 322 ARG cc_start: 0.8332 (ppt170) cc_final: 0.7971 (ppt170) REVERT: D 462 ASP cc_start: 0.8007 (m-30) cc_final: 0.7632 (m-30) REVERT: D 625 MET cc_start: 0.9053 (ttp) cc_final: 0.8820 (ttp) REVERT: D 698 MET cc_start: 0.9275 (tpt) cc_final: 0.8923 (tpp) REVERT: D 795 TYR cc_start: 0.9068 (t80) cc_final: 0.8862 (t80) REVERT: D 822 MET cc_start: 0.8877 (mmp) cc_final: 0.8507 (mmt) REVERT: D 869 CYS cc_start: 0.8073 (m) cc_final: 0.7494 (m) REVERT: D 1144 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9101 (mp) REVERT: D 1215 GLU cc_start: 0.8329 (tp30) cc_final: 0.8001 (mm-30) REVERT: F 18 GLN cc_start: 0.9446 (mm110) cc_final: 0.9129 (mm-40) REVERT: F 52 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 65 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8044 (mm-40) REVERT: F 74 ASP cc_start: 0.8879 (t0) cc_final: 0.8441 (t0) REVERT: F 91 TYR cc_start: 0.8249 (m-80) cc_final: 0.7881 (m-80) outliers start: 65 outliers final: 40 residues processed: 323 average time/residue: 0.1588 time to fit residues: 83.3579 Evaluate side-chains 285 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 91 optimal weight: 0.0010 chunk 248 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 312 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 580 GLN C 952 GLN C 955 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060920 restraints weight = 80734.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.062919 restraints weight = 41028.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064251 restraints weight = 26415.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065138 restraints weight = 19904.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065598 restraints weight = 16677.154| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 26750 Z= 0.230 Angle : 0.642 8.796 36325 Z= 0.336 Chirality : 0.043 0.154 4137 Planarity : 0.004 0.052 4580 Dihedral : 12.788 174.775 4061 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.68 % Allowed : 20.92 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3203 helix: 0.69 (0.16), residues: 1094 sheet: -1.41 (0.25), residues: 409 loop : -2.33 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 687 TYR 0.023 0.002 TYR D 772 PHE 0.013 0.001 PHE C 405 TRP 0.017 0.001 TRP D1193 HIS 0.014 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00528 (26746) covalent geometry : angle 0.64126 (36319) hydrogen bonds : bond 0.04665 ( 1014) hydrogen bonds : angle 4.77088 ( 2798) metal coordination : bond 0.01198 ( 4) metal coordination : angle 2.11840 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 240 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8060 (m-80) cc_final: 0.7622 (m-80) REVERT: B 145 LYS cc_start: 0.8502 (tttt) cc_final: 0.8262 (tppt) REVERT: B 212 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7640 (t0) REVERT: C 46 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7931 (mm-40) REVERT: C 200 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8247 (mmm-85) REVERT: C 403 MET cc_start: 0.8746 (tmm) cc_final: 0.8225 (tmm) REVERT: C 711 ASP cc_start: 0.8180 (m-30) cc_final: 0.7896 (m-30) REVERT: C 826 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7307 (t0) REVERT: C 952 GLN cc_start: 0.9395 (tp40) cc_final: 0.9123 (tp-100) REVERT: C 1059 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6503 (ptm-80) REVERT: C 1304 MET cc_start: 0.8218 (tpt) cc_final: 0.7807 (tpp) REVERT: D 42 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7594 (mm-30) REVERT: D 45 ASN cc_start: 0.8975 (t0) cc_final: 0.8688 (t0) REVERT: D 180 MET cc_start: 0.8395 (ptt) cc_final: 0.7750 (ptt) REVERT: D 237 MET cc_start: 0.8444 (mtm) cc_final: 0.8243 (ttm) REVERT: D 301 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7865 (tm-30) REVERT: D 322 ARG cc_start: 0.8310 (ppt170) cc_final: 0.7965 (ppt170) REVERT: D 587 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9027 (mp) REVERT: D 625 MET cc_start: 0.8987 (ttp) cc_final: 0.8695 (ttp) REVERT: D 698 MET cc_start: 0.9266 (tpt) cc_final: 0.8751 (tpp) REVERT: D 795 TYR cc_start: 0.9016 (t80) cc_final: 0.8798 (t80) REVERT: D 822 MET cc_start: 0.8853 (mmp) cc_final: 0.8513 (mmt) REVERT: D 869 CYS cc_start: 0.8171 (m) cc_final: 0.7546 (m) REVERT: D 898 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7939 (m) REVERT: D 1144 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9169 (mp) REVERT: D 1215 GLU cc_start: 0.8449 (tp30) cc_final: 0.8129 (mm-30) REVERT: F 18 GLN cc_start: 0.9419 (mm110) cc_final: 0.9217 (mm-40) REVERT: F 52 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 65 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8034 (mm-40) REVERT: F 74 ASP cc_start: 0.8833 (t0) cc_final: 0.8395 (t0) REVERT: F 91 TYR cc_start: 0.8264 (m-80) cc_final: 0.7910 (m-80) outliers start: 101 outliers final: 72 residues processed: 315 average time/residue: 0.1562 time to fit residues: 81.4613 Evaluate side-chains 306 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 228 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 271 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062330 restraints weight = 80084.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064365 restraints weight = 40239.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065734 restraints weight = 25805.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066627 restraints weight = 19402.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067160 restraints weight = 16227.942| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26750 Z= 0.142 Angle : 0.594 8.523 36325 Z= 0.310 Chirality : 0.042 0.169 4137 Planarity : 0.004 0.059 4580 Dihedral : 12.699 174.387 4061 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.13 % Allowed : 22.02 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 3203 helix: 0.89 (0.16), residues: 1093 sheet: -1.25 (0.25), residues: 394 loop : -2.16 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 687 TYR 0.015 0.001 TYR D 772 PHE 0.009 0.001 PHE C 405 TRP 0.021 0.001 TRP D1193 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00330 (26746) covalent geometry : angle 0.59370 (36319) hydrogen bonds : bond 0.04126 ( 1014) hydrogen bonds : angle 4.56325 ( 2798) metal coordination : bond 0.00628 ( 4) metal coordination : angle 1.62492 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 253 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8149 (m-80) cc_final: 0.7702 (m-80) REVERT: B 145 LYS cc_start: 0.8501 (tttt) cc_final: 0.8258 (tppt) REVERT: B 182 ARG cc_start: 0.8251 (ttt90) cc_final: 0.7864 (ttt-90) REVERT: B 186 ASN cc_start: 0.8456 (t0) cc_final: 0.8231 (p0) REVERT: B 212 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7454 (t0) REVERT: C 200 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8227 (mmm-85) REVERT: C 239 MET cc_start: 0.6913 (ppp) cc_final: 0.6142 (tmm) REVERT: C 403 MET cc_start: 0.8798 (tmm) cc_final: 0.8272 (tmm) REVERT: C 711 ASP cc_start: 0.8107 (m-30) cc_final: 0.7805 (m-30) REVERT: C 826 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7272 (t0) REVERT: C 951 MET cc_start: 0.8473 (mmt) cc_final: 0.8058 (tpt) REVERT: C 952 GLN cc_start: 0.9377 (tp40) cc_final: 0.9009 (tp-100) REVERT: C 1059 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6517 (ptm-80) REVERT: C 1073 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8418 (ptmm) REVERT: C 1304 MET cc_start: 0.8272 (tpt) cc_final: 0.7829 (tpp) REVERT: D 42 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 45 ASN cc_start: 0.8979 (t0) cc_final: 0.8699 (t0) REVERT: D 180 MET cc_start: 0.7924 (ptt) cc_final: 0.7570 (ptt) REVERT: D 237 MET cc_start: 0.8470 (mtm) cc_final: 0.8261 (ttm) REVERT: D 301 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7810 (tm-30) REVERT: D 322 ARG cc_start: 0.8256 (ppt170) cc_final: 0.7893 (ppt170) REVERT: D 587 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8938 (mp) REVERT: D 625 MET cc_start: 0.9021 (ttp) cc_final: 0.8743 (ttp) REVERT: D 698 MET cc_start: 0.9258 (tpt) cc_final: 0.8733 (tpp) REVERT: D 795 TYR cc_start: 0.9116 (t80) cc_final: 0.8910 (t80) REVERT: D 822 MET cc_start: 0.8874 (mmp) cc_final: 0.8501 (mmt) REVERT: D 869 CYS cc_start: 0.8247 (m) cc_final: 0.7606 (m) REVERT: D 898 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7857 (m) REVERT: D 1144 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9144 (mp) REVERT: D 1215 GLU cc_start: 0.8428 (tp30) cc_final: 0.8047 (mm-30) REVERT: F 18 GLN cc_start: 0.9449 (mm110) cc_final: 0.9242 (mm-40) REVERT: F 52 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8241 (tm-30) REVERT: F 65 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8000 (mm-40) REVERT: F 74 ASP cc_start: 0.8880 (t0) cc_final: 0.8367 (t0) REVERT: F 91 TYR cc_start: 0.8279 (m-80) cc_final: 0.7888 (m-80) outliers start: 86 outliers final: 64 residues processed: 318 average time/residue: 0.1517 time to fit residues: 79.9846 Evaluate side-chains 307 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 237 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 193 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 311 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 11 optimal weight: 0.0070 chunk 38 optimal weight: 0.4980 chunk 210 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.063939 restraints weight = 78966.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.066036 restraints weight = 39127.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.067441 restraints weight = 24800.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068369 restraints weight = 18481.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068908 restraints weight = 15329.937| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26750 Z= 0.112 Angle : 0.572 8.134 36325 Z= 0.299 Chirality : 0.041 0.193 4137 Planarity : 0.004 0.056 4580 Dihedral : 12.576 175.069 4061 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.91 % Allowed : 22.63 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3203 helix: 1.05 (0.16), residues: 1096 sheet: -0.94 (0.27), residues: 375 loop : -2.03 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1033 TYR 0.012 0.001 TYR D1232 PHE 0.009 0.001 PHE C1270 TRP 0.025 0.001 TRP D1193 HIS 0.009 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00254 (26746) covalent geometry : angle 0.57147 (36319) hydrogen bonds : bond 0.03730 ( 1014) hydrogen bonds : angle 4.37611 ( 2798) metal coordination : bond 0.00366 ( 4) metal coordination : angle 1.62771 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 262 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8161 (m-80) cc_final: 0.7731 (m-80) REVERT: B 145 LYS cc_start: 0.8485 (tttt) cc_final: 0.8172 (tppt) REVERT: B 182 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7877 (ttt-90) REVERT: B 212 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7380 (t0) REVERT: C 84 GLU cc_start: 0.8569 (pm20) cc_final: 0.8282 (pm20) REVERT: C 200 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8164 (mmm-85) REVERT: C 369 MET cc_start: 0.8253 (ppp) cc_final: 0.7891 (ppp) REVERT: C 403 MET cc_start: 0.8735 (tmm) cc_final: 0.8288 (tmm) REVERT: C 711 ASP cc_start: 0.7977 (m-30) cc_final: 0.7692 (m-30) REVERT: C 826 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7109 (t0) REVERT: C 951 MET cc_start: 0.8408 (mmt) cc_final: 0.8030 (tpt) REVERT: C 952 GLN cc_start: 0.9424 (tp40) cc_final: 0.8870 (tp-100) REVERT: C 1059 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6278 (ptm-80) REVERT: C 1061 GLN cc_start: 0.7988 (pt0) cc_final: 0.7581 (pm20) REVERT: C 1073 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8350 (ptmm) REVERT: C 1304 MET cc_start: 0.8269 (tpt) cc_final: 0.7848 (tpp) REVERT: D 42 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7737 (mm-30) REVERT: D 45 ASN cc_start: 0.8973 (t0) cc_final: 0.8768 (t0) REVERT: D 180 MET cc_start: 0.7826 (ptt) cc_final: 0.7479 (ptt) REVERT: D 237 MET cc_start: 0.8434 (mtm) cc_final: 0.8210 (ttm) REVERT: D 301 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7819 (tm-30) REVERT: D 321 LYS cc_start: 0.9036 (mppt) cc_final: 0.8755 (mttt) REVERT: D 322 ARG cc_start: 0.8321 (ppt170) cc_final: 0.8039 (ppt170) REVERT: D 335 GLN cc_start: 0.8966 (mp10) cc_final: 0.8647 (mp10) REVERT: D 413 ASP cc_start: 0.8535 (p0) cc_final: 0.8296 (p0) REVERT: D 625 MET cc_start: 0.9046 (ttp) cc_final: 0.8784 (ttp) REVERT: D 641 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8915 (tp) REVERT: D 698 MET cc_start: 0.9273 (tpt) cc_final: 0.8728 (tpp) REVERT: D 822 MET cc_start: 0.8913 (mmp) cc_final: 0.8544 (mmt) REVERT: D 869 CYS cc_start: 0.8151 (m) cc_final: 0.7483 (m) REVERT: D 898 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7859 (m) REVERT: D 1144 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9073 (mp) REVERT: D 1215 GLU cc_start: 0.8341 (tp30) cc_final: 0.7970 (mm-30) REVERT: F 52 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8233 (tm-30) REVERT: F 65 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8042 (mm-40) REVERT: F 74 ASP cc_start: 0.8872 (t0) cc_final: 0.8314 (t0) REVERT: F 91 TYR cc_start: 0.8279 (m-80) cc_final: 0.7895 (m-80) outliers start: 80 outliers final: 58 residues processed: 324 average time/residue: 0.1547 time to fit residues: 82.8451 Evaluate side-chains 312 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 309 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 278 optimal weight: 0.3980 chunk 211 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 296 optimal weight: 0.0370 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.088782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064261 restraints weight = 79507.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066398 restraints weight = 39557.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067817 restraints weight = 25038.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068737 restraints weight = 18675.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.069280 restraints weight = 15539.402| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26750 Z= 0.112 Angle : 0.576 13.350 36325 Z= 0.297 Chirality : 0.041 0.202 4137 Planarity : 0.004 0.055 4580 Dihedral : 12.486 175.822 4061 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.84 % Allowed : 23.18 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3203 helix: 1.12 (0.16), residues: 1097 sheet: -0.77 (0.27), residues: 382 loop : -1.93 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1033 TYR 0.032 0.001 TYR D 795 PHE 0.018 0.001 PHE C1270 TRP 0.020 0.001 TRP D1193 HIS 0.004 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00256 (26746) covalent geometry : angle 0.57524 (36319) hydrogen bonds : bond 0.03647 ( 1014) hydrogen bonds : angle 4.29068 ( 2798) metal coordination : bond 0.00420 ( 4) metal coordination : angle 1.56430 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 269 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8124 (m-80) cc_final: 0.7673 (m-80) REVERT: B 182 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7678 (ttt-90) REVERT: B 212 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7309 (t0) REVERT: C 84 GLU cc_start: 0.8607 (pm20) cc_final: 0.8313 (pm20) REVERT: C 200 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: C 369 MET cc_start: 0.8244 (ppp) cc_final: 0.7855 (ppp) REVERT: C 403 MET cc_start: 0.8740 (tmm) cc_final: 0.8276 (tmm) REVERT: C 490 GLN cc_start: 0.9040 (tt0) cc_final: 0.8490 (tp40) REVERT: C 711 ASP cc_start: 0.7939 (m-30) cc_final: 0.7648 (m-30) REVERT: C 826 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7034 (t0) REVERT: C 951 MET cc_start: 0.8381 (mmt) cc_final: 0.8095 (tpt) REVERT: C 952 GLN cc_start: 0.9455 (tp40) cc_final: 0.8894 (tp-100) REVERT: C 1040 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7164 (p0) REVERT: C 1059 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6311 (ptm-80) REVERT: C 1073 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8405 (ptmm) REVERT: C 1304 MET cc_start: 0.8400 (tpt) cc_final: 0.7947 (tpp) REVERT: D 42 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7704 (mm-30) REVERT: D 180 MET cc_start: 0.7781 (ptt) cc_final: 0.7310 (ptt) REVERT: D 237 MET cc_start: 0.8431 (mtm) cc_final: 0.8185 (ttm) REVERT: D 301 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 321 LYS cc_start: 0.9106 (mppt) cc_final: 0.8845 (mttt) REVERT: D 322 ARG cc_start: 0.8349 (ppt170) cc_final: 0.8058 (ppt170) REVERT: D 335 GLN cc_start: 0.9026 (mp10) cc_final: 0.8721 (mp10) REVERT: D 587 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9147 (mp) REVERT: D 625 MET cc_start: 0.9049 (ttp) cc_final: 0.8777 (ttp) REVERT: D 698 MET cc_start: 0.9263 (tpt) cc_final: 0.8725 (tpp) REVERT: D 869 CYS cc_start: 0.8208 (m) cc_final: 0.7568 (m) REVERT: D 898 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7864 (m) REVERT: D 1144 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9062 (mp) REVERT: D 1215 GLU cc_start: 0.8327 (tp30) cc_final: 0.7958 (mm-30) REVERT: D 1306 LEU cc_start: 0.8577 (tp) cc_final: 0.7921 (tt) REVERT: F 52 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8248 (tm-30) REVERT: F 65 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8043 (mm-40) REVERT: F 74 ASP cc_start: 0.8827 (t0) cc_final: 0.8370 (t0) REVERT: F 91 TYR cc_start: 0.8252 (m-80) cc_final: 0.7873 (m-80) REVERT: F 151 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8970 (mmmm) outliers start: 78 outliers final: 59 residues processed: 331 average time/residue: 0.1539 time to fit residues: 84.0398 Evaluate side-chains 320 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 5 optimal weight: 1.9990 chunk 245 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 272 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 148 optimal weight: 0.3980 chunk 262 optimal weight: 0.0870 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065869 restraints weight = 79098.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068050 restraints weight = 39057.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069499 restraints weight = 24675.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070422 restraints weight = 18353.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070967 restraints weight = 15265.296| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26750 Z= 0.105 Angle : 0.582 13.134 36325 Z= 0.297 Chirality : 0.041 0.247 4137 Planarity : 0.004 0.056 4580 Dihedral : 12.355 176.144 4061 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.51 % Allowed : 23.80 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3203 helix: 1.22 (0.16), residues: 1086 sheet: -0.62 (0.27), residues: 378 loop : -1.76 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 33 TYR 0.014 0.001 TYR D1232 PHE 0.008 0.001 PHE C 186 TRP 0.019 0.001 TRP D1193 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00233 (26746) covalent geometry : angle 0.58216 (36319) hydrogen bonds : bond 0.03390 ( 1014) hydrogen bonds : angle 4.15976 ( 2798) metal coordination : bond 0.00265 ( 4) metal coordination : angle 1.64378 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 SER cc_start: 0.9101 (m) cc_final: 0.8712 (t) REVERT: B 68 TYR cc_start: 0.8126 (m-80) cc_final: 0.7754 (m-80) REVERT: B 182 ARG cc_start: 0.8182 (ttt90) cc_final: 0.7886 (ttt-90) REVERT: B 212 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7239 (t0) REVERT: C 84 GLU cc_start: 0.8635 (pm20) cc_final: 0.8353 (pm20) REVERT: C 176 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7765 (tp) REVERT: C 200 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: C 239 MET cc_start: 0.7227 (tmm) cc_final: 0.6706 (tmm) REVERT: C 369 MET cc_start: 0.8178 (ppp) cc_final: 0.7819 (ppp) REVERT: C 403 MET cc_start: 0.8724 (tmm) cc_final: 0.8256 (tmm) REVERT: C 490 GLN cc_start: 0.8954 (tt0) cc_final: 0.8394 (tp40) REVERT: C 951 MET cc_start: 0.8366 (mmt) cc_final: 0.8013 (tpt) REVERT: C 952 GLN cc_start: 0.9443 (tp40) cc_final: 0.8872 (tp-100) REVERT: C 1040 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6452 (p0) REVERT: C 1059 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6255 (ptm-80) REVERT: C 1073 LYS cc_start: 0.8767 (ptpp) cc_final: 0.8387 (ptmm) REVERT: D 42 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7757 (mm-30) REVERT: D 180 MET cc_start: 0.7102 (ptt) cc_final: 0.6762 (ptt) REVERT: D 237 MET cc_start: 0.8374 (mtm) cc_final: 0.8155 (ttm) REVERT: D 298 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: D 301 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 322 ARG cc_start: 0.8354 (ppt170) cc_final: 0.8067 (ppt170) REVERT: D 335 GLN cc_start: 0.9000 (mp10) cc_final: 0.8721 (mp10) REVERT: D 485 MET cc_start: 0.7772 (mmm) cc_final: 0.7496 (mmm) REVERT: D 625 MET cc_start: 0.9039 (ttp) cc_final: 0.8771 (ttp) REVERT: D 698 MET cc_start: 0.9247 (tpt) cc_final: 0.8682 (tpp) REVERT: D 822 MET cc_start: 0.8907 (mmt) cc_final: 0.8612 (mmt) REVERT: D 869 CYS cc_start: 0.8194 (m) cc_final: 0.7554 (m) REVERT: D 898 CYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7965 (m) REVERT: D 1144 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9050 (mp) REVERT: D 1189 MET cc_start: 0.7968 (tpp) cc_final: 0.7718 (tpp) REVERT: D 1215 GLU cc_start: 0.8390 (tp30) cc_final: 0.7660 (tp30) REVERT: D 1306 LEU cc_start: 0.8332 (tp) cc_final: 0.7940 (tt) REVERT: D 1361 THR cc_start: 0.7688 (p) cc_final: 0.7282 (t) REVERT: F 18 GLN cc_start: 0.9241 (mm-40) cc_final: 0.9015 (mm-40) REVERT: F 52 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8201 (tm-30) REVERT: F 65 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8019 (mm-40) REVERT: F 74 ASP cc_start: 0.8846 (t0) cc_final: 0.8260 (t0) REVERT: F 91 TYR cc_start: 0.8257 (m-80) cc_final: 0.7902 (m-80) REVERT: F 151 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8993 (mmmm) outliers start: 69 outliers final: 44 residues processed: 325 average time/residue: 0.1517 time to fit residues: 82.0843 Evaluate side-chains 308 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 236 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.088892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064531 restraints weight = 78984.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.066646 restraints weight = 39330.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.068043 restraints weight = 24963.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068948 restraints weight = 18618.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069514 restraints weight = 15489.778| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26750 Z= 0.127 Angle : 0.596 12.263 36325 Z= 0.305 Chirality : 0.041 0.283 4137 Planarity : 0.004 0.055 4580 Dihedral : 12.344 176.497 4056 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.15 % Allowed : 24.45 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3203 helix: 1.24 (0.16), residues: 1087 sheet: -0.57 (0.27), residues: 394 loop : -1.73 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.031 0.001 TYR D 795 PHE 0.012 0.001 PHE C1270 TRP 0.016 0.001 TRP D1193 HIS 0.010 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00295 (26746) covalent geometry : angle 0.59543 (36319) hydrogen bonds : bond 0.03608 ( 1014) hydrogen bonds : angle 4.21524 ( 2798) metal coordination : bond 0.00617 ( 4) metal coordination : angle 1.56552 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 SER cc_start: 0.9125 (m) cc_final: 0.8717 (t) REVERT: B 68 TYR cc_start: 0.8087 (m-80) cc_final: 0.7614 (m-80) REVERT: B 212 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7364 (t0) REVERT: C 84 GLU cc_start: 0.8615 (pm20) cc_final: 0.8316 (pm20) REVERT: C 200 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8154 (mmm-85) REVERT: C 239 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.7026 (tmm) REVERT: C 369 MET cc_start: 0.8201 (ppp) cc_final: 0.7850 (ppp) REVERT: C 403 MET cc_start: 0.8734 (tmm) cc_final: 0.8355 (tmm) REVERT: C 490 GLN cc_start: 0.8966 (tt0) cc_final: 0.8409 (tp40) REVERT: C 951 MET cc_start: 0.8375 (mmt) cc_final: 0.8171 (tpt) REVERT: C 952 GLN cc_start: 0.9454 (tp40) cc_final: 0.8886 (tp-100) REVERT: C 1040 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6503 (p0) REVERT: C 1059 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6291 (ptm-80) REVERT: C 1304 MET cc_start: 0.8341 (tpt) cc_final: 0.7985 (tpp) REVERT: C 1321 GLU cc_start: 0.7585 (tp30) cc_final: 0.7290 (tp30) REVERT: D 42 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7753 (mm-30) REVERT: D 180 MET cc_start: 0.7304 (ptt) cc_final: 0.6959 (ptt) REVERT: D 237 MET cc_start: 0.8404 (mtm) cc_final: 0.8204 (ttm) REVERT: D 298 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8335 (mmm) REVERT: D 301 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 322 ARG cc_start: 0.8408 (ppt170) cc_final: 0.8122 (ppt170) REVERT: D 335 GLN cc_start: 0.9009 (mp10) cc_final: 0.8730 (mp10) REVERT: D 462 ASP cc_start: 0.7884 (m-30) cc_final: 0.7598 (m-30) REVERT: D 485 MET cc_start: 0.7805 (mmm) cc_final: 0.7543 (mmm) REVERT: D 625 MET cc_start: 0.9031 (ttp) cc_final: 0.8738 (ttp) REVERT: D 698 MET cc_start: 0.9244 (tpt) cc_final: 0.8718 (tpp) REVERT: D 822 MET cc_start: 0.8900 (mmt) cc_final: 0.8585 (mmt) REVERT: D 869 CYS cc_start: 0.8208 (m) cc_final: 0.7563 (m) REVERT: D 898 CYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8024 (m) REVERT: D 1144 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9075 (mp) REVERT: D 1189 MET cc_start: 0.8058 (tpp) cc_final: 0.7777 (tpp) REVERT: D 1215 GLU cc_start: 0.8446 (tp30) cc_final: 0.8047 (mm-30) REVERT: D 1250 ASP cc_start: 0.8519 (m-30) cc_final: 0.7995 (p0) REVERT: D 1361 THR cc_start: 0.7725 (p) cc_final: 0.7325 (t) REVERT: F 18 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8980 (mm-40) REVERT: F 52 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8210 (tm-30) REVERT: F 65 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8075 (mm-40) REVERT: F 74 ASP cc_start: 0.8826 (t0) cc_final: 0.8342 (t0) REVERT: F 91 TYR cc_start: 0.8221 (m-80) cc_final: 0.7869 (m-80) outliers start: 59 outliers final: 46 residues processed: 302 average time/residue: 0.1507 time to fit residues: 76.1656 Evaluate side-chains 300 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 131 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 199 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 311 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 293 optimal weight: 0.0570 chunk 268 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066040 restraints weight = 78945.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.068222 restraints weight = 39156.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069670 restraints weight = 24811.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070546 restraints weight = 18468.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071157 restraints weight = 15407.806| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26750 Z= 0.105 Angle : 0.587 11.842 36325 Z= 0.299 Chirality : 0.041 0.268 4137 Planarity : 0.004 0.056 4580 Dihedral : 12.264 176.156 4056 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.07 % Allowed : 24.64 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 3203 helix: 1.31 (0.16), residues: 1086 sheet: -0.47 (0.28), residues: 371 loop : -1.63 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.013 0.001 TYR D1232 PHE 0.011 0.001 PHE C 186 TRP 0.018 0.001 TRP D1193 HIS 0.008 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00238 (26746) covalent geometry : angle 0.58625 (36319) hydrogen bonds : bond 0.03360 ( 1014) hydrogen bonds : angle 4.09976 ( 2798) metal coordination : bond 0.00296 ( 4) metal coordination : angle 1.66311 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5567.29 seconds wall clock time: 96 minutes 10.56 seconds (5770.56 seconds total)