Starting phenix.real_space_refine on Sun Sep 13 23:04:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d7c_30604/09_2026/7d7c_30604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d7c_30604/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d7c_30604/09_2026/7d7c_30604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d7c_30604/09_2026/7d7c_30604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d7c_30604/09_2026/7d7c_30604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d7c_30604/09_2026/7d7c_30604.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d7c_30604/09_2026/7d7c_30604.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d7c_30604/09_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-2.2.1-6174/lib/python3.11/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: 5.11, per 1000 atoms: 0.19 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: 2.38 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: 2.92 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: 5.80 Time building geometry restraints manager: 2.99 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=" C3' DA N 30 " pdb=" C2' DA N 30 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT T 23 " pdb=" C2' DT T 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT T 31 " pdb=" C2' DT T 31 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" C1' DT T 29 " pdb=" N1 DT T 29 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.02e+00 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 ... (remaining 26741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 35846 2.64 - 5.28: 443 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=" O4' DC N 51 " pdb=" C4' DC N 51 " pdb=" C3' DC N 51 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" O4' DT N 28 " pdb=" C4' DT N 28 " pdb=" C3' DT N 28 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+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: 2448 0.037 - 0.074: 1181 0.074 - 0.111: 390 0.111 - 0.147: 101 0.147 - 0.184: 17 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: 1.090 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: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 28.470 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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= 0.375 Angle : 0.812 16.220 36325 Z= 0.493 Chirality : 0.048 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/Z covalent geometry : bond 0.00742 / 0.37 (26746) covalent geometry : angle 0.80035 / 0.49 (36319) hydrogen bonds : bond 0.16394 / 11.05 ( 1014) hydrogen bonds : angle 7.47798 / 5.14 ( 2798) metal coordination : bond 0.07406 / 3.82 ( 4) metal coordination : angle 10.64029 / 6.84 ( 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 : 1.125 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: 0.8707 (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: 0.8457 (ttp80) REVERT: F 52 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8338 (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: 0.8018 (m-10) outliers start: 8 outliers final: 6 residues processed: 322 average time/residue: 0.2021 time to fit residues: 98.8424 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 : 0.942 ------------------------------------------------------------------------------- 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... A 66 HIS A 147 GLN B 23 HIS B 117 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 343 HIS C 618 GLN C 856 ASN C 955 GLN C1038 GLN C1070 HIS C1136 GLN C1157 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN D 340 GLN D 365 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN D 805 GLN D 921 GLN D 929 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062425 restraints weight = 79619.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064490 restraints weight = 39581.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065866 restraints weight = 25172.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066769 restraints weight = 18890.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067245 restraints weight = 15736.036| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26750 Z= 0.142 Angle : 0.659 7.946 36325 Z= 0.350 Chirality : 0.045 0.180 4137 Planarity : 0.005 0.073 4580 Dihedral : 13.269 166.801 4065 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.67 % Allowed : 13.83 % Favored : 84.50 % 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: -2.77 (0.13), residues: 3203 helix: -0.32 (0.15), residues: 1097 sheet: -2.18 (0.23), residues: 406 loop : -2.90 (0.13), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1034 TYR 0.016 0.002 TYR F 10 PHE 0.026 0.001 PHE F 58 TRP 0.025 0.002 TRP D1193 HIS 0.010 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (26746) covalent geometry : angle 0.65725 / 0.35 (36319) hydrogen bonds : bond 0.05345 / 3.70 ( 1014) hydrogen bonds : angle 5.38034 / 3.69 ( 2798) metal coordination : bond 0.00638 / 0.32 ( 4) metal coordination : angle 4.20080 / 3.59 ( 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 327 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.749 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: 0.8270 (m-80) cc_final: 0.8009 (m-80) REVERT: B 142 MET cc_start: 0.7822 (ptp) cc_final: 0.7612 (ptp) REVERT: B 145 LYS cc_start: 0.8621 (tttt) cc_final: 0.8213 (tppt) REVERT: C 370 MET cc_start: 0.8946 (mmm) cc_final: 0.8664 (mmm) REVERT: C 403 MET cc_start: 0.8697 (tmm) cc_final: 0.8418 (tmm) REVERT: C 503 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8549 (mptt) REVERT: C 947 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8962 (mt-10) REVERT: C 950 GLU cc_start: 0.8996 (pt0) cc_final: 0.8795 (pt0) REVERT: C 952 GLN cc_start: 0.9478 (tt0) cc_final: 0.9043 (tm-30) REVERT: C 1073 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8609 (ptmm) REVERT: C 1119 MET cc_start: 0.7978 (tpp) cc_final: 0.7486 (tpp) REVERT: C 1319 MET cc_start: 0.7382 (tmm) cc_final: 0.7139 (tmm) REVERT: D 45 ASN cc_start: 0.9010 (t0) cc_final: 0.8748 (t0) REVERT: D 180 MET cc_start: 0.8115 (ptt) cc_final: 0.7423 (ptt) REVERT: D 237 MET cc_start: 0.8657 (mtm) cc_final: 0.8455 (ttm) REVERT: D 301 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7894 (tm-30) REVERT: D 322 ARG cc_start: 0.7915 (ppt170) cc_final: 0.7588 (ppt170) REVERT: D 462 ASP cc_start: 0.8284 (m-30) cc_final: 0.7915 (m-30) REVERT: D 625 MET cc_start: 0.9069 (ttp) cc_final: 0.8842 (ttp) REVERT: D 709 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6595 (pmt-80) REVERT: D 795 TYR cc_start: 0.9087 (t80) cc_final: 0.8868 (t80) REVERT: D 821 MET cc_start: 0.8426 (mmm) cc_final: 0.8147 (mmm) REVERT: D 822 MET cc_start: 0.8759 (mmp) cc_final: 0.8435 (mmt) REVERT: D 1144 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9192 (mp) REVERT: D 1215 GLU cc_start: 0.8319 (tp30) cc_final: 0.8112 (mm-30) REVERT: F 52 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8329 (tm-30) REVERT: F 65 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8076 (mm-40) REVERT: F 74 ASP cc_start: 0.8889 (t0) cc_final: 0.8443 (t0) REVERT: F 91 TYR cc_start: 0.8228 (m-80) cc_final: 0.7866 (m-80) outliers start: 46 outliers final: 22 residues processed: 312 average time/residue: 0.1668 time to fit residues: 83.4826 Evaluate side-chains 260 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1253 LEU 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 709 ARG 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 128 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 136 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 115 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 203 optimal weight: 0.0170 chunk 56 optimal weight: 7.9990 chunk 288 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN D 320 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 962 ASN F 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060835 restraints weight = 80746.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.062836 restraints weight = 40804.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064160 restraints weight = 26246.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064967 restraints weight = 19827.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065575 restraints weight = 16703.055| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 26750 Z= 0.216 Angle : 0.655 12.006 36325 Z= 0.347 Chirality : 0.044 0.245 4137 Planarity : 0.005 0.050 4580 Dihedral : 13.197 169.002 4063 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.62 % Allowed : 16.78 % Favored : 80.60 % 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: -2.39 (0.14), residues: 3203 helix: 0.09 (0.16), residues: 1095 sheet: -1.97 (0.23), residues: 408 loop : -2.75 (0.13), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 473 TYR 0.012 0.002 TYR C1149 PHE 0.012 0.001 PHE C 545 TRP 0.017 0.001 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (26746) covalent geometry : angle 0.65427 / 0.35 (36319) hydrogen bonds : bond 0.05214 / 3.60 ( 1014) hydrogen bonds : angle 5.22642 / 3.60 ( 2798) metal coordination : bond 0.01132 / 0.57 ( 4) metal coordination : angle 2.65602 / 1.84 ( 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 319 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 247 time to evaluate : 0.850 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: 0.8241 (m-80) cc_final: 0.7947 (m-80) REVERT: B 142 MET cc_start: 0.7781 (ptp) cc_final: 0.7544 (ptp) REVERT: B 145 LYS cc_start: 0.8627 (tttt) cc_final: 0.8215 (tppt) REVERT: C 403 MET cc_start: 0.8705 (tmm) cc_final: 0.8341 (tmm) REVERT: C 503 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8573 (mptt) REVERT: C 947 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8876 (mt-10) REVERT: C 952 GLN cc_start: 0.9476 (tt0) cc_final: 0.9066 (tm-30) REVERT: C 1073 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8469 (ptmm) REVERT: C 1119 MET cc_start: 0.8144 (tpp) cc_final: 0.7881 (tpp) REVERT: D 45 ASN cc_start: 0.9043 (t0) cc_final: 0.8784 (t0) REVERT: D 180 MET cc_start: 0.8114 (ptt) cc_final: 0.7500 (ptt) REVERT: D 237 MET cc_start: 0.8593 (mtm) cc_final: 0.8374 (ttm) REVERT: D 301 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7792 (tm-30) REVERT: D 322 ARG cc_start: 0.8210 (ppt170) cc_final: 0.7792 (pmt-80) REVERT: D 462 ASP cc_start: 0.8393 (m-30) cc_final: 0.7761 (m-30) REVERT: D 617 THR cc_start: 0.8981 (m) cc_final: 0.8778 (p) REVERT: D 625 MET cc_start: 0.9043 (ttp) cc_final: 0.8773 (ttp) REVERT: D 795 TYR cc_start: 0.9067 (t80) cc_final: 0.8770 (t80) REVERT: D 822 MET cc_start: 0.8840 (mmp) cc_final: 0.8455 (mmt) REVERT: D 1144 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8912 (mp) REVERT: D 1215 GLU cc_start: 0.8360 (tp30) cc_final: 0.8105 (mm-30) REVERT: F 15 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8528 (tm-30) REVERT: F 52 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8353 (tm-30) REVERT: F 65 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8005 (mm-40) REVERT: F 74 ASP cc_start: 0.8861 (t0) cc_final: 0.8551 (t0) REVERT: F 91 TYR cc_start: 0.8231 (m-80) cc_final: 0.7875 (m-80) outliers start: 72 outliers final: 53 residues processed: 299 average time/residue: 0.1545 time to fit residues: 75.4466 Evaluate side-chains 282 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL 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 805 MET Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1219 GLU 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 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 501 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 759 ILE 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 869 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 915 ILE 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 12 ASN 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 128 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: 6.9990 chunk 283 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 184 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN C 65 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.087058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062534 restraints weight = 79324.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064601 restraints weight = 39590.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065971 restraints weight = 25254.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066815 restraints weight = 18951.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067428 restraints weight = 15895.661| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1882 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= 0.130 Angle : 0.604 10.283 36325 Z= 0.321 Chirality : 0.043 0.203 4137 Planarity : 0.004 0.051 4580 Dihedral : 13.083 170.277 4063 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.98 % Allowed : 18.38 % Favored : 78.64 % 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: -1.97 (0.14), residues: 3203 helix: 0.39 (0.16), residues: 1101 sheet: -1.53 (0.25), residues: 394 loop : -2.52 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1372 TYR 0.012 0.001 TYR C1229 PHE 0.009 0.001 PHE D 620 TRP 0.020 0.001 TRP D1193 HIS 0.007 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (26746) covalent geometry : angle 0.60365 / 0.32 (36319) hydrogen bonds : bond 0.04506 / 3.13 ( 1014) hydrogen bonds : angle 4.87425 / 3.35 ( 2798) metal coordination : bond 0.00436 / 0.22 ( 4) metal coordination : angle 2.15712 / 1.85 ( 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 335 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 1.005 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: A 77 ASP cc_start: 0.7568 (t0) cc_final: 0.7226 (t0) REVERT: B 68 TYR cc_start: 0.8286 (m-80) cc_final: 0.7943 (m-80) REVERT: B 145 LYS cc_start: 0.8628 (tttt) cc_final: 0.8146 (tppt) REVERT: C 84 GLU cc_start: 0.8791 (mp0) cc_final: 0.8538 (pm20) REVERT: C 369 MET cc_start: 0.8272 (ppp) cc_final: 0.7787 (ppp) REVERT: C 403 MET cc_start: 0.8683 (tmm) cc_final: 0.8342 (tmm) REVERT: C 826 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7832 (t0) REVERT: C 952 GLN cc_start: 0.9372 (tt0) cc_final: 0.9038 (tp-100) REVERT: C 1073 LYS cc_start: 0.8810 (ptpp) cc_final: 0.8483 (ptmm) REVERT: C 1119 MET cc_start: 0.8318 (tpp) cc_final: 0.8078 (tpp) REVERT: D 45 ASN cc_start: 0.9004 (t0) cc_final: 0.8779 (t0) REVERT: D 180 MET cc_start: 0.8241 (ptt) cc_final: 0.7492 (ptt) REVERT: D 237 MET cc_start: 0.8577 (mtm) cc_final: 0.8325 (ttm) REVERT: D 298 MET cc_start: 0.8694 (mmm) cc_final: 0.8338 (mmm) REVERT: D 301 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 322 ARG cc_start: 0.8084 (ppt170) cc_final: 0.7614 (ppt170) REVERT: D 587 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8959 (mp) REVERT: D 625 MET cc_start: 0.9051 (ttp) cc_final: 0.8786 (ttp) REVERT: D 795 TYR cc_start: 0.9072 (t80) cc_final: 0.8802 (t80) REVERT: D 821 MET cc_start: 0.8400 (mmm) cc_final: 0.8198 (mmm) REVERT: D 822 MET cc_start: 0.8819 (mmp) cc_final: 0.8424 (mmt) REVERT: D 898 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7798 (m) REVERT: D 1144 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8924 (mp) REVERT: D 1189 MET cc_start: 0.7959 (tpp) cc_final: 0.7689 (tpp) REVERT: D 1215 GLU cc_start: 0.8313 (tp30) cc_final: 0.8027 (mm-30) REVERT: F 52 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8383 (tm-30) REVERT: F 65 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8059 (mm-40) REVERT: F 74 ASP cc_start: 0.8856 (t0) cc_final: 0.8557 (t0) REVERT: F 91 TYR cc_start: 0.8203 (m-80) cc_final: 0.7846 (m-80) outliers start: 82 outliers final: 58 residues processed: 315 average time/residue: 0.1511 time to fit residues: 78.5749 Evaluate side-chains 296 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 471 VAL 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 764 CYS Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 826 ASP 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 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1243 MET 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 171 GLU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 392 THR 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 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 869 CYS 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 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 128 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: 3.9990 chunk 248 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN ** 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 = 0.3498 r_free = 0.3498 target = 0.084506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059966 restraints weight = 81273.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061938 restraints weight = 41526.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063238 restraints weight = 26866.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064103 restraints weight = 20381.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064558 restraints weight = 17091.476| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 26750 Z= 0.300 Angle : 0.711 11.268 36325 Z= 0.371 Chirality : 0.045 0.191 4137 Planarity : 0.005 0.051 4580 Dihedral : 13.163 171.925 4063 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.78 % Allowed : 19.98 % Favored : 76.24 % 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: -2.02 (0.14), residues: 3203 helix: 0.37 (0.16), residues: 1094 sheet: -1.65 (0.24), residues: 411 loop : -2.53 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 195 TYR 0.021 0.002 TYR D 772 PHE 0.021 0.002 PHE C 545 TRP 0.016 0.002 TRP D1193 HIS 0.010 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.30 (26746) covalent geometry : angle 0.70975 / 0.37 (36319) hydrogen bonds : bond 0.05204 / 3.58 ( 1014) hydrogen bonds : angle 5.10643 / 3.53 ( 2798) metal coordination : bond 0.01583 / 0.79 ( 4) metal coordination : angle 2.72416 / 1.57 ( 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 334 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 230 time to evaluate : 1.021 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: 0.8120 (m-80) cc_final: 0.7646 (m-80) REVERT: B 145 LYS cc_start: 0.8635 (tttt) cc_final: 0.8269 (tppt) REVERT: C 46 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7875 (mm-40) REVERT: C 369 MET cc_start: 0.8284 (ppp) cc_final: 0.7857 (ppp) REVERT: C 403 MET cc_start: 0.8677 (tmm) cc_final: 0.8366 (tmm) REVERT: C 503 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8621 (mptt) REVERT: C 826 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7792 (t0) REVERT: C 952 GLN cc_start: 0.9396 (tt0) cc_final: 0.9086 (tp-100) REVERT: C 1059 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6562 (ptm-80) REVERT: C 1073 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8494 (ptmm) REVERT: C 1119 MET cc_start: 0.8172 (tpp) cc_final: 0.7872 (tpp) REVERT: D 45 ASN cc_start: 0.9004 (t0) cc_final: 0.8786 (t0) REVERT: D 180 MET cc_start: 0.8319 (ptt) cc_final: 0.7664 (ptt) REVERT: D 237 MET cc_start: 0.8546 (mtm) cc_final: 0.8342 (ttm) REVERT: D 298 MET cc_start: 0.8671 (mmm) cc_final: 0.7976 (mpp) REVERT: D 301 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7825 (tm-30) REVERT: D 322 ARG cc_start: 0.8145 (ppt170) cc_final: 0.7662 (ppt170) REVERT: D 587 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9055 (mp) REVERT: D 617 THR cc_start: 0.9035 (m) cc_final: 0.8827 (p) REVERT: D 625 MET cc_start: 0.9015 (ttp) cc_final: 0.8716 (ttp) REVERT: D 795 TYR cc_start: 0.8961 (t80) cc_final: 0.8629 (t80) REVERT: D 1189 MET cc_start: 0.8012 (tpp) cc_final: 0.7737 (tpp) REVERT: D 1306 LEU cc_start: 0.8837 (tp) cc_final: 0.8471 (tp) REVERT: F 15 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8421 (tm-30) REVERT: F 52 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8374 (tm-30) REVERT: F 65 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8074 (mm-40) REVERT: F 74 ASP cc_start: 0.8836 (t0) cc_final: 0.8533 (t0) REVERT: F 91 TYR cc_start: 0.8192 (m-80) cc_final: 0.7850 (m-80) outliers start: 104 outliers final: 82 residues processed: 309 average time/residue: 0.1496 time to fit residues: 77.2958 Evaluate side-chains 310 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 225 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 LEU 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 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 433 ILE 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 525 THR 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 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 831 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL 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 1219 GLU 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 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 353 SER 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 548 VAL Chi-restraints excluded: chain D residue 574 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 869 CYS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1328 THR 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 D residue 1370 MET 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 128 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: 1.9990 chunk 82 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** C 519 ASN ** 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 = 0.3541 r_free = 0.3541 target = 0.086801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062213 restraints weight = 79438.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064281 restraints weight = 39826.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065612 restraints weight = 25485.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066531 restraints weight = 19160.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067058 restraints weight = 16045.879| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 26750 Z= 0.131 Angle : 0.606 9.254 36325 Z= 0.320 Chirality : 0.043 0.279 4137 Planarity : 0.004 0.052 4580 Dihedral : 13.042 172.242 4063 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.28 % Allowed : 21.25 % Favored : 75.47 % 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: 0.60 (0.16), residues: 1097 sheet: -1.30 (0.26), residues: 361 loop : -2.29 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 293 TYR 0.013 0.001 TYR D 144 PHE 0.010 0.001 PHE C 545 TRP 0.022 0.001 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26746) covalent geometry : angle 0.60560 / 0.32 (36319) hydrogen bonds : bond 0.04393 / 3.05 ( 1014) hydrogen bonds : angle 4.74127 / 3.26 ( 2798) metal coordination : bond 0.00567 / 0.28 ( 4) metal coordination : angle 2.04819 / 1.75 ( 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 334 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 244 time to evaluate : 0.861 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: 0.8185 (m-80) cc_final: 0.7819 (m-80) REVERT: B 145 LYS cc_start: 0.8519 (tttt) cc_final: 0.8197 (tppt) REVERT: C 84 GLU cc_start: 0.8801 (mp0) cc_final: 0.8558 (pm20) REVERT: C 369 MET cc_start: 0.8303 (ppp) cc_final: 0.7897 (ppp) REVERT: C 951 MET cc_start: 0.8396 (mmt) cc_final: 0.7820 (tpt) REVERT: C 952 GLN cc_start: 0.9266 (tt0) cc_final: 0.8939 (tp-100) REVERT: C 1059 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6436 (ptm-80) REVERT: D 45 ASN cc_start: 0.9013 (t0) cc_final: 0.8790 (t0) REVERT: D 130 MET cc_start: 0.8463 (ptt) cc_final: 0.8000 (tmm) REVERT: D 180 MET cc_start: 0.7961 (ptt) cc_final: 0.7670 (ptt) REVERT: D 237 MET cc_start: 0.8588 (mtm) cc_final: 0.8341 (ttm) REVERT: D 298 MET cc_start: 0.8700 (mmm) cc_final: 0.8258 (mmm) REVERT: D 301 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 322 ARG cc_start: 0.8155 (ppt170) cc_final: 0.7599 (ppt170) REVERT: D 587 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8945 (mp) REVERT: D 625 MET cc_start: 0.9060 (ttp) cc_final: 0.8800 (ttp) REVERT: D 821 MET cc_start: 0.8474 (mmm) cc_final: 0.8211 (mmm) REVERT: D 822 MET cc_start: 0.8792 (mmt) cc_final: 0.8451 (mmt) REVERT: D 898 CYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7861 (m) REVERT: D 1189 MET cc_start: 0.7936 (tpp) cc_final: 0.7675 (tpp) REVERT: D 1215 GLU cc_start: 0.8345 (tp30) cc_final: 0.8023 (mm-30) REVERT: D 1306 LEU cc_start: 0.8681 (tp) cc_final: 0.8374 (tp) REVERT: F 52 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 65 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8076 (mm-40) REVERT: F 74 ASP cc_start: 0.8894 (t0) cc_final: 0.8529 (t0) REVERT: F 91 TYR cc_start: 0.8192 (m-80) cc_final: 0.7831 (m-80) outliers start: 90 outliers final: 62 residues processed: 313 average time/residue: 0.1403 time to fit residues: 73.8528 Evaluate side-chains 294 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 SER 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 C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 471 VAL 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 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1040 ASP 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 1219 GLU Chi-restraints excluded: chain C residue 1225 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 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 356 THR 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 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 869 CYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 193 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 311 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 GLN ** 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 = 0.3527 r_free = 0.3527 target = 0.085976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061495 restraints weight = 79964.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063524 restraints weight = 40328.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064873 restraints weight = 25884.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065731 restraints weight = 19466.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066276 restraints weight = 16322.084| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26750 Z= 0.187 Angle : 0.621 10.158 36325 Z= 0.328 Chirality : 0.043 0.206 4137 Planarity : 0.004 0.051 4580 Dihedral : 13.004 172.822 4062 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.35 % Allowed : 21.87 % Favored : 74.78 % 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: -1.61 (0.15), residues: 3203 helix: 0.64 (0.16), residues: 1098 sheet: -1.31 (0.26), residues: 371 loop : -2.25 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 687 TYR 0.022 0.001 TYR D 795 PHE 0.010 0.001 PHE C 812 TRP 0.019 0.001 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (26746) covalent geometry : angle 0.62111 / 0.33 (36319) hydrogen bonds : bond 0.04516 / 3.12 ( 1014) hydrogen bonds : angle 4.75378 / 3.27 ( 2798) metal coordination : bond 0.00897 / 0.45 ( 4) metal coordination : angle 1.78955 / 1.19 ( 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 322 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 230 time to evaluate : 0.781 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: 0.8125 (m-80) cc_final: 0.7648 (m-80) REVERT: B 145 LYS cc_start: 0.8567 (tttt) cc_final: 0.8121 (tppt) REVERT: B 212 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7516 (t0) REVERT: C 84 GLU cc_start: 0.8827 (mp0) cc_final: 0.8537 (mp0) REVERT: C 315 MET cc_start: 0.6474 (mtp) cc_final: 0.6253 (mtm) REVERT: C 369 MET cc_start: 0.8305 (ppp) cc_final: 0.7882 (ppp) REVERT: C 826 ASP cc_start: 0.8006 (t0) cc_final: 0.7562 (t0) REVERT: C 952 GLN cc_start: 0.9277 (tt0) cc_final: 0.8946 (tp-100) REVERT: C 1059 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6440 (ptm-80) REVERT: D 45 ASN cc_start: 0.9037 (t0) cc_final: 0.8820 (t0) REVERT: D 130 MET cc_start: 0.8478 (ptt) cc_final: 0.7948 (tmm) REVERT: D 180 MET cc_start: 0.8061 (ptt) cc_final: 0.7529 (ptt) REVERT: D 237 MET cc_start: 0.8582 (mtm) cc_final: 0.8345 (ttm) REVERT: D 298 MET cc_start: 0.8707 (mmm) cc_final: 0.7939 (mpp) REVERT: D 301 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 322 ARG cc_start: 0.8149 (ppt170) cc_final: 0.7590 (ppt170) REVERT: D 587 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9029 (mp) REVERT: D 625 MET cc_start: 0.9048 (ttp) cc_final: 0.8762 (ttp) REVERT: D 822 MET cc_start: 0.8825 (mmt) cc_final: 0.8425 (mmt) REVERT: D 898 CYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7828 (m) REVERT: D 1144 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9145 (mp) REVERT: D 1215 GLU cc_start: 0.8408 (tp30) cc_final: 0.8054 (mm-30) REVERT: F 52 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8396 (tm-30) REVERT: F 65 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8000 (mm-40) REVERT: F 74 ASP cc_start: 0.8867 (t0) cc_final: 0.8496 (t0) REVERT: F 91 TYR cc_start: 0.8190 (m-80) cc_final: 0.7844 (m-80) outliers start: 92 outliers final: 74 residues processed: 303 average time/residue: 0.1448 time to fit residues: 73.1079 Evaluate side-chains 303 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 224 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 205 MET 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 91 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL 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 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1046 VAL 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 1219 GLU Chi-restraints excluded: chain C residue 1225 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 151 MET Chi-restraints excluded: chain D residue 171 GLU 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 356 THR 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 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 639 VAL Chi-restraints excluded: chain D residue 717 VAL 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 869 CYS 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 1328 THR 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 12 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 309 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 GLN ** 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 = 0.3532 r_free = 0.3532 target = 0.086335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061755 restraints weight = 80363.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063804 restraints weight = 40414.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065162 restraints weight = 25883.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065955 restraints weight = 19460.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.066587 restraints weight = 16410.414| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26750 Z= 0.166 Angle : 0.619 10.600 36325 Z= 0.325 Chirality : 0.043 0.211 4137 Planarity : 0.004 0.063 4580 Dihedral : 12.980 173.242 4062 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.46 % Allowed : 22.34 % Favored : 74.20 % 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: -1.50 (0.15), residues: 3203 helix: 0.71 (0.16), residues: 1096 sheet: -1.31 (0.26), residues: 379 loop : -2.14 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 200 TYR 0.012 0.001 TYR D 772 PHE 0.020 0.001 PHE C 186 TRP 0.022 0.001 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (26746) covalent geometry : angle 0.61871 / 0.33 (36319) hydrogen bonds : bond 0.04437 / 3.06 ( 1014) hydrogen bonds : angle 4.70364 / 3.24 ( 2798) metal coordination : bond 0.00792 / 0.40 ( 4) metal coordination : angle 1.79972 / 1.32 ( 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 331 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 236 time to evaluate : 0.877 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: 0.8068 (m-80) cc_final: 0.7732 (m-80) REVERT: B 145 LYS cc_start: 0.8614 (tttt) cc_final: 0.8252 (tppt) REVERT: B 212 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7484 (t0) REVERT: C 239 MET cc_start: 0.7139 (tmm) cc_final: 0.6456 (tmm) REVERT: C 315 MET cc_start: 0.6497 (mtp) cc_final: 0.6074 (mtm) REVERT: C 369 MET cc_start: 0.8287 (ppp) cc_final: 0.7858 (ppp) REVERT: C 826 ASP cc_start: 0.7965 (t0) cc_final: 0.7565 (t0) REVERT: C 952 GLN cc_start: 0.9263 (tt0) cc_final: 0.8930 (tp-100) REVERT: C 1059 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6415 (ptm-80) REVERT: D 45 ASN cc_start: 0.9029 (t0) cc_final: 0.8810 (t0) REVERT: D 122 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7685 (p) REVERT: D 130 MET cc_start: 0.8456 (ptt) cc_final: 0.7948 (tmm) REVERT: D 180 MET cc_start: 0.8078 (ptt) cc_final: 0.7419 (ptt) REVERT: D 237 MET cc_start: 0.8582 (mtm) cc_final: 0.8341 (ttm) REVERT: D 298 MET cc_start: 0.8714 (mmm) cc_final: 0.7935 (mpp) REVERT: D 301 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 322 ARG cc_start: 0.8148 (ppt170) cc_final: 0.7754 (ppt170) REVERT: D 587 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8943 (mp) REVERT: D 625 MET cc_start: 0.9039 (ttp) cc_final: 0.8763 (ttp) REVERT: D 822 MET cc_start: 0.8841 (mmt) cc_final: 0.8432 (mmt) REVERT: D 898 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7855 (m) REVERT: D 1040 MET cc_start: -0.2299 (mtp) cc_final: -0.2852 (mtt) REVERT: D 1144 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9142 (mp) REVERT: D 1215 GLU cc_start: 0.8415 (tp30) cc_final: 0.8090 (mm-30) REVERT: F 15 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8458 (tm-30) REVERT: F 52 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8390 (tm-30) REVERT: F 65 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8015 (mm-40) REVERT: F 74 ASP cc_start: 0.8871 (t0) cc_final: 0.8462 (t0) REVERT: F 91 TYR cc_start: 0.8183 (m-80) cc_final: 0.7824 (m-80) outliers start: 95 outliers final: 75 residues processed: 311 average time/residue: 0.1429 time to fit residues: 75.0618 Evaluate side-chains 306 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 225 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 90 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 187 VAL Chi-restraints excluded: chain B residue 205 MET 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 91 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 563 THR 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 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 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 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1219 GLU 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 122 SER Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU 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 356 THR 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 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 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS 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 1328 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 5 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 159 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** C 519 ASN ** 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 = 0.3535 r_free = 0.3535 target = 0.086422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061919 restraints weight = 80197.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063967 restraints weight = 40351.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065338 restraints weight = 25859.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066092 restraints weight = 19431.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066742 restraints weight = 16443.595| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26750 Z= 0.159 Angle : 0.624 13.982 36325 Z= 0.326 Chirality : 0.043 0.212 4137 Planarity : 0.004 0.056 4580 Dihedral : 12.944 173.546 4062 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.35 % Allowed : 22.53 % Favored : 74.13 % 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: -1.41 (0.15), residues: 3203 helix: 0.74 (0.16), residues: 1096 sheet: -1.23 (0.26), residues: 387 loop : -2.07 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1034 TYR 0.013 0.001 TYR D 772 PHE 0.010 0.001 PHE D 141 TRP 0.022 0.001 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (26746) covalent geometry : angle 0.62395 / 0.33 (36319) hydrogen bonds : bond 0.04326 / 2.99 ( 1014) hydrogen bonds : angle 4.65907 / 3.19 ( 2798) metal coordination : bond 0.00768 / 0.38 ( 4) metal coordination : angle 1.44251 / 1.13 ( 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 322 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 230 time to evaluate : 1.092 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: 0.8073 (m-80) cc_final: 0.7733 (m-80) REVERT: B 145 LYS cc_start: 0.8534 (tttt) cc_final: 0.8228 (tppt) REVERT: B 186 ASN cc_start: 0.8380 (t0) cc_final: 0.8172 (p0) REVERT: B 212 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7469 (t0) REVERT: C 84 GLU cc_start: 0.8926 (mp0) cc_final: 0.8686 (pm20) REVERT: C 239 MET cc_start: 0.7231 (tmm) cc_final: 0.6537 (tmm) REVERT: C 369 MET cc_start: 0.8268 (ppp) cc_final: 0.7812 (ppp) REVERT: C 826 ASP cc_start: 0.7897 (t0) cc_final: 0.7492 (t0) REVERT: C 952 GLN cc_start: 0.9259 (tt0) cc_final: 0.8934 (tp-100) REVERT: C 1059 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6363 (ptm-80) REVERT: C 1319 MET cc_start: 0.7841 (tmm) cc_final: 0.7577 (tmm) REVERT: D 45 ASN cc_start: 0.8990 (t0) cc_final: 0.8763 (t0) REVERT: D 130 MET cc_start: 0.8430 (ptt) cc_final: 0.7927 (tmm) REVERT: D 237 MET cc_start: 0.8575 (mtm) cc_final: 0.8337 (mtm) REVERT: D 298 MET cc_start: 0.8710 (mmm) cc_final: 0.7922 (mpp) REVERT: D 301 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7807 (tm-30) REVERT: D 322 ARG cc_start: 0.8186 (ppt170) cc_final: 0.7783 (ppt170) REVERT: D 587 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8920 (mp) REVERT: D 625 MET cc_start: 0.9034 (ttp) cc_final: 0.8764 (ttp) REVERT: D 822 MET cc_start: 0.8885 (mmt) cc_final: 0.8480 (mmt) REVERT: D 898 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7868 (m) REVERT: D 1040 MET cc_start: -0.2313 (mtp) cc_final: -0.2860 (mtt) REVERT: D 1144 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9091 (mp) REVERT: D 1215 GLU cc_start: 0.8420 (tp30) cc_final: 0.8089 (mm-30) REVERT: F 15 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8476 (tm-30) REVERT: F 52 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 65 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8010 (mm-40) REVERT: F 74 ASP cc_start: 0.8845 (t0) cc_final: 0.8461 (t0) REVERT: F 91 TYR cc_start: 0.8209 (m-80) cc_final: 0.7754 (m-80) outliers start: 92 outliers final: 78 residues processed: 302 average time/residue: 0.1684 time to fit residues: 85.0871 Evaluate side-chains 309 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 226 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 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 205 MET 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 91 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 563 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 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 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 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1219 GLU 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 151 MET Chi-restraints excluded: chain D residue 171 GLU 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 356 THR Chi-restraints excluded: chain D residue 357 VAL 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 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 869 CYS 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 967 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 1293 GLU Chi-restraints excluded: chain D residue 1328 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 236 optimal weight: 0.0060 chunk 95 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 259 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 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 = 0.3557 r_free = 0.3557 target = 0.087559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063133 restraints weight = 79283.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065215 restraints weight = 39560.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066597 restraints weight = 25186.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067438 restraints weight = 18849.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068028 restraints weight = 15829.775| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26750 Z= 0.122 Angle : 0.613 11.460 36325 Z= 0.319 Chirality : 0.042 0.220 4137 Planarity : 0.004 0.057 4580 Dihedral : 12.855 173.802 4062 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.77 % Allowed : 23.36 % Favored : 73.87 % 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: -1.25 (0.15), residues: 3203 helix: 0.87 (0.16), residues: 1097 sheet: -0.99 (0.27), residues: 369 loop : -2.01 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1034 TYR 0.032 0.001 TYR D 795 PHE 0.010 0.001 PHE D 620 TRP 0.020 0.001 TRP D1193 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (26746) covalent geometry : angle 0.61287 / 0.32 (36319) hydrogen bonds : bond 0.04017 / 2.80 ( 1014) hydrogen bonds : angle 4.53613 / 3.11 ( 2798) metal coordination : bond 0.00425 / 0.21 ( 4) metal coordination : angle 1.73960 / 1.49 ( 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 318 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 242 time to evaluate : 1.090 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: 0.8088 (m-80) cc_final: 0.7731 (m-80) REVERT: B 142 MET cc_start: 0.8027 (pmm) cc_final: 0.7275 (pmm) REVERT: B 145 LYS cc_start: 0.8445 (tttt) cc_final: 0.8184 (tppt) REVERT: B 212 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7467 (t0) REVERT: C 84 GLU cc_start: 0.8892 (mp0) cc_final: 0.8659 (pm20) REVERT: C 239 MET cc_start: 0.7226 (tmm) cc_final: 0.6488 (tmm) REVERT: C 369 MET cc_start: 0.8228 (ppp) cc_final: 0.7806 (ppp) REVERT: C 488 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7594 (tpt) REVERT: C 711 ASP cc_start: 0.8073 (m-30) cc_final: 0.7792 (m-30) REVERT: C 826 ASP cc_start: 0.7755 (t0) cc_final: 0.7340 (t0) REVERT: C 951 MET cc_start: 0.8398 (mmt) cc_final: 0.7884 (tpt) REVERT: C 952 GLN cc_start: 0.9282 (tt0) cc_final: 0.8971 (tp-100) REVERT: C 1059 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6405 (ptm-80) REVERT: C 1061 GLN cc_start: 0.8065 (pt0) cc_final: 0.7651 (pm20) REVERT: D 42 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7562 (mm-30) REVERT: D 45 ASN cc_start: 0.8967 (t0) cc_final: 0.8737 (t0) REVERT: D 130 MET cc_start: 0.8371 (ptt) cc_final: 0.7868 (tmm) REVERT: D 237 MET cc_start: 0.8443 (mtm) cc_final: 0.8183 (mtm) REVERT: D 298 MET cc_start: 0.8722 (mmm) cc_final: 0.8249 (mmm) REVERT: D 301 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 322 ARG cc_start: 0.8228 (ppt170) cc_final: 0.7786 (ppt170) REVERT: D 587 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8917 (mp) REVERT: D 625 MET cc_start: 0.9048 (ttp) cc_final: 0.8793 (ttp) REVERT: D 698 MET cc_start: 0.9239 (tpt) cc_final: 0.8907 (tpp) REVERT: D 822 MET cc_start: 0.8893 (mmt) cc_final: 0.8483 (mmt) REVERT: D 898 CYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7820 (m) REVERT: D 1040 MET cc_start: -0.2365 (mtp) cc_final: -0.2911 (mtt) REVERT: D 1144 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9096 (mp) REVERT: D 1189 MET cc_start: 0.7882 (tpp) cc_final: 0.7614 (tpp) REVERT: D 1215 GLU cc_start: 0.8372 (tp30) cc_final: 0.7984 (mm-30) REVERT: D 1306 LEU cc_start: 0.8640 (tp) cc_final: 0.8168 (tt) REVERT: F 52 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8265 (tm-30) REVERT: F 65 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7998 (mm-40) REVERT: F 74 ASP cc_start: 0.8870 (t0) cc_final: 0.8457 (t0) REVERT: F 91 TYR cc_start: 0.8206 (m-80) cc_final: 0.7805 (m-80) outliers start: 76 outliers final: 65 residues processed: 302 average time/residue: 0.1648 time to fit residues: 83.3653 Evaluate side-chains 302 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 231 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 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 205 MET 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 91 THR 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 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 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 831 ILE 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 1113 LEU Chi-restraints excluded: chain C residue 1219 GLU 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 151 MET Chi-restraints excluded: chain D residue 171 GLU 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 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 372 MET 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 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 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS 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 967 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 1257 VAL Chi-restraints excluded: chain D residue 1293 GLU 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 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 131 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 104 optimal weight: 0.6980 chunk 199 optimal weight: 7.9990 chunk 282 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.063035 restraints weight = 79257.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065057 restraints weight = 39316.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066403 restraints weight = 25005.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.067295 restraints weight = 18677.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067797 restraints weight = 15569.512| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26750 Z= 0.141 Angle : 0.628 18.284 36325 Z= 0.324 Chirality : 0.042 0.217 4137 Planarity : 0.004 0.056 4580 Dihedral : 12.829 174.181 4061 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.77 % Allowed : 23.58 % Favored : 73.65 % 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: -1.19 (0.15), residues: 3203 helix: 0.90 (0.16), residues: 1091 sheet: -0.93 (0.27), residues: 369 loop : -1.95 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1034 TYR 0.013 0.001 TYR D 772 PHE 0.025 0.001 PHE C 186 TRP 0.018 0.001 TRP D1193 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (26746) covalent geometry : angle 0.62774 / 0.32 (36319) hydrogen bonds : bond 0.04068 / 2.83 ( 1014) hydrogen bonds : angle 4.50784 / 3.09 ( 2798) metal coordination : bond 0.00584 / 0.29 ( 4) metal coordination : angle 1.46411 / 1.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5442.74 seconds wall clock time: 94 minutes 24.53 seconds (5664.53 seconds total)