Starting phenix.real_space_refine on Mon Jul 6 19:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7g_32344/07_2026/7w7g_32344.map" } resolution = 3.2 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= 0.087 sd= 0.155 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 302 5.16 5 C 24796 2.51 5 N 6341 2.21 5 O 6702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38143 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 12097 Classifications: {'peptide': 1528} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 73, 'TRANS': 1454} Unresolved chain links: 1 Chain breaks: 16 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 13777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1711, 13777 Classifications: {'peptide': 1711} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 88, 'TRANS': 1621} Unresolved chain links: 1 Chain breaks: 18 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 10847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1346, 10847 Classifications: {'peptide': 1346} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 1297} Chain breaks: 7 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 3, 'ASP:plan': 8, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7681 SG CYS A1407 75.483 98.695 181.043 1.00106.76 S ATOM 7736 SG CYS A2027 73.403 101.883 181.534 1.00 94.23 S ATOM 7760 SG CYS A2030 76.936 102.155 180.133 1.00100.48 S ATOM 16470 SG CYS B1543 65.869 123.985 180.794 1.00 66.97 S ATOM 16520 SG CYS B1549 67.191 120.399 181.357 1.00 72.76 S ATOM 16553 SG CYS B1553 63.495 120.950 180.349 1.00 51.99 S Time building chain proxies: 7.92, per 1000 atoms: 0.21 Number of scatterers: 38143 At special positions: 0 Unit cell: (132.4, 227.728, 250.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 302 16.00 O 6702 8.00 N 6341 7.00 C 24796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 229 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C1046 " - pdb=" SG CYS C1057 " distance=2.03 Simple disulfide: pdb=" SG CYS C1405 " - pdb=" SG CYS C1417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 200 " - pdb=" SG CYS D 270 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 322 " distance=2.03 Simple disulfide: pdb=" SG CYS D 255 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 313 " - pdb=" SG CYS D 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 386 " distance=2.03 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 385 " distance=2.03 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 370 " distance=2.03 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 Links applied NAG-ASN " NAG C2001 " - " ASN C 210 " " NAG C2002 " - " ASN C1064 " " NAG C2003 " - " ASN C 216 " Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" NE2 HIS A1405 " pdb="ZN ZN A3000 " - pdb=" SG CYS A2030 " pdb="ZN ZN A3000 " - pdb=" SG CYS A2027 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1407 " pdb=" ZN B4000 " pdb="ZN ZN B4000 " - pdb=" ND1 HIS B1545 " pdb="ZN ZN B4000 " - pdb=" SG CYS B1543 " pdb="ZN ZN B4000 " - pdb=" SG CYS B1553 " pdb="ZN ZN B4000 " - pdb=" SG CYS B1549 " Number of angles added : 6 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9172 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 6 sheets defined 75.8% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.779A pdb=" N ARG A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.672A pdb=" N SER A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.749A pdb=" N THR A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.841A pdb=" N THR A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 3.639A pdb=" N SER A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.572A pdb=" N THR A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.828A pdb=" N HIS A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.981A pdb=" N SER A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A 179 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 4.266A pdb=" N HIS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.601A pdb=" N LEU A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.863A pdb=" N ALA A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.520A pdb=" N SER A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 486 removed outlier: 3.911A pdb=" N TYR A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 515 Proline residue: A 501 - end of helix removed outlier: 3.984A pdb=" N THR A 505 " --> pdb=" O PRO A 501 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.556A pdb=" N MET A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 558 Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 564 through 582 Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.556A pdb=" N ARG A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 614 through 620 removed outlier: 3.795A pdb=" N ARG A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.862A pdb=" N GLN A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 639 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 642 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 673 Processing helix chain 'A' and resid 741 through 760 Processing helix chain 'A' and resid 772 through 788 removed outlier: 3.734A pdb=" N ASP A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 826 Processing helix chain 'A' and resid 897 through 911 Processing helix chain 'A' and resid 915 through 930 Processing helix chain 'A' and resid 934 through 943 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 954 through 963 Processing helix chain 'A' and resid 967 through 984 removed outlier: 3.785A pdb=" N SER A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) Proline residue: A 976 - end of helix Processing helix chain 'A' and resid 986 through 1000 removed outlier: 3.740A pdb=" N ILE A 990 " --> pdb=" O HIS A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 3.540A pdb=" N GLU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1027 Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.539A pdb=" N GLU A1048 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 4.042A pdb=" N ASP A1063 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1084 Processing helix chain 'A' and resid 1087 through 1102 Processing helix chain 'A' and resid 1109 through 1130 Processing helix chain 'A' and resid 1152 through 1167 Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 3.515A pdb=" N LYS A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1259 Processing helix chain 'A' and resid 1267 through 1285 Processing helix chain 'A' and resid 1297 through 1304 Processing helix chain 'A' and resid 1304 through 1321 removed outlier: 3.537A pdb=" N ALA A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A1313 " --> pdb=" O ALA A1309 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A1315 " --> pdb=" O ILE A1311 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A1316 " --> pdb=" O ALA A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1341 Proline residue: A1330 - end of helix removed outlier: 3.741A pdb=" N SER A1340 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A1341 " --> pdb=" O LYS A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1349 removed outlier: 3.701A pdb=" N GLN A1349 " --> pdb=" O HIS A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 4.139A pdb=" N GLN A1365 " --> pdb=" O PRO A1361 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A1366 " --> pdb=" O HIS A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1403 removed outlier: 3.915A pdb=" N THR A1388 " --> pdb=" O ASP A1384 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A1403 " --> pdb=" O THR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2038 through 2056 removed outlier: 3.613A pdb=" N LEU A2044 " --> pdb=" O GLU A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2061 Processing helix chain 'A' and resid 2063 through 2077 removed outlier: 3.614A pdb=" N LEU A2074 " --> pdb=" O SER A2070 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A2077 " --> pdb=" O ARG A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2108 Processing helix chain 'A' and resid 2109 through 2111 No H-bonds generated for 'chain 'A' and resid 2109 through 2111' Processing helix chain 'A' and resid 2112 through 2120 Processing helix chain 'A' and resid 2126 through 2135 Processing helix chain 'A' and resid 2142 through 2157 Processing helix chain 'A' and resid 2162 through 2179 removed outlier: 3.577A pdb=" N ILE A2167 " --> pdb=" O GLY A2163 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A2168 " --> pdb=" O GLY A2164 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A2179 " --> pdb=" O THR A2175 " (cutoff:3.500A) Processing helix chain 'A' and resid 2188 through 2201 removed outlier: 4.263A pdb=" N ASN A2194 " --> pdb=" O THR A2190 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2206 Processing helix chain 'A' and resid 2213 through 2224 removed outlier: 3.975A pdb=" N LEU A2217 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2230 through 2249 removed outlier: 5.006A pdb=" N GLU A2237 " --> pdb=" O ARG A2233 " (cutoff:3.500A) Proline residue: A2238 - end of helix Processing helix chain 'A' and resid 2256 through 2266 Processing helix chain 'A' and resid 2270 through 2275 removed outlier: 4.042A pdb=" N PHE A2275 " --> pdb=" O GLU A2271 " (cutoff:3.500A) Processing helix chain 'A' and resid 2275 through 2290 Processing helix chain 'A' and resid 2296 through 2310 Processing helix chain 'A' and resid 2335 through 2353 removed outlier: 3.589A pdb=" N CYS A2339 " --> pdb=" O ALA A2335 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A2343 " --> pdb=" O CYS A2339 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A2345 " --> pdb=" O ARG A2341 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU A2346 " --> pdb=" O GLN A2342 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A2353 " --> pdb=" O GLU A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2355 through 2363 removed outlier: 3.532A pdb=" N SER A2362 " --> pdb=" O THR A2358 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A2363 " --> pdb=" O LYS A2359 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2395 Processing helix chain 'A' and resid 2400 through 2407 Processing helix chain 'A' and resid 2414 through 2418 removed outlier: 3.630A pdb=" N GLN A2418 " --> pdb=" O SER A2415 " (cutoff:3.500A) Processing helix chain 'A' and resid 2420 through 2448 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 4.301A pdb=" N HIS A2465 " --> pdb=" O ASP A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2484 through 2512 removed outlier: 3.741A pdb=" N MET A2488 " --> pdb=" O CYS A2484 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A2491 " --> pdb=" O HIS A2487 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A2492 " --> pdb=" O MET A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2546 Proline residue: A2537 - end of helix removed outlier: 3.973A pdb=" N ASN A2546 " --> pdb=" O LEU A2542 " (cutoff:3.500A) Processing helix chain 'A' and resid 2549 through 2568 Processing helix chain 'A' and resid 2569 through 2585 Proline residue: A2577 - end of helix Proline residue: A2581 - end of helix Processing helix chain 'A' and resid 2586 through 2590 Processing helix chain 'A' and resid 2593 through 2603 removed outlier: 4.279A pdb=" N ASN A2603 " --> pdb=" O GLN A2599 " (cutoff:3.500A) Processing helix chain 'A' and resid 2625 through 2649 Processing helix chain 'B' and resid 22 through 35 removed outlier: 4.319A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.531A pdb=" N GLN B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 95 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 206 through 210 removed outlier: 4.607A pdb=" N SER B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 217 through 220 removed outlier: 3.857A pdb=" N GLU B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 345 through 364 removed outlier: 3.622A pdb=" N HIS B 362 " --> pdb=" O GLN B 358 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 666 Processing helix chain 'B' and resid 670 through 685 Processing helix chain 'B' and resid 787 through 803 Processing helix chain 'B' and resid 825 through 841 Processing helix chain 'B' and resid 841 through 856 removed outlier: 3.981A pdb=" N ARG B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 854 " --> pdb=" O ARG B 850 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 856 " --> pdb=" O TYR B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 870 Processing helix chain 'B' and resid 871 through 874 Processing helix chain 'B' and resid 899 through 918 removed outlier: 4.832A pdb=" N LYS B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.879A pdb=" N SER B 924 " --> pdb=" O HIS B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 945 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 1026 through 1038 Processing helix chain 'B' and resid 1177 through 1195 Processing helix chain 'B' and resid 1202 through 1209 Processing helix chain 'B' and resid 1215 through 1235 Processing helix chain 'B' and resid 1266 through 1294 Processing helix chain 'B' and resid 1312 through 1321 Processing helix chain 'B' and resid 1340 through 1358 Processing helix chain 'B' and resid 1528 through 1538 Processing helix chain 'B' and resid 1553 through 1572 Processing helix chain 'B' and resid 1625 through 1634 Processing helix chain 'B' and resid 1639 through 1648 Processing helix chain 'B' and resid 1649 through 1652 Processing helix chain 'B' and resid 1653 through 1667 Proline residue: B1662 - end of helix Processing helix chain 'B' and resid 1668 through 1670 No H-bonds generated for 'chain 'B' and resid 1668 through 1670' Processing helix chain 'B' and resid 1672 through 1690 Processing helix chain 'B' and resid 1690 through 1703 Processing helix chain 'B' and resid 1706 through 1723 Processing helix chain 'B' and resid 1724 through 1726 No H-bonds generated for 'chain 'B' and resid 1724 through 1726' Processing helix chain 'B' and resid 1727 through 1732 removed outlier: 3.778A pdb=" N GLU B1732 " --> pdb=" O TRP B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1820 Processing helix chain 'B' and resid 1826 through 1831 Processing helix chain 'B' and resid 1912 through 1918 Processing helix chain 'B' and resid 1918 through 1926 Processing helix chain 'B' and resid 1937 through 1953 Processing helix chain 'B' and resid 1953 through 1968 removed outlier: 3.701A pdb=" N VAL B1957 " --> pdb=" O ASP B1953 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N HIS B1960 " --> pdb=" O THR B1956 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE B1961 " --> pdb=" O VAL B1957 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B1965 " --> pdb=" O PHE B1961 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR B1966 " --> pdb=" O LEU B1962 " (cutoff:3.500A) Processing helix chain 'B' and resid 1970 through 1986 removed outlier: 3.665A pdb=" N TYR B1976 " --> pdb=" O ASP B1972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2010 Processing helix chain 'B' and resid 2014 through 2031 removed outlier: 3.798A pdb=" N PHE B2025 " --> pdb=" O ALA B2021 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP B2027 " --> pdb=" O LEU B2023 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU B2028 " --> pdb=" O THR B2024 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B2031 " --> pdb=" O TRP B2027 " (cutoff:3.500A) Processing helix chain 'B' and resid 2037 through 2049 Processing helix chain 'B' and resid 2050 through 2055 removed outlier: 4.269A pdb=" N LEU B2054 " --> pdb=" O CYS B2050 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2099 removed outlier: 3.506A pdb=" N LEU B2091 " --> pdb=" O GLN B2087 " (cutoff:3.500A) Processing helix chain 'B' and resid 2125 through 2130 removed outlier: 3.816A pdb=" N ILE B2129 " --> pdb=" O TYR B2125 " (cutoff:3.500A) Processing helix chain 'B' and resid 2146 through 2179 Processing helix chain 'B' and resid 2183 through 2198 Processing helix chain 'B' and resid 2200 through 2207 Processing helix chain 'B' and resid 2209 through 2214 removed outlier: 4.160A pdb=" N SER B2214 " --> pdb=" O PHE B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2219 through 2242 Processing helix chain 'B' and resid 2252 through 2268 removed outlier: 4.210A pdb=" N LEU B2256 " --> pdb=" O ASP B2252 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B2257 " --> pdb=" O GLU B2253 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B2260 " --> pdb=" O LEU B2256 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B2261 " --> pdb=" O PHE B2257 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2289 Processing helix chain 'B' and resid 2289 through 2294 Processing helix chain 'B' and resid 2297 through 2312 Proline residue: B2303 - end of helix Processing helix chain 'B' and resid 2315 through 2333 Processing helix chain 'B' and resid 2334 through 2346 Processing helix chain 'B' and resid 2364 through 2377 removed outlier: 3.739A pdb=" N LEU B2368 " --> pdb=" O SER B2364 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B2369 " --> pdb=" O ALA B2365 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B2377 " --> pdb=" O GLN B2373 " (cutoff:3.500A) Processing helix chain 'B' and resid 2385 through 2389 Processing helix chain 'B' and resid 2410 through 2425 removed outlier: 3.627A pdb=" N ALA B2425 " --> pdb=" O VAL B2421 " (cutoff:3.500A) Processing helix chain 'B' and resid 2428 through 2456 Proline residue: B2443 - end of helix Processing helix chain 'B' and resid 2457 through 2482 removed outlier: 4.457A pdb=" N ARG B2463 " --> pdb=" O VAL B2459 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B2464 " --> pdb=" O PRO B2460 " (cutoff:3.500A) Processing helix chain 'B' and resid 2547 through 2585 Proline residue: B2560 - end of helix Proline residue: B2577 - end of helix Processing helix chain 'B' and resid 2598 through 2616 Processing helix chain 'B' and resid 2619 through 2624 removed outlier: 3.526A pdb=" N MET B2623 " --> pdb=" O ASP B2619 " (cutoff:3.500A) Processing helix chain 'B' and resid 2625 through 2635 Processing helix chain 'B' and resid 2646 through 2666 removed outlier: 4.032A pdb=" N LEU B2650 " --> pdb=" O VAL B2646 " (cutoff:3.500A) Processing helix chain 'B' and resid 2669 through 2674 Processing helix chain 'B' and resid 2675 through 2693 removed outlier: 3.854A pdb=" N ALA B2679 " --> pdb=" O GLU B2675 " (cutoff:3.500A) Processing helix chain 'B' and resid 2694 through 2698 removed outlier: 3.810A pdb=" N PHE B2698 " --> pdb=" O ILE B2695 " (cutoff:3.500A) Processing helix chain 'B' and resid 2699 through 2714 Processing helix chain 'B' and resid 2738 through 2756 Processing helix chain 'B' and resid 2761 through 2767 Processing helix chain 'B' and resid 2768 through 2770 No H-bonds generated for 'chain 'B' and resid 2768 through 2770' Processing helix chain 'B' and resid 2774 through 2782 Processing helix chain 'B' and resid 2782 through 2792 Processing helix chain 'B' and resid 2801 through 2817 Processing helix chain 'B' and resid 2855 through 2873 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 3.944A pdb=" N GLY B2878 " --> pdb=" O GLU B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2880 through 2895 removed outlier: 3.818A pdb=" N LEU B2884 " --> pdb=" O GLN B2880 " (cutoff:3.500A) Processing helix chain 'B' and resid 2900 through 2912 Processing helix chain 'B' and resid 2913 through 2926 removed outlier: 4.038A pdb=" N VAL B2917 " --> pdb=" O ILE B2913 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B2918 " --> pdb=" O PRO B2914 " (cutoff:3.500A) Proline residue: B2921 - end of helix Processing helix chain 'B' and resid 2934 through 2949 removed outlier: 3.691A pdb=" N ALA B2940 " --> pdb=" O GLU B2936 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B2949 " --> pdb=" O SER B2945 " (cutoff:3.500A) Processing helix chain 'B' and resid 2959 through 2979 removed outlier: 3.629A pdb=" N HIS B2978 " --> pdb=" O LYS B2974 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B2979 " --> pdb=" O GLU B2975 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.855A pdb=" N LYS C 35 " --> pdb=" O TRP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 64 through 91 Processing helix chain 'C' and resid 106 through 130 removed outlier: 4.217A pdb=" N PHE C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.672A pdb=" N GLY C 140 " --> pdb=" O SER C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 154 removed outlier: 4.121A pdb=" N ARG C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 153 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 154 " --> pdb=" O MET C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 154' Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.705A pdb=" N ARG C 159 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 200 Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.571A pdb=" N LEU C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 278 Processing helix chain 'C' and resid 282 through 293 Processing helix chain 'C' and resid 294 through 309 removed outlier: 3.500A pdb=" N SER C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 335 removed outlier: 3.698A pdb=" N PHE C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 383 Processing helix chain 'C' and resid 383 through 403 removed outlier: 3.620A pdb=" N HIS C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 441 Processing helix chain 'C' and resid 441 through 447 Processing helix chain 'C' and resid 450 through 465 removed outlier: 4.139A pdb=" N GLU C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.810A pdb=" N GLN C 478 " --> pdb=" O PHE C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'C' and resid 502 through 528 removed outlier: 3.643A pdb=" N LEU C 506 " --> pdb=" O PRO C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 571 through 603 removed outlier: 4.366A pdb=" N LEU C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 615 Processing helix chain 'C' and resid 659 through 669 removed outlier: 3.630A pdb=" N ARG C 669 " --> pdb=" O GLN C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 718 removed outlier: 4.003A pdb=" N LYS C 709 " --> pdb=" O GLN C 705 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 740 Processing helix chain 'C' and resid 846 through 854 Processing helix chain 'C' and resid 875 through 883 Processing helix chain 'C' and resid 886 through 904 Processing helix chain 'C' and resid 915 through 941 Processing helix chain 'C' and resid 952 through 972 removed outlier: 3.513A pdb=" N VAL C 956 " --> pdb=" O ASP C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 990 Processing helix chain 'C' and resid 991 through 994 Processing helix chain 'C' and resid 995 through 1000 removed outlier: 3.566A pdb=" N VAL C1000 " --> pdb=" O ILE C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1013 removed outlier: 4.190A pdb=" N GLY C1013 " --> pdb=" O GLU C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1040 Processing helix chain 'C' and resid 1053 through 1057 Processing helix chain 'C' and resid 1100 through 1113 Processing helix chain 'C' and resid 1116 through 1128 removed outlier: 3.505A pdb=" N VAL C1120 " --> pdb=" O GLY C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1131 No H-bonds generated for 'chain 'C' and resid 1129 through 1131' Processing helix chain 'C' and resid 1132 through 1145 removed outlier: 3.706A pdb=" N ILE C1136 " --> pdb=" O HIS C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1163 Processing helix chain 'C' and resid 1169 through 1184 removed outlier: 3.632A pdb=" N ILE C1184 " --> pdb=" O SER C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1208 removed outlier: 3.605A pdb=" N MET C1203 " --> pdb=" O PHE C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1209 through 1226 Processing helix chain 'C' and resid 1237 through 1264 removed outlier: 3.965A pdb=" N LEU C1241 " --> pdb=" O VAL C1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 1266 through 1270 Processing helix chain 'C' and resid 1271 through 1294 Processing helix chain 'C' and resid 1296 through 1314 Processing helix chain 'C' and resid 1315 through 1317 No H-bonds generated for 'chain 'C' and resid 1315 through 1317' Processing helix chain 'C' and resid 1318 through 1335 Processing helix chain 'C' and resid 1335 through 1358 Processing helix chain 'C' and resid 1374 through 1386 removed outlier: 3.640A pdb=" N VAL C1386 " --> pdb=" O LEU C1382 " (cutoff:3.500A) Processing helix chain 'C' and resid 1390 through 1399 Processing helix chain 'C' and resid 1419 through 1436 Processing helix chain 'C' and resid 1437 through 1454 Processing helix chain 'C' and resid 1463 through 1478 Processing helix chain 'C' and resid 1486 through 1497 Processing helix chain 'C' and resid 1498 through 1502 removed outlier: 3.659A pdb=" N LEU C1501 " --> pdb=" O ARG C1498 " (cutoff:3.500A) Processing helix chain 'C' and resid 1504 through 1523 removed outlier: 6.716A pdb=" N LEU C1510 " --> pdb=" O ASP C1506 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C1511 " --> pdb=" O LYS C1507 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS C1523 " --> pdb=" O MET C1519 " (cutoff:3.500A) Processing helix chain 'C' and resid 1531 through 1541 Processing helix chain 'C' and resid 1543 through 1548 Processing helix chain 'C' and resid 1549 through 1578 removed outlier: 3.890A pdb=" N LYS C1578 " --> pdb=" O MET C1574 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.577A pdb=" N LEU D 261 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 297 Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.666A pdb=" N SER D 301 " --> pdb=" O TYR D 298 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP D 302 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 326 Processing helix chain 'D' and resid 340 through 350 removed outlier: 4.138A pdb=" N LEU D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1287 through 1288 Processing sheet with id=AA2, first strand: chain 'B' and resid 2078 through 2080 Processing sheet with id=AA3, first strand: chain 'C' and resid 206 through 209 Processing sheet with id=AA4, first strand: chain 'C' and resid 350 through 353 Processing sheet with id=AA5, first strand: chain 'C' and resid 1045 through 1046 removed outlier: 3.534A pdb=" N LYS C1045 " --> pdb=" O ALA C1091 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1060 through 1064 2438 hydrogen bonds defined for protein. 7188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.72 Time building geometry restraints manager: 5.01 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: 7484 1.33 - 1.45: 9024 1.45 - 1.57: 22046 1.57 - 1.69: 0 1.69 - 1.81: 463 Bond restraints: 39017 Sorted by residual: bond pdb=" CA LEU B1644 " pdb=" C LEU B1644 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.29e-02 6.01e+03 2.31e+01 bond pdb=" C LEU B1644 " pdb=" O LEU B1644 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.19e-02 7.06e+03 5.67e+00 bond pdb=" CA THR A 128 " pdb=" C THR A 128 " ideal model delta sigma weight residual 1.522 1.499 0.024 1.36e-02 5.41e+03 3.03e+00 bond pdb=" C LEU B1644 " pdb=" N LEU B1645 " ideal model delta sigma weight residual 1.335 1.313 0.022 1.31e-02 5.83e+03 2.91e+00 bond pdb=" C MET B2667 " pdb=" N PRO B2668 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.91e+00 ... (remaining 39012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 52251 1.84 - 3.68: 522 3.68 - 5.52: 106 5.52 - 7.36: 18 7.36 - 9.19: 4 Bond angle restraints: 52901 Sorted by residual: angle pdb=" N LEU B1644 " pdb=" CA LEU B1644 " pdb=" C LEU B1644 " ideal model delta sigma weight residual 111.40 106.62 4.78 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N LEU B2295 " pdb=" CA LEU B2295 " pdb=" C LEU B2295 " ideal model delta sigma weight residual 114.56 109.93 4.63 1.27e+00 6.20e-01 1.33e+01 angle pdb=" CA LEU B2295 " pdb=" C LEU B2295 " pdb=" N SER B2296 " ideal model delta sigma weight residual 119.26 115.78 3.48 1.14e+00 7.69e-01 9.30e+00 angle pdb=" C ARG B2009 " pdb=" N THR B2010 " pdb=" CA THR B2010 " ideal model delta sigma weight residual 121.61 117.48 4.13 1.39e+00 5.18e-01 8.82e+00 angle pdb=" C MET B1635 " pdb=" N SER B1636 " pdb=" CA SER B1636 " ideal model delta sigma weight residual 122.41 128.17 -5.76 2.09e+00 2.29e-01 7.61e+00 ... (remaining 52896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 22057 17.63 - 35.27: 1082 35.27 - 52.90: 236 52.90 - 70.53: 36 70.53 - 88.17: 11 Dihedral angle restraints: 23422 sinusoidal: 9406 harmonic: 14016 Sorted by residual: dihedral pdb=" CA GLN B1736 " pdb=" C GLN B1736 " pdb=" N GLN B1737 " pdb=" CA GLN B1737 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET B 907 " pdb=" C MET B 907 " pdb=" N PHE B 908 " pdb=" CA PHE B 908 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLN A1350 " pdb=" C GLN A1350 " pdb=" N PRO A1351 " pdb=" CA PRO A1351 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 23419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4082 0.032 - 0.064: 1524 0.064 - 0.096: 402 0.096 - 0.128: 111 0.128 - 0.161: 8 Chirality restraints: 6127 Sorted by residual: chirality pdb=" CG LEU B 928 " pdb=" CB LEU B 928 " pdb=" CD1 LEU B 928 " pdb=" CD2 LEU B 928 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CB ILE B2953 " pdb=" CA ILE B2953 " pdb=" CG1 ILE B2953 " pdb=" CG2 ILE B2953 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA PRO B2914 " pdb=" N PRO B2914 " pdb=" C PRO B2914 " pdb=" CB PRO B2914 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 6124 not shown) Planarity restraints: 6590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1643 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C SER B1643 " -0.046 2.00e-02 2.50e+03 pdb=" O SER B1643 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B1644 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 65 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO C 66 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1134 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A1135 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1135 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1135 " 0.025 5.00e-02 4.00e+02 ... (remaining 6587 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3495 2.74 - 3.28: 40148 3.28 - 3.82: 65944 3.82 - 4.36: 75847 4.36 - 4.90: 130222 Nonbonded interactions: 315656 Sorted by model distance: nonbonded pdb=" OH TYR A1376 " pdb=" O PHE B1763 " model vdw 2.199 3.040 nonbonded pdb=" O ALA B1214 " pdb=" NH1 ARG B1219 " model vdw 2.224 3.120 nonbonded pdb=" O LEU B2788 " pdb=" OG SER B2792 " model vdw 2.228 3.040 nonbonded pdb=" O HIS A2487 " pdb=" OG SER A2490 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A 172 " pdb=" O VAL B2917 " model vdw 2.253 3.040 ... (remaining 315651 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.400 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39039 Z= 0.158 Angle : 0.507 9.194 52938 Z= 0.258 Chirality : 0.037 0.161 6127 Planarity : 0.004 0.048 6587 Dihedral : 11.128 88.167 14217 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.29 % Allowed : 6.11 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 2.19 (0.13), residues: 4660 helix: 2.32 (0.09), residues: 3227 sheet: -0.31 (0.75), residues: 35 loop : -0.62 (0.18), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1358 TYR 0.011 0.001 TYR B2309 PHE 0.015 0.001 PHE C 666 TRP 0.013 0.001 TRP B2027 HIS 0.003 0.001 HIS A 932 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (39017) covalent geometry : angle 0.50658 / 0.26 (52901) SS BOND : bond 0.00107 / 0.07 ( 11) SS BOND : angle 0.56713 / 0.40 ( 22) hydrogen bonds : bond 0.12386 / 8.21 ( 2438) hydrogen bonds : angle 4.96042 / 3.61 ( 7188) metal coordination : bond 0.01002 / 0.73 ( 8) metal coordination : angle 1.11012 / 0.66 ( 6) link_NAG-ASN : bond 0.00144 / 0.06 ( 3) link_NAG-ASN : angle 1.15953 / 0.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 879 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 207 TYR cc_start: 0.6507 (m-80) cc_final: 0.6140 (m-80) REVERT: A 447 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8860 (mp) REVERT: A 500 LYS cc_start: 0.5392 (OUTLIER) cc_final: 0.4985 (mtpt) REVERT: A 1403 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8331 (tp40) REVERT: A 2279 ARG cc_start: 0.7337 (ttp-170) cc_final: 0.7127 (ttm170) REVERT: A 2397 HIS cc_start: 0.8466 (m-70) cc_final: 0.7639 (m90) REVERT: A 2417 MET cc_start: 0.5385 (mmt) cc_final: 0.3682 (tmm) REVERT: A 2433 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7337 (tp) REVERT: A 2444 HIS cc_start: 0.8501 (t-90) cc_final: 0.8278 (t70) REVERT: A 2466 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6887 (pt) REVERT: A 2488 MET cc_start: 0.7313 (mmt) cc_final: 0.7091 (mmp) REVERT: A 2543 MET cc_start: 0.7578 (mtt) cc_final: 0.7295 (mtt) REVERT: A 2634 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8695 (pp30) REVERT: B 27 TRP cc_start: 0.7873 (m100) cc_final: 0.7227 (m100) REVERT: B 344 TRP cc_start: 0.7542 (t60) cc_final: 0.6882 (t60) REVERT: B 350 GLN cc_start: 0.7979 (tt0) cc_final: 0.7748 (tp40) REVERT: B 789 HIS cc_start: 0.7607 (t-90) cc_final: 0.7326 (t-90) REVERT: B 2042 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8099 (mtmm) REVERT: B 2052 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8856 (m) REVERT: B 2063 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8591 (m) REVERT: B 2206 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8904 (mt) REVERT: B 2277 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8238 (tp-100) REVERT: B 2552 ILE cc_start: 0.8920 (mt) cc_final: 0.8553 (mm) REVERT: B 2684 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 2778 MET cc_start: 0.8734 (ttt) cc_final: 0.8475 (tmm) REVERT: B 2873 PHE cc_start: 0.9135 (m-10) cc_final: 0.8832 (m-10) REVERT: B 2920 ARG cc_start: 0.7569 (tpt90) cc_final: 0.7330 (ttp-170) REVERT: B 2972 ILE cc_start: 0.9135 (mt) cc_final: 0.8929 (pt) REVERT: C 51 ILE cc_start: 0.9412 (mt) cc_final: 0.8861 (mt) REVERT: C 110 PHE cc_start: 0.7762 (t80) cc_final: 0.7466 (t80) REVERT: C 124 LEU cc_start: 0.9291 (tp) cc_final: 0.9069 (tp) REVERT: C 144 ILE cc_start: 0.9397 (mt) cc_final: 0.9116 (mm) REVERT: C 177 GLN cc_start: 0.9035 (mt0) cc_final: 0.8760 (mt0) REVERT: C 184 PHE cc_start: 0.8370 (t80) cc_final: 0.7945 (t80) REVERT: C 243 PHE cc_start: 0.8122 (m-80) cc_final: 0.7771 (m-80) REVERT: C 253 LEU cc_start: 0.7312 (mp) cc_final: 0.6699 (mp) REVERT: C 270 ILE cc_start: 0.9037 (mt) cc_final: 0.8715 (mt) REVERT: C 275 GLU cc_start: 0.7974 (tt0) cc_final: 0.7686 (tt0) REVERT: C 286 MET cc_start: 0.8698 (ttt) cc_final: 0.8495 (ttm) REVERT: C 324 THR cc_start: 0.8850 (m) cc_final: 0.8538 (m) REVERT: C 325 PHE cc_start: 0.8936 (m-80) cc_final: 0.8710 (m-10) REVERT: C 381 MET cc_start: 0.8196 (ttp) cc_final: 0.7987 (ttp) REVERT: C 388 MET cc_start: 0.8044 (mtt) cc_final: 0.7518 (mpp) REVERT: C 395 THR cc_start: 0.9076 (m) cc_final: 0.8858 (p) REVERT: C 456 LEU cc_start: 0.9417 (tp) cc_final: 0.9212 (tp) REVERT: C 479 VAL cc_start: 0.9284 (m) cc_final: 0.8909 (p) REVERT: C 482 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8657 (p) REVERT: C 498 LYS cc_start: 0.8382 (tttt) cc_final: 0.7925 (mmmm) REVERT: C 593 LEU cc_start: 0.9115 (mt) cc_final: 0.8896 (mt) REVERT: C 896 THR cc_start: 0.8572 (m) cc_final: 0.8052 (p) REVERT: C 903 MET cc_start: 0.8112 (mtp) cc_final: 0.7690 (ttm) REVERT: C 958 ASP cc_start: 0.7928 (m-30) cc_final: 0.7666 (m-30) REVERT: C 986 MET cc_start: 0.8684 (mtp) cc_final: 0.8290 (mtp) REVERT: C 998 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8585 (tttp) REVERT: C 1016 GLU cc_start: 0.8854 (mp0) cc_final: 0.8448 (mp0) REVERT: C 1029 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9031 (mt) REVERT: C 1096 PHE cc_start: 0.8317 (p90) cc_final: 0.7847 (p90) REVERT: C 1161 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8705 (tm-30) REVERT: C 1203 MET cc_start: 0.7626 (tpp) cc_final: 0.6716 (tpp) REVERT: C 1301 MET cc_start: 0.8756 (ttp) cc_final: 0.8512 (tpt) REVERT: C 1313 SER cc_start: 0.8265 (t) cc_final: 0.7734 (p) REVERT: C 1393 LYS cc_start: 0.8726 (mttt) cc_final: 0.8341 (mttp) REVERT: D 268 THR cc_start: 0.7929 (p) cc_final: 0.7418 (t) REVERT: D 277 TYR cc_start: 0.8389 (m-10) cc_final: 0.7951 (m-80) REVERT: D 280 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7678 (m-10) REVERT: D 281 ASP cc_start: 0.7835 (t70) cc_final: 0.6853 (t0) REVERT: D 297 LYS cc_start: 0.9116 (mttm) cc_final: 0.8708 (mttp) REVERT: D 318 LYS cc_start: 0.8350 (tttt) cc_final: 0.7957 (tttp) REVERT: D 340 LYS cc_start: 0.8649 (mttt) cc_final: 0.8217 (mtpp) REVERT: D 345 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8793 (mm-30) REVERT: D 349 ARG cc_start: 0.8978 (mpt-90) cc_final: 0.8412 (mmm-85) REVERT: D 382 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7270 (mm-30) outliers start: 139 outliers final: 50 residues processed: 996 average time/residue: 0.2467 time to fit residues: 405.6084 Evaluate side-chains 704 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 640 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1382 ASP Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2466 ILE Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2634 GLN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1934 ASP Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2042 LYS Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2063 THR Chi-restraints excluded: chain B residue 2206 ILE Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2456 VAL Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2674 VAL Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1516 CYS Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 360 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2083 GLN A2465 HIS A2493 HIS ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 97 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1736 GLN B2262 ASN B2477 GLN ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN C1524 ASN C1549 GLN D 283 HIS D 296 HIS ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096123 restraints weight = 124537.170| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.31 r_work: 0.3226 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39039 Z= 0.153 Angle : 0.612 11.556 52938 Z= 0.302 Chirality : 0.040 0.223 6127 Planarity : 0.004 0.054 6587 Dihedral : 6.133 80.034 5189 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.46 % Allowed : 11.44 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.99 (0.13), residues: 4660 helix: 2.12 (0.09), residues: 3280 sheet: -0.27 (0.75), residues: 35 loop : -0.67 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2115 TYR 0.028 0.001 TYR C 923 PHE 0.024 0.001 PHE B1961 TRP 0.024 0.001 TRP A 202 HIS 0.006 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (39017) covalent geometry : angle 0.61155 / 0.30 (52901) SS BOND : bond 0.00411 / 0.29 ( 11) SS BOND : angle 1.05779 / 0.85 ( 22) hydrogen bonds : bond 0.04096 / 2.74 ( 2438) hydrogen bonds : angle 4.18132 / 3.03 ( 7188) metal coordination : bond 0.01209 / 0.90 ( 8) metal coordination : angle 0.96595 / 0.51 ( 6) link_NAG-ASN : bond 0.00068 / 0.03 ( 3) link_NAG-ASN : angle 1.39185 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 673 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 202 TRP cc_start: 0.8603 (p90) cc_final: 0.8301 (p90) REVERT: A 223 MET cc_start: 0.7665 (mmp) cc_final: 0.7449 (mmm) REVERT: A 447 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 491 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: A 500 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.5055 (mtpt) REVERT: A 519 MET cc_start: 0.7990 (tpp) cc_final: 0.7343 (tpp) REVERT: A 1403 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: A 2279 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7520 (ttm170) REVERT: A 2397 HIS cc_start: 0.8284 (m-70) cc_final: 0.7309 (m90) REVERT: A 2417 MET cc_start: 0.5086 (mmt) cc_final: 0.3589 (tmm) REVERT: A 2433 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7345 (tm) REVERT: A 2466 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6894 (pt) REVERT: A 2488 MET cc_start: 0.7227 (mmt) cc_final: 0.7004 (mmp) REVERT: A 2561 MET cc_start: 0.8605 (mpp) cc_final: 0.8319 (mpp) REVERT: A 2634 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8733 (pp30) REVERT: B 344 TRP cc_start: 0.7553 (t60) cc_final: 0.7134 (t60) REVERT: B 350 GLN cc_start: 0.7907 (tt0) cc_final: 0.7657 (tp40) REVERT: B 362 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7988 (p-80) REVERT: B 1185 MET cc_start: 0.8331 (mmt) cc_final: 0.7962 (mmm) REVERT: B 1808 GLN cc_start: 0.8246 (pt0) cc_final: 0.7963 (tm-30) REVERT: B 2075 ASP cc_start: 0.5444 (OUTLIER) cc_final: 0.5093 (t0) REVERT: B 2206 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8948 (mt) REVERT: B 2277 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8445 (tp-100) REVERT: B 2320 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7999 (mmp80) REVERT: B 2552 ILE cc_start: 0.9072 (mt) cc_final: 0.8765 (mm) REVERT: B 2972 ILE cc_start: 0.9005 (mt) cc_final: 0.8781 (pt) REVERT: C 51 ILE cc_start: 0.9292 (mt) cc_final: 0.8631 (mt) REVERT: C 54 CYS cc_start: 0.9026 (m) cc_final: 0.8781 (p) REVERT: C 141 MET cc_start: 0.7757 (mtp) cc_final: 0.7498 (mtm) REVERT: C 166 ARG cc_start: 0.8990 (mtt-85) cc_final: 0.8510 (ttm-80) REVERT: C 172 LYS cc_start: 0.8554 (mttt) cc_final: 0.7946 (tptt) REVERT: C 184 PHE cc_start: 0.9023 (t80) cc_final: 0.8462 (t80) REVERT: C 235 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 243 PHE cc_start: 0.8279 (m-80) cc_final: 0.7774 (m-80) REVERT: C 275 GLU cc_start: 0.8679 (tt0) cc_final: 0.8367 (tt0) REVERT: C 327 GLU cc_start: 0.9013 (tp30) cc_final: 0.8802 (tp30) REVERT: C 331 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7817 (mm-40) REVERT: C 388 MET cc_start: 0.8145 (mtt) cc_final: 0.7421 (mmm) REVERT: C 395 THR cc_start: 0.9156 (m) cc_final: 0.8901 (p) REVERT: C 420 LEU cc_start: 0.9154 (mt) cc_final: 0.8870 (pp) REVERT: C 469 LEU cc_start: 0.9189 (mt) cc_final: 0.8870 (mt) REVERT: C 479 VAL cc_start: 0.9193 (m) cc_final: 0.8954 (p) REVERT: C 482 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8818 (p) REVERT: C 498 LYS cc_start: 0.8543 (tttt) cc_final: 0.8065 (mmmm) REVERT: C 547 MET cc_start: 0.8996 (mmp) cc_final: 0.8790 (mmm) REVERT: C 593 LEU cc_start: 0.9061 (mt) cc_final: 0.8698 (mt) REVERT: C 603 GLU cc_start: 0.8288 (tt0) cc_final: 0.7977 (tt0) REVERT: C 606 GLU cc_start: 0.8782 (mp0) cc_final: 0.8296 (pm20) REVERT: C 607 ASP cc_start: 0.8506 (m-30) cc_final: 0.8210 (m-30) REVERT: C 643 MET cc_start: 0.8716 (mmm) cc_final: 0.7794 (mmm) REVERT: C 886 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 903 MET cc_start: 0.8286 (mtp) cc_final: 0.7920 (ttm) REVERT: C 929 MET cc_start: 0.9063 (tpt) cc_final: 0.8564 (tpp) REVERT: C 932 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: C 958 ASP cc_start: 0.8526 (m-30) cc_final: 0.8251 (m-30) REVERT: C 1016 GLU cc_start: 0.9079 (mp0) cc_final: 0.8600 (mp0) REVERT: C 1022 ILE cc_start: 0.9226 (mt) cc_final: 0.9021 (mp) REVERT: C 1029 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9096 (mt) REVERT: C 1096 PHE cc_start: 0.8678 (p90) cc_final: 0.8078 (p90) REVERT: C 1108 LEU cc_start: 0.9519 (mt) cc_final: 0.9132 (mt) REVERT: C 1160 ASN cc_start: 0.8738 (t0) cc_final: 0.8513 (t0) REVERT: C 1161 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8679 (tm-30) REVERT: C 1203 MET cc_start: 0.8582 (tpp) cc_final: 0.7692 (tpp) REVERT: C 1301 MET cc_start: 0.8666 (ttp) cc_final: 0.8270 (tpt) REVERT: C 1309 PHE cc_start: 0.8941 (m-80) cc_final: 0.8568 (m-80) REVERT: C 1313 SER cc_start: 0.9033 (t) cc_final: 0.8499 (p) REVERT: C 1384 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8401 (ptp-170) REVERT: C 1393 LYS cc_start: 0.9323 (mttt) cc_final: 0.9075 (mttp) REVERT: C 1399 MET cc_start: 0.8469 (ttm) cc_final: 0.8143 (ttt) REVERT: C 1449 ASN cc_start: 0.8971 (m110) cc_final: 0.8567 (m110) REVERT: C 1456 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (p) REVERT: C 1519 MET cc_start: 0.8300 (mmt) cc_final: 0.7945 (tpp) REVERT: D 227 LEU cc_start: 0.8807 (mt) cc_final: 0.7973 (tp) REVERT: D 232 LEU cc_start: 0.9112 (tp) cc_final: 0.8567 (tt) REVERT: D 238 TYR cc_start: 0.7788 (m-80) cc_final: 0.7504 (m-80) REVERT: D 241 TRP cc_start: 0.7988 (t-100) cc_final: 0.7682 (t-100) REVERT: D 244 PHE cc_start: 0.8558 (m-80) cc_final: 0.8296 (m-80) REVERT: D 277 TYR cc_start: 0.8952 (m-10) cc_final: 0.8502 (m-80) REVERT: D 278 GLN cc_start: 0.9401 (mt0) cc_final: 0.8712 (tm-30) REVERT: D 280 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: D 281 ASP cc_start: 0.8545 (t70) cc_final: 0.8253 (t70) REVERT: D 289 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 294 VAL cc_start: 0.9372 (t) cc_final: 0.9162 (t) REVERT: D 297 LYS cc_start: 0.9250 (mttm) cc_final: 0.8830 (mttp) REVERT: D 307 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8571 (mmmm) REVERT: D 316 VAL cc_start: 0.8960 (t) cc_final: 0.8598 (p) REVERT: D 318 LYS cc_start: 0.8352 (tttt) cc_final: 0.7960 (tttp) outliers start: 146 outliers final: 80 residues processed: 785 average time/residue: 0.2239 time to fit residues: 296.5527 Evaluate side-chains 713 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 615 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2432 ARG Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2466 ILE Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2634 GLN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1206 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2056 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2116 TRP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2206 ILE Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2455 GLN Chi-restraints excluded: chain B residue 2456 VAL Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2660 MET Chi-restraints excluded: chain B residue 2764 HIS Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1215 THR Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1456 THR Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1528 VAL Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 339 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 423 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 417 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 457 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS A 482 HIS A 502 GLN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2480 GLN ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2584 ASN C 39 HIS C 56 ASN C 177 GLN C 473 GLN D 282 HIS D 296 HIS ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN D 341 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.125569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095292 restraints weight = 124187.216| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.30 r_work: 0.3220 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39039 Z= 0.173 Angle : 0.605 14.402 52938 Z= 0.297 Chirality : 0.040 0.183 6127 Planarity : 0.004 0.076 6587 Dihedral : 5.903 79.984 5165 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.29 % Allowed : 13.05 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.82 (0.13), residues: 4660 helix: 1.99 (0.09), residues: 3280 sheet: -0.33 (0.74), residues: 35 loop : -0.74 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 536 TYR 0.022 0.001 TYR C 274 PHE 0.022 0.001 PHE A2572 TRP 0.020 0.001 TRP A 453 HIS 0.005 0.001 HIS B1960 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (39017) covalent geometry : angle 0.60396 / 0.30 (52901) SS BOND : bond 0.00176 / 0.12 ( 11) SS BOND : angle 1.16779 / 0.98 ( 22) hydrogen bonds : bond 0.03864 / 2.55 ( 2438) hydrogen bonds : angle 4.14736 / 3.01 ( 7188) metal coordination : bond 0.01457 / 1.08 ( 8) metal coordination : angle 1.01045 / 0.60 ( 6) link_NAG-ASN : bond 0.00166 / 0.06 ( 3) link_NAG-ASN : angle 1.28951 / 0.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 645 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8339 (tt0) cc_final: 0.7930 (tp-100) REVERT: A 195 MET cc_start: 0.6597 (mmm) cc_final: 0.6389 (mmm) REVERT: A 447 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 491 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: A 500 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.5041 (mtpt) REVERT: A 519 MET cc_start: 0.8001 (tpp) cc_final: 0.7312 (tpp) REVERT: A 1403 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8559 (tp40) REVERT: A 2279 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7516 (ttm170) REVERT: A 2433 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7325 (tm) REVERT: A 2442 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 2488 MET cc_start: 0.7071 (mmt) cc_final: 0.6700 (mmm) REVERT: A 2561 MET cc_start: 0.8562 (mpp) cc_final: 0.8269 (mpp) REVERT: A 2575 LEU cc_start: 0.8472 (mt) cc_final: 0.8036 (mt) REVERT: B 344 TRP cc_start: 0.7232 (t60) cc_final: 0.7021 (t60) REVERT: B 350 GLN cc_start: 0.7932 (tt0) cc_final: 0.7675 (tp40) REVERT: B 791 LEU cc_start: 0.8614 (tp) cc_final: 0.8326 (tp) REVERT: B 795 MET cc_start: 0.8624 (mtt) cc_final: 0.8378 (mmm) REVERT: B 1808 GLN cc_start: 0.8213 (pt0) cc_final: 0.7883 (tm-30) REVERT: B 2075 ASP cc_start: 0.5208 (OUTLIER) cc_final: 0.4829 (t0) REVERT: B 2206 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8903 (mt) REVERT: B 2277 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (tp-100) REVERT: B 2320 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7969 (mmp80) REVERT: B 2552 ILE cc_start: 0.9086 (mt) cc_final: 0.8824 (mm) REVERT: B 2920 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.7011 (mtp180) REVERT: B 2972 ILE cc_start: 0.9005 (mt) cc_final: 0.8774 (pt) REVERT: C 51 ILE cc_start: 0.9365 (mt) cc_final: 0.8735 (mt) REVERT: C 54 CYS cc_start: 0.9034 (m) cc_final: 0.8671 (p) REVERT: C 141 MET cc_start: 0.7827 (mtp) cc_final: 0.7494 (mtm) REVERT: C 166 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8425 (ttm-80) REVERT: C 172 LYS cc_start: 0.8548 (mttt) cc_final: 0.7979 (tptt) REVERT: C 184 PHE cc_start: 0.9029 (t80) cc_final: 0.8770 (t80) REVERT: C 235 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7990 (mp0) REVERT: C 243 PHE cc_start: 0.8252 (m-80) cc_final: 0.7822 (m-80) REVERT: C 275 GLU cc_start: 0.8697 (tt0) cc_final: 0.8407 (tt0) REVERT: C 331 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7684 (mm-40) REVERT: C 388 MET cc_start: 0.8145 (mtt) cc_final: 0.7509 (mpp) REVERT: C 395 THR cc_start: 0.9146 (m) cc_final: 0.8890 (p) REVERT: C 398 VAL cc_start: 0.9355 (p) cc_final: 0.9133 (m) REVERT: C 469 LEU cc_start: 0.9187 (mt) cc_final: 0.8938 (mt) REVERT: C 479 VAL cc_start: 0.9234 (m) cc_final: 0.9029 (p) REVERT: C 498 LYS cc_start: 0.8521 (tttt) cc_final: 0.8028 (mmmm) REVERT: C 525 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9035 (pp) REVERT: C 527 MET cc_start: 0.8054 (tpp) cc_final: 0.7808 (tpp) REVERT: C 536 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.5700 (mtp180) REVERT: C 540 PHE cc_start: 0.8947 (t80) cc_final: 0.8741 (t80) REVERT: C 547 MET cc_start: 0.9007 (mmp) cc_final: 0.8804 (mmm) REVERT: C 558 ASP cc_start: 0.8731 (t0) cc_final: 0.8349 (t0) REVERT: C 603 GLU cc_start: 0.8276 (tt0) cc_final: 0.8029 (tt0) REVERT: C 606 GLU cc_start: 0.8651 (mp0) cc_final: 0.8276 (pm20) REVERT: C 607 ASP cc_start: 0.8467 (m-30) cc_final: 0.8188 (m-30) REVERT: C 643 MET cc_start: 0.8745 (mmm) cc_final: 0.7820 (mmm) REVERT: C 886 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7682 (p) REVERT: C 903 MET cc_start: 0.8334 (mtp) cc_final: 0.7898 (ttm) REVERT: C 929 MET cc_start: 0.9043 (tpt) cc_final: 0.8445 (tpp) REVERT: C 958 ASP cc_start: 0.8491 (m-30) cc_final: 0.8219 (m-30) REVERT: C 1016 GLU cc_start: 0.9096 (mp0) cc_final: 0.8656 (mp0) REVERT: C 1022 ILE cc_start: 0.9237 (mt) cc_final: 0.9004 (mp) REVERT: C 1029 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9108 (mt) REVERT: C 1096 PHE cc_start: 0.8676 (p90) cc_final: 0.8060 (p90) REVERT: C 1108 LEU cc_start: 0.9489 (mt) cc_final: 0.9049 (mt) REVERT: C 1161 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 1203 MET cc_start: 0.8598 (tpp) cc_final: 0.7752 (tpp) REVERT: C 1259 LYS cc_start: 0.9488 (mtmt) cc_final: 0.9253 (mtpp) REVERT: C 1274 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.7785 (t0) REVERT: C 1277 ASP cc_start: 0.9161 (m-30) cc_final: 0.8881 (p0) REVERT: C 1301 MET cc_start: 0.8698 (ttp) cc_final: 0.8167 (tpt) REVERT: C 1309 PHE cc_start: 0.8994 (m-80) cc_final: 0.8687 (m-80) REVERT: C 1384 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8273 (mtm180) REVERT: C 1449 ASN cc_start: 0.8966 (m110) cc_final: 0.8569 (m110) REVERT: C 1456 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 1564 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8116 (tm-30) REVERT: D 227 LEU cc_start: 0.8716 (mt) cc_final: 0.8370 (mm) REVERT: D 232 LEU cc_start: 0.9113 (tp) cc_final: 0.8606 (tt) REVERT: D 238 TYR cc_start: 0.7751 (m-80) cc_final: 0.7459 (m-80) REVERT: D 244 PHE cc_start: 0.8300 (m-80) cc_final: 0.7925 (m-80) REVERT: D 277 TYR cc_start: 0.8903 (m-10) cc_final: 0.8531 (m-80) REVERT: D 280 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: D 281 ASP cc_start: 0.8557 (t70) cc_final: 0.8227 (t70) REVERT: D 289 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8165 (tm-30) REVERT: D 294 VAL cc_start: 0.9414 (t) cc_final: 0.9196 (t) REVERT: D 297 LYS cc_start: 0.9250 (mttm) cc_final: 0.8761 (mttp) REVERT: D 312 ASP cc_start: 0.8225 (t0) cc_final: 0.7936 (t70) REVERT: D 316 VAL cc_start: 0.9002 (t) cc_final: 0.8639 (p) REVERT: D 318 LYS cc_start: 0.8380 (tttt) cc_final: 0.8034 (tttp) REVERT: D 334 ARG cc_start: 0.9469 (mmp80) cc_final: 0.9265 (mmp80) REVERT: D 335 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8717 (mtmm) REVERT: D 342 TYR cc_start: 0.9127 (m-80) cc_final: 0.8759 (m-10) REVERT: D 349 ARG cc_start: 0.9008 (mmm-85) cc_final: 0.8759 (mmm-85) REVERT: D 354 LEU cc_start: 0.9043 (tp) cc_final: 0.8785 (tt) REVERT: D 387 ASP cc_start: 0.7862 (t0) cc_final: 0.7618 (t0) outliers start: 139 outliers final: 90 residues processed: 750 average time/residue: 0.2398 time to fit residues: 303.8439 Evaluate side-chains 720 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 613 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2432 ARG Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2056 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2116 TRP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2206 ILE Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2455 GLN Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2660 MET Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1215 THR Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1456 THR Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 330 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 HIS ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2584 ASN C 562 GLN C1126 HIS C1558 GLN D 296 HIS ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.125420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094968 restraints weight = 124069.104| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.43 r_work: 0.3398 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39039 Z= 0.173 Angle : 0.597 11.076 52938 Z= 0.294 Chirality : 0.040 0.188 6127 Planarity : 0.004 0.085 6587 Dihedral : 5.863 80.218 5159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.79 % Allowed : 13.57 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.75 (0.13), residues: 4660 helix: 1.94 (0.09), residues: 3286 sheet: -0.21 (0.75), residues: 35 loop : -0.77 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 255 TYR 0.022 0.001 TYR B 662 PHE 0.025 0.001 PHE A2492 TRP 0.038 0.001 TRP B 219 HIS 0.006 0.001 HIS C1126 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (39017) covalent geometry : angle 0.59629 / 0.29 (52901) SS BOND : bond 0.00139 / 0.09 ( 11) SS BOND : angle 0.95578 / 0.79 ( 22) hydrogen bonds : bond 0.03779 / 2.50 ( 2438) hydrogen bonds : angle 4.12223 / 3.00 ( 7188) metal coordination : bond 0.01455 / 1.08 ( 8) metal coordination : angle 1.07664 / 0.63 ( 6) link_NAG-ASN : bond 0.00172 / 0.06 ( 3) link_NAG-ASN : angle 1.21839 / 0.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 636 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8308 (tt0) cc_final: 0.7861 (tp-100) REVERT: A 202 TRP cc_start: 0.8605 (p-90) cc_final: 0.8292 (p-90) REVERT: A 447 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 491 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: A 500 LYS cc_start: 0.5427 (OUTLIER) cc_final: 0.5012 (mtpt) REVERT: A 519 MET cc_start: 0.8033 (tpp) cc_final: 0.7288 (tpp) REVERT: A 1403 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8491 (tp40) REVERT: A 2433 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7361 (tm) REVERT: A 2442 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7877 (mt) REVERT: A 2488 MET cc_start: 0.7106 (mmt) cc_final: 0.6717 (mmm) REVERT: A 2492 PHE cc_start: 0.9077 (t80) cc_final: 0.8833 (t80) REVERT: A 2543 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7077 (ttm) REVERT: A 2561 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8369 (mpp) REVERT: A 2575 LEU cc_start: 0.8301 (mt) cc_final: 0.8070 (mt) REVERT: B 188 PHE cc_start: 0.8218 (t80) cc_final: 0.7961 (t80) REVERT: B 350 GLN cc_start: 0.7917 (tt0) cc_final: 0.7643 (tp40) REVERT: B 359 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7812 (mmm160) REVERT: B 789 HIS cc_start: 0.7858 (t70) cc_final: 0.7568 (t-90) REVERT: B 1033 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7278 (tpm170) REVERT: B 1808 GLN cc_start: 0.8224 (pt0) cc_final: 0.7953 (tm-30) REVERT: B 2075 ASP cc_start: 0.5249 (OUTLIER) cc_final: 0.4882 (t0) REVERT: B 2206 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8821 (mt) REVERT: B 2277 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8382 (tp-100) REVERT: B 2320 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7928 (mmp80) REVERT: B 2552 ILE cc_start: 0.9056 (mt) cc_final: 0.8817 (mm) REVERT: B 2972 ILE cc_start: 0.9015 (mt) cc_final: 0.8788 (pt) REVERT: C 54 CYS cc_start: 0.9035 (m) cc_final: 0.8795 (m) REVERT: C 141 MET cc_start: 0.7806 (mtp) cc_final: 0.7502 (mtm) REVERT: C 166 ARG cc_start: 0.9010 (mtt-85) cc_final: 0.8459 (ttm-80) REVERT: C 172 LYS cc_start: 0.8513 (mttt) cc_final: 0.7904 (tptt) REVERT: C 235 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7986 (mp0) REVERT: C 243 PHE cc_start: 0.8135 (m-80) cc_final: 0.7691 (m-80) REVERT: C 275 GLU cc_start: 0.8725 (tt0) cc_final: 0.8507 (tt0) REVERT: C 327 GLU cc_start: 0.9110 (tp30) cc_final: 0.8887 (tp30) REVERT: C 331 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7645 (mm-40) REVERT: C 350 MET cc_start: 0.8227 (tpp) cc_final: 0.7867 (mmm) REVERT: C 388 MET cc_start: 0.8151 (mtt) cc_final: 0.7521 (mpp) REVERT: C 395 THR cc_start: 0.9140 (m) cc_final: 0.8887 (p) REVERT: C 398 VAL cc_start: 0.9351 (p) cc_final: 0.9143 (m) REVERT: C 469 LEU cc_start: 0.9187 (mt) cc_final: 0.8956 (mt) REVERT: C 498 LYS cc_start: 0.8528 (tttt) cc_final: 0.8044 (mmmm) REVERT: C 525 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9017 (pp) REVERT: C 527 MET cc_start: 0.8111 (tpp) cc_final: 0.7872 (tpp) REVERT: C 536 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.6678 (mtt180) REVERT: C 547 MET cc_start: 0.8981 (mmp) cc_final: 0.8772 (mmm) REVERT: C 593 LEU cc_start: 0.8943 (mt) cc_final: 0.8695 (mp) REVERT: C 603 GLU cc_start: 0.8317 (tt0) cc_final: 0.8106 (tt0) REVERT: C 606 GLU cc_start: 0.8727 (mp0) cc_final: 0.8403 (pm20) REVERT: C 643 MET cc_start: 0.8750 (mmm) cc_final: 0.7858 (mmm) REVERT: C 886 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7695 (p) REVERT: C 903 MET cc_start: 0.8317 (mtp) cc_final: 0.7924 (ttm) REVERT: C 913 MET cc_start: 0.8569 (mtm) cc_final: 0.8344 (mpp) REVERT: C 926 VAL cc_start: 0.9502 (t) cc_final: 0.9277 (m) REVERT: C 929 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8560 (tpp) REVERT: C 957 MET cc_start: 0.8404 (ptp) cc_final: 0.8161 (ptp) REVERT: C 958 ASP cc_start: 0.8428 (m-30) cc_final: 0.8131 (m-30) REVERT: C 962 TYR cc_start: 0.9105 (t80) cc_final: 0.8752 (t80) REVERT: C 1016 GLU cc_start: 0.9112 (mp0) cc_final: 0.8714 (mp0) REVERT: C 1020 VAL cc_start: 0.9320 (t) cc_final: 0.9052 (p) REVERT: C 1029 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9101 (mt) REVERT: C 1096 PHE cc_start: 0.8641 (p90) cc_final: 0.8027 (p90) REVERT: C 1108 LEU cc_start: 0.9459 (mt) cc_final: 0.9005 (mt) REVERT: C 1162 ASN cc_start: 0.7760 (m110) cc_final: 0.7366 (m110) REVERT: C 1203 MET cc_start: 0.8657 (tpp) cc_final: 0.7809 (tpp) REVERT: C 1259 LYS cc_start: 0.9464 (mtmt) cc_final: 0.9258 (mtpp) REVERT: C 1274 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8138 (t0) REVERT: C 1301 MET cc_start: 0.8611 (ttp) cc_final: 0.8147 (tpt) REVERT: C 1309 PHE cc_start: 0.8944 (m-80) cc_final: 0.8629 (m-80) REVERT: C 1449 ASN cc_start: 0.9052 (m110) cc_final: 0.8681 (m110) REVERT: C 1516 CYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 1536 MET cc_start: 0.8538 (ttt) cc_final: 0.8183 (ttt) REVERT: C 1546 LYS cc_start: 0.9362 (ttpt) cc_final: 0.9144 (tttt) REVERT: C 1564 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 232 LEU cc_start: 0.9093 (tp) cc_final: 0.8507 (tt) REVERT: D 238 TYR cc_start: 0.7878 (m-80) cc_final: 0.7322 (m-80) REVERT: D 244 PHE cc_start: 0.8332 (m-80) cc_final: 0.7588 (m-80) REVERT: D 277 TYR cc_start: 0.8891 (m-10) cc_final: 0.8386 (m-80) REVERT: D 280 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7778 (m-10) REVERT: D 281 ASP cc_start: 0.8528 (t70) cc_final: 0.8199 (t70) REVERT: D 289 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 297 LYS cc_start: 0.9296 (mttm) cc_final: 0.8814 (mttp) REVERT: D 316 VAL cc_start: 0.9001 (t) cc_final: 0.8659 (p) REVERT: D 318 LYS cc_start: 0.8474 (tttt) cc_final: 0.8136 (tttp) REVERT: D 340 LYS cc_start: 0.9286 (mttm) cc_final: 0.8510 (mtpp) outliers start: 160 outliers final: 103 residues processed: 755 average time/residue: 0.2294 time to fit residues: 292.8849 Evaluate side-chains 739 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 616 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2432 ARG Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2543 MET Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2116 TRP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2206 ILE Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2455 GLN Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2603 MET Chi-restraints excluded: chain B residue 2660 MET Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1215 THR Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1516 CYS Chi-restraints excluded: chain C residue 1528 VAL Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 97 optimal weight: 1.9990 chunk 331 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 141 optimal weight: 30.0000 chunk 441 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 291 optimal weight: 0.9990 chunk 209 optimal weight: 0.0370 chunk 27 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 ASN ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2584 ASN C 473 GLN D 296 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.126432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096680 restraints weight = 123310.416| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.26 r_work: 0.3424 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39039 Z= 0.117 Angle : 0.572 12.824 52938 Z= 0.280 Chirality : 0.038 0.223 6127 Planarity : 0.004 0.050 6587 Dihedral : 5.728 77.742 5159 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.39 % Allowed : 14.68 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.85 (0.13), residues: 4660 helix: 2.05 (0.09), residues: 3286 sheet: -0.04 (0.80), residues: 35 loop : -0.84 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2951 TYR 0.023 0.001 TYR B 662 PHE 0.025 0.001 PHE A2572 TRP 0.026 0.001 TRP B 219 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (39017) covalent geometry : angle 0.57162 / 0.28 (52901) SS BOND : bond 0.00117 / 0.08 ( 11) SS BOND : angle 1.02701 / 0.85 ( 22) hydrogen bonds : bond 0.03463 / 2.30 ( 2438) hydrogen bonds : angle 3.99992 / 2.92 ( 7188) metal coordination : bond 0.00909 / 0.68 ( 8) metal coordination : angle 0.94845 / 0.55 ( 6) link_NAG-ASN : bond 0.00197 / 0.06 ( 3) link_NAG-ASN : angle 1.06127 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 632 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 195 MET cc_start: 0.6257 (mmm) cc_final: 0.5834 (mmm) REVERT: A 202 TRP cc_start: 0.8614 (p-90) cc_final: 0.8330 (p-90) REVERT: A 491 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: A 500 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.5032 (mtpt) REVERT: A 519 MET cc_start: 0.8058 (tpp) cc_final: 0.7344 (tpp) REVERT: A 922 MET cc_start: 0.9112 (mtt) cc_final: 0.8750 (mtt) REVERT: A 2442 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 2488 MET cc_start: 0.7063 (mmt) cc_final: 0.6681 (mmm) REVERT: A 2492 PHE cc_start: 0.9061 (t80) cc_final: 0.8785 (t80) REVERT: A 2531 PHE cc_start: 0.7267 (t80) cc_final: 0.7064 (t80) REVERT: A 2543 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7174 (ttm) REVERT: A 2561 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8356 (mpp) REVERT: A 2575 LEU cc_start: 0.8293 (mt) cc_final: 0.8082 (mt) REVERT: B 188 PHE cc_start: 0.8200 (t80) cc_final: 0.7978 (t80) REVERT: B 344 TRP cc_start: 0.7680 (t60) cc_final: 0.6756 (t60) REVERT: B 350 GLN cc_start: 0.7859 (tt0) cc_final: 0.7530 (tp40) REVERT: B 1762 MET cc_start: 0.7921 (tpp) cc_final: 0.7394 (tpp) REVERT: B 1808 GLN cc_start: 0.8220 (pt0) cc_final: 0.7926 (tm-30) REVERT: B 2277 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8349 (tp-100) REVERT: B 2320 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7983 (mmp80) REVERT: B 2427 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: B 2552 ILE cc_start: 0.9029 (mt) cc_final: 0.8800 (mm) REVERT: B 2972 ILE cc_start: 0.9029 (mt) cc_final: 0.8808 (pt) REVERT: C 54 CYS cc_start: 0.8994 (m) cc_final: 0.8720 (p) REVERT: C 55 MET cc_start: 0.7222 (mmm) cc_final: 0.6532 (mmm) REVERT: C 141 MET cc_start: 0.7858 (mtp) cc_final: 0.7547 (mtm) REVERT: C 166 ARG cc_start: 0.8998 (mtt-85) cc_final: 0.8507 (ttm-80) REVERT: C 172 LYS cc_start: 0.8524 (mttt) cc_final: 0.7890 (tptt) REVERT: C 197 VAL cc_start: 0.9248 (t) cc_final: 0.8953 (p) REVERT: C 235 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7886 (mp0) REVERT: C 243 PHE cc_start: 0.8032 (m-80) cc_final: 0.7645 (m-80) REVERT: C 331 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7650 (mm-40) REVERT: C 350 MET cc_start: 0.8121 (tpp) cc_final: 0.7798 (mmm) REVERT: C 388 MET cc_start: 0.8179 (mtt) cc_final: 0.7528 (mpp) REVERT: C 395 THR cc_start: 0.9083 (m) cc_final: 0.8826 (p) REVERT: C 469 LEU cc_start: 0.9177 (mt) cc_final: 0.8939 (mt) REVERT: C 498 LYS cc_start: 0.8421 (tttt) cc_final: 0.7945 (mmmm) REVERT: C 547 MET cc_start: 0.8922 (mmp) cc_final: 0.8595 (mmm) REVERT: C 593 LEU cc_start: 0.8960 (mt) cc_final: 0.8702 (mp) REVERT: C 606 GLU cc_start: 0.8641 (mp0) cc_final: 0.8344 (pm20) REVERT: C 643 MET cc_start: 0.8681 (mmm) cc_final: 0.7806 (mmm) REVERT: C 892 MET cc_start: 0.9052 (mmp) cc_final: 0.8707 (mmp) REVERT: C 903 MET cc_start: 0.8243 (mtp) cc_final: 0.7899 (ttm) REVERT: C 926 VAL cc_start: 0.9474 (t) cc_final: 0.9253 (m) REVERT: C 929 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8513 (tpp) REVERT: C 932 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: C 957 MET cc_start: 0.8538 (ptp) cc_final: 0.8311 (ptp) REVERT: C 958 ASP cc_start: 0.8374 (m-30) cc_final: 0.8031 (m-30) REVERT: C 962 TYR cc_start: 0.9139 (t80) cc_final: 0.8792 (t80) REVERT: C 1016 GLU cc_start: 0.9125 (mp0) cc_final: 0.8699 (mp0) REVERT: C 1029 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9087 (mt) REVERT: C 1096 PHE cc_start: 0.8631 (p90) cc_final: 0.8015 (p90) REVERT: C 1108 LEU cc_start: 0.9424 (mt) cc_final: 0.8948 (mt) REVERT: C 1203 MET cc_start: 0.8660 (tpp) cc_final: 0.7809 (tpp) REVERT: C 1274 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.6947 (t0) REVERT: C 1276 TYR cc_start: 0.8749 (t80) cc_final: 0.8544 (t80) REVERT: C 1277 ASP cc_start: 0.9171 (m-30) cc_final: 0.8835 (p0) REVERT: C 1287 TRP cc_start: 0.8844 (t60) cc_final: 0.8598 (t60) REVERT: C 1301 MET cc_start: 0.8495 (ttp) cc_final: 0.7882 (tpt) REVERT: C 1309 PHE cc_start: 0.8971 (m-80) cc_final: 0.8583 (m-80) REVERT: C 1364 GLU cc_start: 0.8470 (tt0) cc_final: 0.8206 (tt0) REVERT: C 1393 LYS cc_start: 0.9340 (mtpt) cc_final: 0.9084 (mtpp) REVERT: C 1449 ASN cc_start: 0.9051 (m110) cc_final: 0.8655 (m110) REVERT: C 1519 MET cc_start: 0.7946 (mmp) cc_final: 0.7732 (mmt) REVERT: C 1546 LYS cc_start: 0.9324 (ttpt) cc_final: 0.9111 (tttt) REVERT: D 232 LEU cc_start: 0.9046 (tp) cc_final: 0.8411 (tt) REVERT: D 238 TYR cc_start: 0.7826 (m-80) cc_final: 0.7247 (m-80) REVERT: D 244 PHE cc_start: 0.8118 (m-80) cc_final: 0.7813 (m-80) REVERT: D 277 TYR cc_start: 0.8865 (m-10) cc_final: 0.8638 (m-80) REVERT: D 280 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7791 (m-10) REVERT: D 285 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8669 (pp30) REVERT: D 289 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8076 (tm-30) REVERT: D 297 LYS cc_start: 0.9255 (mttm) cc_final: 0.8845 (mttp) REVERT: D 316 VAL cc_start: 0.9021 (t) cc_final: 0.8705 (p) REVERT: D 318 LYS cc_start: 0.8414 (tttt) cc_final: 0.8043 (tttp) REVERT: D 340 LYS cc_start: 0.9343 (mttm) cc_final: 0.9052 (mtpp) REVERT: D 342 TYR cc_start: 0.8991 (m-80) cc_final: 0.8629 (m-10) REVERT: D 387 ASP cc_start: 0.7844 (t0) cc_final: 0.7590 (t0) outliers start: 143 outliers final: 95 residues processed: 728 average time/residue: 0.2170 time to fit residues: 267.5456 Evaluate side-chains 714 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 606 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 2209 LEU Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2431 ILE Chi-restraints excluded: chain A residue 2432 ARG Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2543 MET Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2056 VAL Chi-restraints excluded: chain B residue 2116 TRP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2427 GLU Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1286 VAL Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 254 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2455 GLN B2584 ASN C 562 GLN C1162 ASN ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.125530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094507 restraints weight = 124179.778| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.42 r_work: 0.3201 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39039 Z= 0.183 Angle : 0.605 12.686 52938 Z= 0.297 Chirality : 0.040 0.249 6127 Planarity : 0.004 0.047 6587 Dihedral : 5.652 79.708 5148 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.67 % Allowed : 15.04 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.77 (0.13), residues: 4660 helix: 1.96 (0.09), residues: 3288 sheet: -0.13 (0.79), residues: 35 loop : -0.79 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 334 TYR 0.032 0.001 TYR B 662 PHE 0.037 0.001 PHE D 291 TRP 0.021 0.001 TRP A 453 HIS 0.018 0.001 HIS A2430 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (39017) covalent geometry : angle 0.60408 / 0.30 (52901) SS BOND : bond 0.00120 / 0.08 ( 11) SS BOND : angle 0.98521 / 0.81 ( 22) hydrogen bonds : bond 0.03722 / 2.45 ( 2438) hydrogen bonds : angle 4.08656 / 2.99 ( 7188) metal coordination : bond 0.01489 / 1.10 ( 8) metal coordination : angle 1.07157 / 0.67 ( 6) link_NAG-ASN : bond 0.00191 / 0.07 ( 3) link_NAG-ASN : angle 1.18101 / 0.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 622 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8370 (tt0) cc_final: 0.7989 (tp-100) REVERT: A 195 MET cc_start: 0.6448 (mmm) cc_final: 0.6175 (mmm) REVERT: A 202 TRP cc_start: 0.8574 (p-90) cc_final: 0.8272 (p-90) REVERT: A 487 MET cc_start: 0.6436 (ppp) cc_final: 0.6196 (ppp) REVERT: A 491 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: A 500 LYS cc_start: 0.5476 (OUTLIER) cc_final: 0.5035 (mtpt) REVERT: A 519 MET cc_start: 0.7912 (tpp) cc_final: 0.7225 (tpp) REVERT: A 2436 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.6885 (m-10) REVERT: A 2442 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7934 (mt) REVERT: A 2488 MET cc_start: 0.7127 (mmt) cc_final: 0.6717 (mmm) REVERT: A 2543 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7189 (ttm) REVERT: A 2561 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (mpp) REVERT: B 188 PHE cc_start: 0.8131 (t80) cc_final: 0.7907 (t80) REVERT: B 344 TRP cc_start: 0.7574 (t60) cc_final: 0.6802 (t60) REVERT: B 350 GLN cc_start: 0.7778 (tt0) cc_final: 0.7457 (tp40) REVERT: B 789 HIS cc_start: 0.7840 (t70) cc_final: 0.7454 (t-170) REVERT: B 1033 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7311 (tpm170) REVERT: B 1762 MET cc_start: 0.8105 (tpp) cc_final: 0.7417 (tpp) REVERT: B 1808 GLN cc_start: 0.8165 (pt0) cc_final: 0.7888 (tm-30) REVERT: B 2075 ASP cc_start: 0.5311 (OUTLIER) cc_final: 0.4890 (t0) REVERT: B 2277 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8497 (tp-100) REVERT: B 2320 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8044 (mmp80) REVERT: B 2552 ILE cc_start: 0.9074 (mt) cc_final: 0.8810 (mm) REVERT: B 2801 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7626 (mp0) REVERT: B 2972 ILE cc_start: 0.8981 (mt) cc_final: 0.8756 (pt) REVERT: C 54 CYS cc_start: 0.9027 (m) cc_final: 0.8695 (m) REVERT: C 141 MET cc_start: 0.7922 (mtp) cc_final: 0.7605 (mtm) REVERT: C 166 ARG cc_start: 0.8996 (mtt-85) cc_final: 0.8471 (ttm-80) REVERT: C 172 LYS cc_start: 0.8456 (mttt) cc_final: 0.7847 (tptt) REVERT: C 197 VAL cc_start: 0.9308 (t) cc_final: 0.8976 (p) REVERT: C 226 ASP cc_start: 0.8513 (t0) cc_final: 0.7944 (p0) REVERT: C 235 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7935 (mp0) REVERT: C 243 PHE cc_start: 0.8112 (m-80) cc_final: 0.7717 (m-80) REVERT: C 331 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7665 (mm-40) REVERT: C 350 MET cc_start: 0.8288 (tpp) cc_final: 0.7833 (mmm) REVERT: C 388 MET cc_start: 0.8180 (mtt) cc_final: 0.7522 (mpp) REVERT: C 395 THR cc_start: 0.9150 (m) cc_final: 0.8849 (p) REVERT: C 469 LEU cc_start: 0.9232 (mt) cc_final: 0.9001 (mt) REVERT: C 498 LYS cc_start: 0.8342 (tttt) cc_final: 0.7869 (mmmm) REVERT: C 520 MET cc_start: 0.9336 (mmp) cc_final: 0.9091 (mmm) REVERT: C 525 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8924 (pp) REVERT: C 547 MET cc_start: 0.9085 (mmp) cc_final: 0.8747 (mmm) REVERT: C 643 MET cc_start: 0.8782 (mmm) cc_final: 0.7842 (mmm) REVERT: C 892 MET cc_start: 0.9230 (mmp) cc_final: 0.8981 (mmp) REVERT: C 903 MET cc_start: 0.8461 (mtp) cc_final: 0.7998 (ttm) REVERT: C 926 VAL cc_start: 0.9540 (t) cc_final: 0.9309 (m) REVERT: C 929 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8579 (tpp) REVERT: C 932 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: C 962 TYR cc_start: 0.9188 (t80) cc_final: 0.8837 (t80) REVERT: C 1029 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9075 (mt) REVERT: C 1096 PHE cc_start: 0.8670 (p90) cc_final: 0.8054 (p90) REVERT: C 1108 LEU cc_start: 0.9491 (mt) cc_final: 0.9019 (mt) REVERT: C 1203 MET cc_start: 0.8463 (tpp) cc_final: 0.7576 (tpp) REVERT: C 1260 ILE cc_start: 0.9129 (mt) cc_final: 0.8921 (mt) REVERT: C 1274 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8187 (t0) REVERT: C 1276 TYR cc_start: 0.8841 (t80) cc_final: 0.8569 (t80) REVERT: C 1287 TRP cc_start: 0.8940 (t60) cc_final: 0.8642 (t60) REVERT: C 1301 MET cc_start: 0.8516 (ttp) cc_final: 0.7829 (tpt) REVERT: C 1309 PHE cc_start: 0.8915 (m-80) cc_final: 0.8486 (m-80) REVERT: C 1449 ASN cc_start: 0.9112 (m110) cc_final: 0.8660 (m110) REVERT: C 1517 TYR cc_start: 0.7657 (t80) cc_final: 0.7455 (t80) REVERT: C 1519 MET cc_start: 0.8106 (mmp) cc_final: 0.7846 (mmt) REVERT: D 232 LEU cc_start: 0.9165 (tp) cc_final: 0.8803 (tt) REVERT: D 234 PHE cc_start: 0.8685 (t80) cc_final: 0.8247 (t80) REVERT: D 238 TYR cc_start: 0.7866 (m-80) cc_final: 0.7234 (m-80) REVERT: D 277 TYR cc_start: 0.8854 (m-10) cc_final: 0.8541 (m-80) REVERT: D 280 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7690 (m-10) REVERT: D 281 ASP cc_start: 0.8639 (t70) cc_final: 0.8419 (t0) REVERT: D 289 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8200 (tm-30) REVERT: D 297 LYS cc_start: 0.9252 (mttm) cc_final: 0.8844 (mttp) REVERT: D 312 ASP cc_start: 0.8199 (t0) cc_final: 0.7477 (t0) REVERT: D 316 VAL cc_start: 0.9041 (t) cc_final: 0.8751 (p) REVERT: D 318 LYS cc_start: 0.8495 (tttt) cc_final: 0.8086 (tttp) REVERT: D 349 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8487 (mmm-85) outliers start: 155 outliers final: 107 residues processed: 733 average time/residue: 0.2315 time to fit residues: 285.4023 Evaluate side-chains 718 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 595 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 2209 LEU Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2431 ILE Chi-restraints excluded: chain A residue 2432 ARG Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2543 MET Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2660 MET Chi-restraints excluded: chain B residue 2764 HIS Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1020 VAL Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1224 SER Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 40 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 278 optimal weight: 0.6980 chunk 292 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 337 optimal weight: 8.9990 chunk 461 optimal weight: 2.9990 chunk 473 optimal weight: 3.9990 chunk 462 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS C 333 GLN C 549 GLN C1270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094534 restraints weight = 123864.825| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.22 r_work: 0.3221 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39039 Z= 0.134 Angle : 0.593 13.538 52938 Z= 0.290 Chirality : 0.039 0.248 6127 Planarity : 0.004 0.048 6587 Dihedral : 5.612 78.778 5148 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.60 % Allowed : 15.46 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.80 (0.13), residues: 4660 helix: 2.00 (0.09), residues: 3287 sheet: -0.06 (0.79), residues: 35 loop : -0.83 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1468 TYR 0.034 0.001 TYR B 662 PHE 0.040 0.001 PHE D 291 TRP 0.024 0.001 TRP A 453 HIS 0.020 0.001 HIS A2430 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (39017) covalent geometry : angle 0.59245 / 0.29 (52901) SS BOND : bond 0.00139 / 0.10 ( 11) SS BOND : angle 1.00246 / 0.82 ( 22) hydrogen bonds : bond 0.03526 / 2.33 ( 2438) hydrogen bonds : angle 4.02771 / 2.95 ( 7188) metal coordination : bond 0.01112 / 0.83 ( 8) metal coordination : angle 1.09465 / 0.66 ( 6) link_NAG-ASN : bond 0.00190 / 0.06 ( 3) link_NAG-ASN : angle 1.07086 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 605 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 195 MET cc_start: 0.6471 (mmm) cc_final: 0.6173 (mmm) REVERT: A 202 TRP cc_start: 0.8592 (p-90) cc_final: 0.8294 (p-90) REVERT: A 447 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 479 GLN cc_start: 0.7998 (mt0) cc_final: 0.7632 (tt0) REVERT: A 487 MET cc_start: 0.6064 (ppp) cc_final: 0.5735 (ppp) REVERT: A 491 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: A 500 LYS cc_start: 0.5453 (OUTLIER) cc_final: 0.5028 (mtpt) REVERT: A 519 MET cc_start: 0.7902 (tpp) cc_final: 0.7227 (tpp) REVERT: A 922 MET cc_start: 0.9151 (mtt) cc_final: 0.8730 (mtt) REVERT: A 2442 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (mt) REVERT: A 2488 MET cc_start: 0.7028 (mmt) cc_final: 0.6606 (mmm) REVERT: A 2492 PHE cc_start: 0.9090 (t80) cc_final: 0.8869 (t80) REVERT: A 2543 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7110 (ttm) REVERT: A 2561 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8395 (mpp) REVERT: B 188 PHE cc_start: 0.8117 (t80) cc_final: 0.7891 (t80) REVERT: B 350 GLN cc_start: 0.7775 (tt0) cc_final: 0.7452 (tp40) REVERT: B 689 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8212 (m) REVERT: B 1033 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7278 (tpm170) REVERT: B 1808 GLN cc_start: 0.8180 (pt0) cc_final: 0.7887 (tm-30) REVERT: B 2075 ASP cc_start: 0.5230 (OUTLIER) cc_final: 0.4824 (t0) REVERT: B 2277 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8462 (tp-100) REVERT: B 2320 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8038 (mmp80) REVERT: B 2552 ILE cc_start: 0.9054 (mt) cc_final: 0.8798 (mm) REVERT: B 2801 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7640 (mp0) REVERT: B 2972 ILE cc_start: 0.8985 (mt) cc_final: 0.8762 (pt) REVERT: C 141 MET cc_start: 0.7900 (mtp) cc_final: 0.7586 (mtm) REVERT: C 166 ARG cc_start: 0.8938 (mtt-85) cc_final: 0.8344 (ttm-80) REVERT: C 172 LYS cc_start: 0.8420 (mttt) cc_final: 0.7798 (tptt) REVERT: C 189 LEU cc_start: 0.9122 (mt) cc_final: 0.8891 (mt) REVERT: C 197 VAL cc_start: 0.9299 (t) cc_final: 0.8979 (p) REVERT: C 235 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7903 (mp0) REVERT: C 243 PHE cc_start: 0.8058 (m-80) cc_final: 0.7682 (m-80) REVERT: C 275 GLU cc_start: 0.8831 (tt0) cc_final: 0.8522 (tt0) REVERT: C 331 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7837 (mm-40) REVERT: C 388 MET cc_start: 0.8165 (mtt) cc_final: 0.7501 (mpp) REVERT: C 395 THR cc_start: 0.9123 (m) cc_final: 0.8834 (p) REVERT: C 469 LEU cc_start: 0.9203 (mt) cc_final: 0.8981 (mt) REVERT: C 498 LYS cc_start: 0.8328 (tttt) cc_final: 0.7846 (mmmm) REVERT: C 520 MET cc_start: 0.9375 (mmp) cc_final: 0.9156 (mmm) REVERT: C 525 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8876 (pp) REVERT: C 547 MET cc_start: 0.9040 (mmp) cc_final: 0.8695 (mmm) REVERT: C 562 GLN cc_start: 0.8791 (tt0) cc_final: 0.8570 (pt0) REVERT: C 593 LEU cc_start: 0.8877 (mp) cc_final: 0.8614 (mp) REVERT: C 643 MET cc_start: 0.8748 (mmm) cc_final: 0.7790 (mmm) REVERT: C 903 MET cc_start: 0.8435 (mtp) cc_final: 0.8058 (ttm) REVERT: C 926 VAL cc_start: 0.9486 (t) cc_final: 0.9259 (m) REVERT: C 929 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8548 (tpt) REVERT: C 962 TYR cc_start: 0.9135 (t80) cc_final: 0.8796 (t80) REVERT: C 1004 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.7801 (tmt-80) REVERT: C 1096 PHE cc_start: 0.8653 (p90) cc_final: 0.7994 (p90) REVERT: C 1108 LEU cc_start: 0.9465 (mt) cc_final: 0.8988 (mt) REVERT: C 1203 MET cc_start: 0.8440 (tpp) cc_final: 0.7572 (tpp) REVERT: C 1274 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7949 (t0) REVERT: C 1277 ASP cc_start: 0.9180 (m-30) cc_final: 0.8979 (p0) REVERT: C 1287 TRP cc_start: 0.8932 (t60) cc_final: 0.8681 (t60) REVERT: C 1301 MET cc_start: 0.8585 (ttp) cc_final: 0.7921 (tpt) REVERT: C 1309 PHE cc_start: 0.8881 (m-10) cc_final: 0.8463 (m-80) REVERT: C 1449 ASN cc_start: 0.9100 (m110) cc_final: 0.8693 (m110) REVERT: C 1519 MET cc_start: 0.8072 (mmp) cc_final: 0.7818 (mmt) REVERT: D 232 LEU cc_start: 0.9133 (tp) cc_final: 0.8690 (tt) REVERT: D 234 PHE cc_start: 0.8662 (t80) cc_final: 0.8182 (t80) REVERT: D 238 TYR cc_start: 0.7786 (m-80) cc_final: 0.7132 (m-80) REVERT: D 277 TYR cc_start: 0.8876 (m-10) cc_final: 0.8572 (m-80) REVERT: D 280 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: D 285 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8747 (pp30) REVERT: D 289 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8200 (tm-30) REVERT: D 297 LYS cc_start: 0.9178 (mttm) cc_final: 0.8928 (mtmm) REVERT: D 312 ASP cc_start: 0.8176 (t0) cc_final: 0.7917 (t70) REVERT: D 316 VAL cc_start: 0.9000 (t) cc_final: 0.8757 (p) REVERT: D 318 LYS cc_start: 0.8511 (tttt) cc_final: 0.8119 (tttp) REVERT: D 342 TYR cc_start: 0.8975 (m-80) cc_final: 0.8640 (m-10) REVERT: D 349 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8478 (mmm-85) REVERT: D 387 ASP cc_start: 0.7852 (t0) cc_final: 0.7580 (t0) outliers start: 152 outliers final: 106 residues processed: 710 average time/residue: 0.2283 time to fit residues: 273.1928 Evaluate side-chains 707 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 586 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2276 TYR Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2431 ILE Chi-restraints excluded: chain A residue 2432 ARG Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2543 MET Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1032 TRP Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1914 CYS Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2764 HIS Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1020 VAL Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1224 SER Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 380 optimal weight: 2.9990 chunk 200 optimal weight: 0.3980 chunk 246 optimal weight: 7.9990 chunk 347 optimal weight: 0.9990 chunk 452 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 250 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1661 GLN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1270 GLN ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** 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 = 0.4213 r_free = 0.4213 target = 0.126514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096720 restraints weight = 123834.945| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.19 r_work: 0.3426 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39039 Z= 0.122 Angle : 0.609 16.047 52938 Z= 0.293 Chirality : 0.039 0.294 6127 Planarity : 0.004 0.048 6587 Dihedral : 5.552 77.649 5146 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.22 % Allowed : 16.34 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.81 (0.13), residues: 4660 helix: 2.01 (0.09), residues: 3292 sheet: -0.03 (0.81), residues: 35 loop : -0.84 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 334 TYR 0.038 0.001 TYR B 662 PHE 0.026 0.001 PHE D 234 TRP 0.027 0.001 TRP A 453 HIS 0.024 0.001 HIS A2430 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (39017) covalent geometry : angle 0.60832 / 0.29 (52901) SS BOND : bond 0.00319 / 0.19 ( 11) SS BOND : angle 1.22039 / 0.91 ( 22) hydrogen bonds : bond 0.03447 / 2.28 ( 2438) hydrogen bonds : angle 4.00932 / 2.93 ( 7188) metal coordination : bond 0.00929 / 0.70 ( 8) metal coordination : angle 1.05535 / 0.61 ( 6) link_NAG-ASN : bond 0.00174 / 0.05 ( 3) link_NAG-ASN : angle 1.02243 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 617 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 195 MET cc_start: 0.6529 (mmm) cc_final: 0.6217 (mmm) REVERT: A 447 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 479 GLN cc_start: 0.8017 (mt0) cc_final: 0.7630 (tt0) REVERT: A 487 MET cc_start: 0.5992 (ppp) cc_final: 0.5627 (ppp) REVERT: A 491 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: A 500 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.5152 (mtpt) REVERT: A 922 MET cc_start: 0.9119 (mtt) cc_final: 0.8740 (mtt) REVERT: A 2397 HIS cc_start: 0.7851 (m90) cc_final: 0.7578 (m90) REVERT: A 2433 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7246 (tp) REVERT: A 2442 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8016 (mt) REVERT: A 2488 MET cc_start: 0.6905 (mmt) cc_final: 0.6518 (mmm) REVERT: A 2492 PHE cc_start: 0.9065 (t80) cc_final: 0.8848 (t80) REVERT: A 2543 MET cc_start: 0.7326 (ttm) cc_final: 0.7120 (ttm) REVERT: A 2552 MET cc_start: 0.6560 (mtp) cc_final: 0.6253 (ttp) REVERT: A 2561 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (mpp) REVERT: A 2582 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7561 (ptp) REVERT: B 49 PHE cc_start: 0.6072 (m-10) cc_final: 0.5833 (m-10) REVERT: B 350 GLN cc_start: 0.7846 (tt0) cc_final: 0.7512 (tp40) REVERT: B 789 HIS cc_start: 0.7687 (t70) cc_final: 0.7394 (t-170) REVERT: B 1033 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7151 (tpm170) REVERT: B 1762 MET cc_start: 0.7991 (tpp) cc_final: 0.7700 (mmm) REVERT: B 1808 GLN cc_start: 0.8219 (pt0) cc_final: 0.7920 (tm-30) REVERT: B 2075 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4805 (t0) REVERT: B 2277 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8386 (tp-100) REVERT: B 2320 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.8000 (mmp80) REVERT: B 2552 ILE cc_start: 0.9018 (mt) cc_final: 0.8790 (mm) REVERT: B 2972 ILE cc_start: 0.9031 (mt) cc_final: 0.8810 (pt) REVERT: C 114 MET cc_start: 0.8458 (mmt) cc_final: 0.8192 (mmt) REVERT: C 141 MET cc_start: 0.7747 (mtp) cc_final: 0.7442 (mtm) REVERT: C 166 ARG cc_start: 0.8913 (mtt-85) cc_final: 0.8263 (ttm110) REVERT: C 172 LYS cc_start: 0.8319 (mttt) cc_final: 0.7698 (ptpt) REVERT: C 189 LEU cc_start: 0.9147 (mt) cc_final: 0.8912 (mt) REVERT: C 197 VAL cc_start: 0.9261 (t) cc_final: 0.8958 (p) REVERT: C 235 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7914 (mp0) REVERT: C 243 PHE cc_start: 0.7980 (m-80) cc_final: 0.7660 (m-80) REVERT: C 275 GLU cc_start: 0.8757 (tt0) cc_final: 0.8443 (tt0) REVERT: C 331 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7740 (mm110) REVERT: C 388 MET cc_start: 0.8175 (mtt) cc_final: 0.7504 (mpp) REVERT: C 469 LEU cc_start: 0.9173 (mt) cc_final: 0.8946 (mt) REVERT: C 498 LYS cc_start: 0.8332 (tttt) cc_final: 0.7840 (mmmm) REVERT: C 520 MET cc_start: 0.9265 (mmp) cc_final: 0.9053 (mmm) REVERT: C 525 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8890 (pp) REVERT: C 578 TYR cc_start: 0.9187 (t80) cc_final: 0.8731 (t80) REVERT: C 643 MET cc_start: 0.8688 (mmm) cc_final: 0.7786 (mmm) REVERT: C 892 MET cc_start: 0.9006 (mmp) cc_final: 0.8644 (mmp) REVERT: C 903 MET cc_start: 0.8236 (mtp) cc_final: 0.7967 (ttm) REVERT: C 929 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8533 (tpt) REVERT: C 932 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: C 962 TYR cc_start: 0.9037 (t80) cc_final: 0.8695 (t80) REVERT: C 995 ARG cc_start: 0.8930 (mtp-110) cc_final: 0.8545 (mmm160) REVERT: C 998 LYS cc_start: 0.8901 (tttm) cc_final: 0.8660 (ttmt) REVERT: C 1004 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.7811 (tmt-80) REVERT: C 1019 LEU cc_start: 0.9381 (tp) cc_final: 0.9094 (tp) REVERT: C 1096 PHE cc_start: 0.8591 (p90) cc_final: 0.7941 (p90) REVERT: C 1108 LEU cc_start: 0.9391 (mt) cc_final: 0.8891 (mt) REVERT: C 1203 MET cc_start: 0.8432 (tpp) cc_final: 0.7558 (tpp) REVERT: C 1274 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7999 (t0) REVERT: C 1276 TYR cc_start: 0.8883 (t80) cc_final: 0.8673 (t80) REVERT: C 1277 ASP cc_start: 0.9070 (m-30) cc_final: 0.8741 (p0) REVERT: C 1301 MET cc_start: 0.8611 (ttp) cc_final: 0.7959 (tpt) REVERT: C 1309 PHE cc_start: 0.8851 (m-10) cc_final: 0.8542 (m-80) REVERT: C 1393 LYS cc_start: 0.9138 (mttm) cc_final: 0.8821 (mtpp) REVERT: C 1449 ASN cc_start: 0.9014 (m110) cc_final: 0.8641 (m110) REVERT: C 1519 MET cc_start: 0.8208 (mmp) cc_final: 0.7883 (mmt) REVERT: D 234 PHE cc_start: 0.8529 (t80) cc_final: 0.7747 (t80) REVERT: D 238 TYR cc_start: 0.7625 (m-80) cc_final: 0.7097 (m-80) REVERT: D 244 PHE cc_start: 0.8043 (m-80) cc_final: 0.7160 (m-80) REVERT: D 277 TYR cc_start: 0.8813 (m-10) cc_final: 0.8492 (m-80) REVERT: D 280 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: D 285 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8629 (pp30) REVERT: D 289 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8140 (tm-30) REVERT: D 297 LYS cc_start: 0.9208 (mttm) cc_final: 0.8963 (mtmm) REVERT: D 318 LYS cc_start: 0.8526 (tttt) cc_final: 0.8176 (tttp) REVERT: D 342 TYR cc_start: 0.8872 (m-80) cc_final: 0.8575 (m-10) REVERT: D 348 THR cc_start: 0.9166 (m) cc_final: 0.8950 (p) REVERT: D 387 ASP cc_start: 0.7859 (t0) cc_final: 0.7614 (t0) outliers start: 136 outliers final: 105 residues processed: 711 average time/residue: 0.2381 time to fit residues: 286.0810 Evaluate side-chains 713 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 592 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2276 TYR Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2431 ILE Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 PHE Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1032 TRP Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2207 ASP Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2295 LEU Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2387 GLU Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2764 HIS Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1020 VAL Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1224 SER Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 106 optimal weight: 4.9990 chunk 344 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 437 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 319 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 358 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2092 ASN A2556 HIS ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.126865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096932 restraints weight = 124594.997| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.27 r_work: 0.3251 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39039 Z= 0.121 Angle : 0.623 17.592 52938 Z= 0.300 Chirality : 0.039 0.268 6127 Planarity : 0.004 0.052 6587 Dihedral : 5.509 76.838 5143 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.75 % Allowed : 17.05 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.85 (0.13), residues: 4660 helix: 2.02 (0.09), residues: 3299 sheet: -0.07 (0.81), residues: 35 loop : -0.78 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 334 TYR 0.033 0.001 TYR B 662 PHE 0.034 0.001 PHE A2572 TRP 0.057 0.001 TRP C1287 HIS 0.026 0.001 HIS A2430 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (39017) covalent geometry : angle 0.62267 / 0.30 (52901) SS BOND : bond 0.00118 / 0.08 ( 11) SS BOND : angle 1.11539 / 0.85 ( 22) hydrogen bonds : bond 0.03414 / 2.26 ( 2438) hydrogen bonds : angle 3.98551 / 2.92 ( 7188) metal coordination : bond 0.00871 / 0.65 ( 8) metal coordination : angle 1.04127 / 0.60 ( 6) link_NAG-ASN : bond 0.00179 / 0.06 ( 3) link_NAG-ASN : angle 0.99703 / 0.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 611 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 175 MET cc_start: 0.8011 (tpt) cc_final: 0.7099 (tpt) REVERT: A 195 MET cc_start: 0.6521 (mmm) cc_final: 0.6204 (mmm) REVERT: A 447 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 479 GLN cc_start: 0.8008 (mt0) cc_final: 0.7651 (tt0) REVERT: A 487 MET cc_start: 0.5886 (ppp) cc_final: 0.5544 (ppp) REVERT: A 491 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: A 500 LYS cc_start: 0.5423 (OUTLIER) cc_final: 0.5133 (mtpt) REVERT: A 519 MET cc_start: 0.7888 (tpp) cc_final: 0.7343 (ttm) REVERT: A 922 MET cc_start: 0.9129 (mtt) cc_final: 0.8771 (mtt) REVERT: A 2397 HIS cc_start: 0.7821 (m90) cc_final: 0.7576 (m90) REVERT: A 2442 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8008 (mt) REVERT: A 2469 HIS cc_start: 0.3494 (OUTLIER) cc_final: 0.2516 (t70) REVERT: A 2492 PHE cc_start: 0.9072 (t80) cc_final: 0.8841 (t80) REVERT: A 2561 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8249 (mpp) REVERT: A 2582 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7590 (ptp) REVERT: B 49 PHE cc_start: 0.6049 (m-10) cc_final: 0.5809 (m-10) REVERT: B 350 GLN cc_start: 0.7780 (tt0) cc_final: 0.7454 (tp40) REVERT: B 789 HIS cc_start: 0.7682 (t70) cc_final: 0.7364 (t-170) REVERT: B 1033 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7101 (tpm170) REVERT: B 1762 MET cc_start: 0.8028 (tpp) cc_final: 0.7730 (mmm) REVERT: B 1808 GLN cc_start: 0.8188 (pt0) cc_final: 0.7875 (tm-30) REVERT: B 2075 ASP cc_start: 0.5092 (OUTLIER) cc_final: 0.4655 (t0) REVERT: B 2277 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8501 (tp-100) REVERT: B 2320 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8101 (mmp80) REVERT: B 2552 ILE cc_start: 0.9079 (mt) cc_final: 0.8811 (mm) REVERT: B 2972 ILE cc_start: 0.9002 (mt) cc_final: 0.8778 (pt) REVERT: C 61 PHE cc_start: 0.7725 (m-10) cc_final: 0.7435 (m-80) REVERT: C 114 MET cc_start: 0.8482 (mmt) cc_final: 0.8217 (mmt) REVERT: C 141 MET cc_start: 0.7708 (mtp) cc_final: 0.7417 (mtm) REVERT: C 166 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.8211 (ttm110) REVERT: C 172 LYS cc_start: 0.8196 (mttt) cc_final: 0.7605 (ptpt) REVERT: C 189 LEU cc_start: 0.9109 (mt) cc_final: 0.8886 (mt) REVERT: C 197 VAL cc_start: 0.9256 (t) cc_final: 0.8941 (p) REVERT: C 235 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7920 (mp0) REVERT: C 243 PHE cc_start: 0.7981 (m-80) cc_final: 0.7586 (m-80) REVERT: C 275 GLU cc_start: 0.8740 (tt0) cc_final: 0.8473 (tt0) REVERT: C 323 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 331 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7555 (mm-40) REVERT: C 388 MET cc_start: 0.8143 (mtt) cc_final: 0.7481 (mpp) REVERT: C 456 LEU cc_start: 0.9284 (tt) cc_final: 0.8971 (pp) REVERT: C 469 LEU cc_start: 0.9203 (mt) cc_final: 0.8938 (mt) REVERT: C 498 LYS cc_start: 0.8308 (tttt) cc_final: 0.7805 (mmmm) REVERT: C 525 LEU cc_start: 0.9223 (tt) cc_final: 0.8918 (pp) REVERT: C 562 GLN cc_start: 0.8815 (tt0) cc_final: 0.8528 (pt0) REVERT: C 578 TYR cc_start: 0.9193 (t80) cc_final: 0.8815 (t80) REVERT: C 593 LEU cc_start: 0.8838 (mt) cc_final: 0.8554 (mp) REVERT: C 643 MET cc_start: 0.8704 (mmm) cc_final: 0.7772 (mmm) REVERT: C 892 MET cc_start: 0.9112 (mmp) cc_final: 0.8723 (mmp) REVERT: C 903 MET cc_start: 0.8413 (mtp) cc_final: 0.8099 (ttm) REVERT: C 929 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8532 (tpt) REVERT: C 932 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: C 962 TYR cc_start: 0.9009 (t80) cc_final: 0.8678 (t80) REVERT: C 995 ARG cc_start: 0.8933 (mtp-110) cc_final: 0.8524 (mmm160) REVERT: C 998 LYS cc_start: 0.9043 (tttm) cc_final: 0.8742 (tptt) REVERT: C 1004 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.7881 (tpt170) REVERT: C 1108 LEU cc_start: 0.9486 (mt) cc_final: 0.8976 (mt) REVERT: C 1141 PHE cc_start: 0.8871 (t80) cc_final: 0.8572 (t80) REVERT: C 1145 MET cc_start: 0.9172 (mmm) cc_final: 0.8574 (mpp) REVERT: C 1203 MET cc_start: 0.8386 (tpp) cc_final: 0.7514 (tpp) REVERT: C 1273 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6664 (ptp90) REVERT: C 1276 TYR cc_start: 0.8970 (t80) cc_final: 0.8612 (t80) REVERT: C 1301 MET cc_start: 0.8476 (ttp) cc_final: 0.7754 (tpt) REVERT: C 1309 PHE cc_start: 0.8857 (m-10) cc_final: 0.8482 (m-80) REVERT: C 1311 PHE cc_start: 0.9218 (t80) cc_final: 0.8988 (t80) REVERT: C 1449 ASN cc_start: 0.9047 (m110) cc_final: 0.8642 (m110) REVERT: C 1519 MET cc_start: 0.8219 (mmp) cc_final: 0.7861 (mmt) REVERT: D 234 PHE cc_start: 0.8610 (t80) cc_final: 0.8171 (t80) REVERT: D 238 TYR cc_start: 0.7590 (m-80) cc_final: 0.6900 (m-80) REVERT: D 244 PHE cc_start: 0.8037 (m-80) cc_final: 0.7150 (m-80) REVERT: D 277 TYR cc_start: 0.8858 (m-10) cc_final: 0.8528 (m-80) REVERT: D 280 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: D 285 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8604 (pp30) REVERT: D 289 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 332 ASN cc_start: 0.7666 (t0) cc_final: 0.7435 (t0) REVERT: D 334 ARG cc_start: 0.9127 (mmp80) cc_final: 0.8344 (mmp80) REVERT: D 335 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8499 (mptt) REVERT: D 340 LYS cc_start: 0.9350 (mttm) cc_final: 0.8557 (mtpp) REVERT: D 342 TYR cc_start: 0.9013 (m-80) cc_final: 0.8307 (m-80) REVERT: D 368 PHE cc_start: 0.8403 (t80) cc_final: 0.8079 (t80) REVERT: D 387 ASP cc_start: 0.7700 (t0) cc_final: 0.7146 (t0) outliers start: 116 outliers final: 91 residues processed: 695 average time/residue: 0.2331 time to fit residues: 273.0412 Evaluate side-chains 701 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 595 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2276 TYR Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2431 ILE Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2469 HIS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1032 TRP Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1359 GLU Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2277 GLN Chi-restraints excluded: chain B residue 2295 LEU Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2387 GLU Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2764 HIS Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1020 VAL Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1224 SER Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1273 ARG Chi-restraints excluded: chain C residue 1274 ASN Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1544 ILE Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 302 optimal weight: 0.9980 chunk 464 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 461 optimal weight: 0.0370 chunk 383 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 240 optimal weight: 1.9990 chunk 413 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 465 optimal weight: 9.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 HIS A2444 HIS B 666 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.127076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097534 restraints weight = 123842.963| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.33 r_work: 0.3441 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39039 Z= 0.120 Angle : 0.624 14.549 52938 Z= 0.302 Chirality : 0.039 0.354 6127 Planarity : 0.004 0.054 6587 Dihedral : 5.428 76.216 5138 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.77 % Allowed : 17.22 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.88 (0.13), residues: 4660 helix: 2.04 (0.09), residues: 3302 sheet: -0.19 (0.81), residues: 35 loop : -0.78 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 334 TYR 0.034 0.001 TYR D 317 PHE 0.038 0.001 PHE C1268 TRP 0.033 0.001 TRP A 453 HIS 0.028 0.001 HIS A2430 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (39017) covalent geometry : angle 0.62381 / 0.30 (52901) SS BOND : bond 0.00124 / 0.08 ( 11) SS BOND : angle 1.07381 / 0.82 ( 22) hydrogen bonds : bond 0.03355 / 2.21 ( 2438) hydrogen bonds : angle 3.98845 / 2.92 ( 7188) metal coordination : bond 0.00786 / 0.59 ( 8) metal coordination : angle 1.01777 / 0.56 ( 6) link_NAG-ASN : bond 0.00163 / 0.06 ( 3) link_NAG-ASN : angle 0.97757 / 0.47 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 611 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 175 MET cc_start: 0.8055 (tpt) cc_final: 0.7132 (tpt) REVERT: A 195 MET cc_start: 0.6519 (mmm) cc_final: 0.6198 (mmm) REVERT: A 447 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 479 GLN cc_start: 0.8012 (mt0) cc_final: 0.7659 (tt0) REVERT: A 487 MET cc_start: 0.5917 (ppp) cc_final: 0.5613 (ppp) REVERT: A 491 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: A 500 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.5010 (mtpt) REVERT: A 519 MET cc_start: 0.8003 (tpp) cc_final: 0.7381 (ttm) REVERT: A 922 MET cc_start: 0.9095 (mtt) cc_final: 0.8766 (mtt) REVERT: A 2397 HIS cc_start: 0.7702 (m90) cc_final: 0.7501 (m90) REVERT: A 2442 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 2469 HIS cc_start: 0.3500 (OUTLIER) cc_final: 0.2422 (t70) REVERT: A 2561 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8224 (mpp) REVERT: A 2582 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7743 (ptp) REVERT: B 49 PHE cc_start: 0.6046 (m-10) cc_final: 0.5845 (m-10) REVERT: B 350 GLN cc_start: 0.7787 (tt0) cc_final: 0.7450 (tp40) REVERT: B 843 ILE cc_start: 0.9185 (mm) cc_final: 0.8836 (tp) REVERT: B 1033 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7105 (tpm170) REVERT: B 1808 GLN cc_start: 0.8225 (pt0) cc_final: 0.7898 (tm-30) REVERT: B 2075 ASP cc_start: 0.5078 (OUTLIER) cc_final: 0.4651 (t0) REVERT: B 2320 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7999 (mmp80) REVERT: B 2552 ILE cc_start: 0.9046 (mt) cc_final: 0.8806 (mm) REVERT: B 2972 ILE cc_start: 0.9015 (mt) cc_final: 0.8795 (pt) REVERT: C 61 PHE cc_start: 0.7682 (m-10) cc_final: 0.7443 (m-80) REVERT: C 114 MET cc_start: 0.8588 (mmt) cc_final: 0.8294 (mmt) REVERT: C 141 MET cc_start: 0.7712 (mtp) cc_final: 0.7431 (mtm) REVERT: C 166 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8149 (ttm110) REVERT: C 172 LYS cc_start: 0.7991 (mttt) cc_final: 0.7396 (ptpt) REVERT: C 179 TRP cc_start: 0.8251 (t-100) cc_final: 0.7733 (t60) REVERT: C 184 PHE cc_start: 0.8929 (t80) cc_final: 0.8547 (t80) REVERT: C 189 LEU cc_start: 0.9125 (mt) cc_final: 0.8893 (mt) REVERT: C 197 VAL cc_start: 0.9241 (t) cc_final: 0.8936 (p) REVERT: C 235 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7916 (mp0) REVERT: C 243 PHE cc_start: 0.7876 (m-80) cc_final: 0.7511 (m-80) REVERT: C 275 GLU cc_start: 0.8644 (tt0) cc_final: 0.8338 (tt0) REVERT: C 286 MET cc_start: 0.8879 (ttm) cc_final: 0.8536 (tpp) REVERT: C 323 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8628 (tm-30) REVERT: C 331 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7612 (mm-40) REVERT: C 388 MET cc_start: 0.8119 (mtt) cc_final: 0.7478 (mpp) REVERT: C 456 LEU cc_start: 0.9292 (tt) cc_final: 0.8979 (pp) REVERT: C 469 LEU cc_start: 0.9181 (mt) cc_final: 0.8936 (mt) REVERT: C 498 LYS cc_start: 0.8294 (tttt) cc_final: 0.7787 (mmmm) REVERT: C 525 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8868 (pp) REVERT: C 562 GLN cc_start: 0.8795 (tt0) cc_final: 0.8519 (pt0) REVERT: C 578 TYR cc_start: 0.9157 (t80) cc_final: 0.8779 (t80) REVERT: C 593 LEU cc_start: 0.8888 (mt) cc_final: 0.8628 (mp) REVERT: C 643 MET cc_start: 0.8638 (mmm) cc_final: 0.7762 (mmm) REVERT: C 892 MET cc_start: 0.9006 (mmp) cc_final: 0.8663 (mmp) REVERT: C 903 MET cc_start: 0.8294 (mtp) cc_final: 0.8062 (ttm) REVERT: C 929 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8477 (tpt) REVERT: C 932 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: C 958 ASP cc_start: 0.8044 (m-30) cc_final: 0.7833 (m-30) REVERT: C 962 TYR cc_start: 0.8954 (t80) cc_final: 0.8675 (t80) REVERT: C 998 LYS cc_start: 0.8917 (tttm) cc_final: 0.8592 (tptt) REVERT: C 1004 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.7853 (tpt170) REVERT: C 1108 LEU cc_start: 0.9457 (mt) cc_final: 0.8948 (mt) REVERT: C 1141 PHE cc_start: 0.8826 (t80) cc_final: 0.8534 (t80) REVERT: C 1145 MET cc_start: 0.9106 (mmm) cc_final: 0.8532 (mpp) REVERT: C 1203 MET cc_start: 0.8361 (tpp) cc_final: 0.7477 (tpp) REVERT: C 1276 TYR cc_start: 0.8912 (t80) cc_final: 0.8465 (t80) REVERT: C 1301 MET cc_start: 0.8413 (ttp) cc_final: 0.7707 (tpt) REVERT: C 1302 MET cc_start: 0.8085 (tmm) cc_final: 0.7678 (mtt) REVERT: C 1309 PHE cc_start: 0.8848 (m-10) cc_final: 0.8434 (m-80) REVERT: C 1311 PHE cc_start: 0.9202 (t80) cc_final: 0.8960 (t80) REVERT: C 1345 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8794 (tt) REVERT: C 1449 ASN cc_start: 0.9010 (m110) cc_final: 0.8644 (m110) REVERT: C 1519 MET cc_start: 0.8158 (mmp) cc_final: 0.7796 (mmt) REVERT: D 238 TYR cc_start: 0.7465 (m-80) cc_final: 0.6840 (m-80) REVERT: D 243 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8857 (mm) REVERT: D 244 PHE cc_start: 0.8030 (m-80) cc_final: 0.7198 (m-80) REVERT: D 277 TYR cc_start: 0.8856 (m-10) cc_final: 0.8501 (m-80) REVERT: D 280 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: D 285 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8609 (pp30) REVERT: D 289 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 297 LYS cc_start: 0.9144 (mttt) cc_final: 0.8657 (mttp) REVERT: D 304 TYR cc_start: 0.8121 (p90) cc_final: 0.7858 (p90) REVERT: D 334 ARG cc_start: 0.9138 (mmp80) cc_final: 0.8920 (mmp80) REVERT: D 340 LYS cc_start: 0.9363 (mttm) cc_final: 0.8652 (mtpp) REVERT: D 341 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8767 (pp30) REVERT: D 342 TYR cc_start: 0.8979 (m-80) cc_final: 0.8178 (m-80) REVERT: D 368 PHE cc_start: 0.8315 (t80) cc_final: 0.8100 (t80) REVERT: D 387 ASP cc_start: 0.7584 (t0) cc_final: 0.7112 (t0) outliers start: 117 outliers final: 89 residues processed: 692 average time/residue: 0.2218 time to fit residues: 259.4289 Evaluate side-chains 705 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 600 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1024 HIS Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1116 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2276 TYR Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2431 ILE Chi-restraints excluded: chain A residue 2436 TRP Chi-restraints excluded: chain A residue 2442 LEU Chi-restraints excluded: chain A residue 2469 HIS Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2561 MET Chi-restraints excluded: chain A residue 2582 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 1031 PHE Chi-restraints excluded: chain B residue 1032 TRP Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain B residue 1331 VAL Chi-restraints excluded: chain B residue 1549 CYS Chi-restraints excluded: chain B residue 1638 SER Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1815 LEU Chi-restraints excluded: chain B residue 1927 GLU Chi-restraints excluded: chain B residue 1988 PHE Chi-restraints excluded: chain B residue 2052 VAL Chi-restraints excluded: chain B residue 2063 THR Chi-restraints excluded: chain B residue 2075 ASP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2256 LEU Chi-restraints excluded: chain B residue 2274 LEU Chi-restraints excluded: chain B residue 2295 LEU Chi-restraints excluded: chain B residue 2320 ARG Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2387 GLU Chi-restraints excluded: chain B residue 2432 LEU Chi-restraints excluded: chain B residue 2596 LEU Chi-restraints excluded: chain B residue 2620 THR Chi-restraints excluded: chain B residue 2764 HIS Chi-restraints excluded: chain B residue 2887 GLN Chi-restraints excluded: chain B residue 2901 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1224 SER Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1253 VAL Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1345 LEU Chi-restraints excluded: chain C residue 1357 PHE Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1400 VAL Chi-restraints excluded: chain C residue 1438 MET Chi-restraints excluded: chain C residue 1465 ASN Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1553 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 155 optimal weight: 0.0370 chunk 168 optimal weight: 9.9990 chunk 463 optimal weight: 10.0000 chunk 332 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 400 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 HIS ** A2092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2277 GLN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.127320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097611 restraints weight = 124457.530| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.29 r_work: 0.3263 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39039 Z= 0.118 Angle : 0.630 14.571 52938 Z= 0.305 Chirality : 0.039 0.274 6127 Planarity : 0.004 0.053 6587 Dihedral : 5.228 59.948 5131 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.65 % Allowed : 17.48 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.87 (0.13), residues: 4660 helix: 2.03 (0.09), residues: 3307 sheet: -0.22 (0.80), residues: 35 loop : -0.78 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 334 TYR 0.039 0.001 TYR D 317 PHE 0.045 0.001 PHE C1268 TRP 0.028 0.001 TRP A 453 HIS 0.028 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (39017) covalent geometry : angle 0.62999 / 0.30 (52901) SS BOND : bond 0.00122 / 0.09 ( 11) SS BOND : angle 1.02166 / 0.79 ( 22) hydrogen bonds : bond 0.03319 / 2.19 ( 2438) hydrogen bonds : angle 3.96607 / 2.90 ( 7188) metal coordination : bond 0.00724 / 0.54 ( 8) metal coordination : angle 1.00898 / 0.56 ( 6) link_NAG-ASN : bond 0.00177 / 0.06 ( 3) link_NAG-ASN : angle 0.94338 / 0.45 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12769.78 seconds wall clock time: 218 minutes 35.24 seconds (13115.24 seconds total)