Starting phenix.real_space_refine on Sat Mar 7 05:16:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7g_32344/03_2026/7w7g_32344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7g_32344/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w7g_32344/03_2026/7w7g_32344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7g_32344/03_2026/7w7g_32344.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7g_32344/03_2026/7w7g_32344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7g_32344/03_2026/7w7g_32344.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 9 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: 8.52, per 1000 atoms: 0.22 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: 3.42 Conformation dependent library (CDL) restraints added in 1.6 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: 1.47 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: 9.54 Time building geometry restraints manager: 4.58 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: 22114 17.63 - 35.27: 1084 35.27 - 52.90: 238 52.90 - 70.53: 38 70.53 - 88.17: 11 Dihedral angle restraints: 23485 sinusoidal: 9469 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 23482 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: 1.920 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 42.240 Find NCS groups from input model: 0.400 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 11.141 88.167 14280 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 covalent geometry : bond 0.00357 (39017) covalent geometry : angle 0.50658 (52901) SS BOND : bond 0.00107 ( 11) SS BOND : angle 0.56713 ( 22) hydrogen bonds : bond 0.12386 ( 2438) hydrogen bonds : angle 4.96042 ( 7188) metal coordination : bond 0.01002 ( 8) metal coordination : angle 1.11012 ( 6) link_NAG-ASN : bond 0.00144 ( 3) link_NAG-ASN : angle 1.15953 ( 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 : 1.477 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: 0.2535 time to fit residues: 414.6180 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 : 1.785 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4206 r_free = 0.4206 target = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095537 restraints weight = 124530.426| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.09 r_work: 0.3225 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39039 Z= 0.154 Angle : 0.614 11.729 52938 Z= 0.303 Chirality : 0.040 0.255 6127 Planarity : 0.004 0.054 6587 Dihedral : 6.201 80.012 5252 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.55 % Allowed : 11.32 % Favored : 85.13 % 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 0.009 0.001 ARG B2115 TYR 0.028 0.001 TYR C 923 PHE 0.025 0.001 PHE B1961 TRP 0.026 0.001 TRP A 202 HIS 0.006 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00353 (39017) covalent geometry : angle 0.61357 (52901) SS BOND : bond 0.00508 ( 11) SS BOND : angle 1.03120 ( 22) hydrogen bonds : bond 0.04062 ( 2438) hydrogen bonds : angle 4.18000 ( 7188) metal coordination : bond 0.01226 ( 8) metal coordination : angle 0.96242 ( 6) link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 1.41471 ( 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 825 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 675 time to evaluate : 1.513 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 TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 202 TRP cc_start: 0.8600 (p90) cc_final: 0.8299 (p90) REVERT: A 447 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 491 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: A 500 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.5063 (mtpt) REVERT: A 519 MET cc_start: 0.8007 (tpp) cc_final: 0.7369 (tpp) REVERT: A 1403 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: A 2279 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7520 (ttm170) REVERT: A 2397 HIS cc_start: 0.8324 (m-70) cc_final: 0.7336 (m90) REVERT: A 2417 MET cc_start: 0.5139 (mmt) cc_final: 0.3581 (tmm) REVERT: A 2433 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7428 (tm) REVERT: A 2466 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6996 (pt) REVERT: A 2488 MET cc_start: 0.7162 (mmt) cc_final: 0.6944 (mmp) REVERT: A 2561 MET cc_start: 0.8609 (mpp) cc_final: 0.8307 (mpp) REVERT: A 2634 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8719 (pp30) REVERT: B 344 TRP cc_start: 0.7457 (t60) cc_final: 0.7127 (t60) REVERT: B 350 GLN cc_start: 0.7955 (tt0) cc_final: 0.7708 (tp40) REVERT: B 359 ARG cc_start: 0.8153 (mmt180) cc_final: 0.7816 (mmm160) REVERT: B 1185 MET cc_start: 0.8317 (mmt) cc_final: 0.7954 (mmm) REVERT: B 1808 GLN cc_start: 0.8246 (pt0) cc_final: 0.7970 (tm-30) REVERT: B 2075 ASP cc_start: 0.5446 (OUTLIER) cc_final: 0.5095 (t0) REVERT: B 2206 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8951 (mt) REVERT: B 2277 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8438 (tp-100) REVERT: B 2320 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8007 (mmp80) REVERT: B 2552 ILE cc_start: 0.9094 (mt) cc_final: 0.8785 (mm) REVERT: B 2972 ILE cc_start: 0.9027 (mt) cc_final: 0.8801 (pt) REVERT: C 51 ILE cc_start: 0.9309 (mt) cc_final: 0.8644 (mt) REVERT: C 54 CYS cc_start: 0.9018 (m) cc_final: 0.8792 (p) REVERT: C 141 MET cc_start: 0.7758 (mtp) cc_final: 0.7499 (mtm) REVERT: C 166 ARG cc_start: 0.8948 (mtt-85) cc_final: 0.8493 (ttm-80) REVERT: C 172 LYS cc_start: 0.8570 (mttt) cc_final: 0.7965 (tptt) REVERT: C 184 PHE cc_start: 0.9001 (t80) cc_final: 0.8452 (t80) REVERT: C 235 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7952 (mp0) REVERT: C 243 PHE cc_start: 0.8259 (m-80) cc_final: 0.7769 (m-80) REVERT: C 327 GLU cc_start: 0.8989 (tp30) cc_final: 0.8786 (tp30) REVERT: C 331 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7820 (mm-40) REVERT: C 388 MET cc_start: 0.8159 (mtt) cc_final: 0.7430 (mmm) REVERT: C 395 THR cc_start: 0.9161 (m) cc_final: 0.8901 (p) REVERT: C 420 LEU cc_start: 0.9159 (mt) cc_final: 0.8870 (pp) REVERT: C 469 LEU cc_start: 0.9189 (mt) cc_final: 0.8880 (mt) REVERT: C 479 VAL cc_start: 0.9185 (m) cc_final: 0.8946 (p) REVERT: C 482 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8802 (p) REVERT: C 498 LYS cc_start: 0.8547 (tttt) cc_final: 0.8066 (mmmm) REVERT: C 547 MET cc_start: 0.8986 (mmp) cc_final: 0.8786 (mmm) REVERT: C 593 LEU cc_start: 0.9082 (mt) cc_final: 0.8716 (mt) REVERT: C 603 GLU cc_start: 0.8278 (tt0) cc_final: 0.7982 (tt0) REVERT: C 606 GLU cc_start: 0.8736 (mp0) cc_final: 0.8262 (pm20) REVERT: C 607 ASP cc_start: 0.8472 (m-30) cc_final: 0.8183 (m-30) REVERT: C 643 MET cc_start: 0.8720 (mmm) cc_final: 0.7800 (mmm) REVERT: C 886 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7636 (p) REVERT: C 903 MET cc_start: 0.8283 (mtp) cc_final: 0.7920 (ttm) REVERT: C 929 MET cc_start: 0.9069 (tpt) cc_final: 0.8570 (tpp) REVERT: C 932 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 958 ASP cc_start: 0.8513 (m-30) cc_final: 0.8237 (m-30) REVERT: C 1016 GLU cc_start: 0.9075 (mp0) cc_final: 0.8598 (mp0) REVERT: C 1022 ILE cc_start: 0.9235 (mt) cc_final: 0.9011 (mp) REVERT: C 1029 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9097 (mt) REVERT: C 1096 PHE cc_start: 0.8688 (p90) cc_final: 0.8088 (p90) REVERT: C 1108 LEU cc_start: 0.9520 (mt) cc_final: 0.9132 (mt) REVERT: C 1160 ASN cc_start: 0.8731 (t0) cc_final: 0.8510 (t0) REVERT: C 1161 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8660 (tm-30) REVERT: C 1203 MET cc_start: 0.8563 (tpp) cc_final: 0.7665 (tpp) REVERT: C 1301 MET cc_start: 0.8670 (ttp) cc_final: 0.8286 (tpt) REVERT: C 1309 PHE cc_start: 0.8954 (m-80) cc_final: 0.8582 (m-80) REVERT: C 1313 SER cc_start: 0.9022 (t) cc_final: 0.8488 (p) REVERT: C 1364 GLU cc_start: 0.8574 (tt0) cc_final: 0.8200 (tt0) REVERT: C 1384 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8402 (ptp-170) REVERT: C 1393 LYS cc_start: 0.9321 (mttt) cc_final: 0.8901 (mttm) REVERT: C 1399 MET cc_start: 0.8498 (ttm) cc_final: 0.8168 (ttt) REVERT: C 1449 ASN cc_start: 0.8963 (m110) cc_final: 0.8572 (m110) REVERT: C 1456 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7918 (p) REVERT: C 1513 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8724 (mmtm) REVERT: C 1519 MET cc_start: 0.8285 (mmt) cc_final: 0.7940 (tpp) REVERT: D 227 LEU cc_start: 0.8763 (mt) cc_final: 0.7971 (tp) REVERT: D 232 LEU cc_start: 0.9115 (tp) cc_final: 0.8574 (tt) REVERT: D 238 TYR cc_start: 0.7753 (m-80) cc_final: 0.7482 (m-80) REVERT: D 241 TRP cc_start: 0.7946 (t-100) cc_final: 0.7649 (t-100) REVERT: D 244 PHE cc_start: 0.8468 (m-80) cc_final: 0.8201 (m-80) REVERT: D 277 TYR cc_start: 0.8915 (m-10) cc_final: 0.8470 (m-80) REVERT: D 278 GLN cc_start: 0.9381 (mt0) cc_final: 0.8682 (tm-30) REVERT: D 280 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7857 (m-10) REVERT: D 281 ASP cc_start: 0.8507 (t70) cc_final: 0.8208 (t70) REVERT: D 289 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 294 VAL cc_start: 0.9374 (t) cc_final: 0.9165 (t) REVERT: D 297 LYS cc_start: 0.9250 (mttm) cc_final: 0.8831 (mttp) REVERT: D 307 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8580 (mmmm) REVERT: D 316 VAL cc_start: 0.8962 (t) cc_final: 0.8597 (p) REVERT: D 318 LYS cc_start: 0.8354 (tttt) cc_final: 0.7962 (tttp) outliers start: 150 outliers final: 82 residues processed: 791 average time/residue: 0.2399 time to fit residues: 319.3294 Evaluate side-chains 716 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 617 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 171 LEU 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 1345 LEU 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: 8.9990 chunk 3 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 423 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 417 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 457 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1115 ASN A2444 HIS 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** B2268 HIS B2584 ASN B2662 ASN C 39 HIS ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 473 GLN D 282 HIS D 296 HIS ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.124775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093768 restraints weight = 124089.357| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.28 r_work: 0.3379 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 39039 Z= 0.235 Angle : 0.637 14.664 52938 Z= 0.314 Chirality : 0.041 0.178 6127 Planarity : 0.004 0.050 6587 Dihedral : 6.074 81.955 5228 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.67 % Allowed : 12.88 % Favored : 83.45 % 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: 1.66 (0.12), residues: 4660 helix: 1.87 (0.09), residues: 3281 sheet: -0.43 (0.72), residues: 35 loop : -0.77 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B2920 TYR 0.022 0.002 TYR C 274 PHE 0.022 0.002 PHE A2492 TRP 0.017 0.001 TRP A 453 HIS 0.006 0.001 HIS B1960 Details of bonding type rmsd covalent geometry : bond 0.00552 (39017) covalent geometry : angle 0.63615 (52901) SS BOND : bond 0.00149 ( 11) SS BOND : angle 1.03516 ( 22) hydrogen bonds : bond 0.04133 ( 2438) hydrogen bonds : angle 4.24150 ( 7188) metal coordination : bond 0.01887 ( 8) metal coordination : angle 1.13364 ( 6) link_NAG-ASN : bond 0.00177 ( 3) link_NAG-ASN : angle 1.44101 ( 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 789 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 634 time to evaluate : 1.546 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: symmetry clash REVERT: A 179 GLN cc_start: 0.8258 (tt0) cc_final: 0.7884 (tp-100) REVERT: A 195 MET cc_start: 0.6647 (mmm) cc_final: 0.6404 (mmm) REVERT: A 447 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 491 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6964 (pm20) REVERT: A 500 LYS cc_start: 0.5392 (OUTLIER) cc_final: 0.4986 (mtpt) REVERT: A 519 MET cc_start: 0.8073 (tpp) cc_final: 0.7319 (tpp) REVERT: A 1403 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8500 (tp40) REVERT: A 2034 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9126 (mp) REVERT: A 2433 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7400 (tp) REVERT: A 2442 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 2466 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6876 (pt) REVERT: A 2469 HIS cc_start: 0.3339 (OUTLIER) cc_final: 0.2892 (t-90) REVERT: A 2488 MET cc_start: 0.7120 (mmt) cc_final: 0.6724 (mmm) REVERT: A 2543 MET cc_start: 0.7934 (mtt) cc_final: 0.7702 (ttm) REVERT: A 2561 MET cc_start: 0.8605 (mpp) cc_final: 0.8343 (mpp) REVERT: A 2575 LEU cc_start: 0.8517 (mt) cc_final: 0.8063 (mt) REVERT: B 350 GLN cc_start: 0.7968 (tt0) cc_final: 0.7712 (tp40) REVERT: B 359 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7862 (mmm160) REVERT: B 791 LEU cc_start: 0.8701 (tp) cc_final: 0.8455 (tp) REVERT: B 1185 MET cc_start: 0.8214 (mmt) cc_final: 0.7888 (mmm) REVERT: B 1808 GLN cc_start: 0.8264 (pt0) cc_final: 0.7949 (tm-30) REVERT: B 2075 ASP cc_start: 0.5308 (OUTLIER) cc_final: 0.4953 (t0) REVERT: B 2206 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8879 (mt) REVERT: B 2277 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (tp-100) REVERT: B 2320 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7882 (mmp80) REVERT: B 2552 ILE cc_start: 0.9065 (mt) cc_final: 0.8763 (mm) REVERT: B 2972 ILE cc_start: 0.9027 (mt) cc_final: 0.8799 (pt) REVERT: C 51 ILE cc_start: 0.9398 (mt) cc_final: 0.8772 (mt) REVERT: C 54 CYS cc_start: 0.9020 (m) cc_final: 0.8676 (p) REVERT: C 141 MET cc_start: 0.7818 (mtp) cc_final: 0.7522 (mtm) REVERT: C 166 ARG cc_start: 0.8972 (mtt-85) cc_final: 0.8663 (ttm-80) REVERT: C 172 LYS cc_start: 0.8562 (mttt) cc_final: 0.7992 (tptt) REVERT: C 235 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8027 (mp0) REVERT: C 243 PHE cc_start: 0.8100 (m-80) cc_final: 0.7669 (m-80) REVERT: C 275 GLU cc_start: 0.8695 (tt0) cc_final: 0.8408 (tt0) REVERT: C 286 MET cc_start: 0.9145 (ttp) cc_final: 0.8927 (ttm) REVERT: C 331 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7821 (mm-40) REVERT: C 380 MET cc_start: 0.7486 (mmt) cc_final: 0.6919 (mmt) REVERT: C 395 THR cc_start: 0.9171 (m) cc_final: 0.8913 (p) REVERT: C 398 VAL cc_start: 0.9358 (p) cc_final: 0.9137 (m) REVERT: C 469 LEU cc_start: 0.9200 (mt) cc_final: 0.8978 (mt) REVERT: C 498 LYS cc_start: 0.8574 (tttt) cc_final: 0.8090 (mmmm) REVERT: C 525 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9039 (pp) REVERT: C 527 MET cc_start: 0.8133 (tpp) cc_final: 0.7899 (tpp) REVERT: C 536 ARG cc_start: 0.7239 (mmm-85) cc_final: 0.5667 (mtp180) REVERT: C 540 PHE cc_start: 0.8930 (t80) cc_final: 0.8729 (t80) REVERT: C 558 ASP cc_start: 0.8716 (t0) cc_final: 0.8282 (t0) REVERT: C 603 GLU cc_start: 0.8290 (tt0) cc_final: 0.8072 (tt0) REVERT: C 606 GLU cc_start: 0.8643 (mp0) cc_final: 0.8283 (pm20) REVERT: C 607 ASP cc_start: 0.8577 (m-30) cc_final: 0.8319 (m-30) REVERT: C 643 MET cc_start: 0.8781 (mmm) cc_final: 0.7882 (mmm) REVERT: C 892 MET cc_start: 0.9139 (mmp) cc_final: 0.8855 (mmp) REVERT: C 903 MET cc_start: 0.8250 (mtp) cc_final: 0.7885 (ttm) REVERT: C 929 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8482 (tpp) REVERT: C 958 ASP cc_start: 0.8406 (m-30) cc_final: 0.8141 (m-30) REVERT: C 1016 GLU cc_start: 0.9099 (mp0) cc_final: 0.8701 (mp0) REVERT: C 1029 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9119 (mt) REVERT: C 1096 PHE cc_start: 0.8672 (p90) cc_final: 0.8103 (p90) REVERT: C 1108 LEU cc_start: 0.9472 (mt) cc_final: 0.9064 (mt) REVERT: C 1161 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8619 (tm-30) REVERT: C 1203 MET cc_start: 0.8652 (tpp) cc_final: 0.7831 (tpp) REVERT: C 1259 LYS cc_start: 0.9491 (mtmt) cc_final: 0.9236 (mtpp) REVERT: C 1274 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8103 (t0) REVERT: C 1301 MET cc_start: 0.8703 (ttp) cc_final: 0.8300 (tpt) REVERT: C 1309 PHE cc_start: 0.9013 (m-80) cc_final: 0.8727 (m-80) REVERT: C 1364 GLU cc_start: 0.8583 (tt0) cc_final: 0.7878 (tt0) REVERT: C 1393 LYS cc_start: 0.9315 (mttt) cc_final: 0.8721 (mttp) REVERT: C 1456 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7817 (p) REVERT: C 1516 CYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8901 (p) REVERT: D 227 LEU cc_start: 0.8725 (mt) cc_final: 0.8396 (mm) REVERT: D 232 LEU cc_start: 0.9061 (tp) cc_final: 0.8554 (tt) REVERT: D 238 TYR cc_start: 0.7783 (m-80) cc_final: 0.7474 (m-80) REVERT: D 244 PHE cc_start: 0.8295 (m-80) cc_final: 0.7914 (m-80) REVERT: D 277 TYR cc_start: 0.8862 (m-10) cc_final: 0.8508 (m-80) REVERT: D 280 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7824 (m-10) REVERT: D 281 ASP cc_start: 0.8517 (t70) cc_final: 0.8194 (t70) REVERT: D 289 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 297 LYS cc_start: 0.9258 (mttm) cc_final: 0.8774 (mttp) REVERT: D 316 VAL cc_start: 0.8998 (t) cc_final: 0.8679 (p) REVERT: D 318 LYS cc_start: 0.8450 (tttt) cc_final: 0.8096 (tttp) REVERT: D 335 LYS cc_start: 0.9131 (mmtm) cc_final: 0.8758 (mtmm) REVERT: D 342 TYR cc_start: 0.9103 (m-80) cc_final: 0.8753 (m-10) REVERT: D 387 ASP cc_start: 0.7891 (t0) cc_final: 0.7632 (t0) outliers start: 155 outliers final: 95 residues processed: 753 average time/residue: 0.2204 time to fit residues: 278.5308 Evaluate side-chains 722 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 607 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 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 2034 LEU 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 2466 ILE Chi-restraints excluded: chain A residue 2469 HIS Chi-restraints excluded: chain A residue 2472 VAL 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 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 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 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 2901 LEU Chi-restraints excluded: chain C residue 50 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 144 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 SER 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 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 893 ILE Chi-restraints excluded: chain C residue 929 MET Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1025 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 1288 VAL Chi-restraints excluded: chain C residue 1291 HIS Chi-restraints excluded: chain C residue 1315 CYS 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 1516 CYS 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 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: 0.9990 chunk 309 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 438 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 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** B2268 HIS B2584 ASN C 56 ASN C 562 GLN C1126 HIS C1558 GLN D 296 HIS ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.125619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095627 restraints weight = 124053.341| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.41 r_work: 0.3232 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39039 Z= 0.143 Angle : 0.586 11.566 52938 Z= 0.289 Chirality : 0.039 0.198 6127 Planarity : 0.004 0.051 6587 Dihedral : 5.854 79.842 5221 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.50 % Allowed : 13.95 % Favored : 82.55 % 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: 1.74 (0.13), residues: 4660 helix: 1.95 (0.09), residues: 3286 sheet: -0.21 (0.76), residues: 35 loop : -0.82 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B2920 TYR 0.023 0.001 TYR B 662 PHE 0.024 0.001 PHE A2492 TRP 0.042 0.001 TRP B 219 HIS 0.006 0.001 HIS C1126 Details of bonding type rmsd covalent geometry : bond 0.00333 (39017) covalent geometry : angle 0.58538 (52901) SS BOND : bond 0.00118 ( 11) SS BOND : angle 0.97783 ( 22) hydrogen bonds : bond 0.03706 ( 2438) hydrogen bonds : angle 4.10262 ( 7188) metal coordination : bond 0.01253 ( 8) metal coordination : angle 1.12310 ( 6) link_NAG-ASN : bond 0.00159 ( 3) link_NAG-ASN : angle 1.26470 ( 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 780 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 632 time to evaluate : 1.458 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 179 GLN cc_start: 0.8389 (tt0) cc_final: 0.7916 (tp-100) REVERT: A 202 TRP cc_start: 0.8618 (p-90) cc_final: 0.8305 (p-90) REVERT: A 207 TYR cc_start: 0.6251 (m-10) cc_final: 0.6031 (m-10) REVERT: A 447 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 491 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: A 500 LYS cc_start: 0.5423 (OUTLIER) cc_final: 0.5039 (mtpt) REVERT: A 519 MET cc_start: 0.8007 (tpp) cc_final: 0.7279 (tpp) REVERT: A 922 MET cc_start: 0.9167 (mtt) cc_final: 0.8959 (mtt) REVERT: A 1403 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8537 (tp40) REVERT: A 2442 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7903 (mt) REVERT: A 2469 HIS cc_start: 0.3610 (OUTLIER) cc_final: 0.3161 (t-90) REVERT: A 2488 MET cc_start: 0.7052 (mmt) cc_final: 0.6681 (mmm) REVERT: A 2492 PHE cc_start: 0.9055 (t80) cc_final: 0.8806 (t80) REVERT: A 2543 MET cc_start: 0.7815 (mtt) cc_final: 0.7516 (ttm) REVERT: A 2561 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8372 (mpp) REVERT: A 2575 LEU cc_start: 0.8317 (mt) cc_final: 0.8083 (mt) REVERT: B 188 PHE cc_start: 0.8199 (t80) cc_final: 0.7949 (t80) REVERT: B 344 TRP cc_start: 0.7696 (t60) cc_final: 0.7211 (t60) REVERT: B 350 GLN cc_start: 0.7924 (tt0) cc_final: 0.7665 (tp40) REVERT: B 789 HIS cc_start: 0.7833 (t70) cc_final: 0.7515 (t-90) REVERT: B 1033 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7202 (tpm170) REVERT: B 1808 GLN cc_start: 0.8208 (pt0) cc_final: 0.7943 (tm-30) REVERT: B 2075 ASP cc_start: 0.5309 (OUTLIER) cc_final: 0.4919 (t0) REVERT: B 2188 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8976 (m) REVERT: B 2206 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8756 (mt) REVERT: B 2277 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8433 (tp-100) REVERT: B 2320 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7997 (mmp80) REVERT: B 2552 ILE cc_start: 0.9088 (mt) cc_final: 0.8823 (mm) REVERT: B 2972 ILE cc_start: 0.9023 (mt) cc_final: 0.8795 (pt) REVERT: C 51 ILE cc_start: 0.9411 (mt) cc_final: 0.8786 (mt) REVERT: C 54 CYS cc_start: 0.9051 (m) cc_final: 0.8726 (p) REVERT: C 141 MET cc_start: 0.7789 (mtp) cc_final: 0.7484 (mtm) REVERT: C 166 ARG cc_start: 0.8944 (mtt-85) cc_final: 0.8449 (ttm-80) REVERT: C 172 LYS cc_start: 0.8526 (mttt) cc_final: 0.7920 (tptt) REVERT: C 197 VAL cc_start: 0.9290 (t) cc_final: 0.8962 (p) REVERT: C 235 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7963 (mp0) REVERT: C 243 PHE cc_start: 0.8089 (m-80) cc_final: 0.7672 (m-80) REVERT: C 275 GLU cc_start: 0.8712 (tt0) cc_final: 0.8434 (tt0) REVERT: C 331 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7665 (mm-40) REVERT: C 350 MET cc_start: 0.8272 (tpp) cc_final: 0.7827 (mmm) REVERT: C 395 THR cc_start: 0.9143 (m) cc_final: 0.8871 (p) REVERT: C 398 VAL cc_start: 0.9338 (p) cc_final: 0.9130 (m) REVERT: C 469 LEU cc_start: 0.9178 (mt) cc_final: 0.8936 (mt) REVERT: C 498 LYS cc_start: 0.8526 (tttt) cc_final: 0.8024 (mmmm) REVERT: C 525 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9015 (pp) REVERT: C 527 MET cc_start: 0.8022 (tpp) cc_final: 0.7774 (tpp) REVERT: C 593 LEU cc_start: 0.8926 (mt) cc_final: 0.8685 (mp) REVERT: C 603 GLU cc_start: 0.8286 (tt0) cc_final: 0.8081 (tt0) REVERT: C 606 GLU cc_start: 0.8670 (mp0) cc_final: 0.8350 (pm20) REVERT: C 643 MET cc_start: 0.8765 (mmm) cc_final: 0.7834 (mmm) REVERT: C 892 MET cc_start: 0.9177 (mmp) cc_final: 0.8914 (mmp) REVERT: C 903 MET cc_start: 0.8429 (mtp) cc_final: 0.7966 (ttm) REVERT: C 926 VAL cc_start: 0.9515 (t) cc_final: 0.9283 (m) REVERT: C 929 MET cc_start: 0.9056 (tpt) cc_final: 0.8575 (tpp) REVERT: C 932 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: C 957 MET cc_start: 0.8384 (ptp) cc_final: 0.8131 (ptp) REVERT: C 958 ASP cc_start: 0.8499 (m-30) cc_final: 0.8174 (m-30) REVERT: C 962 TYR cc_start: 0.9134 (t80) cc_final: 0.8818 (t80) REVERT: C 1016 GLU cc_start: 0.9092 (mp0) cc_final: 0.8693 (mp0) REVERT: C 1020 VAL cc_start: 0.9325 (t) cc_final: 0.9033 (p) REVERT: C 1029 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9095 (mt) REVERT: C 1096 PHE cc_start: 0.8653 (p90) cc_final: 0.8018 (p90) REVERT: C 1108 LEU cc_start: 0.9474 (mt) cc_final: 0.9011 (mt) REVERT: C 1162 ASN cc_start: 0.7746 (m110) cc_final: 0.7347 (m110) REVERT: C 1203 MET cc_start: 0.8605 (tpp) cc_final: 0.7746 (tpp) REVERT: C 1274 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7765 (t0) REVERT: C 1277 ASP cc_start: 0.9139 (m-30) cc_final: 0.8799 (p0) REVERT: C 1301 MET cc_start: 0.8606 (ttp) cc_final: 0.8134 (tpt) REVERT: C 1309 PHE cc_start: 0.8945 (m-80) cc_final: 0.8632 (m-80) REVERT: C 1364 GLU cc_start: 0.8611 (tt0) cc_final: 0.8139 (tt0) REVERT: C 1393 LYS cc_start: 0.9336 (mttt) cc_final: 0.8829 (mttm) REVERT: C 1449 ASN cc_start: 0.8953 (m110) cc_final: 0.8563 (m110) REVERT: C 1456 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7802 (p) REVERT: C 1536 MET cc_start: 0.8603 (ttt) cc_final: 0.8278 (ttt) REVERT: C 1546 LYS cc_start: 0.9344 (ttpt) cc_final: 0.9130 (tttt) REVERT: D 232 LEU cc_start: 0.9069 (tp) cc_final: 0.8591 (tp) REVERT: D 238 TYR cc_start: 0.7830 (m-80) cc_final: 0.7114 (m-80) REVERT: D 244 PHE cc_start: 0.8276 (m-80) cc_final: 0.7523 (m-80) REVERT: D 277 TYR cc_start: 0.8863 (m-10) cc_final: 0.8375 (m-80) REVERT: D 280 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: D 281 ASP cc_start: 0.8520 (t70) cc_final: 0.8191 (t0) REVERT: D 289 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8145 (tm-30) REVERT: D 297 LYS cc_start: 0.9260 (mttm) cc_final: 0.8855 (mttp) REVERT: D 316 VAL cc_start: 0.9031 (t) cc_final: 0.8654 (p) REVERT: D 318 LYS cc_start: 0.8422 (tttt) cc_final: 0.8020 (tttp) REVERT: D 340 LYS cc_start: 0.9328 (mttm) cc_final: 0.8636 (mtpp) outliers start: 148 outliers final: 95 residues processed: 746 average time/residue: 0.2218 time to fit residues: 280.6756 Evaluate side-chains 728 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 614 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 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 1295 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 2151 LEU Chi-restraints excluded: chain A residue 2213 LEU 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 2469 HIS Chi-restraints excluded: chain A residue 2477 PHE 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 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 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 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 2188 VAL 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 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 171 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 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 893 ILE Chi-restraints excluded: chain C residue 932 GLU 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 1224 SER 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 1492 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 193 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 339 CYS Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 97 optimal weight: 0.9980 chunk 331 optimal weight: 0.8980 chunk 259 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 141 optimal weight: 40.0000 chunk 441 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS ** 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 666 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 473 GLN C 549 GLN ** C 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.126076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096096 restraints weight = 123741.761| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.27 r_work: 0.3239 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 39039 Z= 0.122 Angle : 0.577 13.208 52938 Z= 0.283 Chirality : 0.038 0.208 6127 Planarity : 0.004 0.050 6587 Dihedral : 5.726 78.225 5217 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.34 % Allowed : 14.87 % Favored : 81.79 % 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: 1.83 (0.13), residues: 4660 helix: 2.04 (0.09), residues: 3281 sheet: -0.08 (0.79), residues: 35 loop : -0.86 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1028 TYR 0.033 0.001 TYR B 662 PHE 0.027 0.001 PHE C1011 TRP 0.026 0.001 TRP B 219 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00280 (39017) covalent geometry : angle 0.57630 (52901) SS BOND : bond 0.00134 ( 11) SS BOND : angle 1.02865 ( 22) hydrogen bonds : bond 0.03513 ( 2438) hydrogen bonds : angle 4.02849 ( 7188) metal coordination : bond 0.01007 ( 8) metal coordination : angle 0.99385 ( 6) link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 1.17488 ( 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 774 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 633 time to evaluate : 1.503 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: 0.6268 (mmm) cc_final: 0.5843 (mmm) REVERT: A 202 TRP cc_start: 0.8634 (p-90) cc_final: 0.8337 (p-90) REVERT: A 207 TYR cc_start: 0.6215 (m-10) cc_final: 0.5998 (m-10) REVERT: A 491 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: A 500 LYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4998 (mtpt) REVERT: A 519 MET cc_start: 0.7981 (tpp) cc_final: 0.7275 (tpp) REVERT: A 922 MET cc_start: 0.9151 (mtt) cc_final: 0.8746 (mtt) REVERT: A 2442 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7981 (mt) REVERT: A 2469 HIS cc_start: 0.3533 (OUTLIER) cc_final: 0.3160 (t-90) REVERT: A 2488 MET cc_start: 0.7070 (mmt) cc_final: 0.6682 (mmm) REVERT: A 2492 PHE cc_start: 0.9065 (t80) cc_final: 0.8780 (t80) REVERT: A 2543 MET cc_start: 0.7781 (mtt) cc_final: 0.7517 (ttm) REVERT: A 2561 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8363 (mpp) REVERT: B 188 PHE cc_start: 0.8174 (t80) cc_final: 0.7931 (t80) REVERT: B 344 TRP cc_start: 0.7609 (t60) cc_final: 0.6834 (t60) REVERT: B 350 GLN cc_start: 0.7823 (tt0) cc_final: 0.7494 (tp40) REVERT: B 1033 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7210 (tpm170) REVERT: B 1808 GLN cc_start: 0.8208 (pt0) cc_final: 0.7891 (tm-30) REVERT: B 2075 ASP cc_start: 0.5298 (OUTLIER) cc_final: 0.4904 (t0) REVERT: B 2188 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8930 (m) REVERT: B 2277 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8467 (tp-100) REVERT: B 2320 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8037 (mmp80) REVERT: B 2552 ILE cc_start: 0.9073 (mt) cc_final: 0.8820 (mm) REVERT: B 2972 ILE cc_start: 0.9006 (mt) cc_final: 0.8778 (pt) REVERT: C 51 ILE cc_start: 0.9425 (mt) cc_final: 0.8557 (mt) REVERT: C 54 CYS cc_start: 0.9013 (m) cc_final: 0.8634 (p) REVERT: C 55 MET cc_start: 0.7209 (mmm) cc_final: 0.6518 (mmm) REVERT: C 141 MET cc_start: 0.7803 (mtp) cc_final: 0.7510 (mtm) REVERT: C 166 ARG cc_start: 0.8938 (mtt-85) cc_final: 0.8487 (ttm-80) REVERT: C 172 LYS cc_start: 0.8545 (mttt) cc_final: 0.7906 (tptt) REVERT: C 197 VAL cc_start: 0.9266 (t) cc_final: 0.8948 (p) REVERT: C 235 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7963 (mp0) REVERT: C 243 PHE cc_start: 0.8073 (m-80) cc_final: 0.7677 (m-80) REVERT: C 331 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7784 (mm-40) REVERT: C 350 MET cc_start: 0.8250 (tpp) cc_final: 0.7816 (mmm) REVERT: C 388 MET cc_start: 0.8082 (mtt) cc_final: 0.7409 (mpp) REVERT: C 395 THR cc_start: 0.9135 (m) cc_final: 0.8870 (p) REVERT: C 398 VAL cc_start: 0.9349 (p) cc_final: 0.9145 (m) REVERT: C 469 LEU cc_start: 0.9174 (mt) cc_final: 0.8922 (mt) REVERT: C 498 LYS cc_start: 0.8404 (tttt) cc_final: 0.7942 (mmmm) REVERT: C 593 LEU cc_start: 0.8935 (mt) cc_final: 0.8694 (mp) REVERT: C 606 GLU cc_start: 0.8623 (mp0) cc_final: 0.8330 (pm20) REVERT: C 643 MET cc_start: 0.8737 (mmm) cc_final: 0.7816 (mmm) REVERT: C 903 MET cc_start: 0.8407 (mtp) cc_final: 0.8004 (ttm) REVERT: C 913 MET cc_start: 0.8656 (mtm) cc_final: 0.8329 (mpp) REVERT: C 926 VAL cc_start: 0.9505 (t) cc_final: 0.9275 (m) REVERT: C 929 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8524 (tpp) REVERT: C 957 MET cc_start: 0.8498 (ptp) cc_final: 0.8290 (ptp) REVERT: C 958 ASP cc_start: 0.8430 (m-30) cc_final: 0.8151 (m-30) REVERT: C 962 TYR cc_start: 0.9156 (t80) cc_final: 0.8792 (t80) REVERT: C 986 MET cc_start: 0.9333 (mtp) cc_final: 0.9080 (mmm) REVERT: C 1016 GLU cc_start: 0.9107 (mp0) cc_final: 0.8709 (mp0) REVERT: C 1029 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9080 (mt) REVERT: C 1096 PHE cc_start: 0.8632 (p90) cc_final: 0.7965 (p90) REVERT: C 1108 LEU cc_start: 0.9459 (mt) cc_final: 0.8983 (mt) REVERT: C 1203 MET cc_start: 0.8634 (tpp) cc_final: 0.7770 (tpp) REVERT: C 1259 LYS cc_start: 0.9477 (mtpp) cc_final: 0.9193 (tttp) REVERT: C 1274 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7205 (t0) REVERT: C 1287 TRP cc_start: 0.8844 (t60) cc_final: 0.8615 (t60) REVERT: C 1301 MET cc_start: 0.8469 (ttp) cc_final: 0.7849 (tpt) REVERT: C 1309 PHE cc_start: 0.8957 (m-80) cc_final: 0.8585 (m-80) REVERT: C 1364 GLU cc_start: 0.8435 (tt0) cc_final: 0.8049 (tt0) REVERT: C 1393 LYS cc_start: 0.9293 (mttt) cc_final: 0.8714 (mttm) REVERT: C 1449 ASN cc_start: 0.9048 (m110) cc_final: 0.8602 (m110) REVERT: C 1456 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7799 (p) REVERT: C 1546 LYS cc_start: 0.9324 (ttpt) cc_final: 0.9109 (tttt) REVERT: D 232 LEU cc_start: 0.9043 (tp) cc_final: 0.8440 (tt) REVERT: D 238 TYR cc_start: 0.7849 (m-80) cc_final: 0.7265 (m-80) REVERT: D 244 PHE cc_start: 0.8121 (m-80) cc_final: 0.7366 (m-80) REVERT: D 277 TYR cc_start: 0.8885 (m-10) cc_final: 0.8540 (m-80) REVERT: D 280 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: D 285 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8650 (pp30) REVERT: D 289 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8115 (tm-30) REVERT: D 297 LYS cc_start: 0.9234 (mttm) cc_final: 0.8803 (mttp) REVERT: D 316 VAL cc_start: 0.9012 (t) cc_final: 0.8686 (p) REVERT: D 318 LYS cc_start: 0.8389 (tttt) cc_final: 0.8003 (tttp) REVERT: D 340 LYS cc_start: 0.9281 (mttm) cc_final: 0.9015 (mtpp) REVERT: D 349 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8720 (mmm-85) outliers start: 141 outliers final: 96 residues processed: 729 average time/residue: 0.2327 time to fit residues: 286.7661 Evaluate side-chains 715 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 604 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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 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 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 2432 ARG 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 2477 PHE Chi-restraints excluded: chain A residue 2561 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 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 1033 ARG Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1222 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 2075 ASP Chi-restraints excluded: chain B residue 2149 LYS Chi-restraints excluded: chain B residue 2188 VAL 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 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 312 LEU 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 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 1010 LEU Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1151 PHE 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 1288 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 1456 THR 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 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 337 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 341 GLN 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: 0.7980 chunk 82 optimal weight: 0.8980 chunk 249 optimal weight: 0.0980 chunk 262 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B2584 ASN C1162 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.126529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.095145 restraints weight = 124099.463| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.27 r_work: 0.3241 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39039 Z= 0.115 Angle : 0.576 13.327 52938 Z= 0.281 Chirality : 0.038 0.240 6127 Planarity : 0.004 0.049 6587 Dihedral : 5.507 77.174 5208 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.29 % Allowed : 15.08 % Favored : 81.62 % 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: 1.92 (0.13), residues: 4660 helix: 2.10 (0.09), residues: 3289 sheet: -0.00 (0.80), residues: 35 loop : -0.83 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1468 TYR 0.031 0.001 TYR B 662 PHE 0.033 0.001 PHE D 291 TRP 0.022 0.001 TRP A 453 HIS 0.019 0.001 HIS A2430 Details of bonding type rmsd covalent geometry : bond 0.00257 (39017) covalent geometry : angle 0.57569 (52901) SS BOND : bond 0.00096 ( 11) SS BOND : angle 1.03191 ( 22) hydrogen bonds : bond 0.03406 ( 2438) hydrogen bonds : angle 3.98303 ( 7188) metal coordination : bond 0.00822 ( 8) metal coordination : angle 1.00130 ( 6) link_NAG-ASN : bond 0.00201 ( 3) link_NAG-ASN : angle 1.12544 ( 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 750 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 611 time to evaluate : 1.310 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 TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 175 MET cc_start: 0.7946 (tpt) cc_final: 0.7064 (tpt) REVERT: A 195 MET cc_start: 0.6298 (mmm) cc_final: 0.6001 (mmm) REVERT: A 202 TRP cc_start: 0.8629 (p-90) cc_final: 0.8339 (p-90) REVERT: A 207 TYR cc_start: 0.6059 (m-10) cc_final: 0.5848 (m-10) REVERT: A 491 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: A 500 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5173 (mtpt) REVERT: A 922 MET cc_start: 0.9132 (mtt) cc_final: 0.8764 (mtt) REVERT: A 2433 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7114 (tp) REVERT: A 2442 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7940 (mt) REVERT: A 2469 HIS cc_start: 0.3503 (OUTLIER) cc_final: 0.3108 (t-90) REVERT: A 2488 MET cc_start: 0.7026 (mmt) cc_final: 0.6620 (mmm) REVERT: A 2492 PHE cc_start: 0.9067 (t80) cc_final: 0.8770 (t80) REVERT: A 2543 MET cc_start: 0.7747 (mtt) cc_final: 0.7509 (ttm) REVERT: A 2561 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8420 (mpp) REVERT: B 188 PHE cc_start: 0.8150 (t80) cc_final: 0.7947 (t80) REVERT: B 344 TRP cc_start: 0.7508 (t60) cc_final: 0.6688 (t60) REVERT: B 350 GLN cc_start: 0.7790 (tt0) cc_final: 0.7466 (tp40) REVERT: B 789 HIS cc_start: 0.7746 (t70) cc_final: 0.7379 (t-170) REVERT: B 1808 GLN cc_start: 0.8184 (pt0) cc_final: 0.7888 (tm-30) REVERT: B 2075 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4759 (t0) REVERT: B 2188 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8910 (m) REVERT: B 2277 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8425 (tp-100) REVERT: B 2320 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8095 (mmp80) REVERT: B 2552 ILE cc_start: 0.9063 (mt) cc_final: 0.8803 (mm) REVERT: B 2972 ILE cc_start: 0.8987 (mt) cc_final: 0.8762 (pt) REVERT: C 141 MET cc_start: 0.7888 (mtp) cc_final: 0.7556 (mtm) REVERT: C 166 ARG cc_start: 0.8955 (mtt-85) cc_final: 0.8501 (ttm-80) REVERT: C 197 VAL cc_start: 0.9247 (t) cc_final: 0.8931 (p) REVERT: C 235 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7904 (mp0) REVERT: C 243 PHE cc_start: 0.8133 (m-80) cc_final: 0.7733 (m-80) REVERT: C 275 GLU cc_start: 0.8725 (tt0) cc_final: 0.8495 (tt0) REVERT: C 331 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7902 (mm-40) REVERT: C 350 MET cc_start: 0.8213 (tpp) cc_final: 0.7753 (mmm) REVERT: C 388 MET cc_start: 0.8147 (mtt) cc_final: 0.7479 (mpp) REVERT: C 395 THR cc_start: 0.9108 (m) cc_final: 0.8844 (p) REVERT: C 469 LEU cc_start: 0.9195 (mt) cc_final: 0.8967 (mt) REVERT: C 498 LYS cc_start: 0.8354 (tttt) cc_final: 0.7891 (mmmm) REVERT: C 520 MET cc_start: 0.9334 (mmp) cc_final: 0.8937 (mmm) REVERT: C 525 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8980 (pp) REVERT: C 593 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8698 (mp) REVERT: C 643 MET cc_start: 0.8711 (mmm) cc_final: 0.7796 (mmm) REVERT: C 892 MET cc_start: 0.9104 (mmp) cc_final: 0.8747 (mmp) REVERT: C 903 MET cc_start: 0.8436 (mtp) cc_final: 0.8007 (ttm) REVERT: C 926 VAL cc_start: 0.9511 (t) cc_final: 0.9195 (m) REVERT: C 929 MET cc_start: 0.9024 (tpt) cc_final: 0.8468 (tpt) REVERT: C 932 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: C 958 ASP cc_start: 0.8445 (m-30) cc_final: 0.8218 (m-30) REVERT: C 962 TYR cc_start: 0.9182 (t80) cc_final: 0.8842 (t80) REVERT: C 1004 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.7800 (tmt-80) REVERT: C 1016 GLU cc_start: 0.9133 (mp0) cc_final: 0.8723 (mp0) REVERT: C 1028 MET cc_start: 0.9061 (mtp) cc_final: 0.8804 (mtt) REVERT: C 1029 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9063 (mt) REVERT: C 1096 PHE cc_start: 0.8611 (p90) cc_final: 0.7922 (p90) REVERT: C 1108 LEU cc_start: 0.9464 (mt) cc_final: 0.8941 (mt) REVERT: C 1203 MET cc_start: 0.8640 (tpp) cc_final: 0.7770 (tpp) REVERT: C 1258 MET cc_start: 0.8514 (mmt) cc_final: 0.8307 (mmt) REVERT: C 1259 LYS cc_start: 0.9467 (mtpp) cc_final: 0.9193 (tttp) REVERT: C 1274 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7229 (t0) REVERT: C 1276 TYR cc_start: 0.8877 (t80) cc_final: 0.8634 (t80) REVERT: C 1287 TRP cc_start: 0.8846 (t60) cc_final: 0.8587 (t60) REVERT: C 1301 MET cc_start: 0.8500 (ttp) cc_final: 0.7821 (tpt) REVERT: C 1309 PHE cc_start: 0.8904 (m-80) cc_final: 0.8594 (m-80) REVERT: C 1364 GLU cc_start: 0.8597 (tt0) cc_final: 0.8116 (tt0) REVERT: C 1393 LYS cc_start: 0.9330 (mttt) cc_final: 0.8721 (mttm) REVERT: C 1449 ASN cc_start: 0.9097 (m110) cc_final: 0.8689 (m110) REVERT: C 1546 LYS cc_start: 0.9334 (ttpt) cc_final: 0.9118 (tttt) REVERT: D 234 PHE cc_start: 0.8714 (t80) cc_final: 0.8091 (t80) REVERT: D 238 TYR cc_start: 0.7802 (m-80) cc_final: 0.7167 (m-80) REVERT: D 277 TYR cc_start: 0.8827 (m-10) cc_final: 0.8537 (m-80) REVERT: D 280 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: D 281 ASP cc_start: 0.8634 (t70) cc_final: 0.8410 (t0) REVERT: D 289 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 297 LYS cc_start: 0.9219 (mttm) cc_final: 0.8881 (mttp) REVERT: D 316 VAL cc_start: 0.9029 (t) cc_final: 0.8740 (p) REVERT: D 318 LYS cc_start: 0.8436 (tttt) cc_final: 0.8022 (tttp) REVERT: D 340 LYS cc_start: 0.9297 (mttm) cc_final: 0.9021 (mtpp) REVERT: D 342 TYR cc_start: 0.8950 (m-80) cc_final: 0.8593 (m-10) outliers start: 139 outliers final: 94 residues processed: 708 average time/residue: 0.2261 time to fit residues: 270.7864 Evaluate side-chains 698 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 588 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 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 1322 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2295 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 2469 HIS 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 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 1196 GLU Chi-restraints excluded: chain B residue 1222 LEU 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 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 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2223 PHE Chi-restraints excluded: chain B residue 2255 MET 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 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 431 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 733 CYS 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 1151 PHE Chi-restraints excluded: chain C residue 1182 LEU 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 1313 SER 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 1536 MET 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 313 CYS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 341 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 40 optimal weight: 6.9990 chunk 106 optimal weight: 0.0170 chunk 58 optimal weight: 5.9990 chunk 278 optimal weight: 0.9980 chunk 292 optimal weight: 0.0000 chunk 155 optimal weight: 0.0870 chunk 337 optimal weight: 8.9990 chunk 461 optimal weight: 2.9990 chunk 473 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2556 HIS B 666 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1661 GLN C 333 GLN C 549 GLN C1270 GLN D 272 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN D 347 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.126554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.095853 restraints weight = 123739.852| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.25 r_work: 0.3228 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39039 Z= 0.119 Angle : 0.584 13.539 52938 Z= 0.285 Chirality : 0.039 0.243 6127 Planarity : 0.004 0.048 6587 Dihedral : 5.442 76.909 5205 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.41 % Allowed : 15.51 % Favored : 81.08 % 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: 1.92 (0.13), residues: 4660 helix: 2.10 (0.09), residues: 3291 sheet: -0.04 (0.82), residues: 35 loop : -0.84 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 334 TYR 0.036 0.001 TYR B 662 PHE 0.039 0.001 PHE D 291 TRP 0.026 0.001 TRP A 453 HIS 0.020 0.001 HIS A2430 Details of bonding type rmsd covalent geometry : bond 0.00268 (39017) covalent geometry : angle 0.58361 (52901) SS BOND : bond 0.00109 ( 11) SS BOND : angle 1.01836 ( 22) hydrogen bonds : bond 0.03380 ( 2438) hydrogen bonds : angle 3.97471 ( 7188) metal coordination : bond 0.00864 ( 8) metal coordination : angle 1.00107 ( 6) link_NAG-ASN : bond 0.00182 ( 3) link_NAG-ASN : angle 1.09089 ( 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 759 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 615 time to evaluate : 1.536 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 175 MET cc_start: 0.7930 (tpt) cc_final: 0.7117 (tpt) REVERT: A 202 TRP cc_start: 0.8637 (p-90) cc_final: 0.8366 (p-90) REVERT: A 207 TYR cc_start: 0.6022 (m-10) cc_final: 0.5793 (m-10) REVERT: A 447 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8586 (mp) REVERT: A 479 GLN cc_start: 0.8000 (mt0) cc_final: 0.7631 (tt0) REVERT: A 491 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: A 500 LYS cc_start: 0.5449 (OUTLIER) cc_final: 0.5129 (mtpt) REVERT: A 519 MET cc_start: 0.7899 (tpp) cc_final: 0.7282 (ttm) REVERT: A 922 MET cc_start: 0.9143 (mtt) cc_final: 0.8770 (mtt) REVERT: A 2397 HIS cc_start: 0.7869 (m90) cc_final: 0.7596 (m90) REVERT: A 2433 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7186 (tp) REVERT: A 2442 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (mt) REVERT: A 2469 HIS cc_start: 0.3544 (OUTLIER) cc_final: 0.3092 (t-90) REVERT: A 2488 MET cc_start: 0.6997 (mmt) cc_final: 0.6613 (mmm) REVERT: A 2543 MET cc_start: 0.7789 (mtt) cc_final: 0.7537 (ttm) REVERT: A 2552 MET cc_start: 0.6582 (mtp) cc_final: 0.6191 (ttp) REVERT: A 2561 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8417 (mpp) REVERT: B 49 PHE cc_start: 0.6027 (m-10) cc_final: 0.5791 (m-10) REVERT: B 188 PHE cc_start: 0.8170 (t80) cc_final: 0.7957 (t80) REVERT: B 350 GLN cc_start: 0.7813 (tt0) cc_final: 0.7486 (tp40) REVERT: B 1808 GLN cc_start: 0.8174 (pt0) cc_final: 0.7877 (tm-30) REVERT: B 2075 ASP cc_start: 0.5114 (OUTLIER) cc_final: 0.4726 (t0) REVERT: B 2188 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8910 (m) REVERT: B 2277 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8458 (tp-100) REVERT: B 2320 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (mmp80) REVERT: B 2552 ILE cc_start: 0.9089 (mt) cc_final: 0.8822 (mm) REVERT: B 2972 ILE cc_start: 0.9004 (mt) cc_final: 0.8773 (pt) REVERT: C 141 MET cc_start: 0.7901 (mtp) cc_final: 0.7587 (mtm) REVERT: C 166 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8430 (ttm-80) REVERT: C 197 VAL cc_start: 0.9255 (t) cc_final: 0.8946 (p) REVERT: C 235 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7902 (mp0) REVERT: C 243 PHE cc_start: 0.8169 (m-80) cc_final: 0.7765 (m-80) REVERT: C 275 GLU cc_start: 0.8743 (tt0) cc_final: 0.8531 (tt0) REVERT: C 331 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7742 (mm-40) REVERT: C 350 MET cc_start: 0.8257 (tpp) cc_final: 0.7798 (mmm) REVERT: C 388 MET cc_start: 0.8065 (mtt) cc_final: 0.7387 (mpp) REVERT: C 395 THR cc_start: 0.9125 (m) cc_final: 0.8820 (p) REVERT: C 456 LEU cc_start: 0.9294 (tt) cc_final: 0.8819 (pp) REVERT: C 469 LEU cc_start: 0.9207 (mt) cc_final: 0.8978 (mt) REVERT: C 498 LYS cc_start: 0.8349 (tttt) cc_final: 0.7876 (mmmm) REVERT: C 520 MET cc_start: 0.9363 (mmp) cc_final: 0.9124 (mmm) REVERT: C 525 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8971 (pp) REVERT: C 643 MET cc_start: 0.8714 (mmm) cc_final: 0.7807 (mmm) REVERT: C 892 MET cc_start: 0.9118 (mmp) cc_final: 0.8771 (mmp) REVERT: C 903 MET cc_start: 0.8473 (mtp) cc_final: 0.8026 (ttm) REVERT: C 929 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8488 (tpt) REVERT: C 932 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: C 962 TYR cc_start: 0.9172 (t80) cc_final: 0.8785 (t80) REVERT: C 972 MET cc_start: 0.8476 (tpp) cc_final: 0.7874 (tpp) REVERT: C 1004 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.7812 (tmt-80) REVERT: C 1016 GLU cc_start: 0.9145 (mp0) cc_final: 0.8710 (mp0) REVERT: C 1096 PHE cc_start: 0.8649 (p90) cc_final: 0.7882 (p90) REVERT: C 1108 LEU cc_start: 0.9451 (mt) cc_final: 0.8935 (mt) REVERT: C 1123 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9343 (p) REVERT: C 1203 MET cc_start: 0.8551 (tpp) cc_final: 0.7734 (tpp) REVERT: C 1258 MET cc_start: 0.8541 (mmt) cc_final: 0.8326 (mmt) REVERT: C 1274 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7273 (t0) REVERT: C 1301 MET cc_start: 0.8587 (ttp) cc_final: 0.7930 (tpt) REVERT: C 1309 PHE cc_start: 0.8918 (m-10) cc_final: 0.8515 (m-80) REVERT: C 1326 LEU cc_start: 0.9527 (mt) cc_final: 0.9311 (mt) REVERT: C 1364 GLU cc_start: 0.8572 (tt0) cc_final: 0.8061 (tt0) REVERT: C 1393 LYS cc_start: 0.9314 (mttt) cc_final: 0.8673 (mttm) REVERT: C 1449 ASN cc_start: 0.9111 (m110) cc_final: 0.8705 (m110) REVERT: C 1528 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8358 (t) REVERT: C 1536 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8756 (ttt) REVERT: C 1546 LYS cc_start: 0.9355 (ttpt) cc_final: 0.9146 (tttt) REVERT: D 238 TYR cc_start: 0.7748 (m-80) cc_final: 0.7123 (m-80) REVERT: D 243 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8754 (mm) REVERT: D 277 TYR cc_start: 0.8893 (m-10) cc_final: 0.8575 (m-80) REVERT: D 280 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: D 285 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8790 (pp30) REVERT: D 289 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8231 (tm-30) REVERT: D 297 LYS cc_start: 0.9223 (mttm) cc_final: 0.8987 (mtmm) REVERT: D 312 ASP cc_start: 0.7986 (t0) cc_final: 0.7598 (t70) REVERT: D 316 VAL cc_start: 0.9021 (t) cc_final: 0.8760 (p) REVERT: D 318 LYS cc_start: 0.8450 (tttt) cc_final: 0.8048 (tttp) REVERT: D 334 ARG cc_start: 0.9213 (mmp80) cc_final: 0.8773 (mmp80) REVERT: D 340 LYS cc_start: 0.9290 (mttm) cc_final: 0.8599 (mtpp) REVERT: D 342 TYR cc_start: 0.8915 (m-80) cc_final: 0.8584 (m-10) REVERT: D 387 ASP cc_start: 0.7929 (t0) cc_final: 0.7649 (t0) outliers start: 144 outliers final: 102 residues processed: 720 average time/residue: 0.2255 time to fit residues: 275.2604 Evaluate side-chains 707 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 585 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 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 1358 SER Chi-restraints excluded: chain A residue 2151 LEU 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 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 2469 HIS 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 2575 LEU 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 1196 GLU Chi-restraints excluded: chain B residue 1222 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 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 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2188 VAL 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 50 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 111 ASP 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 273 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 525 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 1123 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 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 1528 VAL Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1536 MET 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 272 GLN 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 339 CYS Chi-restraints excluded: chain D residue 341 GLN 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: 0.0030 chunk 246 optimal weight: 7.9990 chunk 347 optimal weight: 0.9990 chunk 452 optimal weight: 8.9990 chunk 193 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2584 ASN C 63 HIS ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.126392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096475 restraints weight = 123745.647| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.28 r_work: 0.3239 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39039 Z= 0.141 Angle : 0.610 14.893 52938 Z= 0.297 Chirality : 0.040 0.324 6127 Planarity : 0.004 0.050 6587 Dihedral : 5.455 77.743 5202 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.60 % Allowed : 15.82 % Favored : 80.58 % 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: 2.05 (0.09), residues: 3295 sheet: -0.13 (0.79), residues: 35 loop : -0.81 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 271 TYR 0.031 0.001 TYR B 662 PHE 0.029 0.001 PHE D 234 TRP 0.040 0.001 TRP C1287 HIS 0.023 0.001 HIS A2430 Details of bonding type rmsd covalent geometry : bond 0.00328 (39017) covalent geometry : angle 0.60947 (52901) SS BOND : bond 0.00162 ( 11) SS BOND : angle 1.10796 ( 22) hydrogen bonds : bond 0.03509 ( 2438) hydrogen bonds : angle 4.00898 ( 7188) metal coordination : bond 0.01087 ( 8) metal coordination : angle 0.96695 ( 6) link_NAG-ASN : bond 0.00171 ( 3) link_NAG-ASN : angle 1.13115 ( 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 750 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 598 time to evaluate : 1.572 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: A 175 MET cc_start: 0.7938 (tpt) cc_final: 0.7127 (tpt) REVERT: A 195 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4469 (mmm) REVERT: A 202 TRP cc_start: 0.8618 (p-90) cc_final: 0.8326 (p-90) REVERT: A 447 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 479 GLN cc_start: 0.7983 (mt0) cc_final: 0.7627 (tt0) REVERT: A 491 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: A 500 LYS cc_start: 0.5446 (OUTLIER) cc_final: 0.5143 (mtpt) REVERT: A 519 MET cc_start: 0.7925 (tpp) cc_final: 0.7281 (ttm) REVERT: A 922 MET cc_start: 0.9161 (mtt) cc_final: 0.8744 (mtt) REVERT: A 2397 HIS cc_start: 0.7860 (m90) cc_final: 0.7586 (m90) REVERT: A 2433 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7162 (tp) REVERT: A 2442 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 2469 HIS cc_start: 0.3584 (OUTLIER) cc_final: 0.3131 (t-90) REVERT: A 2488 MET cc_start: 0.6882 (mmt) cc_final: 0.6492 (mmm) REVERT: A 2543 MET cc_start: 0.7803 (mtt) cc_final: 0.7545 (ttm) REVERT: A 2552 MET cc_start: 0.6574 (mtp) cc_final: 0.6223 (ttp) REVERT: A 2582 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7462 (ptp) REVERT: B 49 PHE cc_start: 0.6043 (m-10) cc_final: 0.5762 (m-10) REVERT: B 188 PHE cc_start: 0.8178 (t80) cc_final: 0.7955 (t80) REVERT: B 350 GLN cc_start: 0.7813 (tt0) cc_final: 0.7482 (tp40) REVERT: B 789 HIS cc_start: 0.7730 (t70) cc_final: 0.7412 (t-170) REVERT: B 1033 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7080 (tpm170) REVERT: B 1808 GLN cc_start: 0.8195 (pt0) cc_final: 0.7886 (tm-30) REVERT: B 2075 ASP cc_start: 0.5125 (OUTLIER) cc_final: 0.4726 (t0) REVERT: B 2188 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8927 (m) REVERT: B 2277 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8493 (tp-100) REVERT: B 2320 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8089 (mmp80) REVERT: B 2552 ILE cc_start: 0.9055 (mt) cc_final: 0.8799 (mm) REVERT: B 2972 ILE cc_start: 0.8998 (mt) cc_final: 0.8773 (pt) REVERT: C 61 PHE cc_start: 0.7754 (m-10) cc_final: 0.7472 (m-80) REVERT: C 141 MET cc_start: 0.7754 (mtp) cc_final: 0.7442 (mtm) REVERT: C 166 ARG cc_start: 0.8929 (mtt-85) cc_final: 0.8132 (ttm110) REVERT: C 172 LYS cc_start: 0.8418 (mttt) cc_final: 0.7823 (ptpt) REVERT: C 189 LEU cc_start: 0.9110 (mt) cc_final: 0.8901 (mt) REVERT: C 197 VAL cc_start: 0.9283 (t) cc_final: 0.8971 (p) REVERT: C 235 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7946 (mp0) REVERT: C 243 PHE cc_start: 0.7923 (m-80) cc_final: 0.7574 (m-80) REVERT: C 323 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 331 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7735 (mm110) REVERT: C 388 MET cc_start: 0.8145 (mtt) cc_final: 0.7475 (mpp) REVERT: C 456 LEU cc_start: 0.9293 (tt) cc_final: 0.8895 (pp) REVERT: C 469 LEU cc_start: 0.9211 (mt) cc_final: 0.8989 (mt) REVERT: C 498 LYS cc_start: 0.8368 (tttt) cc_final: 0.7879 (mmmm) REVERT: C 520 MET cc_start: 0.9392 (mmp) cc_final: 0.9189 (mmm) REVERT: C 525 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8944 (pp) REVERT: C 540 PHE cc_start: 0.8905 (t80) cc_final: 0.8704 (t80) REVERT: C 554 GLU cc_start: 0.8364 (tp30) cc_final: 0.7739 (tp30) REVERT: C 578 TYR cc_start: 0.9209 (t80) cc_final: 0.8818 (t80) REVERT: C 593 LEU cc_start: 0.8887 (mp) cc_final: 0.8611 (mp) REVERT: C 643 MET cc_start: 0.8723 (mmm) cc_final: 0.7827 (mmm) REVERT: C 892 MET cc_start: 0.9118 (mmp) cc_final: 0.8784 (mmp) REVERT: C 903 MET cc_start: 0.8398 (mtp) cc_final: 0.8027 (ttm) REVERT: C 913 MET cc_start: 0.8669 (mmm) cc_final: 0.8399 (mmp) REVERT: C 929 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8545 (tpt) REVERT: C 932 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: C 962 TYR cc_start: 0.9121 (t80) cc_final: 0.8788 (t80) REVERT: C 972 MET cc_start: 0.8665 (tpp) cc_final: 0.8126 (tpp) REVERT: C 1004 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.7827 (tmt-80) REVERT: C 1016 GLU cc_start: 0.9133 (mp0) cc_final: 0.8694 (mp0) REVERT: C 1096 PHE cc_start: 0.8648 (p90) cc_final: 0.7867 (p90) REVERT: C 1108 LEU cc_start: 0.9469 (mt) cc_final: 0.8985 (mt) REVERT: C 1123 VAL cc_start: 0.9564 (OUTLIER) cc_final: 0.9338 (p) REVERT: C 1203 MET cc_start: 0.8421 (tpp) cc_final: 0.7529 (tpp) REVERT: C 1227 LEU cc_start: 0.9396 (mt) cc_final: 0.9136 (mp) REVERT: C 1287 TRP cc_start: 0.8353 (t60) cc_final: 0.8145 (t60) REVERT: C 1301 MET cc_start: 0.8495 (ttp) cc_final: 0.7771 (tpt) REVERT: C 1309 PHE cc_start: 0.8840 (m-10) cc_final: 0.8542 (m-80) REVERT: C 1311 PHE cc_start: 0.9239 (t80) cc_final: 0.9012 (t80) REVERT: C 1326 LEU cc_start: 0.9537 (mt) cc_final: 0.9320 (mt) REVERT: C 1345 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8880 (tt) REVERT: C 1364 GLU cc_start: 0.8598 (tt0) cc_final: 0.8078 (tt0) REVERT: C 1393 LYS cc_start: 0.9333 (mttt) cc_final: 0.8681 (mttm) REVERT: C 1449 ASN cc_start: 0.9080 (m110) cc_final: 0.8657 (m110) REVERT: C 1519 MET cc_start: 0.7998 (mmp) cc_final: 0.7655 (mmt) REVERT: C 1528 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8407 (t) REVERT: D 238 TYR cc_start: 0.7660 (m-80) cc_final: 0.7126 (m-80) REVERT: D 243 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8780 (mm) REVERT: D 244 PHE cc_start: 0.8080 (m-80) cc_final: 0.7255 (m-80) REVERT: D 277 TYR cc_start: 0.8847 (m-10) cc_final: 0.8480 (m-80) REVERT: D 280 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: D 285 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8691 (pp30) REVERT: D 289 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8223 (tm-30) REVERT: D 297 LYS cc_start: 0.9248 (mttm) cc_final: 0.8961 (mtmm) REVERT: D 316 VAL cc_start: 0.8988 (t) cc_final: 0.8753 (p) REVERT: D 318 LYS cc_start: 0.8427 (tttt) cc_final: 0.8074 (tttp) REVERT: D 334 ARG cc_start: 0.9189 (mmp80) cc_final: 0.8832 (mmp80) REVERT: D 340 LYS cc_start: 0.9260 (mttm) cc_final: 0.8574 (mtpp) REVERT: D 342 TYR cc_start: 0.8871 (m-80) cc_final: 0.8643 (m-10) REVERT: D 348 THR cc_start: 0.9241 (m) cc_final: 0.9015 (p) REVERT: D 387 ASP cc_start: 0.7919 (t0) cc_final: 0.6027 (m-30) outliers start: 152 outliers final: 109 residues processed: 704 average time/residue: 0.2200 time to fit residues: 262.6739 Evaluate side-chains 712 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 582 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 195 MET 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 448 SER 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 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 2151 LEU Chi-restraints excluded: chain A residue 2209 LEU 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 2433 LEU 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 2575 LEU 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 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 1222 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 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 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2188 VAL 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 2387 GLU 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 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 109 VAL Chi-restraints excluded: chain C residue 111 ASP 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 253 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 525 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 1119 GLU Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1182 LEU 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 1288 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 1485 ILE Chi-restraints excluded: chain C residue 1488 PHE Chi-restraints excluded: chain C residue 1492 PHE Chi-restraints excluded: chain C residue 1528 VAL 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 232 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 339 CYS 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: 0.8980 chunk 344 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 323 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 437 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 319 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 358 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.126580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096801 restraints weight = 124616.892| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.36 r_work: 0.3240 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39039 Z= 0.132 Angle : 0.619 14.138 52938 Z= 0.301 Chirality : 0.039 0.270 6127 Planarity : 0.004 0.053 6587 Dihedral : 5.381 77.706 5197 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.13 % Allowed : 16.65 % Favored : 80.23 % 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: 3298 sheet: -0.15 (0.79), residues: 35 loop : -0.78 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1468 TYR 0.040 0.001 TYR B 662 PHE 0.034 0.001 PHE A2572 TRP 0.028 0.001 TRP A 453 HIS 0.026 0.001 HIS A2430 Details of bonding type rmsd covalent geometry : bond 0.00305 (39017) covalent geometry : angle 0.61863 (52901) SS BOND : bond 0.00252 ( 11) SS BOND : angle 1.28243 ( 22) hydrogen bonds : bond 0.03455 ( 2438) hydrogen bonds : angle 4.00953 ( 7188) metal coordination : bond 0.01002 ( 8) metal coordination : angle 1.01234 ( 6) link_NAG-ASN : bond 0.00179 ( 3) link_NAG-ASN : angle 1.10994 ( 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 722 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 590 time to evaluate : 1.590 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: A 175 MET cc_start: 0.7931 (tpt) cc_final: 0.7129 (tpt) REVERT: A 202 TRP cc_start: 0.8608 (p-90) cc_final: 0.8366 (p-90) REVERT: A 447 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 479 GLN cc_start: 0.7963 (mt0) cc_final: 0.7571 (tt0) REVERT: A 491 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: A 500 LYS cc_start: 0.5434 (OUTLIER) cc_final: 0.5142 (mtpt) REVERT: A 519 MET cc_start: 0.7925 (tpp) cc_final: 0.7278 (ttm) REVERT: A 922 MET cc_start: 0.9145 (mtt) cc_final: 0.8749 (mtt) REVERT: A 2087 MET cc_start: 0.6861 (mmm) cc_final: 0.6381 (tpp) REVERT: A 2397 HIS cc_start: 0.7842 (m90) cc_final: 0.7598 (m90) REVERT: A 2430 HIS cc_start: 0.7555 (m170) cc_final: 0.6908 (m170) REVERT: A 2433 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7176 (tp) REVERT: A 2442 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7987 (mt) REVERT: A 2469 HIS cc_start: 0.3555 (OUTLIER) cc_final: 0.2441 (t-90) REVERT: A 2543 MET cc_start: 0.7815 (mtt) cc_final: 0.7556 (ttm) REVERT: A 2552 MET cc_start: 0.6592 (mtp) cc_final: 0.6217 (ttp) REVERT: A 2582 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7445 (ptp) REVERT: B 49 PHE cc_start: 0.6032 (m-10) cc_final: 0.5795 (m-10) REVERT: B 188 PHE cc_start: 0.8170 (t80) cc_final: 0.7948 (t80) REVERT: B 350 GLN cc_start: 0.7768 (tt0) cc_final: 0.7445 (tp40) REVERT: B 789 HIS cc_start: 0.7693 (t70) cc_final: 0.7382 (t-170) REVERT: B 1808 GLN cc_start: 0.8231 (pt0) cc_final: 0.7918 (tm-30) REVERT: B 1962 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 2075 ASP cc_start: 0.5210 (OUTLIER) cc_final: 0.4805 (t0) REVERT: B 2188 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8924 (m) REVERT: B 2277 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8474 (tp-100) REVERT: B 2320 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8172 (mmp80) REVERT: B 2552 ILE cc_start: 0.9055 (mt) cc_final: 0.8804 (mm) REVERT: B 2972 ILE cc_start: 0.8999 (mt) cc_final: 0.8777 (pt) REVERT: C 61 PHE cc_start: 0.7718 (m-10) cc_final: 0.7476 (m-80) REVERT: C 141 MET cc_start: 0.7690 (mtp) cc_final: 0.7365 (mtm) REVERT: C 166 ARG cc_start: 0.8851 (mtt-85) cc_final: 0.8236 (ttm-80) REVERT: C 172 LYS cc_start: 0.8300 (mttt) cc_final: 0.7723 (ptpt) REVERT: C 189 LEU cc_start: 0.9106 (mt) cc_final: 0.8894 (mt) REVERT: C 197 VAL cc_start: 0.9272 (t) cc_final: 0.8964 (p) REVERT: C 235 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7945 (mp0) REVERT: C 243 PHE cc_start: 0.7901 (m-80) cc_final: 0.7584 (m-80) REVERT: C 275 GLU cc_start: 0.8550 (tt0) cc_final: 0.7994 (tm-30) REVERT: C 323 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 331 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7846 (mm-40) REVERT: C 388 MET cc_start: 0.8054 (mtt) cc_final: 0.7365 (mpp) REVERT: C 456 LEU cc_start: 0.9291 (tt) cc_final: 0.8899 (pp) REVERT: C 469 LEU cc_start: 0.9196 (mt) cc_final: 0.8944 (mt) REVERT: C 498 LYS cc_start: 0.8371 (tttt) cc_final: 0.7880 (mmmm) REVERT: C 525 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8929 (pp) REVERT: C 540 PHE cc_start: 0.8877 (t80) cc_final: 0.8664 (t80) REVERT: C 578 TYR cc_start: 0.9172 (t80) cc_final: 0.8798 (t80) REVERT: C 643 MET cc_start: 0.8721 (mmm) cc_final: 0.7816 (mmm) REVERT: C 892 MET cc_start: 0.9096 (mmp) cc_final: 0.8752 (mmp) REVERT: C 903 MET cc_start: 0.8400 (mtp) cc_final: 0.8050 (ttm) REVERT: C 913 MET cc_start: 0.8642 (mmm) cc_final: 0.8373 (mmp) REVERT: C 929 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8516 (tpt) REVERT: C 932 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: C 962 TYR cc_start: 0.8998 (t80) cc_final: 0.8668 (t80) REVERT: C 972 MET cc_start: 0.8683 (tpp) cc_final: 0.8094 (tpp) REVERT: C 1004 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.7841 (tmt-80) REVERT: C 1016 GLU cc_start: 0.9150 (mp0) cc_final: 0.8723 (mp0) REVERT: C 1096 PHE cc_start: 0.8633 (p90) cc_final: 0.7858 (p90) REVERT: C 1108 LEU cc_start: 0.9486 (mt) cc_final: 0.8975 (mt) REVERT: C 1123 VAL cc_start: 0.9551 (OUTLIER) cc_final: 0.9320 (p) REVERT: C 1203 MET cc_start: 0.8509 (tpp) cc_final: 0.7576 (tpp) REVERT: C 1231 TRP cc_start: 0.7697 (m-10) cc_final: 0.7297 (m-10) REVERT: C 1263 MET cc_start: 0.8373 (ptp) cc_final: 0.8151 (ppp) REVERT: C 1301 MET cc_start: 0.8411 (ttp) cc_final: 0.7706 (tpt) REVERT: C 1309 PHE cc_start: 0.8824 (m-10) cc_final: 0.8533 (m-80) REVERT: C 1311 PHE cc_start: 0.9227 (t80) cc_final: 0.8976 (t80) REVERT: C 1326 LEU cc_start: 0.9539 (mt) cc_final: 0.9318 (mt) REVERT: C 1345 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8886 (tt) REVERT: C 1364 GLU cc_start: 0.8596 (tt0) cc_final: 0.8069 (tt0) REVERT: C 1393 LYS cc_start: 0.9301 (mttt) cc_final: 0.8604 (mttm) REVERT: C 1449 ASN cc_start: 0.9065 (m110) cc_final: 0.8654 (m110) REVERT: C 1519 MET cc_start: 0.7999 (mmp) cc_final: 0.7630 (mmt) REVERT: C 1528 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8459 (t) REVERT: D 238 TYR cc_start: 0.7530 (m-80) cc_final: 0.7003 (m-80) REVERT: D 243 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 244 PHE cc_start: 0.8168 (m-80) cc_final: 0.7497 (m-80) REVERT: D 277 TYR cc_start: 0.8879 (m-10) cc_final: 0.8531 (m-80) REVERT: D 280 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7666 (m-10) REVERT: D 285 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8693 (pp30) REVERT: D 289 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8207 (tm-30) REVERT: D 316 VAL cc_start: 0.9039 (t) cc_final: 0.8821 (p) REVERT: D 334 ARG cc_start: 0.9200 (mmp80) cc_final: 0.8900 (mmp80) REVERT: D 342 TYR cc_start: 0.8879 (m-80) cc_final: 0.8475 (m-10) REVERT: D 348 THR cc_start: 0.9211 (m) cc_final: 0.9006 (p) REVERT: D 349 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8177 (mtp85) REVERT: D 387 ASP cc_start: 0.7770 (t0) cc_final: 0.6152 (m-30) outliers start: 132 outliers final: 101 residues processed: 688 average time/residue: 0.2314 time to fit residues: 271.4130 Evaluate side-chains 698 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 577 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 448 SER 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 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 2151 LEU Chi-restraints excluded: chain A residue 2209 LEU 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 2433 LEU 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 2575 LEU 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 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 1222 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 1927 GLU Chi-restraints excluded: chain B residue 1962 LEU 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 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2188 VAL 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 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 109 VAL Chi-restraints excluded: chain C residue 111 ASP 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 273 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 525 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 1119 GLU Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1182 LEU 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 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 1528 VAL 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 280 TYR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 339 CYS 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: 10.0000 chunk 136 optimal weight: 4.9990 chunk 461 optimal weight: 20.0000 chunk 383 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 240 optimal weight: 0.9980 chunk 413 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 465 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.126837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096893 restraints weight = 123629.120| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.28 r_work: 0.3254 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39039 Z= 0.127 Angle : 0.628 17.837 52938 Z= 0.305 Chirality : 0.040 0.334 6127 Planarity : 0.004 0.057 6587 Dihedral : 5.377 76.984 5197 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.98 % Allowed : 16.74 % Favored : 80.27 % 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: 1.86 (0.13), residues: 4660 helix: 2.03 (0.09), residues: 3299 sheet: -0.14 (0.80), residues: 35 loop : -0.78 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1468 TYR 0.035 0.001 TYR D 317 PHE 0.035 0.001 PHE C1011 TRP 0.060 0.001 TRP C1287 HIS 0.023 0.001 HIS A2430 Details of bonding type rmsd covalent geometry : bond 0.00291 (39017) covalent geometry : angle 0.62800 (52901) SS BOND : bond 0.00236 ( 11) SS BOND : angle 1.06297 ( 22) hydrogen bonds : bond 0.03425 ( 2438) hydrogen bonds : angle 4.01274 ( 7188) metal coordination : bond 0.00923 ( 8) metal coordination : angle 1.02318 ( 6) link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 1.08607 ( 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 719 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 593 time to evaluate : 1.722 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 TARDY: cannot create tardy model for: "MET D 267 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 175 MET cc_start: 0.7934 (tpt) cc_final: 0.7135 (tpt) REVERT: A 447 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 479 GLN cc_start: 0.7980 (mt0) cc_final: 0.7626 (tt0) REVERT: A 491 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: A 500 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.5024 (mtpt) REVERT: A 519 MET cc_start: 0.7904 (tpp) cc_final: 0.7278 (ttm) REVERT: A 922 MET cc_start: 0.9133 (mtt) cc_final: 0.8723 (mtt) REVERT: A 2397 HIS cc_start: 0.7734 (m90) cc_final: 0.7498 (m90) REVERT: A 2430 HIS cc_start: 0.7669 (m170) cc_final: 0.7060 (m170) REVERT: A 2433 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7203 (tp) REVERT: A 2442 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 2469 HIS cc_start: 0.3577 (OUTLIER) cc_final: 0.2408 (t-90) REVERT: A 2543 MET cc_start: 0.7823 (mtt) cc_final: 0.7550 (ttm) REVERT: A 2552 MET cc_start: 0.6569 (mtp) cc_final: 0.6217 (ptm) REVERT: A 2582 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7485 (ptp) REVERT: B 49 PHE cc_start: 0.6017 (m-10) cc_final: 0.5779 (m-10) REVERT: B 350 GLN cc_start: 0.7761 (tt0) cc_final: 0.7431 (tp40) REVERT: B 1033 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7087 (tpm170) REVERT: B 1762 MET cc_start: 0.7832 (tpp) cc_final: 0.7424 (tpp) REVERT: B 1808 GLN cc_start: 0.8215 (pt0) cc_final: 0.7903 (tm-30) REVERT: B 1962 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8143 (mm) REVERT: B 2075 ASP cc_start: 0.5144 (OUTLIER) cc_final: 0.4784 (t0) REVERT: B 2188 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8907 (m) REVERT: B 2277 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8464 (tp-100) REVERT: B 2320 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8165 (mmp80) REVERT: B 2552 ILE cc_start: 0.9078 (mt) cc_final: 0.8815 (mm) REVERT: B 2972 ILE cc_start: 0.9002 (mt) cc_final: 0.8778 (pt) REVERT: C 61 PHE cc_start: 0.7718 (m-10) cc_final: 0.7464 (m-80) REVERT: C 86 MET cc_start: 0.9593 (tpt) cc_final: 0.9341 (tpp) REVERT: C 141 MET cc_start: 0.7705 (mtp) cc_final: 0.7410 (mtm) REVERT: C 166 ARG cc_start: 0.8890 (mtt-85) cc_final: 0.8180 (ttm110) REVERT: C 172 LYS cc_start: 0.8023 (mttt) cc_final: 0.7458 (ptpt) REVERT: C 179 TRP cc_start: 0.8263 (t-100) cc_final: 0.7735 (t60) REVERT: C 189 LEU cc_start: 0.9094 (mt) cc_final: 0.8886 (mt) REVERT: C 197 VAL cc_start: 0.9235 (t) cc_final: 0.8935 (p) REVERT: C 235 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7947 (mp0) REVERT: C 243 PHE cc_start: 0.7950 (m-80) cc_final: 0.7609 (m-80) REVERT: C 275 GLU cc_start: 0.8560 (tt0) cc_final: 0.7977 (tm-30) REVERT: C 323 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8540 (tm-30) REVERT: C 331 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7626 (mm110) REVERT: C 388 MET cc_start: 0.8024 (mtt) cc_final: 0.7375 (mpp) REVERT: C 456 LEU cc_start: 0.9275 (tt) cc_final: 0.8957 (pp) REVERT: C 469 LEU cc_start: 0.9202 (mt) cc_final: 0.8936 (mt) REVERT: C 498 LYS cc_start: 0.8349 (tttt) cc_final: 0.7861 (mmmm) REVERT: C 525 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8914 (pp) REVERT: C 540 PHE cc_start: 0.8875 (t80) cc_final: 0.8661 (t80) REVERT: C 578 TYR cc_start: 0.9164 (t80) cc_final: 0.8800 (t80) REVERT: C 593 LEU cc_start: 0.8836 (mt) cc_final: 0.8556 (mp) REVERT: C 643 MET cc_start: 0.8695 (mmm) cc_final: 0.7798 (mmm) REVERT: C 892 MET cc_start: 0.9121 (mmp) cc_final: 0.8713 (mmp) REVERT: C 903 MET cc_start: 0.8399 (mtp) cc_final: 0.8060 (ttm) REVERT: C 913 MET cc_start: 0.8636 (mmm) cc_final: 0.8343 (mmp) REVERT: C 929 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8539 (tpt) REVERT: C 932 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: C 962 TYR cc_start: 0.9005 (t80) cc_final: 0.8704 (t80) REVERT: C 972 MET cc_start: 0.8730 (tpp) cc_final: 0.8091 (tpp) REVERT: C 1004 ARG cc_start: 0.8811 (mtm-85) cc_final: 0.7828 (tmt-80) REVERT: C 1016 GLU cc_start: 0.9153 (mp0) cc_final: 0.8707 (mp0) REVERT: C 1096 PHE cc_start: 0.8598 (p90) cc_final: 0.7799 (p90) REVERT: C 1108 LEU cc_start: 0.9492 (mt) cc_final: 0.8980 (mt) REVERT: C 1123 VAL cc_start: 0.9554 (OUTLIER) cc_final: 0.9320 (p) REVERT: C 1203 MET cc_start: 0.8464 (tpp) cc_final: 0.7539 (tpp) REVERT: C 1263 MET cc_start: 0.8554 (ptp) cc_final: 0.8319 (ppp) REVERT: C 1273 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6616 (ptp90) REVERT: C 1301 MET cc_start: 0.8222 (ttp) cc_final: 0.7105 (tpt) REVERT: C 1302 MET cc_start: 0.8147 (tmm) cc_final: 0.7519 (mmm) REVERT: C 1305 CYS cc_start: 0.8857 (m) cc_final: 0.8154 (m) REVERT: C 1309 PHE cc_start: 0.8814 (m-10) cc_final: 0.8553 (m-80) REVERT: C 1311 PHE cc_start: 0.9207 (t80) cc_final: 0.8936 (t80) REVERT: C 1326 LEU cc_start: 0.9536 (mt) cc_final: 0.9315 (mt) REVERT: C 1345 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8903 (tt) REVERT: C 1364 GLU cc_start: 0.8675 (tt0) cc_final: 0.8147 (tt0) REVERT: C 1393 LYS cc_start: 0.9321 (mttt) cc_final: 0.8644 (mttm) REVERT: C 1449 ASN cc_start: 0.9054 (m110) cc_final: 0.8641 (m110) REVERT: C 1519 MET cc_start: 0.8067 (mmp) cc_final: 0.7698 (mmt) REVERT: C 1528 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8590 (p) REVERT: D 191 PHE cc_start: 0.6907 (m-80) cc_final: 0.6689 (m-80) REVERT: D 238 TYR cc_start: 0.7466 (m-80) cc_final: 0.6848 (m-80) REVERT: D 243 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8707 (mm) REVERT: D 244 PHE cc_start: 0.8065 (m-80) cc_final: 0.7243 (m-80) REVERT: D 272 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8909 (mm110) REVERT: D 277 TYR cc_start: 0.8881 (m-10) cc_final: 0.8507 (m-80) REVERT: D 280 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7702 (m-10) REVERT: D 285 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8676 (pp30) REVERT: D 289 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 297 LYS cc_start: 0.9169 (mttt) cc_final: 0.8673 (mttp) REVERT: D 312 ASP cc_start: 0.8088 (p0) cc_final: 0.7885 (p0) REVERT: D 334 ARG cc_start: 0.9185 (mmp80) cc_final: 0.8919 (mmp80) REVERT: D 340 LYS cc_start: 0.9209 (mttm) cc_final: 0.8574 (mtpp) REVERT: D 342 TYR cc_start: 0.8882 (m-80) cc_final: 0.8619 (m-10) REVERT: D 349 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8008 (mtp85) REVERT: D 387 ASP cc_start: 0.7662 (t0) cc_final: 0.7453 (t0) outliers start: 126 outliers final: 95 residues processed: 682 average time/residue: 0.2313 time to fit residues: 268.7256 Evaluate side-chains 699 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 581 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 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 1322 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2151 LEU 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 2433 LEU 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 2582 MET Chi-restraints excluded: chain B residue 99 LEU 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 1222 LEU 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 1927 GLU Chi-restraints excluded: chain B residue 1962 LEU 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 2149 LYS Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2188 VAL 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 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 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 57 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 VAL 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 273 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 1119 GLU Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1151 PHE Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1224 SER 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 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 1528 VAL 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 232 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 GLN 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 339 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 463 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 HIS A2092 ASN B 666 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.125751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.095124 restraints weight = 124193.430| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.28 r_work: 0.3410 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39039 Z= 0.189 Angle : 0.660 16.563 52938 Z= 0.325 Chirality : 0.041 0.287 6127 Planarity : 0.004 0.050 6587 Dihedral : 5.492 79.144 5197 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.08 % Allowed : 16.65 % Favored : 80.27 % 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: 1.76 (0.13), residues: 4660 helix: 1.94 (0.09), residues: 3302 sheet: -0.20 (0.76), residues: 35 loop : -0.79 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 271 TYR 0.041 0.002 TYR D 317 PHE 0.036 0.001 PHE A2572 TRP 0.038 0.001 TRP A 202 HIS 0.029 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00445 (39017) covalent geometry : angle 0.65824 (52901) SS BOND : bond 0.00333 ( 11) SS BOND : angle 2.49266 ( 22) hydrogen bonds : bond 0.03708 ( 2438) hydrogen bonds : angle 4.10244 ( 7188) metal coordination : bond 0.01472 ( 8) metal coordination : angle 1.07006 ( 6) link_NAG-ASN : bond 0.00184 ( 3) link_NAG-ASN : angle 1.21459 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12959.16 seconds wall clock time: 221 minutes 38.92 seconds (13298.92 seconds total)