Starting phenix.real_space_refine on Wed Mar 4 21:30:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xja_22204/03_2026/6xja_22204.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xja_22204/03_2026/6xja_22204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xja_22204/03_2026/6xja_22204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xja_22204/03_2026/6xja_22204.map" model { file = "/net/cci-nas-00/data/ceres_data/6xja_22204/03_2026/6xja_22204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xja_22204/03_2026/6xja_22204.cif" } resolution = 4.0 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= 0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10337 2.51 5 N 2810 2.21 5 O 3244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s 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: 16441 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 10159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10159 Classifications: {'peptide': 1286} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 32, 'TRANS': 1253} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1598 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain: "B" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1604 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 17, 'TRANS': 192} Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1541 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1539 Classifications: {'peptide': 232} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 213} Residues with excluded nonbonded symmetry interactions: 25 residue: pdb=" N SER L 7 " occ=0.40 ... (4 atoms not shown) pdb=" OG SER L 7 " occ=0.40 residue: pdb=" N SER L 61 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 61 " occ=0.70 residue: pdb=" N SER L 68 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER L 68 " occ=0.60 residue: pdb=" N LYS L 112 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS L 112 " occ=0.50 residue: pdb=" N SER L 119 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 119 " occ=0.70 residue: pdb=" N ASP L 127 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP L 127 " occ=0.60 residue: pdb=" N LYS L 154 " occ=0.70 ... (7 atoms not shown) pdb=" NZ LYS L 154 " occ=0.70 residue: pdb=" N LYS L 188 " occ=0.70 ... (7 atoms not shown) pdb=" NZ LYS L 188 " occ=0.70 residue: pdb=" N GLU L 192 " occ=0.60 ... (7 atoms not shown) pdb=" OE2 GLU L 192 " occ=0.60 residue: pdb=" N CYS L 199 " occ=0.60 ... (4 atoms not shown) pdb=" SG CYS L 199 " occ=0.60 residue: pdb=" N SER L 208 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 208 " occ=0.70 residue: pdb=" N SER L 213 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 213 " occ=0.70 ... (remaining 13 not shown) Time building chain proxies: 3.00, per 1000 atoms: 0.18 Number of scatterers: 16441 At special positions: 0 Unit cell: (96.99, 131.97, 192.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3244 8.00 N 2810 7.00 C 10337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 196 " - pdb=" SG CYS H 220 " distance=2.04 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 700.5 milliseconds 4268 Ramachandran restraints generated. 2134 Oldfield, 0 Emsley, 2134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 28 sheets defined 22.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'P' and resid 782 through 793 removed outlier: 4.011A pdb=" N LYS P 788 " --> pdb=" O SER P 784 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN P 791 " --> pdb=" O VAL P 787 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN P 792 " --> pdb=" O LYS P 788 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN P 793 " --> pdb=" O ALA P 789 " (cutoff:3.500A) Processing helix chain 'P' and resid 1010 through 1015 removed outlier: 4.579A pdb=" N GLY P1015 " --> pdb=" O GLU P1011 " (cutoff:3.500A) Processing helix chain 'P' and resid 1075 through 1083 removed outlier: 3.530A pdb=" N SER P1079 " --> pdb=" O MET P1075 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE P1081 " --> pdb=" O ASP P1077 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL P1082 " --> pdb=" O ALA P1078 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER P1083 " --> pdb=" O SER P1079 " (cutoff:3.500A) Processing helix chain 'P' and resid 1119 through 1128 removed outlier: 3.582A pdb=" N LYS P1128 " --> pdb=" O LYS P1124 " (cutoff:3.500A) Processing helix chain 'P' and resid 1134 through 1144 removed outlier: 3.780A pdb=" N LEU P1144 " --> pdb=" O LYS P1140 " (cutoff:3.500A) Processing helix chain 'P' and resid 1169 through 1174 removed outlier: 3.544A pdb=" N SER P1173 " --> pdb=" O THR P1169 " (cutoff:3.500A) Processing helix chain 'P' and resid 1211 through 1213 No H-bonds generated for 'chain 'P' and resid 1211 through 1213' Processing helix chain 'P' and resid 1225 through 1238 removed outlier: 3.996A pdb=" N GLU P1231 " --> pdb=" O SER P1227 " (cutoff:3.500A) Proline residue: P1234 - end of helix removed outlier: 3.679A pdb=" N LYS P1238 " --> pdb=" O PRO P1234 " (cutoff:3.500A) Processing helix chain 'P' and resid 1243 through 1250 removed outlier: 3.719A pdb=" N ARG P1247 " --> pdb=" O SER P1243 " (cutoff:3.500A) Processing helix chain 'P' and resid 1263 through 1273 Processing helix chain 'P' and resid 1273 through 1286 removed outlier: 4.147A pdb=" N SER P1277 " --> pdb=" O ASN P1273 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA P1286 " --> pdb=" O LEU P1282 " (cutoff:3.500A) Processing helix chain 'P' and resid 1292 through 1306 removed outlier: 4.630A pdb=" N ARG P1296 " --> pdb=" O ASN P1292 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN P1306 " --> pdb=" O LYS P1302 " (cutoff:3.500A) Processing helix chain 'P' and resid 1306 through 1320 Processing helix chain 'P' and resid 1347 through 1357 removed outlier: 3.562A pdb=" N LEU P1352 " --> pdb=" O PRO P1348 " (cutoff:3.500A) Processing helix chain 'P' and resid 1367 through 1375 removed outlier: 3.757A pdb=" N TYR P1372 " --> pdb=" O ASN P1368 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY P1373 " --> pdb=" O VAL P1369 " (cutoff:3.500A) Processing helix chain 'P' and resid 1384 through 1396 Processing helix chain 'P' and resid 1401 through 1410 Processing helix chain 'P' and resid 1421 through 1430 removed outlier: 3.709A pdb=" N GLY P1429 " --> pdb=" O LYS P1425 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU P1430 " --> pdb=" O THR P1426 " (cutoff:3.500A) Processing helix chain 'P' and resid 1438 through 1444 Processing helix chain 'P' and resid 1450 through 1452 No H-bonds generated for 'chain 'P' and resid 1450 through 1452' Processing helix chain 'P' and resid 1453 through 1459 removed outlier: 3.618A pdb=" N LEU P1457 " --> pdb=" O MET P1453 " (cutoff:3.500A) Processing helix chain 'P' and resid 1480 through 1482 No H-bonds generated for 'chain 'P' and resid 1480 through 1482' Processing helix chain 'P' and resid 1490 through 1519 Processing helix chain 'P' and resid 1523 through 1527 Processing helix chain 'P' and resid 1558 through 1564 Processing helix chain 'P' and resid 1595 through 1610 removed outlier: 3.964A pdb=" N ALA P1599 " --> pdb=" O ASP P1595 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE P1600 " --> pdb=" O LYS P1596 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR P1601 " --> pdb=" O ASP P1597 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS P1604 " --> pdb=" O ILE P1600 " (cutoff:3.500A) Processing helix chain 'P' and resid 1658 through 1662 Processing helix chain 'P' and resid 1669 through 1674 Processing helix chain 'P' and resid 1676 through 1705 Processing helix chain 'P' and resid 1707 through 1714 removed outlier: 3.603A pdb=" N ALA P1713 " --> pdb=" O TYR P1709 " (cutoff:3.500A) Processing helix chain 'P' and resid 1742 through 1748 removed outlier: 3.901A pdb=" N ASN P1748 " --> pdb=" O ALA P1744 " (cutoff:3.500A) Processing helix chain 'P' and resid 1751 through 1758 removed outlier: 3.766A pdb=" N ILE P1756 " --> pdb=" O PHE P1752 " (cutoff:3.500A) Processing helix chain 'P' and resid 1798 through 1812 removed outlier: 3.762A pdb=" N ARG P1803 " --> pdb=" O LEU P1799 " (cutoff:3.500A) Processing helix chain 'P' and resid 1817 through 1823 Processing helix chain 'P' and resid 1826 through 1834 Processing helix chain 'P' and resid 1848 through 1857 Processing helix chain 'P' and resid 1863 through 1880 Processing helix chain 'P' and resid 1904 through 1921 removed outlier: 3.716A pdb=" N LEU P1908 " --> pdb=" O ASN P1904 " (cutoff:3.500A) Processing helix chain 'P' and resid 1930 through 1933 Processing helix chain 'P' and resid 1934 through 1951 removed outlier: 3.683A pdb=" N THR P1951 " --> pdb=" O TYR P1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.754A pdb=" N LYS A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.632A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 removed outlier: 3.832A pdb=" N HIS B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.540A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 194 removed outlier: 3.694A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'P' and resid 699 through 700 removed outlier: 3.874A pdb=" N ARG P 699 " --> pdb=" O SER P 692 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER P 732 " --> pdb=" O THR P 747 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE P 765 " --> pdb=" O ALA P 748 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 699 through 700 removed outlier: 3.874A pdb=" N ARG P 699 " --> pdb=" O SER P 692 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 755 through 757 Processing sheet with id=AA4, first strand: chain 'P' and resid 797 through 799 removed outlier: 6.168A pdb=" N TYR P 798 " --> pdb=" O GLY P 829 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE P 828 " --> pdb=" O GLU P 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'P' and resid 804 through 805 removed outlier: 6.630A pdb=" N LEU P 804 " --> pdb=" O TYR P 839 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'P' and resid 858 through 866 removed outlier: 3.666A pdb=" N ASN P 861 " --> pdb=" O ASP P 889 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL P 891 " --> pdb=" O ASN P 861 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA P 863 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA P 893 " --> pdb=" O ALA P 863 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER P 865 " --> pdb=" O ALA P 893 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 858 through 866 removed outlier: 3.666A pdb=" N ASN P 861 " --> pdb=" O ASP P 889 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL P 891 " --> pdb=" O ASN P 861 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA P 863 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA P 893 " --> pdb=" O ALA P 863 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER P 865 " --> pdb=" O ALA P 893 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL P 920 " --> pdb=" O GLY P 890 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU P 892 " --> pdb=" O VAL P 920 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE P 919 " --> pdb=" O SER P 955 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 870 through 871 removed outlier: 6.176A pdb=" N ILE P 870 " --> pdb=" O GLY P 899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 874 through 877 removed outlier: 6.933A pdb=" N ASN P 875 " --> pdb=" O LEU P 902 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 883 through 884 removed outlier: 6.583A pdb=" N ILE P 883 " --> pdb=" O ALA P 911 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE P 945 " --> pdb=" O GLN P 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 930 through 931 Processing sheet with id=AB3, first strand: chain 'P' and resid 1020 through 1021 removed outlier: 6.397A pdb=" N VAL P1020 " --> pdb=" O PHE P1046 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'P' and resid 1159 through 1161 removed outlier: 3.855A pdb=" N LYS P1196 " --> pdb=" O ASN P1208 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU P1214 " --> pdb=" O LEU P1209 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 1324 through 1325 Processing sheet with id=AB6, first strand: chain 'P' and resid 1413 through 1417 removed outlier: 3.858A pdb=" N GLU P1417 " --> pdb=" O SER P1469 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU P1474 " --> pdb=" O LEU P1533 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU P1532 " --> pdb=" O VAL P1586 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR P1588 " --> pdb=" O LEU P1532 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR P1534 " --> pdb=" O TYR P1588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 1734 through 1739 Processing sheet with id=AB8, first strand: chain 'P' and resid 1836 through 1839 Processing sheet with id=AB9, first strand: chain 'A' and resid 245 through 246 removed outlier: 4.151A pdb=" N CYS A 266 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 306 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 322 through 325 removed outlier: 4.405A pdb=" N ALA A 325 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 334 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.728A pdb=" N ARG B 401 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 412 " --> pdb=" O ARG B 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.155A pdb=" N ALA L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR L 54 " --> pdb=" O ALA L 58 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.530A pdb=" N SER L 119 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 141 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.076A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS L 150 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU L 200 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.572A pdb=" N ALA H 82 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 95 through 96 removed outlier: 3.577A pdb=" N TYR H 96 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.783A pdb=" N LYS H 126 " --> pdb=" O GLN H 148 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA H 144 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR H 185 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY H 149 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR H 183 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER H 186 " --> pdb=" O PHE H 172 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE H 172 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.529A pdb=" N SER H 157 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 202 " --> pdb=" O VAL H 218 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1101 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: 3.09 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.47: 8299 1.47 - 1.83: 8471 1.83 - 2.18: 3 2.18 - 2.53: 2 2.53 - 2.88: 1 Bond restraints: 16776 Sorted by residual: bond pdb=" C GLN P 673 " pdb=" N THR P 674 " ideal model delta sigma weight residual 1.333 2.878 -1.545 1.29e-02 6.01e+03 1.43e+04 bond pdb=" C LEU P1091 " pdb=" N THR P1092 " ideal model delta sigma weight residual 1.332 2.386 -1.053 1.40e-02 5.10e+03 5.66e+03 bond pdb=" CA HIS B 243 " pdb=" CB HIS B 243 " ideal model delta sigma weight residual 1.530 2.514 -0.984 1.58e-02 4.01e+03 3.88e+03 bond pdb=" C ILE P1958 " pdb=" N PHE P1959 " ideal model delta sigma weight residual 1.331 2.007 -0.676 1.40e-02 5.10e+03 2.33e+03 bond pdb=" CA VAL B 307 " pdb=" CB VAL B 307 " ideal model delta sigma weight residual 1.543 2.093 -0.550 1.32e-02 5.74e+03 1.73e+03 ... (remaining 16771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.32: 22744 15.32 - 30.65: 24 30.65 - 45.97: 9 45.97 - 61.30: 0 61.30 - 76.62: 3 Bond angle restraints: 22780 Sorted by residual: angle pdb=" C GLN P 673 " pdb=" N THR P 674 " pdb=" CA THR P 674 " ideal model delta sigma weight residual 122.63 46.01 76.62 1.44e+00 4.82e-01 2.83e+03 angle pdb=" O CYS B 242 " pdb=" C CYS B 242 " pdb=" N HIS B 243 " ideal model delta sigma weight residual 122.28 60.26 62.02 1.30e+00 5.92e-01 2.28e+03 angle pdb=" O GLN P 673 " pdb=" C GLN P 673 " pdb=" N THR P 674 " ideal model delta sigma weight residual 122.13 51.58 70.55 1.50e+00 4.44e-01 2.21e+03 angle pdb=" CA HIS B 243 " pdb=" CB HIS B 243 " pdb=" CG HIS B 243 " ideal model delta sigma weight residual 113.80 152.90 -39.10 1.00e+00 1.00e+00 1.53e+03 angle pdb=" O ILE P1958 " pdb=" C ILE P1958 " pdb=" N PHE P1959 " ideal model delta sigma weight residual 123.18 83.88 39.30 1.04e+00 9.25e-01 1.43e+03 ... (remaining 22775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 9291 26.92 - 53.84: 691 53.84 - 80.76: 125 80.76 - 107.68: 6 107.68 - 134.60: 1 Dihedral angle restraints: 10114 sinusoidal: 3845 harmonic: 6269 Sorted by residual: dihedral pdb=" CA TYR L 145 " pdb=" C TYR L 145 " pdb=" N PRO L 146 " pdb=" CA PRO L 146 " ideal model delta harmonic sigma weight residual 180.00 45.40 134.60 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" C VAL B 307 " pdb=" N VAL B 307 " pdb=" CA VAL B 307 " pdb=" CB VAL B 307 " ideal model delta harmonic sigma weight residual -122.00 -166.14 44.14 0 2.50e+00 1.60e-01 3.12e+02 dihedral pdb=" CA ALA H 85 " pdb=" C ALA H 85 " pdb=" N ALA H 86 " pdb=" CA ALA H 86 " ideal model delta harmonic sigma weight residual 180.00 -92.22 -87.78 0 5.00e+00 4.00e-02 3.08e+02 ... (remaining 10111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.615: 2562 0.615 - 1.230: 4 1.230 - 1.844: 0 1.844 - 2.459: 0 2.459 - 3.074: 1 Chirality restraints: 2567 Sorted by residual: chirality pdb=" CB VAL B 307 " pdb=" CA VAL B 307 " pdb=" CG1 VAL B 307 " pdb=" CG2 VAL B 307 " both_signs ideal model delta sigma weight residual False -2.63 0.44 -3.07 2.00e-01 2.50e+01 2.36e+02 chirality pdb=" CA ALA H 86 " pdb=" N ALA H 86 " pdb=" C ALA H 86 " pdb=" CB ALA H 86 " both_signs ideal model delta sigma weight residual False 2.48 1.30 1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 1.35 1.09 2.00e-01 2.50e+01 2.99e+01 ... (remaining 2564 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 673 " -0.185 2.00e-02 2.50e+03 2.71e-01 7.35e+02 pdb=" C GLN P 673 " 0.440 2.00e-02 2.50e+03 pdb=" O GLN P 673 " -0.257 2.00e-02 2.50e+03 pdb=" N THR P 674 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P1958 " -0.178 2.00e-02 2.50e+03 2.67e-01 7.15e+02 pdb=" C ILE P1958 " 0.444 2.00e-02 2.50e+03 pdb=" O ILE P1958 " -0.237 2.00e-02 2.50e+03 pdb=" N PHE P1959 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P1091 " -0.156 2.00e-02 2.50e+03 2.48e-01 6.14e+02 pdb=" C LEU P1091 " 0.419 2.00e-02 2.50e+03 pdb=" O LEU P1091 " -0.206 2.00e-02 2.50e+03 pdb=" N THR P1092 " -0.056 2.00e-02 2.50e+03 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.35: 24 1.35 - 2.24: 222 2.24 - 3.13: 13705 3.13 - 4.01: 43048 4.01 - 4.90: 75031 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132030 Sorted by model distance: nonbonded pdb=" O CYS A 299 " pdb=" SG CYS B 241 " model vdw 0.468 3.400 nonbonded pdb=" ND2 ASN P 684 " pdb=" N ASP P1106 " model vdw 0.682 3.200 nonbonded pdb=" CG GLU P 924 " pdb=" OD1 ASN P1361 " model vdw 0.697 3.440 nonbonded pdb=" CZ ARG B 250 " pdb=" OG1 THR B 267 " model vdw 0.767 3.270 nonbonded pdb=" NE ARG B 250 " pdb=" OG1 THR B 267 " model vdw 0.881 3.120 ... (remaining 132025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 242 through 450) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 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 : 0.024 1.545 16791 Z= 1.874 Angle : 1.934 76.622 22798 Z= 1.414 Chirality : 0.118 3.074 2567 Planarity : 0.012 0.271 2961 Dihedral : 18.035 134.597 6059 Min Nonbonded Distance : 0.468 Molprobity Statistics. All-atom Clashscore : 73.67 Ramachandran Plot: Outliers : 1.73 % Allowed : 6.09 % Favored : 92.17 % Rotamer: Outliers : 18.43 % Allowed : 10.79 % Favored : 70.78 % Cbeta Deviations : 1.54 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 5.38 % Twisted General : 0.19 % 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: -1.93 (0.17), residues: 2134 helix: -0.64 (0.23), residues: 438 sheet: -0.34 (0.27), residues: 405 loop : -1.91 (0.15), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P1747 TYR 0.017 0.001 TYR P 982 PHE 0.017 0.001 PHE P1396 TRP 0.019 0.001 TRP H 109 HIS 0.046 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.02301 (16776) covalent geometry : angle 1.93410 (22780) SS BOND : bond 0.00795 ( 9) SS BOND : angle 1.00521 ( 18) hydrogen bonds : bond 0.24363 ( 386) hydrogen bonds : angle 7.85206 ( 1101) Misc. bond : bond 0.42445 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4268 Ramachandran restraints generated. 2134 Oldfield, 0 Emsley, 2134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4268 Ramachandran restraints generated. 2134 Oldfield, 0 Emsley, 2134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 383 time to evaluate : 0.516 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 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: P 788 LYS cc_start: 0.8594 (mttt) cc_final: 0.8320 (tmtt) REVERT: P 846 PHE cc_start: 0.7762 (m-80) cc_final: 0.7530 (m-10) REVERT: P 971 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7386 (tp) REVERT: P 1024 VAL cc_start: 0.8445 (p) cc_final: 0.8228 (p) REVERT: P 1053 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.7021 (p) REVERT: P 1291 ASP cc_start: 0.6640 (t0) cc_final: 0.6365 (m-30) REVERT: P 1345 ASN cc_start: 0.6315 (t0) cc_final: 0.5827 (t0) REVERT: P 1388 THR cc_start: 0.7082 (m) cc_final: 0.6239 (m) REVERT: P 1471 MET cc_start: 0.6996 (ttt) cc_final: 0.5685 (pmm) REVERT: P 1515 TRP cc_start: 0.6471 (m100) cc_final: 0.6184 (m100) REVERT: P 1554 PHE cc_start: 0.5586 (m-80) cc_final: 0.5164 (m-10) REVERT: P 1603 THR cc_start: 0.6971 (t) cc_final: 0.6763 (t) REVERT: P 1611 ASP cc_start: 0.6390 (t70) cc_final: 0.6107 (t70) REVERT: P 1614 ILE cc_start: 0.7185 (mm) cc_final: 0.6853 (mm) REVERT: P 1634 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5954 (pp) REVERT: P 1809 LEU cc_start: 0.6146 (tp) cc_final: 0.5761 (tp) REVERT: P 1894 TRP cc_start: 0.1263 (OUTLIER) cc_final: 0.0757 (t60) REVERT: A 260 SER cc_start: -0.1195 (OUTLIER) cc_final: -0.1548 (m) REVERT: A 280 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8946 (p) REVERT: A 319 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4135 (tmtt) REVERT: A 356 SER cc_start: -0.1075 (OUTLIER) cc_final: -0.1494 (m) REVERT: A 358 GLU cc_start: 0.3379 (OUTLIER) cc_final: 0.2906 (tm-30) REVERT: A 383 TRP cc_start: 0.2837 (m100) cc_final: 0.2540 (t-100) REVERT: A 393 GLU cc_start: 0.1517 (OUTLIER) cc_final: 0.0847 (pm20) REVERT: A 394 LYS cc_start: 0.4161 (OUTLIER) cc_final: 0.2984 (mptt) REVERT: A 395 TYR cc_start: 0.2706 (OUTLIER) cc_final: 0.1525 (t80) REVERT: A 404 PRO cc_start: 0.4425 (Cg_endo) cc_final: 0.4221 (Cg_exo) REVERT: A 408 THR cc_start: 0.4136 (OUTLIER) cc_final: 0.3556 (p) REVERT: A 416 ILE cc_start: 0.4750 (OUTLIER) cc_final: 0.4376 (pt) REVERT: A 426 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5608 (tptm) REVERT: B 272 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5028 (mtp85) REVERT: B 291 GLN cc_start: 0.1375 (OUTLIER) cc_final: 0.0995 (mt0) REVERT: B 316 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8098 (m110) REVERT: B 348 GLU cc_start: 0.3181 (OUTLIER) cc_final: 0.2888 (tt0) REVERT: B 352 LEU cc_start: 0.2558 (OUTLIER) cc_final: 0.2233 (tt) REVERT: B 394 LYS cc_start: 0.0137 (OUTLIER) cc_final: -0.0118 (mttt) REVERT: B 402 GLN cc_start: -0.1701 (OUTLIER) cc_final: -0.2064 (tp40) REVERT: B 422 GLU cc_start: 0.2674 (OUTLIER) cc_final: 0.1723 (mm-30) REVERT: L 160 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7240 (tp40) REVERT: L 212 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6543 (mtpt) REVERT: L 215 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7510 (p0) REVERT: H 128 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.5919 (m-80) REVERT: H 136 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5277 (mt0) REVERT: H 200 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6921 (tppt) outliers start: 321 outliers final: 119 residues processed: 657 average time/residue: 0.1387 time to fit residues: 131.8040 Evaluate side-chains 382 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 234 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 776 GLU Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 971 LEU Chi-restraints excluded: chain P residue 1053 VAL Chi-restraints excluded: chain P residue 1068 SER Chi-restraints excluded: chain P residue 1081 ILE Chi-restraints excluded: chain P residue 1082 VAL Chi-restraints excluded: chain P residue 1087 GLU Chi-restraints excluded: chain P residue 1200 ASP Chi-restraints excluded: chain P residue 1444 THR Chi-restraints excluded: chain P residue 1551 GLU Chi-restraints excluded: chain P residue 1634 LEU Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 TYR Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain L residue 207 SER Chi-restraints excluded: chain L residue 210 VAL Chi-restraints excluded: chain L residue 212 LYS Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 GLN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 153 GLN Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 220 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 673 GLN P 684 ASN P 835 ASN P 840 ASN P 868 ASN P1089 ASN P1114 HIS P1166 GLN ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1903 ASN A 249 HIS ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 129 GLN ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.138448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.118837 restraints weight = 62109.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.121343 restraints weight = 35286.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.123037 restraints weight = 22810.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.124233 restraints weight = 16315.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.124952 restraints weight = 12606.268| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4355 r_free = 0.4355 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 16791 Z= 0.239 Angle : 0.914 18.941 22798 Z= 0.477 Chirality : 0.052 0.407 2567 Planarity : 0.007 0.098 2961 Dihedral : 12.669 89.045 2618 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.68 % Favored : 92.99 % Rotamer: Outliers : 10.33 % Allowed : 19.46 % Favored : 70.21 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.15 % 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: -2.03 (0.17), residues: 2140 helix: -0.31 (0.24), residues: 444 sheet: -0.64 (0.27), residues: 388 loop : -2.04 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 372 TYR 0.027 0.003 TYR H 97 PHE 0.027 0.003 PHE B 430 TRP 0.033 0.003 TRP H 160 HIS 0.024 0.003 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00544 (16776) covalent geometry : angle 0.91419 (22780) SS BOND : bond 0.00390 ( 9) SS BOND : angle 1.08750 ( 18) hydrogen bonds : bond 0.04922 ( 386) hydrogen bonds : angle 6.20127 ( 1101) Misc. bond : bond 0.00856 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 234 time to evaluate : 0.614 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 REVERT: P 712 ASP cc_start: 0.7594 (p0) cc_final: 0.7360 (p0) REVERT: P 769 LEU cc_start: 0.3729 (OUTLIER) cc_final: 0.3461 (mp) REVERT: P 770 ASP cc_start: 0.3275 (OUTLIER) cc_final: 0.3001 (m-30) REVERT: P 788 LYS cc_start: 0.8797 (mttt) cc_final: 0.8433 (tmtt) REVERT: P 957 ASN cc_start: 0.7353 (t0) cc_final: 0.7096 (m110) REVERT: P 971 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.6876 (tp) REVERT: P 1053 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7650 (p) REVERT: P 1345 ASN cc_start: 0.6618 (t0) cc_final: 0.6043 (t0) REVERT: P 1372 TYR cc_start: 0.6997 (t80) cc_final: 0.6565 (t80) REVERT: P 1430 LEU cc_start: 0.8404 (tp) cc_final: 0.8058 (tp) REVERT: P 1458 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5630 (tt) REVERT: P 1471 MET cc_start: 0.7153 (ttt) cc_final: 0.5437 (pmm) REVERT: P 1507 ARG cc_start: 0.5034 (mtm-85) cc_final: 0.3061 (mmp80) REVERT: P 1561 MET cc_start: 0.7385 (tmm) cc_final: 0.7098 (tmm) REVERT: P 1614 ILE cc_start: 0.6859 (mm) cc_final: 0.6623 (mm) REVERT: P 1715 LEU cc_start: 0.8660 (mt) cc_final: 0.8352 (tp) REVERT: P 1745 GLU cc_start: 0.7916 (mp0) cc_final: 0.7714 (mp0) REVERT: P 1800 MET cc_start: 0.5907 (mmm) cc_final: 0.5566 (mmm) REVERT: P 1828 GLU cc_start: 0.7781 (pm20) cc_final: 0.7249 (tp30) REVERT: P 1894 TRP cc_start: 0.1248 (OUTLIER) cc_final: 0.0421 (t60) REVERT: P 1924 ARG cc_start: 0.3723 (mmm160) cc_final: 0.3259 (ptt90) REVERT: A 290 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 299 CYS cc_start: 0.4768 (OUTLIER) cc_final: 0.3653 (t) REVERT: A 302 TYR cc_start: 0.5759 (t80) cc_final: 0.5387 (t80) REVERT: A 306 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7331 (t) REVERT: A 358 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2679 (tm-30) REVERT: A 393 GLU cc_start: 0.2231 (OUTLIER) cc_final: 0.1444 (pm20) REVERT: A 395 TYR cc_start: 0.2844 (OUTLIER) cc_final: 0.2342 (t80) REVERT: A 416 ILE cc_start: 0.5609 (OUTLIER) cc_final: 0.5022 (pt) REVERT: A 417 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.3792 (tp) REVERT: A 426 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.5351 (tptm) REVERT: A 450 ARG cc_start: 0.2756 (OUTLIER) cc_final: 0.2332 (ttt180) REVERT: B 266 CYS cc_start: 0.0675 (OUTLIER) cc_final: -0.0102 (p) REVERT: B 316 ASN cc_start: 0.8398 (t0) cc_final: 0.7972 (m110) REVERT: B 393 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6040 (mm-30) REVERT: B 422 GLU cc_start: 0.2683 (OUTLIER) cc_final: 0.1774 (mm-30) REVERT: L 175 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.6951 (p0) REVERT: L 215 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7700 (p0) REVERT: H 138 ASP cc_start: 0.5642 (p0) cc_final: 0.5355 (p0) REVERT: H 200 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7010 (tppt) outliers start: 180 outliers final: 93 residues processed: 394 average time/residue: 0.1358 time to fit residues: 79.6019 Evaluate side-chains 299 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 185 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 769 LEU Chi-restraints excluded: chain P residue 770 ASP Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 971 LEU Chi-restraints excluded: chain P residue 981 SER Chi-restraints excluded: chain P residue 993 PHE Chi-restraints excluded: chain P residue 1038 THR Chi-restraints excluded: chain P residue 1045 THR Chi-restraints excluded: chain P residue 1048 SER Chi-restraints excluded: chain P residue 1053 VAL Chi-restraints excluded: chain P residue 1065 SER Chi-restraints excluded: chain P residue 1068 SER Chi-restraints excluded: chain P residue 1081 ILE Chi-restraints excluded: chain P residue 1082 VAL Chi-restraints excluded: chain P residue 1089 ASN Chi-restraints excluded: chain P residue 1125 ASN Chi-restraints excluded: chain P residue 1144 LEU Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1396 PHE Chi-restraints excluded: chain P residue 1410 THR Chi-restraints excluded: chain P residue 1443 ILE Chi-restraints excluded: chain P residue 1458 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1534 TYR Chi-restraints excluded: chain P residue 1537 TYR Chi-restraints excluded: chain P residue 1551 GLU Chi-restraints excluded: chain P residue 1634 LEU Chi-restraints excluded: chain P residue 1667 VAL Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1735 THR Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1899 THR Chi-restraints excluded: chain P residue 1956 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 220 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 173 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 921 ASN P1025 ASN ** P1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1143 ASN ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1838 ASN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.136999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.115274 restraints weight = 62445.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.117582 restraints weight = 35562.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.119134 restraints weight = 23143.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.120237 restraints weight = 16885.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.121076 restraints weight = 13448.526| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4373 r_free = 0.4373 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4373 r_free = 0.4373 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16791 Z= 0.165 Angle : 0.772 16.668 22798 Z= 0.398 Chirality : 0.047 0.492 2567 Planarity : 0.006 0.083 2961 Dihedral : 10.695 172.032 2452 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.45 % Favored : 93.27 % Rotamer: Outliers : 7.58 % Allowed : 22.04 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2140 helix: -0.18 (0.24), residues: 451 sheet: -0.70 (0.26), residues: 382 loop : -2.09 (0.15), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P1924 TYR 0.023 0.002 TYR P1588 PHE 0.023 0.002 PHE P1879 TRP 0.018 0.002 TRP H 109 HIS 0.013 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00378 (16776) covalent geometry : angle 0.77229 (22780) SS BOND : bond 0.00253 ( 9) SS BOND : angle 0.64845 ( 18) hydrogen bonds : bond 0.04206 ( 386) hydrogen bonds : angle 5.62776 ( 1101) Misc. bond : bond 0.00436 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 198 time to evaluate : 0.607 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: P 712 ASP cc_start: 0.7832 (p0) cc_final: 0.7380 (p0) REVERT: P 788 LYS cc_start: 0.8837 (mttt) cc_final: 0.8424 (tmtt) REVERT: P 846 PHE cc_start: 0.8367 (m-80) cc_final: 0.8119 (m-10) REVERT: P 913 SER cc_start: 0.8907 (p) cc_final: 0.8437 (t) REVERT: P 948 SER cc_start: 0.9242 (p) cc_final: 0.8715 (t) REVERT: P 971 LEU cc_start: 0.7902 (tp) cc_final: 0.7410 (tp) REVERT: P 973 ASP cc_start: 0.7688 (m-30) cc_final: 0.7372 (m-30) REVERT: P 1040 MET cc_start: 0.7794 (mmm) cc_final: 0.7562 (mmm) REVERT: P 1053 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7616 (p) REVERT: P 1075 MET cc_start: 0.6233 (mpp) cc_final: 0.5922 (mpp) REVERT: P 1162 MET cc_start: 0.6224 (ttp) cc_final: 0.5957 (ttp) REVERT: P 1315 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7766 (p) REVERT: P 1462 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7224 (tm-30) REVERT: P 1471 MET cc_start: 0.7415 (ttt) cc_final: 0.4560 (pmm) REVERT: P 1507 ARG cc_start: 0.5194 (mtm-85) cc_final: 0.3306 (mmp80) REVERT: P 1561 MET cc_start: 0.7193 (tmm) cc_final: 0.6191 (tmm) REVERT: P 1614 ILE cc_start: 0.6849 (mm) cc_final: 0.6516 (mm) REVERT: P 1745 GLU cc_start: 0.7947 (mp0) cc_final: 0.7343 (mp0) REVERT: P 1844 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6522 (ptm160) REVERT: P 1894 TRP cc_start: 0.1055 (OUTLIER) cc_final: 0.0220 (t60) REVERT: A 395 TYR cc_start: 0.1834 (OUTLIER) cc_final: 0.1467 (t80) REVERT: A 426 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5801 (tmtt) REVERT: B 266 CYS cc_start: 0.0177 (OUTLIER) cc_final: -0.0926 (p) REVERT: B 316 ASN cc_start: 0.8357 (t0) cc_final: 0.8007 (m110) REVERT: B 393 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6827 (mm-30) REVERT: B 422 GLU cc_start: 0.2452 (OUTLIER) cc_final: 0.2002 (mm-30) REVERT: B 446 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6418 (tttt) REVERT: L 54 TYR cc_start: 0.4974 (p90) cc_final: 0.4107 (t80) REVERT: L 153 TRP cc_start: 0.6938 (t-100) cc_final: 0.6737 (t-100) REVERT: L 175 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.7389 (p0) REVERT: L 215 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7730 (p0) REVERT: H 138 ASP cc_start: 0.5770 (p0) cc_final: 0.5538 (p0) REVERT: H 200 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6779 (tppt) outliers start: 132 outliers final: 77 residues processed: 324 average time/residue: 0.1227 time to fit residues: 61.8216 Evaluate side-chains 259 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 170 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 679 LYS Chi-restraints excluded: chain P residue 702 VAL Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 770 ASP Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 981 SER Chi-restraints excluded: chain P residue 1053 VAL Chi-restraints excluded: chain P residue 1076 LEU Chi-restraints excluded: chain P residue 1081 ILE Chi-restraints excluded: chain P residue 1082 VAL Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1315 THR Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1410 THR Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1534 TYR Chi-restraints excluded: chain P residue 1634 LEU Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1735 THR Chi-restraints excluded: chain P residue 1737 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1844 ARG Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1956 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 220 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 151 optimal weight: 0.0020 chunk 195 optimal weight: 0.0670 chunk 83 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1089 ASN ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1511 HIS ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.137368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.115854 restraints weight = 61278.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.118274 restraints weight = 35511.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.119766 restraints weight = 23156.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.120813 restraints weight = 17010.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.121712 restraints weight = 13664.382| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16791 Z= 0.138 Angle : 0.712 15.096 22798 Z= 0.361 Chirality : 0.044 0.313 2567 Planarity : 0.006 0.094 2961 Dihedral : 9.345 168.791 2412 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.36 % Rotamer: Outliers : 5.97 % Allowed : 24.91 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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 (0.17), residues: 2140 helix: 0.06 (0.25), residues: 442 sheet: -0.87 (0.26), residues: 381 loop : -2.04 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P1924 TYR 0.022 0.002 TYR P1615 PHE 0.021 0.002 PHE P1879 TRP 0.036 0.002 TRP P1515 HIS 0.012 0.001 HIS P1184 Details of bonding type rmsd covalent geometry : bond 0.00317 (16776) covalent geometry : angle 0.71225 (22780) SS BOND : bond 0.00311 ( 9) SS BOND : angle 0.83136 ( 18) hydrogen bonds : bond 0.03737 ( 386) hydrogen bonds : angle 5.33728 ( 1101) Misc. bond : bond 0.00292 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 193 time to evaluate : 0.619 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: P 712 ASP cc_start: 0.7824 (p0) cc_final: 0.7353 (p0) REVERT: P 788 LYS cc_start: 0.8849 (mttt) cc_final: 0.8412 (tmtt) REVERT: P 846 PHE cc_start: 0.8299 (m-80) cc_final: 0.8026 (m-10) REVERT: P 876 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7006 (tm-30) REVERT: P 912 GLU cc_start: 0.8398 (mp0) cc_final: 0.8049 (mp0) REVERT: P 913 SER cc_start: 0.8854 (p) cc_final: 0.8437 (t) REVERT: P 922 THR cc_start: 0.7065 (p) cc_final: 0.5971 (t) REVERT: P 948 SER cc_start: 0.9252 (p) cc_final: 0.8671 (t) REVERT: P 957 ASN cc_start: 0.7389 (t0) cc_final: 0.7041 (m-40) REVERT: P 971 LEU cc_start: 0.7979 (tp) cc_final: 0.7390 (tp) REVERT: P 973 ASP cc_start: 0.7599 (m-30) cc_final: 0.7304 (m-30) REVERT: P 1125 ASN cc_start: 0.6359 (OUTLIER) cc_final: 0.5956 (t0) REVERT: P 1162 MET cc_start: 0.6351 (ttp) cc_final: 0.6095 (ttp) REVERT: P 1462 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7177 (tm-30) REVERT: P 1471 MET cc_start: 0.7409 (ttt) cc_final: 0.4195 (pmm) REVERT: P 1507 ARG cc_start: 0.4952 (mtm-85) cc_final: 0.3032 (mmp80) REVERT: P 1553 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6903 (tppt) REVERT: P 1600 ILE cc_start: 0.7456 (mm) cc_final: 0.7247 (mm) REVERT: P 1606 MET cc_start: 0.6585 (mmm) cc_final: 0.6205 (mtt) REVERT: P 1712 MET cc_start: 0.6153 (mmm) cc_final: 0.5293 (mmm) REVERT: P 1745 GLU cc_start: 0.8082 (mp0) cc_final: 0.7789 (mp0) REVERT: P 1828 GLU cc_start: 0.7892 (pm20) cc_final: 0.7361 (tp30) REVERT: P 1894 TRP cc_start: 0.0838 (OUTLIER) cc_final: 0.0317 (t60) REVERT: A 393 GLU cc_start: 0.2588 (OUTLIER) cc_final: 0.2065 (pm20) REVERT: A 395 TYR cc_start: 0.1829 (OUTLIER) cc_final: 0.1338 (t80) REVERT: B 266 CYS cc_start: -0.0302 (OUTLIER) cc_final: -0.1031 (p) REVERT: B 316 ASN cc_start: 0.8433 (t0) cc_final: 0.8100 (m110) REVERT: B 393 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7038 (mm-30) REVERT: B 410 THR cc_start: 0.0846 (OUTLIER) cc_final: 0.0609 (p) REVERT: B 446 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6359 (tttt) REVERT: L 54 TYR cc_start: 0.4943 (p90) cc_final: 0.4048 (t80) REVERT: L 175 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7522 (p0) REVERT: L 215 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8104 (p0) REVERT: H 138 ASP cc_start: 0.5700 (p0) cc_final: 0.5446 (p0) outliers start: 104 outliers final: 69 residues processed: 290 average time/residue: 0.1199 time to fit residues: 54.6248 Evaluate side-chains 255 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 176 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 1076 LEU Chi-restraints excluded: chain P residue 1082 VAL Chi-restraints excluded: chain P residue 1125 ASN Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1243 SER Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1534 TYR Chi-restraints excluded: chain P residue 1553 LYS Chi-restraints excluded: chain P residue 1634 LEU Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1735 THR Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1956 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 220 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 151 optimal weight: 0.0770 chunk 111 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 673 GLN ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1324 ASN P1380 HIS P1399 ASN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1774 ASN ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.129520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.107023 restraints weight = 62404.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.109169 restraints weight = 36789.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.110482 restraints weight = 24690.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.111524 restraints weight = 18645.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.112225 restraints weight = 15317.665| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 16791 Z= 0.210 Angle : 0.757 17.092 22798 Z= 0.387 Chirality : 0.046 0.285 2567 Planarity : 0.006 0.093 2961 Dihedral : 9.067 169.091 2395 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.66 % Favored : 92.01 % Rotamer: Outliers : 7.23 % Allowed : 24.86 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % 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: -2.12 (0.17), residues: 2140 helix: -0.20 (0.24), residues: 429 sheet: -1.05 (0.26), residues: 391 loop : -2.03 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P1072 TYR 0.028 0.003 TYR P1615 PHE 0.018 0.002 PHE P1887 TRP 0.022 0.002 TRP P1004 HIS 0.009 0.002 HIS P1184 Details of bonding type rmsd covalent geometry : bond 0.00463 (16776) covalent geometry : angle 0.75654 (22780) SS BOND : bond 0.00296 ( 9) SS BOND : angle 0.92989 ( 18) hydrogen bonds : bond 0.04145 ( 386) hydrogen bonds : angle 5.64953 ( 1101) Misc. bond : bond 0.00248 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 189 time to evaluate : 0.610 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: P 712 ASP cc_start: 0.7687 (p0) cc_final: 0.7473 (p0) REVERT: P 788 LYS cc_start: 0.8864 (mttt) cc_final: 0.8520 (tmtt) REVERT: P 876 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7130 (tm-30) REVERT: P 913 SER cc_start: 0.8477 (p) cc_final: 0.8251 (t) REVERT: P 948 SER cc_start: 0.9354 (p) cc_final: 0.8962 (t) REVERT: P 971 LEU cc_start: 0.8522 (tp) cc_final: 0.7680 (tp) REVERT: P 973 ASP cc_start: 0.7678 (m-30) cc_final: 0.7302 (m-30) REVERT: P 1125 ASN cc_start: 0.6511 (OUTLIER) cc_final: 0.6125 (t0) REVERT: P 1162 MET cc_start: 0.6451 (ttp) cc_final: 0.6235 (ttp) REVERT: P 1233 LEU cc_start: 0.7352 (tp) cc_final: 0.7015 (tt) REVERT: P 1372 TYR cc_start: 0.7071 (t80) cc_final: 0.6355 (t80) REVERT: P 1462 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7175 (tm-30) REVERT: P 1471 MET cc_start: 0.7225 (ttt) cc_final: 0.4104 (pmm) REVERT: P 1496 PHE cc_start: 0.6614 (t80) cc_final: 0.6157 (t80) REVERT: P 1507 ARG cc_start: 0.5187 (mtm-85) cc_final: 0.3098 (mmt-90) REVERT: P 1588 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5266 (m-80) REVERT: P 1606 MET cc_start: 0.7326 (mmm) cc_final: 0.7102 (mtt) REVERT: P 1712 MET cc_start: 0.7033 (mmm) cc_final: 0.6601 (mmm) REVERT: P 1772 GLU cc_start: 0.7001 (tp30) cc_final: 0.6217 (tp30) REVERT: P 1894 TRP cc_start: 0.0484 (OUTLIER) cc_final: -0.0061 (t60) REVERT: A 395 TYR cc_start: 0.1257 (OUTLIER) cc_final: 0.0662 (t80) REVERT: B 316 ASN cc_start: 0.8387 (t0) cc_final: 0.8026 (m110) REVERT: B 413 VAL cc_start: 0.2802 (OUTLIER) cc_final: 0.2446 (p) REVERT: H 96 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6412 (m-80) outliers start: 126 outliers final: 93 residues processed: 306 average time/residue: 0.1120 time to fit residues: 54.2848 Evaluate side-chains 261 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 162 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 688 ILE Chi-restraints excluded: chain P residue 702 VAL Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 822 THR Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 855 GLU Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 977 HIS Chi-restraints excluded: chain P residue 990 VAL Chi-restraints excluded: chain P residue 1020 VAL Chi-restraints excluded: chain P residue 1038 THR Chi-restraints excluded: chain P residue 1048 SER Chi-restraints excluded: chain P residue 1076 LEU Chi-restraints excluded: chain P residue 1088 ILE Chi-restraints excluded: chain P residue 1125 ASN Chi-restraints excluded: chain P residue 1144 LEU Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1169 THR Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1212 THR Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1291 ASP Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1410 THR Chi-restraints excluded: chain P residue 1457 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1493 LEU Chi-restraints excluded: chain P residue 1534 TYR Chi-restraints excluded: chain P residue 1553 LYS Chi-restraints excluded: chain P residue 1588 TYR Chi-restraints excluded: chain P residue 1634 LEU Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1667 VAL Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1737 VAL Chi-restraints excluded: chain P residue 1774 ASN Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1937 HIS Chi-restraints excluded: chain P residue 1956 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 220 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 673 GLN ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1558 ASN P1563 ASN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1903 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.124830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.102402 restraints weight = 63108.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.104194 restraints weight = 37379.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.105422 restraints weight = 25399.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.106241 restraints weight = 19114.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.106867 restraints weight = 15755.745| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16791 Z= 0.247 Angle : 0.810 16.619 22798 Z= 0.418 Chirality : 0.047 0.289 2567 Planarity : 0.006 0.086 2961 Dihedral : 9.006 169.919 2386 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.08 % Favored : 91.59 % Rotamer: Outliers : 7.81 % Allowed : 25.83 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % 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: -2.34 (0.17), residues: 2140 helix: -0.67 (0.23), residues: 430 sheet: -0.98 (0.27), residues: 377 loop : -2.13 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P1773 TYR 0.028 0.003 TYR P1722 PHE 0.021 0.003 PHE P1887 TRP 0.028 0.003 TRP P1004 HIS 0.010 0.002 HIS P1654 Details of bonding type rmsd covalent geometry : bond 0.00546 (16776) covalent geometry : angle 0.80943 (22780) SS BOND : bond 0.00663 ( 9) SS BOND : angle 1.05189 ( 18) hydrogen bonds : bond 0.04406 ( 386) hydrogen bonds : angle 6.04075 ( 1101) Misc. bond : bond 0.00237 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 165 time to evaluate : 0.608 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: P 712 ASP cc_start: 0.7294 (p0) cc_final: 0.6954 (p0) REVERT: P 876 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7770 (tm-30) REVERT: P 901 LEU cc_start: 0.8510 (mm) cc_final: 0.8073 (mm) REVERT: P 912 GLU cc_start: 0.8554 (mp0) cc_final: 0.8229 (mp0) REVERT: P 971 LEU cc_start: 0.8840 (tp) cc_final: 0.8312 (tp) REVERT: P 1125 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.5992 (t0) REVERT: P 1233 LEU cc_start: 0.7686 (tp) cc_final: 0.7305 (tt) REVERT: P 1302 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7931 (tttt) REVERT: P 1372 TYR cc_start: 0.7251 (t80) cc_final: 0.6710 (t80) REVERT: P 1462 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6769 (tm-30) REVERT: P 1471 MET cc_start: 0.7831 (ttt) cc_final: 0.7382 (tmm) REVERT: P 1496 PHE cc_start: 0.6564 (t80) cc_final: 0.6134 (t80) REVERT: P 1507 ARG cc_start: 0.5343 (mtm-85) cc_final: 0.3082 (mmt-90) REVERT: P 1575 ASN cc_start: 0.2204 (OUTLIER) cc_final: 0.1997 (p0) REVERT: P 1588 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5138 (m-80) REVERT: P 1712 MET cc_start: 0.7653 (mmm) cc_final: 0.7369 (mmm) REVERT: P 1772 GLU cc_start: 0.6936 (tp30) cc_final: 0.6729 (tp30) REVERT: P 1894 TRP cc_start: 0.0640 (OUTLIER) cc_final: -0.0094 (t60) REVERT: P 1947 TYR cc_start: 0.5837 (t80) cc_final: 0.5577 (t80) REVERT: B 316 ASN cc_start: 0.8479 (t0) cc_final: 0.8084 (m110) REVERT: H 96 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6765 (m-80) outliers start: 136 outliers final: 99 residues processed: 285 average time/residue: 0.1152 time to fit residues: 51.4278 Evaluate side-chains 261 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 157 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 679 LYS Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 688 ILE Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 822 THR Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 873 LEU Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 977 HIS Chi-restraints excluded: chain P residue 999 VAL Chi-restraints excluded: chain P residue 1020 VAL Chi-restraints excluded: chain P residue 1038 THR Chi-restraints excluded: chain P residue 1045 THR Chi-restraints excluded: chain P residue 1048 SER Chi-restraints excluded: chain P residue 1081 ILE Chi-restraints excluded: chain P residue 1088 ILE Chi-restraints excluded: chain P residue 1125 ASN Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1169 THR Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1212 THR Chi-restraints excluded: chain P residue 1230 LYS Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1291 ASP Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1363 LEU Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1405 TRP Chi-restraints excluded: chain P residue 1457 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1493 LEU Chi-restraints excluded: chain P residue 1553 LYS Chi-restraints excluded: chain P residue 1575 ASN Chi-restraints excluded: chain P residue 1588 TYR Chi-restraints excluded: chain P residue 1603 THR Chi-restraints excluded: chain P residue 1634 LEU Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1702 ILE Chi-restraints excluded: chain P residue 1723 VAL Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1867 PHE Chi-restraints excluded: chain P residue 1882 LEU Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1937 HIS Chi-restraints excluded: chain P residue 1956 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 220 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 147 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.129148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.106542 restraints weight = 61779.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.108628 restraints weight = 36506.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.110068 restraints weight = 24585.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.110860 restraints weight = 18371.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.111688 restraints weight = 15184.902| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4180 r_free = 0.4180 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4180 r_free = 0.4180 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.4180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16791 Z= 0.137 Angle : 0.714 17.388 22798 Z= 0.358 Chirality : 0.043 0.250 2567 Planarity : 0.005 0.071 2961 Dihedral : 8.469 175.078 2375 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.73 % Favored : 93.04 % Rotamer: Outliers : 5.05 % Allowed : 28.47 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % 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: -2.18 (0.17), residues: 2140 helix: -0.28 (0.24), residues: 432 sheet: -0.95 (0.27), residues: 366 loop : -2.10 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P1517 TYR 0.027 0.002 TYR P1336 PHE 0.031 0.002 PHE A 443 TRP 0.028 0.002 TRP L 153 HIS 0.010 0.001 HIS P1184 Details of bonding type rmsd covalent geometry : bond 0.00312 (16776) covalent geometry : angle 0.71348 (22780) SS BOND : bond 0.00231 ( 9) SS BOND : angle 1.06075 ( 18) hydrogen bonds : bond 0.03694 ( 386) hydrogen bonds : angle 5.57421 ( 1101) Misc. bond : bond 0.00162 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 180 time to evaluate : 0.589 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: P 712 ASP cc_start: 0.7077 (p0) cc_final: 0.6772 (p0) REVERT: P 733 ILE cc_start: 0.7604 (mp) cc_final: 0.7374 (mp) REVERT: P 804 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8827 (pp) REVERT: P 844 PRO cc_start: 0.8133 (Cg_exo) cc_final: 0.7792 (Cg_endo) REVERT: P 901 LEU cc_start: 0.8509 (mm) cc_final: 0.7866 (mm) REVERT: P 922 THR cc_start: 0.7281 (p) cc_final: 0.6440 (t) REVERT: P 971 LEU cc_start: 0.8598 (tp) cc_final: 0.8363 (tp) REVERT: P 1074 THR cc_start: 0.4050 (OUTLIER) cc_final: 0.3587 (m) REVERT: P 1125 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.5471 (t0) REVERT: P 1299 LEU cc_start: 0.8018 (tp) cc_final: 0.7479 (pp) REVERT: P 1372 TYR cc_start: 0.6797 (t80) cc_final: 0.6424 (t80) REVERT: P 1496 PHE cc_start: 0.6513 (t80) cc_final: 0.6078 (t80) REVERT: P 1507 ARG cc_start: 0.5204 (mtm-85) cc_final: 0.3016 (mmt-90) REVERT: P 1588 TYR cc_start: 0.5534 (OUTLIER) cc_final: 0.4834 (m-10) REVERT: P 1593 MET cc_start: 0.4046 (ttp) cc_final: 0.3497 (ttm) REVERT: P 1632 LYS cc_start: 0.7146 (tptt) cc_final: 0.6944 (tptp) REVERT: P 1712 MET cc_start: 0.7648 (mmm) cc_final: 0.6970 (mmm) REVERT: P 1882 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5539 (mp) REVERT: P 1894 TRP cc_start: 0.0344 (OUTLIER) cc_final: -0.0284 (t60) REVERT: B 316 ASN cc_start: 0.8459 (t0) cc_final: 0.8074 (m110) REVERT: B 413 VAL cc_start: 0.2568 (OUTLIER) cc_final: 0.2196 (p) REVERT: L 131 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7714 (mmtm) REVERT: H 96 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6283 (m-80) outliers start: 88 outliers final: 66 residues processed: 256 average time/residue: 0.1171 time to fit residues: 47.0645 Evaluate side-chains 237 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 162 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 767 PHE Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 822 THR Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 1074 THR Chi-restraints excluded: chain P residue 1081 ILE Chi-restraints excluded: chain P residue 1082 VAL Chi-restraints excluded: chain P residue 1125 ASN Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1169 THR Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1363 LEU Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1534 TYR Chi-restraints excluded: chain P residue 1588 TYR Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1723 VAL Chi-restraints excluded: chain P residue 1737 VAL Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1882 LEU Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 196 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 684 ASN ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1774 ASN P1838 ASN P1878 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.123487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.100485 restraints weight = 63245.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.102469 restraints weight = 37686.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.103850 restraints weight = 25828.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.104612 restraints weight = 19817.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.105489 restraints weight = 16549.393| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16791 Z= 0.233 Angle : 0.781 16.076 22798 Z= 0.400 Chirality : 0.046 0.235 2567 Planarity : 0.006 0.078 2961 Dihedral : 8.313 170.844 2362 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.97 % Favored : 90.79 % Rotamer: Outliers : 5.97 % Allowed : 28.42 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % 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: -2.32 (0.17), residues: 2140 helix: -0.53 (0.24), residues: 434 sheet: -1.15 (0.27), residues: 371 loop : -2.11 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 250 TYR 0.036 0.003 TYR P1336 PHE 0.027 0.003 PHE A 443 TRP 0.024 0.002 TRP P1004 HIS 0.012 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00521 (16776) covalent geometry : angle 0.78085 (22780) SS BOND : bond 0.01154 ( 9) SS BOND : angle 1.31004 ( 18) hydrogen bonds : bond 0.04241 ( 386) hydrogen bonds : angle 5.93847 ( 1101) Misc. bond : bond 0.00208 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 154 time to evaluate : 0.633 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: P 820 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5586 (mmmt) REVERT: P 901 LEU cc_start: 0.8598 (mm) cc_final: 0.7932 (mm) REVERT: P 971 LEU cc_start: 0.8853 (tp) cc_final: 0.8593 (tp) REVERT: P 1075 MET cc_start: 0.6043 (mpp) cc_final: 0.5834 (mpp) REVERT: P 1084 LYS cc_start: 0.7530 (mtmm) cc_final: 0.7021 (mmtm) REVERT: P 1162 MET cc_start: 0.6726 (ttp) cc_final: 0.6259 (ttt) REVERT: P 1372 TYR cc_start: 0.7229 (t80) cc_final: 0.6751 (t80) REVERT: P 1496 PHE cc_start: 0.6555 (t80) cc_final: 0.6140 (t80) REVERT: P 1588 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: P 1593 MET cc_start: 0.4269 (ttp) cc_final: 0.3932 (ttm) REVERT: P 1712 MET cc_start: 0.7845 (mmm) cc_final: 0.7128 (mmm) REVERT: P 1772 GLU cc_start: 0.7265 (tp30) cc_final: 0.7026 (tp30) REVERT: P 1894 TRP cc_start: 0.0619 (OUTLIER) cc_final: -0.0188 (t60) REVERT: P 1947 TYR cc_start: 0.5806 (t80) cc_final: 0.5504 (t80) REVERT: B 316 ASN cc_start: 0.8472 (t0) cc_final: 0.8081 (m110) REVERT: B 413 VAL cc_start: 0.2820 (OUTLIER) cc_final: 0.2446 (p) REVERT: H 96 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: H 138 ASP cc_start: 0.5837 (p0) cc_final: 0.5578 (p0) outliers start: 104 outliers final: 82 residues processed: 244 average time/residue: 0.1161 time to fit residues: 45.3007 Evaluate side-chains 229 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 142 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 688 ILE Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 770 ASP Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 804 LEU Chi-restraints excluded: chain P residue 820 LYS Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 855 GLU Chi-restraints excluded: chain P residue 873 LEU Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 944 SER Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 977 HIS Chi-restraints excluded: chain P residue 990 VAL Chi-restraints excluded: chain P residue 999 VAL Chi-restraints excluded: chain P residue 1144 LEU Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1169 THR Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1243 SER Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1363 LEU Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1457 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1531 ILE Chi-restraints excluded: chain P residue 1588 TYR Chi-restraints excluded: chain P residue 1603 THR Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1723 VAL Chi-restraints excluded: chain P residue 1737 VAL Chi-restraints excluded: chain P residue 1774 ASN Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1867 PHE Chi-restraints excluded: chain P residue 1882 LEU Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1937 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1838 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.126641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.103660 restraints weight = 62309.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.105734 restraints weight = 36832.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.107354 restraints weight = 25088.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.108398 restraints weight = 18824.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.108908 restraints weight = 15423.589| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16791 Z= 0.139 Angle : 0.719 16.385 22798 Z= 0.364 Chirality : 0.044 0.242 2567 Planarity : 0.005 0.068 2961 Dihedral : 8.161 175.186 2360 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.01 % Favored : 92.76 % Rotamer: Outliers : 4.88 % Allowed : 29.39 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % 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: -2.22 (0.17), residues: 2140 helix: -0.26 (0.24), residues: 426 sheet: -1.07 (0.27), residues: 362 loop : -2.10 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P1773 TYR 0.016 0.002 TYR P 929 PHE 0.026 0.002 PHE A 443 TRP 0.024 0.002 TRP P1004 HIS 0.010 0.001 HIS P1184 Details of bonding type rmsd covalent geometry : bond 0.00319 (16776) covalent geometry : angle 0.71810 (22780) SS BOND : bond 0.00514 ( 9) SS BOND : angle 1.14037 ( 18) hydrogen bonds : bond 0.03694 ( 386) hydrogen bonds : angle 5.59890 ( 1101) Misc. bond : bond 0.00115 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 162 time to evaluate : 0.639 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: P 733 ILE cc_start: 0.7823 (mp) cc_final: 0.7593 (mp) REVERT: P 820 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5532 (mmmt) REVERT: P 844 PRO cc_start: 0.8082 (Cg_exo) cc_final: 0.7641 (Cg_endo) REVERT: P 846 PHE cc_start: 0.8553 (m-10) cc_final: 0.7971 (m-10) REVERT: P 901 LEU cc_start: 0.8511 (mm) cc_final: 0.7749 (mm) REVERT: P 971 LEU cc_start: 0.8821 (tp) cc_final: 0.8591 (tp) REVERT: P 1162 MET cc_start: 0.6642 (ttp) cc_final: 0.6218 (ttt) REVERT: P 1372 TYR cc_start: 0.6798 (t80) cc_final: 0.6461 (t80) REVERT: P 1379 GLN cc_start: 0.7581 (mm110) cc_final: 0.7367 (mm110) REVERT: P 1496 PHE cc_start: 0.6478 (t80) cc_final: 0.6078 (t80) REVERT: P 1507 ARG cc_start: 0.5341 (mtm-85) cc_final: 0.2929 (mmt-90) REVERT: P 1588 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.4945 (m-10) REVERT: P 1593 MET cc_start: 0.4201 (ttp) cc_final: 0.3580 (ttm) REVERT: P 1712 MET cc_start: 0.7608 (mmm) cc_final: 0.6979 (mmm) REVERT: P 1772 GLU cc_start: 0.7027 (tp30) cc_final: 0.6745 (tp30) REVERT: P 1882 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5524 (mp) REVERT: P 1894 TRP cc_start: 0.1145 (OUTLIER) cc_final: 0.0335 (t60) REVERT: B 316 ASN cc_start: 0.8460 (t0) cc_final: 0.8080 (m110) REVERT: B 413 VAL cc_start: 0.2581 (OUTLIER) cc_final: 0.2244 (p) REVERT: H 96 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: H 138 ASP cc_start: 0.5919 (p0) cc_final: 0.5657 (p0) outliers start: 85 outliers final: 69 residues processed: 237 average time/residue: 0.1149 time to fit residues: 43.3132 Evaluate side-chains 231 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 156 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 770 ASP Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 820 LYS Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 944 SER Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 977 HIS Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1169 THR Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1243 SER Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1363 LEU Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1531 ILE Chi-restraints excluded: chain P residue 1534 TYR Chi-restraints excluded: chain P residue 1588 TYR Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1737 VAL Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1882 LEU Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1937 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 180 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 0.0970 chunk 175 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** 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 = 0.4332 r_free = 0.4332 target = 0.119730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.096785 restraints weight = 63650.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.098708 restraints weight = 38232.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.100109 restraints weight = 26301.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100858 restraints weight = 20154.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.101713 restraints weight = 16903.509| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16791 Z= 0.310 Angle : 0.886 15.765 22798 Z= 0.459 Chirality : 0.050 0.289 2567 Planarity : 0.007 0.093 2961 Dihedral : 8.592 169.161 2360 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.09 % Favored : 89.67 % Rotamer: Outliers : 5.51 % Allowed : 28.65 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -2.76 (0.17), residues: 2140 helix: -0.99 (0.23), residues: 432 sheet: -1.53 (0.25), residues: 408 loop : -2.33 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P1517 TYR 0.045 0.004 TYR P1947 PHE 0.031 0.003 PHE P1564 TRP 0.040 0.004 TRP L 153 HIS 0.015 0.003 HIS P1654 Details of bonding type rmsd covalent geometry : bond 0.00676 (16776) covalent geometry : angle 0.88555 (22780) SS BOND : bond 0.00467 ( 9) SS BOND : angle 1.64869 ( 18) hydrogen bonds : bond 0.04829 ( 386) hydrogen bonds : angle 6.43382 ( 1101) Misc. bond : bond 0.00199 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 148 time to evaluate : 1.088 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: P 850 SER cc_start: 0.7569 (t) cc_final: 0.7185 (m) REVERT: P 876 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7792 (tm-30) REVERT: P 971 LEU cc_start: 0.8794 (tp) cc_final: 0.8517 (tp) REVERT: P 1162 MET cc_start: 0.6793 (ttp) cc_final: 0.6352 (ttt) REVERT: P 1233 LEU cc_start: 0.7642 (tp) cc_final: 0.7308 (tt) REVERT: P 1372 TYR cc_start: 0.7173 (t80) cc_final: 0.6732 (t80) REVERT: P 1496 PHE cc_start: 0.6589 (t80) cc_final: 0.6137 (t80) REVERT: P 1553 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7304 (tptp) REVERT: P 1588 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.5827 (m-80) REVERT: P 1593 MET cc_start: 0.4846 (ttp) cc_final: 0.4490 (ttp) REVERT: P 1712 MET cc_start: 0.7652 (mmm) cc_final: 0.6950 (mmm) REVERT: P 1772 GLU cc_start: 0.7653 (tp30) cc_final: 0.7337 (tp30) REVERT: P 1894 TRP cc_start: 0.0202 (OUTLIER) cc_final: -0.0609 (t60) REVERT: A 306 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7498 (t) REVERT: B 413 VAL cc_start: 0.2026 (OUTLIER) cc_final: 0.1452 (p) REVERT: H 96 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: H 138 ASP cc_start: 0.6070 (p0) cc_final: 0.5787 (p0) outliers start: 96 outliers final: 78 residues processed: 234 average time/residue: 0.1080 time to fit residues: 40.7909 Evaluate side-chains 224 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 140 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 688 ILE Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 770 ASP Chi-restraints excluded: chain P residue 774 LYS Chi-restraints excluded: chain P residue 778 THR Chi-restraints excluded: chain P residue 781 THR Chi-restraints excluded: chain P residue 828 ILE Chi-restraints excluded: chain P residue 854 VAL Chi-restraints excluded: chain P residue 925 THR Chi-restraints excluded: chain P residue 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 944 SER Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 977 HIS Chi-restraints excluded: chain P residue 990 VAL Chi-restraints excluded: chain P residue 999 VAL Chi-restraints excluded: chain P residue 1161 MET Chi-restraints excluded: chain P residue 1169 THR Chi-restraints excluded: chain P residue 1172 VAL Chi-restraints excluded: chain P residue 1243 SER Chi-restraints excluded: chain P residue 1252 ILE Chi-restraints excluded: chain P residue 1256 VAL Chi-restraints excluded: chain P residue 1328 VAL Chi-restraints excluded: chain P residue 1363 LEU Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1396 PHE Chi-restraints excluded: chain P residue 1457 LEU Chi-restraints excluded: chain P residue 1487 HIS Chi-restraints excluded: chain P residue 1493 LEU Chi-restraints excluded: chain P residue 1531 ILE Chi-restraints excluded: chain P residue 1553 LYS Chi-restraints excluded: chain P residue 1588 TYR Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1735 THR Chi-restraints excluded: chain P residue 1737 VAL Chi-restraints excluded: chain P residue 1863 THR Chi-restraints excluded: chain P residue 1867 PHE Chi-restraints excluded: chain P residue 1882 LEU Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1902 ILE Chi-restraints excluded: chain P residue 1937 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 203 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 180 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 792 GLN ** P1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1143 ASN ** P1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1758 HIS ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.124833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.102374 restraints weight = 62365.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.104329 restraints weight = 36752.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.105714 restraints weight = 24544.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.106520 restraints weight = 18445.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.106964 restraints weight = 15345.717| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16791 Z= 0.151 Angle : 0.744 15.999 22798 Z= 0.376 Chirality : 0.045 0.236 2567 Planarity : 0.005 0.078 2961 Dihedral : 8.293 175.305 2356 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.92 % Favored : 92.90 % Rotamer: Outliers : 4.59 % Allowed : 29.39 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -2.45 (0.17), residues: 2140 helix: -0.40 (0.24), residues: 432 sheet: -1.25 (0.26), residues: 388 loop : -2.28 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 960 TYR 0.019 0.002 TYR P1947 PHE 0.029 0.002 PHE P1564 TRP 0.037 0.002 TRP L 153 HIS 0.010 0.001 HIS P1184 Details of bonding type rmsd covalent geometry : bond 0.00347 (16776) covalent geometry : angle 0.74385 (22780) SS BOND : bond 0.00424 ( 9) SS BOND : angle 1.10126 ( 18) hydrogen bonds : bond 0.03843 ( 386) hydrogen bonds : angle 5.86132 ( 1101) Misc. bond : bond 0.00101 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.71 seconds wall clock time: 60 minutes 15.27 seconds (3615.27 seconds total)