Starting phenix.real_space_refine on Sat Jun 14 21:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xja_22204/06_2025/6xja_22204.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xja_22204/06_2025/6xja_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_22204/06_2025/6xja_22204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xja_22204/06_2025/6xja_22204.map" model { file = "/net/cci-nas-00/data/ceres_data/6xja_22204/06_2025/6xja_22204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xja_22204/06_2025/6xja_22204.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.58, per 1000 atoms: 0.52 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: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.82 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: 6.17 Time building geometry restraints manager: 4.79 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: 0.470 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- 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 : 73.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP H 109 HIS 0.046 0.002 HIS B 243 PHE 0.017 0.001 PHE P1396 TYR 0.017 0.001 TYR P 982 ARG 0.003 0.000 ARG P1747 Details of bonding type rmsd hydrogen bonds : bond 0.24363 ( 386) hydrogen bonds : angle 7.85206 ( 1101) SS BOND : bond 0.00795 ( 9) SS BOND : angle 1.00521 ( 18) covalent geometry : bond 0.02301 (16776) covalent geometry : angle 1.93410 (22780) 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 : 1.678 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: 0.7761 (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: 0.6470 (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: 0.4222 (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: 0.7241 (tp40) REVERT: L 212 LYS cc_start: 0.7027 (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: 0.3220 time to fit residues: 303.4495 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 : 1.812 ------------------------------------------------------------------------------- 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 179 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P1114 HIS P1166 GLN ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1380 HIS ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1825 GLN ** 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 H 111 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.136785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.116981 restraints weight = 62456.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.119445 restraints weight = 35609.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.121130 restraints weight = 23149.921| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4302 r_free = 0.4302 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4286 r_free = 0.4286 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 16791 Z= 0.270 Angle : 0.936 20.117 22798 Z= 0.491 Chirality : 0.053 0.573 2567 Planarity : 0.007 0.098 2961 Dihedral : 12.637 89.121 2618 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.73 % Favored : 92.94 % Rotamer: Outliers : 10.39 % Allowed : 19.52 % Favored : 70.09 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2140 helix: -0.37 (0.24), residues: 445 sheet: -0.67 (0.27), residues: 391 loop : -2.00 (0.15), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 160 HIS 0.022 0.003 HIS B 243 PHE 0.026 0.003 PHE P1879 TYR 0.029 0.003 TYR H 97 ARG 0.024 0.001 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 386) hydrogen bonds : angle 6.24880 ( 1101) SS BOND : bond 0.00440 ( 9) SS BOND : angle 1.24309 ( 18) covalent geometry : bond 0.00613 (16776) covalent geometry : angle 0.93535 (22780) Misc. bond : bond 0.00828 ( 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 411 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 230 time to evaluate : 1.694 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: 0.7613 (p0) cc_final: 0.7285 (p0) REVERT: P 769 LEU cc_start: 0.3908 (OUTLIER) cc_final: 0.3612 (mp) REVERT: P 788 LYS cc_start: 0.8702 (mttt) cc_final: 0.8412 (tmtt) REVERT: P 971 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7205 (tp) REVERT: P 1051 ASN cc_start: 0.5662 (OUTLIER) cc_final: 0.5462 (p0) REVERT: P 1053 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7680 (p) REVERT: P 1372 TYR cc_start: 0.6946 (t80) cc_final: 0.6669 (t80) REVERT: P 1449 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5457 (mtmt) REVERT: P 1458 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5672 (tt) REVERT: P 1471 MET cc_start: 0.7067 (ttt) cc_final: 0.5519 (pmm) REVERT: P 1507 ARG cc_start: 0.5272 (mtm-85) cc_final: 0.3374 (mmp80) REVERT: P 1513 ASP cc_start: 0.7443 (t0) cc_final: 0.7193 (t0) REVERT: P 1561 MET cc_start: 0.7219 (tmm) cc_final: 0.6884 (tmm) REVERT: P 1603 THR cc_start: 0.7442 (t) cc_final: 0.7239 (t) REVERT: P 1614 ILE cc_start: 0.6904 (mm) cc_final: 0.6678 (mm) REVERT: P 1748 ASN cc_start: 0.8072 (m-40) cc_final: 0.7796 (p0) REVERT: P 1800 MET cc_start: 0.5839 (mmm) cc_final: 0.5446 (mmm) REVERT: P 1894 TRP cc_start: 0.1450 (OUTLIER) cc_final: 0.0549 (t60) REVERT: A 290 VAL cc_start: 0.8911 (t) cc_final: 0.8658 (p) REVERT: A 302 TYR cc_start: 0.5681 (t80) cc_final: 0.5253 (t80) REVERT: A 306 SER cc_start: 0.7970 (OUTLIER) cc_final: 0.7612 (t) REVERT: A 358 GLU cc_start: 0.3013 (OUTLIER) cc_final: 0.2709 (tm-30) REVERT: A 393 GLU cc_start: 0.2228 (OUTLIER) cc_final: 0.1446 (pm20) REVERT: A 395 TYR cc_start: 0.2854 (OUTLIER) cc_final: 0.2357 (t80) REVERT: A 416 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.5116 (pt) REVERT: A 417 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4081 (tp) REVERT: A 426 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5264 (tptm) REVERT: A 450 ARG cc_start: 0.2651 (OUTLIER) cc_final: 0.2289 (ttt180) REVERT: B 266 CYS cc_start: 0.0908 (OUTLIER) cc_final: 0.0059 (p) REVERT: B 316 ASN cc_start: 0.8413 (t0) cc_final: 0.7974 (m110) REVERT: B 393 GLU cc_start: 0.7011 (tm-30) cc_final: 0.5478 (mm-30) REVERT: B 401 ARG cc_start: -0.1110 (OUTLIER) cc_final: -0.2720 (tmt170) REVERT: B 422 GLU cc_start: 0.2831 (OUTLIER) cc_final: 0.1906 (mm-30) REVERT: B 433 MET cc_start: 0.2943 (ptp) cc_final: 0.2656 (ptp) REVERT: L 175 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.6969 (p0) REVERT: L 215 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7647 (p0) REVERT: H 138 ASP cc_start: 0.5662 (p0) cc_final: 0.5367 (p0) REVERT: H 200 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7000 (tppt) outliers start: 181 outliers final: 98 residues processed: 395 average time/residue: 0.2901 time to fit residues: 170.6983 Evaluate side-chains 294 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 175 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 769 LEU 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 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 1020 VAL Chi-restraints excluded: chain P residue 1038 THR Chi-restraints excluded: chain P residue 1048 SER Chi-restraints excluded: chain P residue 1051 ASN 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 1256 VAL 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 1449 LYS 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 1877 ASP 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 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 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 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 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 126 SER 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 111 GLN 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 205 HIS Chi-restraints excluded: chain H residue 216 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 80 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 146 optimal weight: 0.0980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 P1089 ASN P1143 ASN ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1324 ASN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.132231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.109934 restraints weight = 61706.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.112195 restraints weight = 36020.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.113710 restraints weight = 23934.996| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16791 Z= 0.197 Angle : 0.809 16.113 22798 Z= 0.416 Chirality : 0.047 0.306 2567 Planarity : 0.007 0.127 2961 Dihedral : 10.838 173.679 2456 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.92 % Favored : 92.76 % Rotamer: Outliers : 8.50 % Allowed : 22.22 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2140 helix: -0.44 (0.24), residues: 441 sheet: -0.64 (0.28), residues: 341 loop : -2.05 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P1004 HIS 0.016 0.002 HIS B 243 PHE 0.023 0.003 PHE P1879 TYR 0.022 0.003 TYR H 97 ARG 0.024 0.001 ARG P1844 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 386) hydrogen bonds : angle 5.94422 ( 1101) SS BOND : bond 0.00330 ( 9) SS BOND : angle 0.82900 ( 18) covalent geometry : bond 0.00444 (16776) covalent geometry : angle 0.80856 (22780) Misc. bond : bond 0.00465 ( 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 351 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 203 time to evaluate : 1.822 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: 0.7626 (p0) cc_final: 0.7311 (p0) REVERT: P 788 LYS cc_start: 0.8810 (mttt) cc_final: 0.8494 (tmtt) REVERT: P 922 THR cc_start: 0.6457 (p) cc_final: 0.5758 (t) REVERT: P 971 LEU cc_start: 0.8363 (tp) cc_final: 0.7869 (tp) REVERT: P 973 ASP cc_start: 0.7885 (m-30) cc_final: 0.7530 (m-30) REVERT: P 1053 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7690 (p) REVERT: P 1125 ASN cc_start: 0.6944 (OUTLIER) cc_final: 0.6487 (t0) REVERT: P 1162 MET cc_start: 0.6472 (ttp) cc_final: 0.5969 (ttt) REVERT: P 1458 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5906 (tt) REVERT: P 1471 MET cc_start: 0.7342 (ttt) cc_final: 0.4386 (pmm) REVERT: P 1507 ARG cc_start: 0.5241 (mtm-85) cc_final: 0.3160 (mmt-90) REVERT: P 1561 MET cc_start: 0.7416 (tmm) cc_final: 0.7061 (tmm) REVERT: P 1715 LEU cc_start: 0.8661 (mp) cc_final: 0.8218 (tp) REVERT: P 1745 GLU cc_start: 0.7840 (mp0) cc_final: 0.7437 (mp0) REVERT: P 1894 TRP cc_start: 0.0481 (OUTLIER) cc_final: -0.0270 (t60) REVERT: A 358 GLU cc_start: 0.1806 (OUTLIER) cc_final: 0.1603 (tm-30) REVERT: A 395 TYR cc_start: 0.1188 (OUTLIER) cc_final: 0.0765 (t80) REVERT: A 426 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6073 (ptmt) REVERT: B 266 CYS cc_start: 0.0404 (OUTLIER) cc_final: -0.0425 (p) REVERT: B 316 ASN cc_start: 0.8291 (t0) cc_final: 0.7910 (m110) REVERT: L 175 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.7405 (p0) REVERT: H 138 ASP cc_start: 0.5966 (p0) cc_final: 0.5746 (p0) REVERT: H 160 TRP cc_start: 0.7817 (m100) cc_final: 0.7479 (m100) REVERT: H 200 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7006 (tppt) outliers start: 148 outliers final: 99 residues processed: 338 average time/residue: 0.2628 time to fit residues: 137.7693 Evaluate side-chains 281 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 172 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 686 SER 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 925 THR Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 1020 VAL Chi-restraints excluded: chain P residue 1045 THR Chi-restraints excluded: chain P residue 1053 VAL Chi-restraints excluded: chain P residue 1065 SER 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 1125 ASN 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 1385 LEU Chi-restraints excluded: chain P residue 1410 THR Chi-restraints excluded: chain P residue 1457 LEU Chi-restraints excluded: chain P residue 1458 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 1537 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 1706 LEU Chi-restraints excluded: chain P residue 1723 VAL 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 1894 TRP Chi-restraints excluded: chain P residue 1899 THR 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 290 VAL 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 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 426 LYS Chi-restraints excluded: chain A residue 430 PHE 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 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 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 214 PHE 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 218 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 176 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 879 ASN ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1379 GLN P1399 ASN P1511 HIS P1563 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** P1838 ASN P1903 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.129940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.105828 restraints weight = 60010.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.107915 restraints weight = 36471.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.109196 restraints weight = 24030.518| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16791 Z= 0.219 Angle : 0.777 14.820 22798 Z= 0.404 Chirality : 0.047 0.266 2567 Planarity : 0.007 0.146 2961 Dihedral : 9.597 162.505 2415 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.43 % Favored : 92.24 % Rotamer: Outliers : 8.50 % Allowed : 23.94 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2140 helix: -0.58 (0.24), residues: 434 sheet: -0.90 (0.26), residues: 377 loop : -2.10 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 424 HIS 0.024 0.002 HIS L 203 PHE 0.022 0.003 PHE P1879 TYR 0.024 0.003 TYR P1602 ARG 0.006 0.001 ARG P1844 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 386) hydrogen bonds : angle 5.92044 ( 1101) SS BOND : bond 0.00285 ( 9) SS BOND : angle 0.64361 ( 18) covalent geometry : bond 0.00493 (16776) covalent geometry : angle 0.77688 (22780) Misc. bond : bond 0.00378 ( 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 319 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 171 time to evaluate : 1.700 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: P 712 ASP cc_start: 0.7612 (p0) cc_final: 0.7343 (p0) REVERT: P 788 LYS cc_start: 0.8962 (mttt) cc_final: 0.8561 (tmtt) REVERT: P 876 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7614 (tm-30) REVERT: P 901 LEU cc_start: 0.8325 (mm) cc_final: 0.7782 (mm) REVERT: P 912 GLU cc_start: 0.8654 (mp0) cc_final: 0.8330 (mp0) REVERT: P 922 THR cc_start: 0.8083 (p) cc_final: 0.7619 (p) REVERT: P 971 LEU cc_start: 0.8733 (tp) cc_final: 0.8228 (tp) REVERT: P 973 ASP cc_start: 0.8191 (m-30) cc_final: 0.7819 (m-30) REVERT: P 1125 ASN cc_start: 0.6643 (OUTLIER) cc_final: 0.6173 (t0) REVERT: P 1240 ASP cc_start: 0.7480 (t0) cc_final: 0.7129 (p0) REVERT: P 1302 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7894 (tttt) REVERT: P 1372 TYR cc_start: 0.6969 (t80) cc_final: 0.6307 (t80) REVERT: P 1471 MET cc_start: 0.8051 (ttt) cc_final: 0.7481 (tmm) REVERT: P 1507 ARG cc_start: 0.5460 (mtm-85) cc_final: 0.3299 (mmt-90) REVERT: P 1561 MET cc_start: 0.7723 (tmm) cc_final: 0.7510 (tmm) REVERT: P 1588 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.5229 (m-80) REVERT: P 1589 MET cc_start: 0.7993 (mpp) cc_final: 0.7672 (mpp) REVERT: P 1712 MET cc_start: 0.7670 (mmm) cc_final: 0.6790 (mmm) REVERT: P 1715 LEU cc_start: 0.8651 (mp) cc_final: 0.8425 (mm) REVERT: P 1717 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8283 (ttpp) REVERT: P 1745 GLU cc_start: 0.8001 (mp0) cc_final: 0.7744 (mp0) REVERT: P 1774 ASN cc_start: 0.8257 (p0) cc_final: 0.8054 (p0) REVERT: P 1894 TRP cc_start: 0.0904 (OUTLIER) cc_final: 0.0240 (t60) REVERT: A 358 GLU cc_start: 0.2072 (OUTLIER) cc_final: 0.1741 (tm-30) REVERT: A 395 TYR cc_start: 0.1248 (OUTLIER) cc_final: 0.0623 (t80) REVERT: A 426 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6167 (tppt) REVERT: B 266 CYS cc_start: 0.0062 (OUTLIER) cc_final: -0.0917 (p) REVERT: B 308 LEU cc_start: 0.2114 (OUTLIER) cc_final: 0.1779 (pp) REVERT: B 316 ASN cc_start: 0.8451 (t0) cc_final: 0.8062 (m110) REVERT: H 138 ASP cc_start: 0.6088 (p0) cc_final: 0.5832 (p0) outliers start: 148 outliers final: 110 residues processed: 309 average time/residue: 0.2649 time to fit residues: 127.0720 Evaluate side-chains 277 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 159 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 728 ILE 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 855 GLU Chi-restraints excluded: chain P residue 879 ASN Chi-restraints excluded: chain P residue 913 SER 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 990 VAL 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 1076 LEU 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 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 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 1410 THR Chi-restraints excluded: chain P residue 1455 LEU 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 1584 ASP Chi-restraints excluded: chain P residue 1588 TYR 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 1723 VAL 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 1894 TRP Chi-restraints excluded: chain P residue 1899 THR 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 351 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 426 LYS Chi-restraints excluded: chain A residue 430 PHE 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 256 LEU Chi-restraints excluded: chain B residue 266 CYS 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 308 LEU 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 53 ILE Chi-restraints excluded: chain L residue 131 LYS Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 214 PHE 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 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 218 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 11 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 121 optimal weight: 0.0670 chunk 129 optimal weight: 6.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- 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** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1838 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** 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 = 0.4481 r_free = 0.4481 target = 0.128884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.106742 restraints weight = 62586.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.108752 restraints weight = 36726.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.110100 restraints weight = 24500.601| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4137 r_free = 0.4137 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4137 r_free = 0.4137 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16791 Z= 0.150 Angle : 0.713 16.827 22798 Z= 0.364 Chirality : 0.044 0.241 2567 Planarity : 0.006 0.121 2961 Dihedral : 9.238 171.595 2400 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 7.41 % Allowed : 25.77 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2140 helix: -0.28 (0.24), residues: 434 sheet: -0.77 (0.27), residues: 359 loop : -2.10 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 398 HIS 0.010 0.002 HIS L 203 PHE 0.030 0.002 PHE A 443 TYR 0.020 0.002 TYR L 145 ARG 0.019 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 386) hydrogen bonds : angle 5.64084 ( 1101) SS BOND : bond 0.00301 ( 9) SS BOND : angle 0.72344 ( 18) covalent geometry : bond 0.00339 (16776) covalent geometry : angle 0.71267 (22780) Misc. bond : bond 0.00237 ( 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 302 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 173 time to evaluate : 1.958 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 788 LYS cc_start: 0.8812 (mttt) cc_final: 0.8531 (tmtt) REVERT: P 820 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5514 (mmmt) REVERT: P 844 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: P 901 LEU cc_start: 0.8460 (mm) cc_final: 0.8064 (mm) REVERT: P 960 ARG cc_start: 0.6616 (tpp80) cc_final: 0.6369 (tpp-160) REVERT: P 971 LEU cc_start: 0.8765 (tp) cc_final: 0.8214 (tp) REVERT: P 1125 ASN cc_start: 0.6858 (OUTLIER) cc_final: 0.6436 (t0) REVERT: P 1302 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7934 (tttt) REVERT: P 1372 TYR cc_start: 0.6906 (t80) cc_final: 0.6409 (t80) REVERT: P 1507 ARG cc_start: 0.5537 (mtm-85) cc_final: 0.3168 (mmt-90) REVERT: P 1588 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.5007 (m-10) REVERT: P 1712 MET cc_start: 0.7415 (mmm) cc_final: 0.7063 (mmm) REVERT: P 1715 LEU cc_start: 0.8768 (mp) cc_final: 0.8540 (mm) REVERT: P 1745 GLU cc_start: 0.7793 (mp0) cc_final: 0.7360 (mp0) REVERT: P 1855 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7682 (mmmt) REVERT: P 1894 TRP cc_start: 0.1406 (OUTLIER) cc_final: 0.0657 (t60) REVERT: B 268 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6158 (mt) REVERT: B 316 ASN cc_start: 0.8435 (t0) cc_final: 0.8032 (m110) REVERT: B 410 THR cc_start: 0.1573 (OUTLIER) cc_final: 0.1347 (p) REVERT: B 446 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6327 (tttt) REVERT: H 96 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: H 138 ASP cc_start: 0.6173 (p0) cc_final: 0.5964 (p0) outliers start: 129 outliers final: 96 residues processed: 298 average time/residue: 0.2778 time to fit residues: 127.8155 Evaluate side-chains 263 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 158 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 679 LYS Chi-restraints excluded: chain P residue 680 LEU 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 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 990 VAL Chi-restraints excluded: chain P residue 1045 THR Chi-restraints excluded: chain P residue 1048 SER 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 1125 ASN 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 1396 PHE 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 1531 ILE 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 1680 LEU Chi-restraints excluded: chain P residue 1723 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1855 LYS Chi-restraints excluded: chain P residue 1894 TRP Chi-restraints excluded: chain P residue 1937 HIS 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 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 430 PHE 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 268 LEU Chi-restraints excluded: chain B residue 271 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 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 411 PHE 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 185 THR 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 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 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 218 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 192 optimal weight: 40.0000 chunk 202 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 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** P1878 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.123384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.100792 restraints weight = 63810.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.102492 restraints weight = 38025.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.103739 restraints weight = 25519.443| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16791 Z= 0.252 Angle : 0.792 13.169 22798 Z= 0.410 Chirality : 0.046 0.284 2567 Planarity : 0.006 0.097 2961 Dihedral : 9.043 169.243 2387 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.25 % Favored : 90.47 % Rotamer: Outliers : 7.98 % Allowed : 26.18 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2140 helix: -0.84 (0.23), residues: 444 sheet: -1.08 (0.27), residues: 368 loop : -2.24 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 153 HIS 0.012 0.002 HIS L 203 PHE 0.024 0.003 PHE A 443 TYR 0.025 0.003 TYR P1602 ARG 0.009 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 386) hydrogen bonds : angle 6.13853 ( 1101) SS BOND : bond 0.00431 ( 9) SS BOND : angle 1.03044 ( 18) covalent geometry : bond 0.00549 (16776) covalent geometry : angle 0.79145 (22780) Misc. bond : bond 0.00256 ( 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 310 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 171 time to evaluate : 2.068 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: P 712 ASP cc_start: 0.7510 (p0) cc_final: 0.7286 (p0) REVERT: P 820 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5721 (mmmt) REVERT: P 901 LEU cc_start: 0.8555 (mm) cc_final: 0.7874 (mm) REVERT: P 971 LEU cc_start: 0.8811 (tp) cc_final: 0.8466 (tp) REVERT: P 1040 MET cc_start: 0.7260 (mmm) cc_final: 0.6881 (mmm) REVERT: P 1125 ASN cc_start: 0.6606 (OUTLIER) cc_final: 0.6380 (t0) REVERT: P 1162 MET cc_start: 0.6705 (ttp) cc_final: 0.6240 (ttt) REVERT: P 1182 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5326 (mm) REVERT: P 1233 LEU cc_start: 0.7547 (tp) cc_final: 0.7234 (tt) REVERT: P 1372 TYR cc_start: 0.7009 (t80) cc_final: 0.6364 (t80) REVERT: P 1462 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7179 (tm-30) REVERT: P 1600 ILE cc_start: 0.8173 (mm) cc_final: 0.7878 (mm) REVERT: P 1712 MET cc_start: 0.7806 (mmm) cc_final: 0.7479 (mmm) REVERT: P 1715 LEU cc_start: 0.8744 (mp) cc_final: 0.8503 (mm) REVERT: P 1745 GLU cc_start: 0.7889 (mp0) cc_final: 0.7263 (mp0) REVERT: P 1766 TYR cc_start: 0.7902 (m-80) cc_final: 0.7649 (m-80) REVERT: P 1894 TRP cc_start: 0.0781 (OUTLIER) cc_final: -0.0024 (t60) REVERT: A 302 TYR cc_start: 0.5553 (t80) cc_final: 0.5303 (t80) REVERT: H 96 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: H 138 ASP cc_start: 0.5930 (p0) cc_final: 0.5617 (p0) outliers start: 139 outliers final: 114 residues processed: 292 average time/residue: 0.3064 time to fit residues: 138.9299 Evaluate side-chains 275 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 156 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 679 LYS Chi-restraints excluded: chain P residue 680 LEU 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 820 LYS 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 935 VAL Chi-restraints excluded: chain P residue 939 THR Chi-restraints excluded: chain P residue 944 SER Chi-restraints excluded: chain P residue 948 SER Chi-restraints excluded: chain P residue 964 THR Chi-restraints excluded: chain P residue 973 ASP 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 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 1076 LEU Chi-restraints excluded: chain P residue 1081 ILE Chi-restraints excluded: chain P residue 1082 VAL 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 1182 LEU 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 1396 PHE Chi-restraints excluded: chain P residue 1405 TRP Chi-restraints excluded: chain P residue 1443 ILE 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 1534 TYR Chi-restraints excluded: chain P residue 1553 LYS Chi-restraints excluded: chain P residue 1584 ASP 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 1819 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1863 THR 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 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 377 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 430 PHE 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 278 THR 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 411 PHE 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 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 98 CYS 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 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 218 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 176 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 700 GLN ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 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 ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 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 = 0.4428 r_free = 0.4428 target = 0.125349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.102917 restraints weight = 63129.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.104503 restraints weight = 37205.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.105922 restraints weight = 24984.236| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4075 r_free = 0.4075 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.7383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16791 Z= 0.166 Angle : 0.723 13.695 22798 Z= 0.371 Chirality : 0.044 0.237 2567 Planarity : 0.005 0.086 2961 Dihedral : 8.815 173.595 2382 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.76 % Favored : 92.01 % Rotamer: Outliers : 6.49 % Allowed : 27.44 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 2140 helix: -0.53 (0.24), residues: 431 sheet: -0.92 (0.28), residues: 356 loop : -2.23 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 153 HIS 0.010 0.002 HIS P1184 PHE 0.025 0.002 PHE A 443 TYR 0.017 0.002 TYR P1947 ARG 0.008 0.001 ARG P 960 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 386) hydrogen bonds : angle 5.84529 ( 1101) SS BOND : bond 0.00335 ( 9) SS BOND : angle 0.87381 ( 18) covalent geometry : bond 0.00376 (16776) covalent geometry : angle 0.72294 (22780) Misc. bond : bond 0.00176 ( 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 287 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 174 time to evaluate : 1.864 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: 0.7357 (p0) cc_final: 0.7066 (p0) REVERT: P 820 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5655 (mmmt) REVERT: P 844 PRO cc_start: 0.8381 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: P 901 LEU cc_start: 0.8492 (mm) cc_final: 0.7784 (mm) REVERT: P 1125 ASN cc_start: 0.6022 (OUTLIER) cc_final: 0.5803 (t0) REVERT: P 1162 MET cc_start: 0.6716 (ttp) cc_final: 0.6036 (mmm) REVERT: P 1291 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.6084 (p0) REVERT: P 1302 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7502 (tttt) REVERT: P 1372 TYR cc_start: 0.7030 (t80) cc_final: 0.6544 (t80) REVERT: P 1529 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5722 (ptt-90) REVERT: P 1712 MET cc_start: 0.7654 (mmm) cc_final: 0.6858 (mmm) REVERT: P 1894 TRP cc_start: 0.0652 (OUTLIER) cc_final: -0.0134 (t60) REVERT: A 302 TYR cc_start: 0.5612 (t80) cc_final: 0.5381 (t80) REVERT: B 316 ASN cc_start: 0.8576 (t0) cc_final: 0.8267 (m-40) REVERT: B 379 VAL cc_start: 0.1965 (OUTLIER) cc_final: 0.1715 (m) REVERT: B 413 VAL cc_start: 0.1993 (OUTLIER) cc_final: 0.1653 (p) REVERT: H 96 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: H 138 ASP cc_start: 0.6237 (p0) cc_final: 0.5908 (p0) REVERT: H 189 LEU cc_start: 0.8481 (mt) cc_final: 0.8179 (mt) outliers start: 113 outliers final: 90 residues processed: 275 average time/residue: 0.2793 time to fit residues: 118.9240 Evaluate side-chains 259 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 161 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 680 LEU 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 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 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 948 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 1038 THR Chi-restraints excluded: chain P residue 1045 THR Chi-restraints excluded: chain P residue 1048 SER 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 1291 ASP 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 1529 ARG Chi-restraints excluded: chain P residue 1531 ILE 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 1819 VAL 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 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 351 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 430 PHE 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 257 LEU Chi-restraints excluded: chain B residue 278 THR 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 348 GLU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 379 VAL 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 201 VAL 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 98 CYS 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 161 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 218 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 110 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 169 optimal weight: 0.0770 chunk 164 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1025 ASN ** P1188 HIS ** 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 ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 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 = 0.4422 r_free = 0.4422 target = 0.124934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.102206 restraints weight = 62660.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.104338 restraints weight = 36710.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.105729 restraints weight = 24492.374| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.7626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16791 Z= 0.160 Angle : 0.709 13.656 22798 Z= 0.361 Chirality : 0.043 0.226 2567 Planarity : 0.005 0.098 2961 Dihedral : 8.589 173.467 2373 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.11 % Favored : 90.65 % Rotamer: Outliers : 6.60 % Allowed : 27.90 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.17), residues: 2140 helix: -0.44 (0.24), residues: 434 sheet: -0.91 (0.28), residues: 344 loop : -2.24 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 153 HIS 0.009 0.001 HIS P1184 PHE 0.028 0.002 PHE P1132 TYR 0.023 0.002 TYR P1947 ARG 0.005 0.001 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 386) hydrogen bonds : angle 5.77761 ( 1101) SS BOND : bond 0.00394 ( 9) SS BOND : angle 1.05464 ( 18) covalent geometry : bond 0.00365 (16776) covalent geometry : angle 0.70823 (22780) Misc. bond : bond 0.00125 ( 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 281 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 166 time to evaluate : 1.906 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: 0.7273 (p0) cc_final: 0.7025 (p0) REVERT: P 733 ILE cc_start: 0.7887 (mp) cc_final: 0.7663 (mp) REVERT: P 844 PRO cc_start: 0.8355 (Cg_exo) cc_final: 0.7985 (Cg_endo) REVERT: P 850 SER cc_start: 0.7703 (t) cc_final: 0.7451 (m) REVERT: P 901 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7736 (mm) REVERT: P 912 GLU cc_start: 0.8578 (mp0) cc_final: 0.8291 (mp0) REVERT: P 1087 GLU cc_start: 0.5581 (pm20) cc_final: 0.4949 (tp30) REVERT: P 1162 MET cc_start: 0.6742 (ttp) cc_final: 0.6055 (mmm) REVERT: P 1291 ASP cc_start: 0.6173 (OUTLIER) cc_final: 0.5862 (p0) REVERT: P 1372 TYR cc_start: 0.7055 (t80) cc_final: 0.6566 (t80) REVERT: P 1529 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6059 (ptt-90) REVERT: P 1712 MET cc_start: 0.7632 (mmm) cc_final: 0.6832 (mmm) REVERT: P 1882 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5549 (mp) REVERT: P 1894 TRP cc_start: 0.0662 (OUTLIER) cc_final: -0.0131 (t60) REVERT: B 287 LYS cc_start: 0.5979 (pttm) cc_final: 0.5393 (tmtt) REVERT: B 413 VAL cc_start: 0.2991 (OUTLIER) cc_final: 0.2630 (p) REVERT: L 4 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5533 (tmm) REVERT: H 96 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: H 138 ASP cc_start: 0.6397 (p0) cc_final: 0.6032 (p0) outliers start: 115 outliers final: 95 residues processed: 265 average time/residue: 0.2632 time to fit residues: 110.5913 Evaluate side-chains 255 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 152 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 707 ILE Chi-restraints excluded: chain P residue 726 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 855 GLU Chi-restraints excluded: chain P residue 901 LEU 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 948 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 1045 THR Chi-restraints excluded: chain P residue 1048 SER 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 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 1363 LEU Chi-restraints excluded: chain P residue 1385 LEU Chi-restraints excluded: chain P residue 1396 PHE 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 1529 ARG Chi-restraints excluded: chain P residue 1531 ILE Chi-restraints excluded: chain P residue 1584 ASP Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1863 THR 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 P residue 1956 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 290 VAL 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 351 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 430 PHE 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 278 THR 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 348 GLU 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 411 PHE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain L residue 4 MET 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 201 VAL 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 98 CYS 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 161 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 184 optimal weight: 0.0020 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 172 optimal weight: 50.0000 chunk 156 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 989 ASN ** P1188 HIS ** 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** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.127745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.105760 restraints weight = 61561.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.107795 restraints weight = 35989.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.109125 restraints weight = 23790.654| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16791 Z= 0.129 Angle : 0.697 14.121 22798 Z= 0.349 Chirality : 0.043 0.199 2567 Planarity : 0.005 0.079 2961 Dihedral : 8.306 175.882 2367 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.43 % Rotamer: Outliers : 5.68 % Allowed : 28.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 2140 helix: -0.22 (0.25), residues: 436 sheet: -0.86 (0.28), residues: 335 loop : -2.22 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP P1515 HIS 0.012 0.001 HIS B 243 PHE 0.044 0.002 PHE P1132 TYR 0.015 0.002 TYR P1336 ARG 0.007 0.001 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 386) hydrogen bonds : angle 5.51122 ( 1101) SS BOND : bond 0.00364 ( 9) SS BOND : angle 0.86373 ( 18) covalent geometry : bond 0.00298 (16776) covalent geometry : angle 0.69669 (22780) Misc. bond : bond 0.00114 ( 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 275 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 176 time to evaluate : 1.859 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: P 712 ASP cc_start: 0.7026 (p0) cc_final: 0.6799 (p0) REVERT: P 733 ILE cc_start: 0.7776 (mp) cc_final: 0.7551 (mp) REVERT: P 844 PRO cc_start: 0.8085 (Cg_exo) cc_final: 0.7685 (Cg_endo) REVERT: P 846 PHE cc_start: 0.8506 (m-10) cc_final: 0.8009 (m-10) REVERT: P 901 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.7931 (mm) REVERT: P 912 GLU cc_start: 0.8474 (mp0) cc_final: 0.8218 (mp0) REVERT: P 1125 ASN cc_start: 0.5543 (OUTLIER) cc_final: 0.5040 (t0) REVERT: P 1162 MET cc_start: 0.6710 (ttp) cc_final: 0.6283 (ttt) REVERT: P 1299 LEU cc_start: 0.8298 (tp) cc_final: 0.8016 (tp) REVERT: P 1372 TYR cc_start: 0.6911 (t80) cc_final: 0.6479 (t80) REVERT: P 1507 ARG cc_start: 0.5674 (mtm-85) cc_final: 0.3155 (mmt-90) REVERT: P 1529 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5623 (ptt-90) REVERT: P 1712 MET cc_start: 0.7476 (mmm) cc_final: 0.6731 (mmm) REVERT: P 1882 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5438 (mp) REVERT: P 1894 TRP cc_start: 0.1321 (OUTLIER) cc_final: 0.0510 (t60) REVERT: B 287 LYS cc_start: 0.5776 (pttm) cc_final: 0.5241 (tmtt) REVERT: B 316 ASN cc_start: 0.8589 (t0) cc_final: 0.8273 (m110) REVERT: B 346 ARG cc_start: 0.6681 (mmt-90) cc_final: 0.6087 (mmm160) REVERT: B 379 VAL cc_start: 0.2083 (OUTLIER) cc_final: 0.1867 (m) REVERT: B 413 VAL cc_start: 0.0910 (OUTLIER) cc_final: 0.0569 (p) REVERT: L 4 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5535 (tmm) REVERT: H 138 ASP cc_start: 0.6132 (p0) cc_final: 0.5733 (p0) REVERT: H 189 LEU cc_start: 0.8439 (mt) cc_final: 0.8138 (mt) outliers start: 99 outliers final: 73 residues processed: 259 average time/residue: 0.2594 time to fit residues: 106.4541 Evaluate side-chains 246 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 726 VAL Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 767 PHE 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 901 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 990 VAL Chi-restraints excluded: chain P residue 999 VAL 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 1082 VAL Chi-restraints excluded: chain P residue 1125 ASN 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 1529 ARG Chi-restraints excluded: chain P residue 1531 ILE Chi-restraints excluded: chain P residue 1584 ASP Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1838 ASN Chi-restraints excluded: chain P residue 1863 THR 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 351 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain B residue 248 LEU 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 348 GLU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 379 VAL 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 4 MET Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 201 VAL 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 115 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 220 CYS 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 169 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 192 optimal weight: 40.0000 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 989 ASN ** P1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1604 HIS ** 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** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.127337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.104982 restraints weight = 62273.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.106928 restraints weight = 36277.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.108300 restraints weight = 24186.957| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.7724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.257 16791 Z= 0.268 Angle : 0.913 59.197 22798 Z= 0.501 Chirality : 0.046 0.610 2567 Planarity : 0.005 0.080 2961 Dihedral : 8.101 175.816 2361 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.43 % Rotamer: Outliers : 5.22 % Allowed : 29.51 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 2140 helix: -0.22 (0.25), residues: 436 sheet: -0.86 (0.28), residues: 335 loop : -2.21 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP P1515 HIS 0.008 0.001 HIS P1184 PHE 0.052 0.002 PHE P1109 TYR 0.075 0.002 TYR H 96 ARG 0.007 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 386) hydrogen bonds : angle 5.52818 ( 1101) SS BOND : bond 0.00528 ( 9) SS BOND : angle 1.87805 ( 18) covalent geometry : bond 0.00598 (16776) covalent geometry : angle 0.91218 (22780) Misc. bond : bond 0.00115 ( 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 252 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 161 time to evaluate : 2.097 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: 0.7111 (p0) cc_final: 0.6875 (p0) REVERT: P 733 ILE cc_start: 0.7818 (mp) cc_final: 0.7583 (mp) REVERT: P 844 PRO cc_start: 0.8135 (Cg_exo) cc_final: 0.7720 (Cg_endo) REVERT: P 846 PHE cc_start: 0.8535 (m-10) cc_final: 0.8056 (m-10) REVERT: P 901 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.7905 (mm) REVERT: P 912 GLU cc_start: 0.8493 (mp0) cc_final: 0.8230 (mp0) REVERT: P 1125 ASN cc_start: 0.5529 (OUTLIER) cc_final: 0.4993 (t0) REVERT: P 1299 LEU cc_start: 0.8323 (tp) cc_final: 0.8034 (tp) REVERT: P 1372 TYR cc_start: 0.6914 (t80) cc_final: 0.6486 (t80) REVERT: P 1507 ARG cc_start: 0.5670 (mtm-85) cc_final: 0.3164 (mmt-90) REVERT: P 1712 MET cc_start: 0.7478 (mmm) cc_final: 0.6744 (mmm) REVERT: P 1882 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5450 (mp) REVERT: P 1894 TRP cc_start: 0.1280 (OUTLIER) cc_final: 0.0472 (t60) REVERT: B 287 LYS cc_start: 0.5946 (pttm) cc_final: 0.5399 (tmtt) REVERT: B 316 ASN cc_start: 0.8594 (t0) cc_final: 0.8300 (m110) REVERT: B 346 ARG cc_start: 0.6688 (mmt-90) cc_final: 0.6153 (mmm160) REVERT: B 413 VAL cc_start: 0.2101 (OUTLIER) cc_final: 0.1764 (p) REVERT: L 4 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5548 (tmm) REVERT: H 138 ASP cc_start: 0.6184 (p0) cc_final: 0.5736 (p0) REVERT: H 189 LEU cc_start: 0.8449 (mt) cc_final: 0.8150 (mt) outliers start: 91 outliers final: 79 residues processed: 239 average time/residue: 0.2650 time to fit residues: 100.8327 Evaluate side-chains 245 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 160 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 671 ASN Chi-restraints excluded: chain P residue 680 LEU Chi-restraints excluded: chain P residue 688 ILE Chi-restraints excluded: chain P residue 726 VAL Chi-restraints excluded: chain P residue 728 ILE Chi-restraints excluded: chain P residue 743 VAL Chi-restraints excluded: chain P residue 767 PHE 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 901 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 990 VAL Chi-restraints excluded: chain P residue 999 VAL 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 1082 VAL Chi-restraints excluded: chain P residue 1088 ILE Chi-restraints excluded: chain P residue 1125 ASN 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 1405 TRP 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 1553 LYS Chi-restraints excluded: chain P residue 1584 ASP Chi-restraints excluded: chain P residue 1648 ILE Chi-restraints excluded: chain P residue 1680 LEU Chi-restraints excluded: chain P residue 1819 VAL Chi-restraints excluded: chain P residue 1863 THR 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 351 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain B residue 248 LEU 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 348 GLU 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 4 MET Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 201 VAL 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 146 LEU Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 220 CYS 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 93 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 166 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1604 HIS ** 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 ** 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.127234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.105028 restraints weight = 62419.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.106967 restraints weight = 36497.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.108331 restraints weight = 24460.933| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.257 16791 Z= 0.268 Angle : 0.913 59.197 22798 Z= 0.501 Chirality : 0.046 0.610 2567 Planarity : 0.005 0.080 2961 Dihedral : 8.101 175.816 2361 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.38 % Favored : 92.43 % Rotamer: Outliers : 4.88 % Allowed : 29.79 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 2140 helix: -0.22 (0.25), residues: 436 sheet: -0.86 (0.28), residues: 335 loop : -2.21 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP P1515 HIS 0.008 0.001 HIS P1184 PHE 0.052 0.002 PHE P1109 TYR 0.075 0.002 TYR H 96 ARG 0.007 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 386) hydrogen bonds : angle 5.52818 ( 1101) SS BOND : bond 0.00528 ( 9) SS BOND : angle 1.87805 ( 18) covalent geometry : bond 0.00598 (16776) covalent geometry : angle 0.91217 (22780) Misc. bond : bond 0.00115 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6601.01 seconds wall clock time: 116 minutes 53.66 seconds (7013.66 seconds total)