Starting phenix.real_space_refine on Fri Mar 6 09:23:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7peb_13351/03_2026/7peb_13351.cif Found real_map, /net/cci-nas-00/data/ceres_data/7peb_13351/03_2026/7peb_13351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7peb_13351/03_2026/7peb_13351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7peb_13351/03_2026/7peb_13351.map" model { file = "/net/cci-nas-00/data/ceres_data/7peb_13351/03_2026/7peb_13351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7peb_13351/03_2026/7peb_13351.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 193 5.16 5 C 18556 2.51 5 N 5084 2.21 5 O 5301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1862 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 15606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1949, 15606 Classifications: {'peptide': 1949} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 80, 'TRANS': 1868} Chain breaks: 12 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 25, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.30, per 1000 atoms: 0.22 Number of scatterers: 29140 At special positions: 0 Unit cell: (247.976, 169.024, 152.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 193 16.00 P 6 15.00 O 5301 8.00 N 5084 7.00 C 18556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 24 sheets defined 65.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.789A pdb=" N UNK A 52 " --> pdb=" O UNK A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.938A pdb=" N LEU A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.600A pdb=" N SER A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.216A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.731A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.683A pdb=" N VAL A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.632A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.290A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 387 through 404 Proline residue: A 397 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.849A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.690A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.592A pdb=" N VAL A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.716A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 4.402A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.723A pdb=" N ALA A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 549 removed outlier: 3.925A pdb=" N HIS A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.168A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.722A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Processing helix chain 'A' and resid 645 through 666 Processing helix chain 'A' and resid 668 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.583A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 Processing helix chain 'A' and resid 722 through 744 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.903A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 816 through 829 Processing helix chain 'A' and resid 836 through 852 Processing helix chain 'A' and resid 855 through 861 Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.919A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 891 removed outlier: 3.582A pdb=" N LEU A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 942 through 960 Proline residue: A 948 - end of helix removed outlier: 3.843A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 960 " --> pdb=" O MET A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 983 removed outlier: 7.232A pdb=" N THR A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET A 970 " --> pdb=" O HIS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.524A pdb=" N VAL A 987 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1006 through 1024 removed outlier: 4.342A pdb=" N GLU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1042 removed outlier: 4.553A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 Processing helix chain 'A' and resid 1065 through 1069 removed outlier: 3.811A pdb=" N LYS A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1084 removed outlier: 3.703A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 3.652A pdb=" N LEU A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 3.564A pdb=" N ASP A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A1109 " --> pdb=" O ASN A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1110 through 1124 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1146 removed outlier: 3.611A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1166 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1186 through 1190 removed outlier: 4.102A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.629A pdb=" N HIS A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1219 Processing helix chain 'A' and resid 1263 through 1270 Processing helix chain 'A' and resid 1276 through 1295 removed outlier: 3.619A pdb=" N TRP A1280 " --> pdb=" O SER A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.597A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1317 removed outlier: 3.994A pdb=" N ALA A1314 " --> pdb=" O TYR A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 Processing helix chain 'A' and resid 1331 through 1347 Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1380 Processing helix chain 'A' and resid 1381 through 1390 Processing helix chain 'A' and resid 1392 through 1407 Processing helix chain 'A' and resid 1409 through 1423 Processing helix chain 'A' and resid 1425 through 1441 removed outlier: 3.619A pdb=" N ALA A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 4.035A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1470 Processing helix chain 'A' and resid 1473 through 1488 Processing helix chain 'A' and resid 1489 through 1500 Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 4.480A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1536 removed outlier: 3.600A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1556 through 1581 removed outlier: 4.506A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1608 removed outlier: 3.727A pdb=" N ALA A1586 " --> pdb=" O SER A1582 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1626 Processing helix chain 'A' and resid 1629 through 1641 Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1663 removed outlier: 3.968A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 Processing helix chain 'A' and resid 1693 through 1707 removed outlier: 3.555A pdb=" N LYS A1706 " --> pdb=" O LYS A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1732 Processing helix chain 'A' and resid 1737 through 1762 removed outlier: 3.569A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 3.846A pdb=" N LYS A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1812 removed outlier: 3.631A pdb=" N TRP A1790 " --> pdb=" O TRP A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1896 removed outlier: 3.540A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix removed outlier: 3.502A pdb=" N SER A1895 " --> pdb=" O SER A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 Processing helix chain 'A' and resid 1916 through 1930 Processing helix chain 'A' and resid 1933 through 1937 Processing helix chain 'A' and resid 1938 through 1945 removed outlier: 3.695A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1967 removed outlier: 3.792A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1971 Processing helix chain 'A' and resid 1972 through 1981 removed outlier: 3.539A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2002 removed outlier: 3.618A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2021 Processing helix chain 'A' and resid 2022 through 2039 Processing helix chain 'A' and resid 2043 through 2059 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2091 removed outlier: 3.645A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 3.735A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.709A pdb=" N LEU A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2212 Processing helix chain 'A' and resid 2212 through 2219 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2293 Processing helix chain 'A' and resid 2297 through 2307 Processing helix chain 'A' and resid 2309 through 2335 removed outlier: 3.557A pdb=" N ASP A2315 " --> pdb=" O GLU A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2363 through 2368 Processing helix chain 'A' and resid 2380 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2424 removed outlier: 3.588A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2427 through 2435 removed outlier: 4.303A pdb=" N LEU A2431 " --> pdb=" O LEU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2510 Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2541 removed outlier: 3.688A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A2541 " --> pdb=" O ASN A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 89 through 94 removed outlier: 4.047A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY E 94 " --> pdb=" O PRO E 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 94' Processing helix chain 'E' and resid 94 through 114 removed outlier: 4.029A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 179 through 186 removed outlier: 3.593A pdb=" N MET E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 219 removed outlier: 4.135A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 6.331A pdb=" N CYS E 283 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 removed outlier: 3.688A pdb=" N ARG E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.857A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 390 removed outlier: 4.223A pdb=" N GLN E 380 " --> pdb=" O HIS E 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 422 removed outlier: 4.030A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.622A pdb=" N LEU E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 removed outlier: 3.506A pdb=" N GLY E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 486 through 502 removed outlier: 4.522A pdb=" N LEU E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 Processing helix chain 'E' and resid 514 through 523 removed outlier: 3.515A pdb=" N PHE E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 521 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.826A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 629 removed outlier: 4.001A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 649 removed outlier: 3.911A pdb=" N THR E 638 " --> pdb=" O THR E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 674 removed outlier: 3.563A pdb=" N LEU E 670 " --> pdb=" O ALA E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.720A pdb=" N THR E 680 " --> pdb=" O SER E 676 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.548A pdb=" N ILE E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 removed outlier: 3.627A pdb=" N ALA E 953 " --> pdb=" O PHE E 950 " (cutoff:3.500A) Processing helix chain 'E' and resid 958 through 969 removed outlier: 4.008A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1008 Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'I' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.707A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.195A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.733A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 91 removed outlier: 6.501A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 102 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 110 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.641A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 228 removed outlier: 3.623A pdb=" N GLN C 225 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 277 through 278 removed outlier: 6.783A pdb=" N ALA C 294 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU C 307 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 296 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 123 removed outlier: 3.542A pdb=" N LEU E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER E 59 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N HIS E 149 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA E 61 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASN E 151 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL E 63 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AB4, first strand: chain 'E' and resid 1015 through 1016 removed outlier: 3.989A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E1020 " --> pdb=" O ILE E1325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1015 through 1016 removed outlier: 3.989A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER E1326 " --> pdb=" O VAL E1318 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL E1318 " --> pdb=" O SER E1326 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E1316 " --> pdb=" O TYR E1328 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 4.318A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E1030 " --> pdb=" O ALA E1039 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E1039 " --> pdb=" O LYS E1030 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE E1048 " --> pdb=" O ASP E1058 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1070 through 1073 removed outlier: 3.848A pdb=" N ALA E1072 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E1087 " --> pdb=" O ALA E1072 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 1127 through 1128 Processing sheet with id=AB9, first strand: chain 'E' and resid 1131 through 1132 removed outlier: 3.660A pdb=" N GLU E1132 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E1137 " --> pdb=" O GLU E1132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 1146 through 1151 removed outlier: 4.164A pdb=" N GLN E1159 " --> pdb=" O ILE E1149 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP E1151 " --> pdb=" O LYS E1157 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS E1157 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 3.665A pdb=" N SER E1171 " --> pdb=" O GLY E1184 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1227 through 1230 removed outlier: 3.919A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 1268 through 1269 removed outlier: 3.868A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 329 through 333 removed outlier: 5.014A pdb=" N SER I 374 " --> pdb=" O GLU I 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.540A pdb=" N VAL I 343 " --> pdb=" O GLN I 353 " (cutoff:3.500A) 1642 hydrogen bonds defined for protein. 4818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.43 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9584 1.34 - 1.46: 6072 1.46 - 1.58: 13789 1.58 - 1.69: 6 1.69 - 1.81: 310 Bond restraints: 29761 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.602 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.444 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.623 0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C1 IHP A2601 " pdb=" O11 IHP A2601 " ideal model delta sigma weight residual 1.392 1.443 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 29756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 39633 1.56 - 3.11: 587 3.11 - 4.67: 125 4.67 - 6.23: 34 6.23 - 7.78: 11 Bond angle restraints: 40390 Sorted by residual: angle pdb=" C LEU A 757 " pdb=" N GLY A 758 " pdb=" CA GLY A 758 " ideal model delta sigma weight residual 119.99 123.82 -3.83 1.13e+00 7.83e-01 1.15e+01 angle pdb=" C GLY I 323 " pdb=" N ALA I 324 " pdb=" CA ALA I 324 " ideal model delta sigma weight residual 121.80 128.61 -6.81 2.44e+00 1.68e-01 7.79e+00 angle pdb=" CA LYS A1024 " pdb=" CB LYS A1024 " pdb=" CG LYS A1024 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.61e+00 angle pdb=" C PRO E 80 " pdb=" N CYS E 81 " pdb=" CA CYS E 81 " ideal model delta sigma weight residual 121.76 127.64 -5.88 2.19e+00 2.09e-01 7.20e+00 angle pdb=" CA PHE A 610 " pdb=" CB PHE A 610 " pdb=" CG PHE A 610 " ideal model delta sigma weight residual 113.80 116.47 -2.67 1.00e+00 1.00e+00 7.10e+00 ... (remaining 40385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 16257 17.27 - 34.54: 1355 34.54 - 51.82: 288 51.82 - 69.09: 74 69.09 - 86.36: 18 Dihedral angle restraints: 17992 sinusoidal: 7263 harmonic: 10729 Sorted by residual: dihedral pdb=" CA UNK A 17 " pdb=" C UNK A 17 " pdb=" N UNK A 18 " pdb=" CA UNK A 18 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA ALA I 324 " pdb=" C ALA I 324 " pdb=" N PRO I 325 " pdb=" CA PRO I 325 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 17989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3999 0.058 - 0.117: 532 0.117 - 0.175: 59 0.175 - 0.233: 1 0.233 - 0.292: 3 Chirality restraints: 4594 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.61 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU A 395 " pdb=" CB LEU A 395 " pdb=" CD1 LEU A 395 " pdb=" CD2 LEU A 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4591 not shown) Planarity restraints: 5143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1157 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A1158 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 324 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO I 325 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO I 325 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 325 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E1105 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E1106 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E1106 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E1106 " -0.031 5.00e-02 4.00e+02 ... (remaining 5140 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5152 2.78 - 3.31: 28662 3.31 - 3.84: 47389 3.84 - 4.37: 55716 4.37 - 4.90: 94964 Nonbonded interactions: 231883 Sorted by model distance: nonbonded pdb=" O GLY A2337 " pdb=" NH1 ARG A2339 " model vdw 2.245 3.120 nonbonded pdb=" O ALA A1268 " pdb=" NE1 TRP A1283 " model vdw 2.251 3.120 nonbonded pdb=" O THR E1163 " pdb=" OH TYR E1193 " model vdw 2.255 3.040 nonbonded pdb=" O THR A 484 " pdb=" OG SER A 487 " model vdw 2.259 3.040 nonbonded pdb=" O LEU I 319 " pdb=" OH TYR I 326 " model vdw 2.281 3.040 ... (remaining 231878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.880 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.002 0.077 29761 Z= 0.110 Angle : 0.521 7.784 40390 Z= 0.280 Chirality : 0.040 0.292 4594 Planarity : 0.005 0.057 5143 Dihedral : 13.932 86.360 11000 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 6.14 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.12), residues: 3559 helix: -1.44 (0.10), residues: 2088 sheet: -3.26 (0.23), residues: 348 loop : -1.44 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1161 TYR 0.012 0.001 TYR E 475 PHE 0.025 0.001 PHE A 610 TRP 0.018 0.001 TRP A2023 HIS 0.007 0.001 HIS E1315 Details of bonding type rmsd covalent geometry : bond 0.00228 (29761) covalent geometry : angle 0.52081 (40390) hydrogen bonds : bond 0.22447 ( 1642) hydrogen bonds : angle 7.38438 ( 4818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 674 time to evaluate : 0.967 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: A 532 LYS cc_start: 0.2684 (OUTLIER) cc_final: 0.2381 (tptt) REVERT: A 780 ILE cc_start: 0.9036 (mt) cc_final: 0.8693 (pt) REVERT: A 805 LEU cc_start: 0.9192 (mt) cc_final: 0.8861 (mt) REVERT: A 808 VAL cc_start: 0.7858 (t) cc_final: 0.7538 (t) REVERT: A 1074 LEU cc_start: 0.9120 (mt) cc_final: 0.8499 (mp) REVERT: A 1362 GLU cc_start: 0.7977 (tt0) cc_final: 0.7754 (tp30) REVERT: A 1401 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 1455 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7928 (tp30) REVERT: A 1546 TYR cc_start: 0.8341 (m-80) cc_final: 0.7986 (m-80) REVERT: A 1673 LEU cc_start: 0.9278 (mt) cc_final: 0.9017 (mt) REVERT: A 1752 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 1809 GLN cc_start: 0.8283 (mt0) cc_final: 0.7966 (tm-30) REVERT: A 1913 TYR cc_start: 0.7417 (m-80) cc_final: 0.7156 (m-80) REVERT: A 2021 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9052 (pt) REVERT: A 2051 LEU cc_start: 0.8674 (mt) cc_final: 0.8437 (pp) REVERT: A 2161 GLN cc_start: 0.8083 (tm130) cc_final: 0.7827 (tm-30) REVERT: A 2199 MET cc_start: 0.8769 (mmt) cc_final: 0.8410 (mmt) REVERT: C 155 TRP cc_start: 0.7411 (t60) cc_final: 0.7122 (t60) REVERT: C 197 TRP cc_start: 0.7049 (m100) cc_final: 0.6094 (m100) REVERT: C 315 VAL cc_start: 0.7012 (t) cc_final: 0.6658 (t) REVERT: E 89 ASP cc_start: 0.8756 (t0) cc_final: 0.8287 (t0) REVERT: E 585 TRP cc_start: 0.4133 (p90) cc_final: 0.3872 (p90) REVERT: E 831 MET cc_start: 0.6292 (tpp) cc_final: 0.5524 (tpt) REVERT: E 1131 TRP cc_start: 0.8028 (t-100) cc_final: 0.7374 (t-100) REVERT: E 1132 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7162 (mm-30) REVERT: E 1172 LEU cc_start: 0.8611 (tt) cc_final: 0.8181 (tp) REVERT: E 1181 ILE cc_start: 0.8423 (mp) cc_final: 0.8222 (mm) REVERT: E 1224 ASP cc_start: 0.7763 (m-30) cc_final: 0.7011 (p0) REVERT: E 1236 VAL cc_start: 0.6529 (t) cc_final: 0.6285 (t) REVERT: E 1309 PHE cc_start: 0.6166 (m-80) cc_final: 0.5484 (m-10) REVERT: I 373 VAL cc_start: 0.7865 (m) cc_final: 0.7202 (t) REVERT: I 405 GLU cc_start: 0.6879 (tt0) cc_final: 0.6482 (tt0) outliers start: 85 outliers final: 11 residues processed: 735 average time/residue: 0.2053 time to fit residues: 233.1892 Evaluate side-chains 347 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 333 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1652 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 1323 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN E 151 ASN E 636 HIS ** E 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.109499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.090292 restraints weight = 124489.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.093239 restraints weight = 68484.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.093024 restraints weight = 39530.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.093943 restraints weight = 33753.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.093817 restraints weight = 28422.262| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29761 Z= 0.207 Angle : 0.718 11.648 40390 Z= 0.367 Chirality : 0.045 0.369 4594 Planarity : 0.006 0.084 5143 Dihedral : 5.220 50.603 4023 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 2.69 % Allowed : 12.33 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3559 helix: 0.82 (0.11), residues: 2116 sheet: -3.03 (0.22), residues: 348 loop : -1.00 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 270 TYR 0.021 0.002 TYR A 451 PHE 0.038 0.002 PHE A2421 TRP 0.035 0.002 TRP C 27 HIS 0.008 0.001 HIS E1312 Details of bonding type rmsd covalent geometry : bond 0.00455 (29761) covalent geometry : angle 0.71849 (40390) hydrogen bonds : bond 0.05386 ( 1642) hydrogen bonds : angle 4.89206 ( 4818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LYS cc_start: 0.3015 (OUTLIER) cc_final: 0.2659 (tptp) REVERT: A 548 MET cc_start: 0.4098 (mtt) cc_final: 0.3533 (mmt) REVERT: A 772 MET cc_start: 0.7328 (tpt) cc_final: 0.6387 (tpp) REVERT: A 825 MET cc_start: 0.7707 (tpt) cc_final: 0.7287 (tpt) REVERT: A 1477 MET cc_start: 0.8670 (tpp) cc_final: 0.8195 (tpp) REVERT: A 1535 MET cc_start: 0.6482 (mtm) cc_final: 0.6106 (mtm) REVERT: A 1546 TYR cc_start: 0.8512 (m-80) cc_final: 0.8190 (m-80) REVERT: A 1809 GLN cc_start: 0.8505 (mt0) cc_final: 0.8134 (tm-30) REVERT: A 2051 LEU cc_start: 0.8605 (mt) cc_final: 0.8397 (pp) REVERT: A 2057 MET cc_start: 0.9208 (tmm) cc_final: 0.8799 (tmm) REVERT: A 2135 ASP cc_start: 0.7722 (t0) cc_final: 0.7485 (t0) REVERT: A 2161 GLN cc_start: 0.8157 (tm130) cc_final: 0.7759 (tm-30) REVERT: A 2199 MET cc_start: 0.8827 (mmt) cc_final: 0.8385 (mmt) REVERT: C 100 MET cc_start: 0.8738 (tmm) cc_final: 0.8461 (tmm) REVERT: C 273 MET cc_start: 0.7863 (ttm) cc_final: 0.7617 (ttm) REVERT: E 28 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7720 (mm) REVERT: E 31 MET cc_start: 0.8309 (ppp) cc_final: 0.7394 (mmm) REVERT: E 89 ASP cc_start: 0.8798 (t0) cc_final: 0.8448 (t0) REVERT: E 342 LEU cc_start: 0.7930 (tp) cc_final: 0.7604 (tp) REVERT: E 378 MET cc_start: 0.8959 (mmm) cc_final: 0.8378 (mmm) REVERT: E 431 GLU cc_start: 0.7222 (pt0) cc_final: 0.6963 (tt0) REVERT: E 585 TRP cc_start: 0.4652 (p90) cc_final: 0.3731 (p90) REVERT: E 1010 ILE cc_start: 0.6681 (mm) cc_final: 0.6351 (tp) REVERT: E 1012 ARG cc_start: 0.4774 (mmp80) cc_final: 0.4229 (mmp80) REVERT: E 1037 CYS cc_start: 0.5498 (m) cc_final: 0.5098 (m) REVERT: E 1073 MET cc_start: 0.7094 (mtp) cc_final: 0.6800 (mtm) REVERT: E 1156 MET cc_start: 0.6884 (mmm) cc_final: 0.6682 (mmt) REVERT: E 1172 LEU cc_start: 0.8529 (tt) cc_final: 0.8250 (tt) REVERT: E 1224 ASP cc_start: 0.7760 (m-30) cc_final: 0.7085 (p0) REVERT: E 1309 PHE cc_start: 0.6199 (m-80) cc_final: 0.5744 (m-10) REVERT: I 329 LYS cc_start: 0.7151 (ttpt) cc_final: 0.6942 (ttpp) REVERT: I 356 ASP cc_start: 0.8544 (p0) cc_final: 0.8338 (p0) REVERT: I 370 GLN cc_start: 0.8170 (mt0) cc_final: 0.7952 (mt0) outliers start: 85 outliers final: 46 residues processed: 417 average time/residue: 0.1838 time to fit residues: 124.4931 Evaluate side-chains 328 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain E residue 1325 ILE Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 281 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 19 optimal weight: 20.0000 chunk 242 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 258 optimal weight: 0.2980 chunk 240 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 311 HIS E 281 GLN ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 GLN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1210 HIS ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 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 = 0.4240 r_free = 0.4240 target = 0.109890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.089923 restraints weight = 124902.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.091846 restraints weight = 61922.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.092955 restraints weight = 38530.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.093669 restraints weight = 28193.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.094135 restraints weight = 22928.268| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29761 Z= 0.132 Angle : 0.616 10.712 40390 Z= 0.308 Chirality : 0.041 0.248 4594 Planarity : 0.005 0.060 5143 Dihedral : 4.816 51.906 4012 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 12.49 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3559 helix: 1.43 (0.11), residues: 2109 sheet: -2.68 (0.24), residues: 353 loop : -0.93 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1375 TYR 0.029 0.001 TYR A 451 PHE 0.027 0.001 PHE A2421 TRP 0.021 0.001 TRP A2101 HIS 0.006 0.001 HIS E1315 Details of bonding type rmsd covalent geometry : bond 0.00288 (29761) covalent geometry : angle 0.61645 (40390) hydrogen bonds : bond 0.04453 ( 1642) hydrogen bonds : angle 4.44967 ( 4818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 309 time to evaluate : 1.186 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: A 135 MET cc_start: 0.0426 (mtt) cc_final: 0.0166 (mpp) REVERT: A 439 LEU cc_start: -0.2544 (OUTLIER) cc_final: -0.3025 (mt) REVERT: A 548 MET cc_start: 0.4279 (mtt) cc_final: 0.3658 (mmt) REVERT: A 772 MET cc_start: 0.7618 (tpt) cc_final: 0.7283 (tpt) REVERT: A 825 MET cc_start: 0.8099 (tpt) cc_final: 0.7899 (tpt) REVERT: A 1031 MET cc_start: 0.7965 (tpt) cc_final: 0.7735 (tpp) REVERT: A 1507 GLU cc_start: 0.8691 (mp0) cc_final: 0.8447 (pm20) REVERT: A 1535 MET cc_start: 0.6632 (mtm) cc_final: 0.6296 (mtm) REVERT: A 1581 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: A 1673 LEU cc_start: 0.9149 (mt) cc_final: 0.8938 (mt) REVERT: A 2051 LEU cc_start: 0.8372 (mt) cc_final: 0.8167 (pp) REVERT: A 2080 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: A 2161 GLN cc_start: 0.8137 (tm130) cc_final: 0.7883 (tm-30) REVERT: C 100 MET cc_start: 0.8804 (tmm) cc_final: 0.8404 (tmm) REVERT: E 89 ASP cc_start: 0.8715 (t0) cc_final: 0.8338 (t0) REVERT: E 378 MET cc_start: 0.8941 (mmm) cc_final: 0.8543 (mmm) REVERT: E 424 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7533 (p) REVERT: E 976 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: E 1012 ARG cc_start: 0.4909 (mmp80) cc_final: 0.4519 (mmp80) REVERT: E 1127 MET cc_start: 0.6838 (tpt) cc_final: 0.6575 (tpp) REVERT: E 1224 ASP cc_start: 0.7685 (m-30) cc_final: 0.7183 (p0) REVERT: E 1309 PHE cc_start: 0.6228 (m-80) cc_final: 0.5827 (m-10) outliers start: 75 outliers final: 34 residues processed: 366 average time/residue: 0.1757 time to fit residues: 106.0328 Evaluate side-chains 312 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 222 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 362 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 285 optimal weight: 0.1980 chunk 326 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.109243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.089280 restraints weight = 123867.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.091264 restraints weight = 61785.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.092408 restraints weight = 38659.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.093205 restraints weight = 28491.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.093648 restraints weight = 23094.660| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29761 Z= 0.132 Angle : 0.604 11.470 40390 Z= 0.299 Chirality : 0.041 0.355 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.699 52.582 4008 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 2.75 % Allowed : 13.25 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3559 helix: 1.61 (0.11), residues: 2107 sheet: -2.42 (0.25), residues: 346 loop : -0.92 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 616 TYR 0.030 0.001 TYR A 451 PHE 0.022 0.001 PHE A2421 TRP 0.020 0.001 TRP A1916 HIS 0.011 0.001 HIS A2410 Details of bonding type rmsd covalent geometry : bond 0.00290 (29761) covalent geometry : angle 0.60382 (40390) hydrogen bonds : bond 0.04117 ( 1642) hydrogen bonds : angle 4.33413 ( 4818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 288 time to evaluate : 0.994 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: A 439 LEU cc_start: -0.2435 (OUTLIER) cc_final: -0.2871 (mt) REVERT: A 532 LYS cc_start: 0.2582 (OUTLIER) cc_final: 0.2355 (tptt) REVERT: A 548 MET cc_start: 0.3865 (mtt) cc_final: 0.3350 (mmt) REVERT: A 772 MET cc_start: 0.7588 (tpt) cc_final: 0.7214 (tpt) REVERT: A 825 MET cc_start: 0.8188 (tpt) cc_final: 0.6886 (tmm) REVERT: A 827 MET cc_start: 0.8480 (tmm) cc_final: 0.8014 (tmm) REVERT: A 1477 MET cc_start: 0.8806 (tpp) cc_final: 0.8284 (tpp) REVERT: A 1481 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7194 (mtt) REVERT: A 1507 GLU cc_start: 0.8759 (mp0) cc_final: 0.8492 (pm20) REVERT: A 1535 MET cc_start: 0.6831 (mtm) cc_final: 0.6487 (mtm) REVERT: A 1546 TYR cc_start: 0.8447 (m-80) cc_final: 0.8081 (m-80) REVERT: A 1581 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: A 1673 LEU cc_start: 0.9172 (mt) cc_final: 0.8921 (mt) REVERT: A 2051 LEU cc_start: 0.8462 (mt) cc_final: 0.8256 (pp) REVERT: A 2080 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: A 2199 MET cc_start: 0.8709 (mmt) cc_final: 0.8242 (mmt) REVERT: C 100 MET cc_start: 0.8818 (tmm) cc_final: 0.8325 (tmm) REVERT: E 31 MET cc_start: 0.8290 (ppp) cc_final: 0.7005 (mmm) REVERT: E 72 PRO cc_start: 0.6146 (Cg_exo) cc_final: 0.5813 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8789 (t0) cc_final: 0.8368 (t0) REVERT: E 237 MET cc_start: 0.7589 (pmm) cc_final: 0.7357 (pmm) REVERT: E 424 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7647 (p) REVERT: E 976 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: E 1012 ARG cc_start: 0.5062 (mmp80) cc_final: 0.4678 (mmp80) REVERT: E 1061 HIS cc_start: 0.7588 (t-90) cc_final: 0.7136 (t-90) REVERT: E 1127 MET cc_start: 0.6862 (tpt) cc_final: 0.6652 (mpp) REVERT: E 1224 ASP cc_start: 0.7670 (m-30) cc_final: 0.7205 (p0) REVERT: E 1309 PHE cc_start: 0.6178 (m-80) cc_final: 0.5748 (m-10) outliers start: 87 outliers final: 49 residues processed: 350 average time/residue: 0.1716 time to fit residues: 100.1352 Evaluate side-chains 317 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2041 GLU Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 249 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 275 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 334 optimal weight: 0.0000 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 HIS E 326 ASN ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.110259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.090196 restraints weight = 124763.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.092165 restraints weight = 62105.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093322 restraints weight = 38734.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.094045 restraints weight = 28469.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.094443 restraints weight = 23312.446| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29761 Z= 0.114 Angle : 0.593 10.730 40390 Z= 0.290 Chirality : 0.040 0.225 4594 Planarity : 0.004 0.065 5143 Dihedral : 4.556 54.029 4007 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 2.59 % Allowed : 13.69 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3559 helix: 1.81 (0.11), residues: 2091 sheet: -2.21 (0.26), residues: 334 loop : -0.89 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1811 TYR 0.022 0.001 TYR A 451 PHE 0.022 0.001 PHE A 610 TRP 0.015 0.001 TRP E1131 HIS 0.007 0.001 HIS A2410 Details of bonding type rmsd covalent geometry : bond 0.00246 (29761) covalent geometry : angle 0.59313 (40390) hydrogen bonds : bond 0.03716 ( 1642) hydrogen bonds : angle 4.16975 ( 4818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 283 time to evaluate : 1.157 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: A 532 LYS cc_start: 0.2576 (OUTLIER) cc_final: 0.2332 (tptt) REVERT: A 686 HIS cc_start: 0.7966 (m90) cc_final: 0.6837 (m-70) REVERT: A 827 MET cc_start: 0.8355 (tmm) cc_final: 0.7952 (tmm) REVERT: A 1313 MET cc_start: 0.8138 (mmp) cc_final: 0.7882 (mmp) REVERT: A 1477 MET cc_start: 0.8711 (tpp) cc_final: 0.8279 (tpp) REVERT: A 1507 GLU cc_start: 0.8687 (mp0) cc_final: 0.8480 (pm20) REVERT: A 1546 TYR cc_start: 0.8420 (m-80) cc_final: 0.8133 (m-80) REVERT: A 1581 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 1590 MET cc_start: 0.8059 (mmm) cc_final: 0.7803 (mtp) REVERT: A 2031 LEU cc_start: 0.8791 (mp) cc_final: 0.8357 (tt) REVERT: A 2051 LEU cc_start: 0.8447 (mt) cc_final: 0.8245 (pp) REVERT: A 2080 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: A 2199 MET cc_start: 0.8680 (mmt) cc_final: 0.8187 (mmt) REVERT: C 100 MET cc_start: 0.8782 (tmm) cc_final: 0.8273 (tmm) REVERT: E 43 LYS cc_start: 0.8216 (tmtt) cc_final: 0.7900 (tmtt) REVERT: E 72 PRO cc_start: 0.6308 (Cg_exo) cc_final: 0.5983 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8727 (t0) cc_final: 0.8116 (t0) REVERT: E 93 MET cc_start: 0.6254 (ppp) cc_final: 0.6013 (ppp) REVERT: E 602 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 976 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: E 1008 LYS cc_start: 0.7676 (mttt) cc_final: 0.7253 (tttt) REVERT: E 1012 ARG cc_start: 0.5136 (mmp80) cc_final: 0.4807 (mmp80) REVERT: E 1073 MET cc_start: 0.7747 (mtp) cc_final: 0.7166 (mtm) REVERT: E 1224 ASP cc_start: 0.7573 (m-30) cc_final: 0.7184 (p0) REVERT: E 1276 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5386 (t80) REVERT: I 328 ARG cc_start: 0.7791 (tmm160) cc_final: 0.7556 (tmm-80) outliers start: 82 outliers final: 43 residues processed: 348 average time/residue: 0.1662 time to fit residues: 96.7153 Evaluate side-chains 311 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1156 MET Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 52 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 247 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.109098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.089130 restraints weight = 124034.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.091082 restraints weight = 62147.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092180 restraints weight = 39036.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092918 restraints weight = 28827.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.093374 restraints weight = 23549.354| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29761 Z= 0.131 Angle : 0.599 11.705 40390 Z= 0.293 Chirality : 0.041 0.315 4594 Planarity : 0.004 0.066 5143 Dihedral : 4.526 55.154 4006 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.06 % Allowed : 14.93 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3559 helix: 1.87 (0.11), residues: 2099 sheet: -2.19 (0.26), residues: 334 loop : -0.82 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1811 TYR 0.019 0.001 TYR A 451 PHE 0.035 0.001 PHE A2421 TRP 0.018 0.001 TRP C 197 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00292 (29761) covalent geometry : angle 0.59890 (40390) hydrogen bonds : bond 0.03703 ( 1642) hydrogen bonds : angle 4.20462 ( 4818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 1.073 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: A 135 MET cc_start: 0.0587 (mtt) cc_final: 0.0331 (mpp) REVERT: A 548 MET cc_start: 0.3879 (mtt) cc_final: 0.3400 (mmt) REVERT: A 686 HIS cc_start: 0.8099 (m90) cc_final: 0.7025 (m-70) REVERT: A 827 MET cc_start: 0.8449 (tmm) cc_final: 0.8152 (tmm) REVERT: A 1031 MET cc_start: 0.8263 (tpt) cc_final: 0.8012 (tpp) REVERT: A 1507 GLU cc_start: 0.8722 (mp0) cc_final: 0.8518 (pm20) REVERT: A 1546 TYR cc_start: 0.8402 (m-80) cc_final: 0.8140 (m-80) REVERT: A 1581 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: A 2199 MET cc_start: 0.8736 (mmt) cc_final: 0.8246 (mmt) REVERT: A 2327 MET cc_start: 0.8259 (mmm) cc_final: 0.8023 (tpt) REVERT: C 100 MET cc_start: 0.8764 (tmm) cc_final: 0.8212 (tmm) REVERT: E 72 PRO cc_start: 0.6368 (Cg_exo) cc_final: 0.6068 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8710 (t0) cc_final: 0.8182 (t0) REVERT: E 93 MET cc_start: 0.6418 (ppp) cc_final: 0.6092 (ppp) REVERT: E 297 LYS cc_start: 0.8973 (pptt) cc_final: 0.8737 (ptmm) REVERT: E 602 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7705 (mm-30) REVERT: E 976 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: E 1008 LYS cc_start: 0.7692 (mttt) cc_final: 0.7358 (tttt) REVERT: E 1073 MET cc_start: 0.7686 (mtp) cc_final: 0.7196 (mtm) REVERT: E 1224 ASP cc_start: 0.7610 (m-30) cc_final: 0.7334 (p0) REVERT: E 1276 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.5495 (t80) REVERT: I 328 ARG cc_start: 0.7845 (tmm160) cc_final: 0.7616 (tmm-80) REVERT: I 370 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7845 (mp10) outliers start: 65 outliers final: 43 residues processed: 332 average time/residue: 0.1726 time to fit residues: 95.8404 Evaluate side-chains 307 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 201 optimal weight: 0.6980 chunk 347 optimal weight: 5.9990 chunk 2 optimal weight: 40.0000 chunk 162 optimal weight: 0.7980 chunk 159 optimal weight: 0.0870 chunk 269 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.109114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.089084 restraints weight = 124357.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.091006 restraints weight = 63012.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092160 restraints weight = 39762.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.092904 restraints weight = 29227.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093362 restraints weight = 23861.070| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29761 Z= 0.122 Angle : 0.604 12.532 40390 Z= 0.292 Chirality : 0.040 0.252 4594 Planarity : 0.004 0.065 5143 Dihedral : 4.504 57.030 4006 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.25 % Allowed : 15.31 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3559 helix: 1.94 (0.11), residues: 2092 sheet: -2.11 (0.26), residues: 334 loop : -0.78 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 488 TYR 0.020 0.001 TYR A 451 PHE 0.032 0.001 PHE A2421 TRP 0.021 0.001 TRP C 99 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00274 (29761) covalent geometry : angle 0.60393 (40390) hydrogen bonds : bond 0.03613 ( 1642) hydrogen bonds : angle 4.17054 ( 4818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 1.055 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: A 686 HIS cc_start: 0.8079 (m90) cc_final: 0.7010 (m-70) REVERT: A 1477 MET cc_start: 0.8684 (tpp) cc_final: 0.8410 (tpp) REVERT: A 1507 GLU cc_start: 0.8725 (mp0) cc_final: 0.8498 (pm20) REVERT: A 1581 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: A 2027 TRP cc_start: 0.7815 (m100) cc_final: 0.7556 (m100) REVERT: A 2080 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: A 2199 MET cc_start: 0.8691 (mmt) cc_final: 0.8203 (mmt) REVERT: A 2366 MET cc_start: 0.8071 (mtt) cc_final: 0.7685 (mtt) REVERT: C 100 MET cc_start: 0.8662 (tmm) cc_final: 0.8112 (tmm) REVERT: E 72 PRO cc_start: 0.6832 (Cg_exo) cc_final: 0.6555 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8675 (t0) cc_final: 0.8146 (t0) REVERT: E 93 MET cc_start: 0.6527 (ppp) cc_final: 0.6209 (ppp) REVERT: E 297 LYS cc_start: 0.8912 (pptt) cc_final: 0.8710 (ptmm) REVERT: E 976 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: E 1008 LYS cc_start: 0.7655 (mttt) cc_final: 0.7356 (tttt) REVERT: E 1073 MET cc_start: 0.7619 (mtp) cc_final: 0.7107 (mtm) REVERT: E 1156 MET cc_start: 0.6441 (mmm) cc_final: 0.5958 (mmm) REVERT: E 1224 ASP cc_start: 0.7568 (m-30) cc_final: 0.7313 (p0) REVERT: I 328 ARG cc_start: 0.7874 (tmm160) cc_final: 0.7645 (tmm-80) outliers start: 71 outliers final: 49 residues processed: 325 average time/residue: 0.1678 time to fit residues: 92.2486 Evaluate side-chains 309 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 405 GLU Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 8 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 341 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 221 optimal weight: 0.0770 chunk 202 optimal weight: 0.8980 chunk 335 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 295 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.109011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089080 restraints weight = 124353.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.091128 restraints weight = 62490.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092235 restraints weight = 38725.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.092927 restraints weight = 28571.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.093370 restraints weight = 23514.760| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29761 Z= 0.121 Angle : 0.608 12.597 40390 Z= 0.295 Chirality : 0.040 0.238 4594 Planarity : 0.004 0.065 5143 Dihedral : 4.487 58.572 4006 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 1.90 % Allowed : 15.56 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3559 helix: 1.96 (0.11), residues: 2089 sheet: -1.95 (0.26), residues: 332 loop : -0.79 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 488 TYR 0.018 0.001 TYR A 451 PHE 0.031 0.001 PHE A2421 TRP 0.021 0.001 TRP C 99 HIS 0.009 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00272 (29761) covalent geometry : angle 0.60805 (40390) hydrogen bonds : bond 0.03586 ( 1642) hydrogen bonds : angle 4.14750 ( 4818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 1.202 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: A 548 MET cc_start: 0.4242 (mtt) cc_final: 0.3742 (mmt) REVERT: A 686 HIS cc_start: 0.8110 (m90) cc_final: 0.7037 (m-70) REVERT: A 1467 MET cc_start: 0.8352 (mmt) cc_final: 0.8126 (mmt) REVERT: A 1546 TYR cc_start: 0.8440 (m-80) cc_final: 0.8111 (m-80) REVERT: A 1581 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: A 2031 LEU cc_start: 0.8566 (mp) cc_final: 0.8224 (tt) REVERT: A 2057 MET cc_start: 0.9363 (tmm) cc_final: 0.9069 (tmm) REVERT: A 2080 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: A 2199 MET cc_start: 0.8712 (mmt) cc_final: 0.8225 (mmt) REVERT: A 2366 MET cc_start: 0.8089 (mtt) cc_final: 0.7700 (mtt) REVERT: C 100 MET cc_start: 0.8591 (tmm) cc_final: 0.8019 (tmm) REVERT: C 255 MET cc_start: 0.7712 (tpp) cc_final: 0.7507 (tpp) REVERT: E 43 LYS cc_start: 0.8304 (tmtt) cc_final: 0.8091 (tmtt) REVERT: E 72 PRO cc_start: 0.6849 (Cg_exo) cc_final: 0.6578 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8685 (t0) cc_final: 0.8151 (t0) REVERT: E 93 MET cc_start: 0.6547 (ppp) cc_final: 0.6294 (ppp) REVERT: E 976 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: E 1008 LYS cc_start: 0.7661 (mttt) cc_final: 0.7298 (tttt) REVERT: E 1073 MET cc_start: 0.7620 (mtp) cc_final: 0.7108 (mtm) REVERT: E 1127 MET cc_start: 0.7433 (mmm) cc_final: 0.7142 (mmt) REVERT: E 1139 MET cc_start: 0.6477 (pmm) cc_final: 0.5975 (pmm) REVERT: E 1156 MET cc_start: 0.6963 (mmm) cc_final: 0.6531 (mmm) REVERT: E 1224 ASP cc_start: 0.7560 (m-30) cc_final: 0.7317 (p0) REVERT: E 1243 MET cc_start: 0.3202 (ppp) cc_final: 0.2936 (ppp) REVERT: E 1276 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.5220 (t80) REVERT: I 328 ARG cc_start: 0.7876 (tmm160) cc_final: 0.7657 (tmm-80) REVERT: I 370 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8021 (pm20) outliers start: 60 outliers final: 48 residues processed: 314 average time/residue: 0.1658 time to fit residues: 87.9993 Evaluate side-chains 310 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 338 optimal weight: 8.9990 chunk 219 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 332 optimal weight: 0.7980 chunk 265 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.108761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.088819 restraints weight = 124358.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.090729 restraints weight = 63587.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.091929 restraints weight = 39866.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.092712 restraints weight = 29112.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093135 restraints weight = 23853.098| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29761 Z= 0.129 Angle : 0.623 12.652 40390 Z= 0.302 Chirality : 0.041 0.293 4594 Planarity : 0.004 0.065 5143 Dihedral : 4.494 59.830 4006 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 15.97 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.14), residues: 3559 helix: 1.93 (0.11), residues: 2094 sheet: -1.88 (0.26), residues: 329 loop : -0.82 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1811 TYR 0.019 0.001 TYR A2125 PHE 0.030 0.001 PHE A2421 TRP 0.020 0.001 TRP C 99 HIS 0.006 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00292 (29761) covalent geometry : angle 0.62252 (40390) hydrogen bonds : bond 0.03648 ( 1642) hydrogen bonds : angle 4.15727 ( 4818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 1.048 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: A 548 MET cc_start: 0.4041 (mtt) cc_final: 0.3572 (mmt) REVERT: A 686 HIS cc_start: 0.8132 (m90) cc_final: 0.7092 (m-70) REVERT: A 752 GLN cc_start: 0.8540 (mt0) cc_final: 0.8153 (tm-30) REVERT: A 1467 MET cc_start: 0.8346 (mmt) cc_final: 0.8143 (mmt) REVERT: A 1477 MET cc_start: 0.8554 (tpp) cc_final: 0.7865 (tpp) REVERT: A 1546 TYR cc_start: 0.8474 (m-80) cc_final: 0.8107 (m-80) REVERT: A 1581 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: A 2031 LEU cc_start: 0.8559 (mp) cc_final: 0.8221 (tt) REVERT: A 2080 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: A 2199 MET cc_start: 0.8728 (mmt) cc_final: 0.8227 (mmt) REVERT: A 2366 MET cc_start: 0.8165 (mtt) cc_final: 0.7837 (mtt) REVERT: C 84 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6788 (m) REVERT: C 100 MET cc_start: 0.8536 (tmm) cc_final: 0.7938 (tmm) REVERT: C 255 MET cc_start: 0.7825 (tpp) cc_final: 0.7547 (tpp) REVERT: E 31 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.7400 (mmp) REVERT: E 72 PRO cc_start: 0.6884 (Cg_exo) cc_final: 0.6616 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8685 (t0) cc_final: 0.8151 (t0) REVERT: E 93 MET cc_start: 0.6496 (ppp) cc_final: 0.6266 (ppp) REVERT: E 976 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: E 1008 LYS cc_start: 0.7581 (mttt) cc_final: 0.7191 (tttt) REVERT: E 1073 MET cc_start: 0.7607 (mtp) cc_final: 0.7091 (mtm) REVERT: E 1127 MET cc_start: 0.7602 (mmm) cc_final: 0.7293 (mmt) REVERT: E 1156 MET cc_start: 0.7182 (mmm) cc_final: 0.6731 (mmm) REVERT: E 1243 MET cc_start: 0.3143 (ppp) cc_final: 0.2889 (ppp) REVERT: I 328 ARG cc_start: 0.7901 (tmm160) cc_final: 0.7683 (tmm-80) REVERT: I 370 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (pm20) outliers start: 70 outliers final: 50 residues processed: 317 average time/residue: 0.1662 time to fit residues: 89.7232 Evaluate side-chains 311 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 405 GLU Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 258 optimal weight: 0.5980 chunk 271 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 306 optimal weight: 0.1980 chunk 361 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 326 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.109338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.090612 restraints weight = 123039.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.093652 restraints weight = 68989.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093617 restraints weight = 37719.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.094190 restraints weight = 30340.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.094222 restraints weight = 28655.379| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29761 Z= 0.121 Angle : 0.630 12.979 40390 Z= 0.303 Chirality : 0.041 0.229 4594 Planarity : 0.004 0.067 5143 Dihedral : 4.318 52.829 4002 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 16.29 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 3559 helix: 1.93 (0.11), residues: 2099 sheet: -1.75 (0.26), residues: 328 loop : -0.80 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1811 TYR 0.024 0.001 TYR A2125 PHE 0.030 0.001 PHE A2421 TRP 0.017 0.001 TRP C 99 HIS 0.011 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00271 (29761) covalent geometry : angle 0.63032 (40390) hydrogen bonds : bond 0.03552 ( 1642) hydrogen bonds : angle 4.11919 ( 4818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 0.724 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: A 548 MET cc_start: 0.3740 (mtt) cc_final: 0.3216 (mmt) REVERT: A 686 HIS cc_start: 0.8098 (m90) cc_final: 0.7041 (m-70) REVERT: A 752 GLN cc_start: 0.8583 (mt0) cc_final: 0.8191 (tm-30) REVERT: A 772 MET cc_start: 0.7681 (mmm) cc_final: 0.7235 (tpt) REVERT: A 1477 MET cc_start: 0.8480 (tpp) cc_final: 0.7647 (tpp) REVERT: A 1481 MET cc_start: 0.7713 (mtt) cc_final: 0.7382 (mtm) REVERT: A 1546 TYR cc_start: 0.8349 (m-80) cc_final: 0.8013 (m-80) REVERT: A 2031 LEU cc_start: 0.8644 (mp) cc_final: 0.8281 (tt) REVERT: A 2080 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: A 2199 MET cc_start: 0.8644 (mmt) cc_final: 0.8212 (mmt) REVERT: A 2366 MET cc_start: 0.8091 (mtt) cc_final: 0.7703 (mtt) REVERT: C 84 VAL cc_start: 0.7268 (OUTLIER) cc_final: 0.6880 (m) REVERT: C 100 MET cc_start: 0.8548 (tmm) cc_final: 0.8038 (tmm) REVERT: C 255 MET cc_start: 0.7784 (tpp) cc_final: 0.7464 (tpp) REVERT: C 273 MET cc_start: 0.7319 (ptm) cc_final: 0.6696 (ptm) REVERT: E 31 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7461 (mmt) REVERT: E 72 PRO cc_start: 0.6909 (Cg_exo) cc_final: 0.6630 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8739 (t0) cc_final: 0.8183 (t0) REVERT: E 976 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: E 1008 LYS cc_start: 0.7559 (mttt) cc_final: 0.7143 (tmtt) REVERT: E 1073 MET cc_start: 0.7613 (mtp) cc_final: 0.7077 (mtm) REVERT: E 1127 MET cc_start: 0.7603 (mmm) cc_final: 0.7205 (mmt) REVERT: E 1139 MET cc_start: 0.6611 (pmm) cc_final: 0.6165 (pmm) REVERT: E 1156 MET cc_start: 0.7117 (mmm) cc_final: 0.6662 (mmm) REVERT: E 1243 MET cc_start: 0.3041 (ppp) cc_final: 0.2808 (ppp) REVERT: I 328 ARG cc_start: 0.8019 (tmm160) cc_final: 0.7743 (tmm-80) REVERT: I 370 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7978 (pm20) outliers start: 60 outliers final: 46 residues processed: 311 average time/residue: 0.1697 time to fit residues: 89.0876 Evaluate side-chains 306 residues out of total 3164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 976 GLU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 31 optimal weight: 0.5980 chunk 339 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 354 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.109323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.090557 restraints weight = 124374.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.093368 restraints weight = 69006.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093553 restraints weight = 38829.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.095048 restraints weight = 30429.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.094653 restraints weight = 27441.544| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29761 Z= 0.122 Angle : 0.638 12.904 40390 Z= 0.307 Chirality : 0.041 0.216 4594 Planarity : 0.004 0.067 5143 Dihedral : 4.305 52.465 4002 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 1.71 % Allowed : 16.64 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.14), residues: 3559 helix: 1.94 (0.11), residues: 2102 sheet: -1.71 (0.26), residues: 331 loop : -0.81 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 98 TYR 0.018 0.001 TYR A 451 PHE 0.030 0.001 PHE A2421 TRP 0.023 0.001 TRP A2027 HIS 0.007 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00276 (29761) covalent geometry : angle 0.63790 (40390) hydrogen bonds : bond 0.03533 ( 1642) hydrogen bonds : angle 4.12728 ( 4818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6099.47 seconds wall clock time: 105 minutes 33.69 seconds (6333.69 seconds total)