Starting phenix.real_space_refine on Fri Nov 21 01:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctk_45909/11_2025/9ctk_45909_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctk_45909/11_2025/9ctk_45909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctk_45909/11_2025/9ctk_45909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctk_45909/11_2025/9ctk_45909.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctk_45909/11_2025/9ctk_45909_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctk_45909/11_2025/9ctk_45909_trim.cif" } resolution = 2.92 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= 0.002 sd= 0.061 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 110 5.16 5 C 13104 2.51 5 N 3514 2.21 5 O 4078 1.98 5 H 20442 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41254 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 20468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1301, 20405 Classifications: {'peptide': 1301} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1237} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1301, 20405 Classifications: {'peptide': 1301} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1237} Chain breaks: 2 bond proxies already assigned to first conformer: 20566 Chain: "B" Number of atoms: 20468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1301, 20405 Classifications: {'peptide': 1301} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1237} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1301, 20405 Classifications: {'peptide': 1301} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1237} Chain breaks: 2 bond proxies already assigned to first conformer: 20566 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 14.13, per 1000 atoms: 0.34 Number of scatterers: 41254 At special positions: 0 Unit cell: (206.7, 103.88, 93.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 6 15.00 O 4078 8.00 N 3514 7.00 C 13104 6.00 H 20442 1.00 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: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 22 sheets defined 41.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.722A pdb=" N LEU A 900 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 915 through 929 Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 994 through 998 Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1014 through 1023 removed outlier: 3.521A pdb=" N GLU A1020 " --> pdb=" O GLU A1016 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A1021 " --> pdb=" O ILE A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1033 removed outlier: 3.627A pdb=" N GLN A1033 " --> pdb=" O ALA A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1030 through 1033' Processing helix chain 'A' and resid 1052 through 1067 removed outlier: 3.675A pdb=" N MET A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1187 Processing helix chain 'A' and resid 1194 through 1208 Processing helix chain 'A' and resid 1218 through 1231 Processing helix chain 'A' and resid 1240 through 1252 removed outlier: 3.581A pdb=" N GLU A1244 " --> pdb=" O HIS A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1269 through 1275 removed outlier: 4.204A pdb=" N LEU A1273 " --> pdb=" O VAL A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 Processing helix chain 'A' and resid 1284 through 1299 removed outlier: 3.576A pdb=" N ASN A1298 " --> pdb=" O THR A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1324 Proline residue: A1322 - end of helix Processing helix chain 'A' and resid 1325 through 1328 removed outlier: 3.572A pdb=" N PHE A1328 " --> pdb=" O LEU A1325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1325 through 1328' Processing helix chain 'A' and resid 1344 through 1349 removed outlier: 4.096A pdb=" N GLU A1348 " --> pdb=" O ASP A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1369 Processing helix chain 'A' and resid 1386 through 1395 Processing helix chain 'A' and resid 1416 through 1423 removed outlier: 3.625A pdb=" N ILE A1422 " --> pdb=" O PRO A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1455 removed outlier: 3.726A pdb=" N HIS A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1506 Processing helix chain 'A' and resid 1526 through 1539 removed outlier: 3.940A pdb=" N GLU A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.749A pdb=" N LYS A1573 " --> pdb=" O GLU A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1600 Processing helix chain 'A' and resid 1616 through 1618 No H-bonds generated for 'chain 'A' and resid 1616 through 1618' Processing helix chain 'A' and resid 1626 through 1630 Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.672A pdb=" N LYS A1639 " --> pdb=" O LEU A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1665 removed outlier: 3.695A pdb=" N ILE A1661 " --> pdb=" O ASN A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1673 Processing helix chain 'A' and resid 1674 through 1678 Processing helix chain 'A' and resid 1726 through 1731 Processing helix chain 'A' and resid 1732 through 1745 removed outlier: 4.333A pdb=" N ALA A1736 " --> pdb=" O THR A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1763 through 1776 Processing helix chain 'A' and resid 1786 through 1797 Processing helix chain 'A' and resid 1801 through 1803 No H-bonds generated for 'chain 'A' and resid 1801 through 1803' Processing helix chain 'A' and resid 1812 through 1821 removed outlier: 3.691A pdb=" N TYR A1816 " --> pdb=" O SER A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1843 Processing helix chain 'A' and resid 1859 through 1868 Processing helix chain 'A' and resid 1876 through 1885 removed outlier: 3.560A pdb=" N GLU A1883 " --> pdb=" O ASP A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1902 Processing helix chain 'A' and resid 1917 through 1928 Processing helix chain 'A' and resid 1975 through 1989 Processing helix chain 'A' and resid 2003 through 2017 Processing helix chain 'A' and resid 2029 through 2044 Processing helix chain 'A' and resid 2060 through 2064 removed outlier: 3.588A pdb=" N MET A2064 " --> pdb=" O PHE A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2070 Processing helix chain 'A' and resid 2073 through 2078 Processing helix chain 'A' and resid 2081 through 2088 removed outlier: 3.619A pdb=" N LYS A2086 " --> pdb=" O LEU A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2091 through 2096 removed outlier: 3.512A pdb=" N THR A2095 " --> pdb=" O PRO A2091 " (cutoff:3.500A) Processing helix chain 'A' and resid 2106 through 2108 No H-bonds generated for 'chain 'A' and resid 2106 through 2108' Processing helix chain 'A' and resid 2114 through 2134 Processing helix chain 'A' and resid 2170 through 2183 removed outlier: 3.651A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A2180 " --> pdb=" O SER A2176 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 removed outlier: 3.723A pdb=" N LEU B 900 " --> pdb=" O GLU B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 929 Processing helix chain 'B' and resid 931 through 935 Processing helix chain 'B' and resid 994 through 998 Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1014 through 1023 removed outlier: 3.520A pdb=" N GLU B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B1021 " --> pdb=" O ILE B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1033 removed outlier: 3.635A pdb=" N GLN B1033 " --> pdb=" O ALA B1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1030 through 1033' Processing helix chain 'B' and resid 1052 through 1067 removed outlier: 3.694A pdb=" N MET B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1089 Processing helix chain 'B' and resid 1162 through 1187 Processing helix chain 'B' and resid 1194 through 1208 Processing helix chain 'B' and resid 1218 through 1231 Processing helix chain 'B' and resid 1240 through 1252 removed outlier: 3.598A pdb=" N GLU B1244 " --> pdb=" O HIS B1240 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1269 through 1275 removed outlier: 4.206A pdb=" N LEU B1273 " --> pdb=" O VAL B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1281 Processing helix chain 'B' and resid 1284 through 1299 removed outlier: 3.605A pdb=" N ASN B1298 " --> pdb=" O THR B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1324 Proline residue: B1322 - end of helix Processing helix chain 'B' and resid 1325 through 1328 removed outlier: 3.571A pdb=" N PHE B1328 " --> pdb=" O LEU B1325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1325 through 1328' Processing helix chain 'B' and resid 1344 through 1349 removed outlier: 4.128A pdb=" N GLU B1348 " --> pdb=" O ASP B1345 " (cutoff:3.500A) Processing helix chain 'B' and resid 1365 through 1369 Processing helix chain 'B' and resid 1386 through 1395 Processing helix chain 'B' and resid 1416 through 1422 removed outlier: 3.719A pdb=" N ILE B1422 " --> pdb=" O PRO B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1455 removed outlier: 3.686A pdb=" N HIS B1455 " --> pdb=" O LEU B1451 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1506 Processing helix chain 'B' and resid 1526 through 1539 removed outlier: 3.503A pdb=" N ARG B1532 " --> pdb=" O LEU B1528 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B1537 " --> pdb=" O SER B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1574 removed outlier: 3.750A pdb=" N LYS B1573 " --> pdb=" O GLU B1569 " (cutoff:3.500A) Processing helix chain 'B' and resid 1596 through 1600 Processing helix chain 'B' and resid 1616 through 1618 No H-bonds generated for 'chain 'B' and resid 1616 through 1618' Processing helix chain 'B' and resid 1626 through 1630 Processing helix chain 'B' and resid 1636 through 1641 removed outlier: 3.665A pdb=" N LYS B1639 " --> pdb=" O LEU B1636 " (cutoff:3.500A) Processing helix chain 'B' and resid 1657 through 1665 removed outlier: 3.711A pdb=" N ILE B1661 " --> pdb=" O ASN B1657 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1673 Processing helix chain 'B' and resid 1674 through 1678 Processing helix chain 'B' and resid 1726 through 1731 Processing helix chain 'B' and resid 1732 through 1745 removed outlier: 4.335A pdb=" N ALA B1736 " --> pdb=" O THR B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1763 through 1776 Processing helix chain 'B' and resid 1786 through 1797 Processing helix chain 'B' and resid 1801 through 1803 No H-bonds generated for 'chain 'B' and resid 1801 through 1803' Processing helix chain 'B' and resid 1812 through 1821 removed outlier: 3.696A pdb=" N TYR B1816 " --> pdb=" O SER B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1843 Processing helix chain 'B' and resid 1859 through 1868 Processing helix chain 'B' and resid 1876 through 1885 removed outlier: 3.566A pdb=" N GLU B1883 " --> pdb=" O ASP B1879 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1902 Processing helix chain 'B' and resid 1917 through 1928 Processing helix chain 'B' and resid 1975 through 1989 Processing helix chain 'B' and resid 2003 through 2017 Processing helix chain 'B' and resid 2029 through 2044 Processing helix chain 'B' and resid 2060 through 2064 removed outlier: 3.600A pdb=" N MET B2064 " --> pdb=" O PHE B2061 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2070 Processing helix chain 'B' and resid 2073 through 2078 Processing helix chain 'B' and resid 2081 through 2088 removed outlier: 3.610A pdb=" N LYS B2086 " --> pdb=" O LEU B2082 " (cutoff:3.500A) Processing helix chain 'B' and resid 2091 through 2096 removed outlier: 3.513A pdb=" N THR B2095 " --> pdb=" O PRO B2091 " (cutoff:3.500A) Processing helix chain 'B' and resid 2106 through 2108 No H-bonds generated for 'chain 'B' and resid 2106 through 2108' Processing helix chain 'B' and resid 2114 through 2134 Processing helix chain 'B' and resid 2170 through 2183 removed outlier: 3.669A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B2180 " --> pdb=" O SER B2176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 886 through 891 removed outlier: 3.516A pdb=" N GLY A 954 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE A 969 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER A 980 " --> pdb=" O PHE A 969 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 971 " --> pdb=" O ILE A 978 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 982 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN A 941 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 984 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N MET A 939 " --> pdb=" O THR A 984 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER A 986 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 937 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A1080 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN A 943 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A1078 " --> pdb=" O GLN A 943 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A1073 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS A1125 " --> pdb=" O THR A1077 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A1079 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER A1123 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER A1081 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A1121 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A1083 " --> pdb=" O VAL A1119 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A1119 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A1101 " --> pdb=" O TRP A1049 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP A1044 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A1038 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP A1046 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 908 through 909 Processing sheet with id=AA3, first strand: chain 'A' and resid 1485 through 1488 removed outlier: 6.588A pdb=" N ILE A1485 " --> pdb=" O TRP A1517 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A1519 " --> pdb=" O ILE A1485 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A1487 " --> pdb=" O VAL A1519 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A1516 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A1546 " --> pdb=" O LEU A1516 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A1518 " --> pdb=" O ILE A1546 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE A1548 " --> pdb=" O LEU A1518 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A1520 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ASN A1578 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N CYS A1545 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A1580 " --> pdb=" O CYS A1545 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A1547 " --> pdb=" O PHE A1580 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N TYR A1577 " --> pdb=" O TYR A1588 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A1588 " --> pdb=" O TYR A1577 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A2188 " --> pdb=" O PHE A1143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1485 through 1488 removed outlier: 6.588A pdb=" N ILE A1485 " --> pdb=" O TRP A1517 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A1519 " --> pdb=" O ILE A1485 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A1487 " --> pdb=" O VAL A1519 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A1516 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A1546 " --> pdb=" O LEU A1516 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A1518 " --> pdb=" O ILE A1546 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE A1548 " --> pdb=" O LEU A1518 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A1520 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ASN A1578 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N CYS A1545 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A1580 " --> pdb=" O CYS A1545 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A1547 " --> pdb=" O PHE A1580 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N TYR A1577 " --> pdb=" O TYR A1588 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A1588 " --> pdb=" O TYR A1577 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A2188 " --> pdb=" O PHE A1143 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A2193 " --> pdb=" O TYR A2167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1351 through 1355 removed outlier: 9.149A pdb=" N LYS A1352 " --> pdb=" O TRP A1333 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR A1335 " --> pdb=" O LYS A1352 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET A1354 " --> pdb=" O TYR A1335 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A1337 " --> pdb=" O MET A1354 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N VAL A1303 " --> pdb=" O CYS A1372 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU A1374 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU A1305 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A1376 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A1307 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP A1373 " --> pdb=" O PHE A1403 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU A1405 " --> pdb=" O ASP A1373 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A1375 " --> pdb=" O LEU A1405 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A1407 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A1475 " --> pdb=" O GLN A1459 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLN A1459 " --> pdb=" O ARG A1475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1602 through 1604 Processing sheet with id=AA7, first strand: chain 'A' and resid 1607 through 1611 Processing sheet with id=AA8, first strand: chain 'A' and resid 1710 through 1714 removed outlier: 6.681A pdb=" N SER A1689 " --> pdb=" O TYR A1652 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA A1654 " --> pdb=" O GLU A1687 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLU A1687 " --> pdb=" O ALA A1654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1710 through 1714 removed outlier: 4.347A pdb=" N ILE A1934 " --> pdb=" O LEU A1656 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1805 through 1807 removed outlier: 6.182A pdb=" N VAL A1756 " --> pdb=" O PHE A1781 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU A1783 " --> pdb=" O VAL A1756 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A1758 " --> pdb=" O LEU A1783 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A1755 " --> pdb=" O VAL A1826 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP A1827 " --> pdb=" O LYS A1850 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A1852 " --> pdb=" O ASP A1827 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A1829 " --> pdb=" O VAL A1852 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2019 through 2024 removed outlier: 5.718A pdb=" N SER A1967 " --> pdb=" O VAL A2046 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A2048 " --> pdb=" O SER A1967 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A2047 " --> pdb=" O HIS A2098 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N VAL A2100 " --> pdb=" O GLY A2047 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A2049 " --> pdb=" O VAL A2100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 886 through 891 removed outlier: 3.513A pdb=" N GLY B 954 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE B 969 " --> pdb=" O SER B 980 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 980 " --> pdb=" O PHE B 969 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 971 " --> pdb=" O ILE B 978 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 982 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASN B 941 " --> pdb=" O VAL B 982 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 984 " --> pdb=" O MET B 939 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET B 939 " --> pdb=" O THR B 984 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 986 " --> pdb=" O VAL B 937 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL B 937 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU B1080 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN B 943 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B1078 " --> pdb=" O GLN B 943 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN B1073 " --> pdb=" O ALA B1129 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS B1125 " --> pdb=" O THR B1077 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU B1079 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER B1123 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B1081 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE B1121 " --> pdb=" O SER B1081 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B1083 " --> pdb=" O VAL B1119 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B1119 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B1101 " --> pdb=" O TRP B1049 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP B1044 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B1038 " --> pdb=" O ASP B1044 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B1046 " --> pdb=" O GLN B1036 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 908 through 909 Processing sheet with id=AB5, first strand: chain 'B' and resid 1485 through 1488 removed outlier: 6.476A pdb=" N ILE B1485 " --> pdb=" O TRP B1517 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1519 " --> pdb=" O ILE B1485 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B1487 " --> pdb=" O VAL B1519 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ASN B1578 " --> pdb=" O LEU B1543 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B1545 " --> pdb=" O ASN B1578 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE B1580 " --> pdb=" O CYS B1545 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN B1547 " --> pdb=" O PHE B1580 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N TYR B1577 " --> pdb=" O TYR B1588 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B1588 " --> pdb=" O TYR B1577 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL B2188 " --> pdb=" O PHE B1143 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B2140 " --> pdb=" O THR B2189 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER B2191 " --> pdb=" O THR B2140 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN B2142 " --> pdb=" O SER B2191 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL B2193 " --> pdb=" O GLN B2142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1485 through 1488 removed outlier: 6.476A pdb=" N ILE B1485 " --> pdb=" O TRP B1517 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1519 " --> pdb=" O ILE B1485 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B1487 " --> pdb=" O VAL B1519 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ASN B1578 " --> pdb=" O LEU B1543 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B1545 " --> pdb=" O ASN B1578 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE B1580 " --> pdb=" O CYS B1545 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN B1547 " --> pdb=" O PHE B1580 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N TYR B1577 " --> pdb=" O TYR B1588 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B1588 " --> pdb=" O TYR B1577 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL B2188 " --> pdb=" O PHE B1143 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B2193 " --> pdb=" O TYR B2167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1351 through 1355 removed outlier: 9.218A pdb=" N LYS B1352 " --> pdb=" O TRP B1333 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR B1335 " --> pdb=" O LYS B1352 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET B1354 " --> pdb=" O TYR B1335 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B1337 " --> pdb=" O MET B1354 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N VAL B1303 " --> pdb=" O CYS B1372 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU B1374 " --> pdb=" O VAL B1303 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU B1305 " --> pdb=" O LEU B1374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B1376 " --> pdb=" O GLU B1305 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B1307 " --> pdb=" O VAL B1376 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B1373 " --> pdb=" O PHE B1403 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU B1405 " --> pdb=" O ASP B1373 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B1375 " --> pdb=" O LEU B1405 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B1407 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG B1475 " --> pdb=" O GLN B1459 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN B1459 " --> pdb=" O ARG B1475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1602 through 1604 Processing sheet with id=AB9, first strand: chain 'B' and resid 1607 through 1611 Processing sheet with id=AC1, first strand: chain 'B' and resid 1710 through 1714 removed outlier: 6.685A pdb=" N SER B1689 " --> pdb=" O TYR B1652 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA B1654 " --> pdb=" O GLU B1687 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU B1687 " --> pdb=" O ALA B1654 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1710 through 1714 removed outlier: 4.343A pdb=" N ILE B1934 " --> pdb=" O LEU B1656 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1805 through 1807 removed outlier: 6.184A pdb=" N VAL B1756 " --> pdb=" O PHE B1781 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU B1783 " --> pdb=" O VAL B1756 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B1758 " --> pdb=" O LEU B1783 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1755 " --> pdb=" O VAL B1826 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP B1827 " --> pdb=" O LYS B1850 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL B1852 " --> pdb=" O ASP B1827 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B1829 " --> pdb=" O VAL B1852 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 2019 through 2024 removed outlier: 5.714A pdb=" N SER B1967 " --> pdb=" O VAL B2046 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B2048 " --> pdb=" O SER B1967 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY B2047 " --> pdb=" O HIS B2098 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B2100 " --> pdb=" O GLY B2047 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE B2049 " --> pdb=" O VAL B2100 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2495 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: 13.86 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20406 1.03 - 1.23: 157 1.23 - 1.42: 8635 1.42 - 1.62: 12112 1.62 - 1.81: 190 Bond restraints: 41500 Sorted by residual: bond pdb=" C TYR A2192 " pdb=" O TYR A2192 " ideal model delta sigma weight residual 1.234 1.130 0.104 1.22e-02 6.72e+03 7.31e+01 bond pdb=" C ILE A2190 " pdb=" O ILE A2190 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.10e-02 8.26e+03 3.82e+01 bond pdb=" O2B NAP A5001 " pdb=" P2B NAP A5001 " ideal model delta sigma weight residual 1.736 1.619 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C PHE B1813 " pdb=" O PHE B1813 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.29e-02 6.01e+03 2.59e+01 bond pdb=" C ASN B1831 " pdb=" O ASN B1831 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.22e-02 6.72e+03 2.55e+01 ... (remaining 41495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 73865 2.38 - 4.77: 1127 4.77 - 7.15: 100 7.15 - 9.53: 12 9.53 - 11.91: 6 Bond angle restraints: 75110 Sorted by residual: angle pdb=" CA PHE A1781 " pdb=" C PHE A1781 " pdb=" O PHE A1781 " ideal model delta sigma weight residual 120.36 112.34 8.02 1.08e+00 8.57e-01 5.51e+01 angle pdb=" CA PHE B1781 " pdb=" C PHE B1781 " pdb=" O PHE B1781 " ideal model delta sigma weight residual 120.36 112.39 7.97 1.08e+00 8.57e-01 5.45e+01 angle pdb=" CA TYR A2192 " pdb=" C TYR A2192 " pdb=" O TYR A2192 " ideal model delta sigma weight residual 120.99 113.45 7.54 1.12e+00 7.97e-01 4.53e+01 angle pdb=" CA GLY A2110 " pdb=" C GLY A2110 " pdb=" O GLY A2110 " ideal model delta sigma weight residual 122.29 117.10 5.19 8.10e-01 1.52e+00 4.10e+01 angle pdb=" CA ASN A1578 " pdb=" C ASN A1578 " pdb=" O ASN A1578 " ideal model delta sigma weight residual 120.30 114.01 6.29 1.07e+00 8.73e-01 3.46e+01 ... (remaining 75105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 17042 17.51 - 35.01: 1730 35.01 - 52.52: 612 52.52 - 70.02: 190 70.02 - 87.53: 26 Dihedral angle restraints: 19600 sinusoidal: 10734 harmonic: 8866 Sorted by residual: dihedral pdb=" CD ARG A1263 " pdb=" NE ARG A1263 " pdb=" CZ ARG A1263 " pdb=" NH1 ARG A1263 " ideal model delta sinusoidal sigma weight residual 0.00 -83.43 83.43 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CD ARG A1544 " pdb=" NE ARG A1544 " pdb=" CZ ARG A1544 " pdb=" NH1 ARG A1544 " ideal model delta sinusoidal sigma weight residual 0.00 68.75 -68.75 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CA VAL B1733 " pdb=" C VAL B1733 " pdb=" N PRO B1734 " pdb=" CA PRO B1734 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 19597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2561 0.050 - 0.101: 414 0.101 - 0.151: 167 0.151 - 0.202: 15 0.202 - 0.252: 5 Chirality restraints: 3162 Sorted by residual: chirality pdb=" CB VAL B1299 " pdb=" CA VAL B1299 " pdb=" CG1 VAL B1299 " pdb=" CG2 VAL B1299 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL A1299 " pdb=" CA VAL A1299 " pdb=" CG1 VAL A1299 " pdb=" CG2 VAL A1299 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ARG A1544 " pdb=" N ARG A1544 " pdb=" C ARG A1544 " pdb=" CB ARG A1544 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3159 not shown) Planarity restraints: 6148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1503 " 0.646 9.50e-02 1.11e+02 5.19e-01 5.05e+03 pdb=" NE ARG B1503 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG B1503 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG B1503 " -0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG B1503 " 0.038 2.00e-02 2.50e+03 pdb="HH11 ARG B1503 " 0.656 2.00e-02 2.50e+03 pdb="HH12 ARG B1503 " -0.831 2.00e-02 2.50e+03 pdb="HH21 ARG B1503 " -0.620 2.00e-02 2.50e+03 pdb="HH22 ARG B1503 " 0.699 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1515 " -0.483 9.50e-02 1.11e+02 4.07e-01 3.17e+03 pdb=" NE ARG A1515 " -0.403 2.00e-02 2.50e+03 pdb=" CZ ARG A1515 " -0.098 2.00e-02 2.50e+03 pdb=" NH1 ARG A1515 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG A1515 " 0.052 2.00e-02 2.50e+03 pdb="HH11 ARG A1515 " -0.501 2.00e-02 2.50e+03 pdb="HH12 ARG A1515 " 0.715 2.00e-02 2.50e+03 pdb="HH21 ARG A1515 " 0.483 2.00e-02 2.50e+03 pdb="HH22 ARG A1515 " -0.286 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1503 " -0.143 9.50e-02 1.11e+02 3.50e-01 2.70e+03 pdb=" NE ARG A1503 " 0.155 2.00e-02 2.50e+03 pdb=" CZ ARG A1503 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A1503 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1503 " -0.038 2.00e-02 2.50e+03 pdb="HH11 ARG A1503 " -0.736 2.00e-02 2.50e+03 pdb="HH12 ARG A1503 " 0.711 2.00e-02 2.50e+03 pdb="HH21 ARG A1503 " -0.063 2.00e-02 2.50e+03 pdb="HH22 ARG A1503 " -0.049 2.00e-02 2.50e+03 ... (remaining 6145 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 712 2.07 - 2.71: 68713 2.71 - 3.34: 123322 3.34 - 3.97: 164253 3.97 - 4.60: 259662 Nonbonded interactions: 616662 Sorted by model distance: nonbonded pdb=" HE1 PHE A1417 " pdb="HD11 LEU A1427 " model vdw 1.443 2.270 nonbonded pdb=" H ALA A1438 " pdb=" O PHE A1442 " model vdw 1.633 2.450 nonbonded pdb=" O CYS B1545 " pdb="HD21 ASN B1578 " model vdw 1.643 2.450 nonbonded pdb=" O LEU B1290 " pdb=" HG1 THR B1294 " model vdw 1.651 2.450 nonbonded pdb=" O GLU B1283 " pdb=" HZ3 LYS B1323 " model vdw 1.652 2.450 ... (remaining 616657 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 883 through 1597 or resid 1599 through 1817 or resid 1819 \ through 1841 or resid 1843 through 5001)) selection = (chain 'B' and (resid 883 through 1597 or resid 1599 through 1817 or resid 1819 \ through 1841 or resid 1843 through 5001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 51.220 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 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:9.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.005 0.117 21058 Z= 0.343 Angle : 0.859 8.677 28542 Z= 0.557 Chirality : 0.046 0.252 3162 Planarity : 0.013 0.493 3672 Dihedral : 17.482 87.530 7914 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 1.89 % Allowed : 23.83 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.23 (0.16), residues: 2596 helix: -0.74 (0.17), residues: 898 sheet: -0.75 (0.23), residues: 520 loop : -0.72 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1182 TYR 0.020 0.001 TYR A1018 PHE 0.020 0.001 PHE A1837 TRP 0.025 0.002 TRP B1496 HIS 0.007 0.001 HIS A1455 Details of bonding type rmsd covalent geometry : bond 0.00522 (21058) covalent geometry : angle 0.85888 (28542) hydrogen bonds : bond 0.23655 ( 853) hydrogen bonds : angle 9.24276 ( 2495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 1.074 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: A 1204 MET cc_start: 0.6897 (ptp) cc_final: 0.6521 (ptp) REVERT: A 1809 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 1847 LYS cc_start: 0.8450 (mttt) cc_final: 0.7885 (mppt) REVERT: A 1930 GLU cc_start: 0.7628 (tt0) cc_final: 0.6751 (pm20) REVERT: A 2064 MET cc_start: 0.8438 (ttp) cc_final: 0.8196 (ttp) REVERT: A 2182 MET cc_start: 0.9018 (mtp) cc_final: 0.8676 (mtp) REVERT: A 2199 MET cc_start: 0.6592 (mtm) cc_final: 0.5821 (ttp) REVERT: B 1175 PHE cc_start: 0.8065 (t80) cc_final: 0.7719 (t80) REVERT: B 1809 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 1847 LYS cc_start: 0.8443 (mttt) cc_final: 0.7849 (mppt) REVERT: B 1930 GLU cc_start: 0.7700 (tt0) cc_final: 0.6749 (pm20) REVERT: B 2182 MET cc_start: 0.8998 (mtp) cc_final: 0.8649 (mtp) REVERT: B 2199 MET cc_start: 0.6779 (mtm) cc_final: 0.6457 (mtt) outliers start: 40 outliers final: 22 residues processed: 297 average time/residue: 1.6948 time to fit residues: 564.6727 Evaluate side-chains 273 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1183 TRP Chi-restraints excluded: chain A residue 1296 SER Chi-restraints excluded: chain A residue 1418 PRO Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1475 ARG Chi-restraints excluded: chain A residue 1545 CYS Chi-restraints excluded: chain A residue 1574 ASP Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1933 LYS Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain B residue 1296 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1475 ARG Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1662 ILE Chi-restraints excluded: chain B residue 1933 LYS Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2068 GLN B1194 ASN ** B1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1578 ASN ** B2068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109950 restraints weight = 80661.804| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.92 r_work: 0.2853 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21058 Z= 0.137 Angle : 0.576 6.910 28542 Z= 0.302 Chirality : 0.042 0.174 3162 Planarity : 0.006 0.171 3672 Dihedral : 7.411 58.831 3006 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 2.47 % Allowed : 22.71 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 (0.16), residues: 2596 helix: 0.21 (0.17), residues: 892 sheet: -0.71 (0.22), residues: 530 loop : -0.59 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1544 TYR 0.020 0.001 TYR A1018 PHE 0.020 0.001 PHE B1417 TRP 0.022 0.001 TRP A1889 HIS 0.005 0.001 HIS A1267 Details of bonding type rmsd covalent geometry : bond 0.00297 (21058) covalent geometry : angle 0.57592 (28542) hydrogen bonds : bond 0.05055 ( 853) hydrogen bonds : angle 5.81284 ( 2495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1204 MET cc_start: 0.6769 (ptp) cc_final: 0.6323 (ptp) REVERT: A 1427 LEU cc_start: 0.8264 (tt) cc_final: 0.7975 (tt) REVERT: A 1809 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 1847 LYS cc_start: 0.8446 (mttt) cc_final: 0.7735 (mppt) REVERT: A 1930 GLU cc_start: 0.7571 (tt0) cc_final: 0.6735 (pm20) REVERT: A 2185 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7724 (t0) REVERT: A 2199 MET cc_start: 0.6684 (mtm) cc_final: 0.5799 (ttp) REVERT: B 1204 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6376 (ptp) REVERT: B 1302 GLN cc_start: 0.8257 (tp40) cc_final: 0.7359 (tp-100) REVERT: B 1370 GLU cc_start: 0.7557 (mp0) cc_final: 0.7165 (mp0) REVERT: B 1503 ARG cc_start: 0.6854 (mmt-90) cc_final: 0.6444 (mmp80) REVERT: B 1809 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 1847 LYS cc_start: 0.8418 (mttt) cc_final: 0.7772 (mppt) REVERT: B 1930 GLU cc_start: 0.7774 (tt0) cc_final: 0.6776 (pm20) REVERT: B 2031 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7664 (mttm) REVERT: B 2096 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8463 (tt) REVERT: B 2199 MET cc_start: 0.6518 (mtm) cc_final: 0.6133 (ttp) outliers start: 53 outliers final: 23 residues processed: 292 average time/residue: 1.5830 time to fit residues: 521.5911 Evaluate side-chains 267 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1296 SER Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1545 CYS Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1933 LYS Chi-restraints excluded: chain A residue 1939 ARG Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2185 ASP Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1204 MET Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1933 LYS Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2052 MET Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 23 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105998 restraints weight = 86066.769| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.93 r_work: 0.2812 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 21058 Z= 0.296 Angle : 0.633 6.995 28542 Z= 0.332 Chirality : 0.046 0.180 3162 Planarity : 0.006 0.066 3672 Dihedral : 7.333 57.766 2986 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.79 % Allowed : 22.84 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.73 (0.16), residues: 2596 helix: 0.21 (0.17), residues: 890 sheet: -0.75 (0.22), residues: 534 loop : -0.78 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1263 TYR 0.028 0.002 TYR B1018 PHE 0.017 0.002 PHE B1417 TRP 0.021 0.002 TRP A1889 HIS 0.007 0.001 HIS B 903 Details of bonding type rmsd covalent geometry : bond 0.00711 (21058) covalent geometry : angle 0.63346 (28542) hydrogen bonds : bond 0.05429 ( 853) hydrogen bonds : angle 5.65175 ( 2495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1302 GLN cc_start: 0.8374 (tp40) cc_final: 0.7575 (tp-100) REVERT: A 1396 LYS cc_start: 0.8417 (mttp) cc_final: 0.8006 (mttp) REVERT: A 1809 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 1847 LYS cc_start: 0.8446 (mttt) cc_final: 0.7773 (mppt) REVERT: A 1930 GLU cc_start: 0.7712 (tt0) cc_final: 0.6789 (pm20) REVERT: A 1939 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8454 (mtm-85) REVERT: A 2199 MET cc_start: 0.6716 (mtm) cc_final: 0.5807 (ttp) REVERT: B 1204 MET cc_start: 0.6797 (ptp) cc_final: 0.6347 (ptp) REVERT: B 1302 GLN cc_start: 0.8400 (tp40) cc_final: 0.7629 (tp-100) REVERT: B 1396 LYS cc_start: 0.8420 (mttp) cc_final: 0.8085 (mttp) REVERT: B 1503 ARG cc_start: 0.7153 (mmt-90) cc_final: 0.6679 (mmp80) REVERT: B 1809 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7542 (mm-30) REVERT: B 1847 LYS cc_start: 0.8424 (mttt) cc_final: 0.7756 (mppt) REVERT: B 1930 GLU cc_start: 0.7821 (tt0) cc_final: 0.6799 (pm20) REVERT: B 2196 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6526 (pp20) REVERT: B 2199 MET cc_start: 0.6582 (mtm) cc_final: 0.6172 (ttp) outliers start: 60 outliers final: 27 residues processed: 299 average time/residue: 1.5104 time to fit residues: 511.0646 Evaluate side-chains 283 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1545 CYS Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1939 ARG Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2008 ARG Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1545 CYS Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1716 SER Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2002 THR Chi-restraints excluded: chain B residue 2009 LYS Chi-restraints excluded: chain B residue 2043 MET Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2196 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 176 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 934 GLN A1657 ASN B 934 GLN B1578 ASN B1657 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109130 restraints weight = 91053.318| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.89 r_work: 0.2854 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21058 Z= 0.121 Angle : 0.543 5.966 28542 Z= 0.280 Chirality : 0.041 0.157 3162 Planarity : 0.005 0.054 3672 Dihedral : 6.842 59.053 2977 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 2.43 % Allowed : 22.48 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.49 (0.16), residues: 2596 helix: 0.55 (0.18), residues: 890 sheet: -0.83 (0.22), residues: 530 loop : -0.66 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2165 TYR 0.022 0.001 TYR A1018 PHE 0.012 0.001 PHE A1567 TRP 0.021 0.001 TRP A1889 HIS 0.006 0.001 HIS A1267 Details of bonding type rmsd covalent geometry : bond 0.00279 (21058) covalent geometry : angle 0.54251 (28542) hydrogen bonds : bond 0.04045 ( 853) hydrogen bonds : angle 5.16280 ( 2495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 934 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7661 (mp10) REVERT: A 1302 GLN cc_start: 0.8378 (tp40) cc_final: 0.7488 (tp-100) REVERT: A 1396 LYS cc_start: 0.8464 (mttp) cc_final: 0.8045 (mttp) REVERT: A 1809 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 1847 LYS cc_start: 0.8387 (mttt) cc_final: 0.7789 (mppt) REVERT: A 1930 GLU cc_start: 0.7701 (tt0) cc_final: 0.6851 (pm20) REVERT: A 2182 MET cc_start: 0.8949 (mtp) cc_final: 0.8705 (mtp) REVERT: A 2199 MET cc_start: 0.6705 (mtm) cc_final: 0.5813 (ttp) REVERT: B 934 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7644 (mp10) REVERT: B 1204 MET cc_start: 0.6976 (ptp) cc_final: 0.6564 (ptp) REVERT: B 1292 MET cc_start: 0.8921 (mmt) cc_final: 0.8717 (mmt) REVERT: B 1302 GLN cc_start: 0.8441 (tp40) cc_final: 0.7540 (tp-100) REVERT: B 1370 GLU cc_start: 0.7664 (mp0) cc_final: 0.7217 (mp0) REVERT: B 1396 LYS cc_start: 0.8458 (mttp) cc_final: 0.8060 (mttp) REVERT: B 1503 ARG cc_start: 0.7181 (mmt-90) cc_final: 0.6735 (mmp80) REVERT: B 1809 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 1847 LYS cc_start: 0.8421 (mttt) cc_final: 0.7821 (mppt) REVERT: B 1930 GLU cc_start: 0.7746 (tt0) cc_final: 0.6808 (pm20) REVERT: B 2068 GLN cc_start: 0.8266 (mt0) cc_final: 0.7922 (mt0) REVERT: B 2199 MET cc_start: 0.6623 (mtm) cc_final: 0.6243 (ttp) outliers start: 52 outliers final: 24 residues processed: 288 average time/residue: 1.5049 time to fit residues: 489.7270 Evaluate side-chains 271 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1545 CYS Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1902 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 228 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.092939 restraints weight = 83491.637| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.97 r_work: 0.2820 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21058 Z= 0.129 Angle : 0.532 6.145 28542 Z= 0.273 Chirality : 0.041 0.151 3162 Planarity : 0.005 0.055 3672 Dihedral : 6.597 59.859 2977 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 2.20 % Allowed : 22.71 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.33 (0.17), residues: 2596 helix: 0.75 (0.18), residues: 892 sheet: -0.83 (0.22), residues: 534 loop : -0.56 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1602 TYR 0.022 0.001 TYR B1018 PHE 0.013 0.001 PHE A2171 TRP 0.020 0.001 TRP A1889 HIS 0.006 0.001 HIS A1267 Details of bonding type rmsd covalent geometry : bond 0.00303 (21058) covalent geometry : angle 0.53178 (28542) hydrogen bonds : bond 0.03843 ( 853) hydrogen bonds : angle 4.95819 ( 2495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7600 (mp10) REVERT: A 1302 GLN cc_start: 0.8442 (tp40) cc_final: 0.7599 (tp-100) REVERT: A 1396 LYS cc_start: 0.8393 (mttp) cc_final: 0.8001 (mttp) REVERT: A 1809 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 1847 LYS cc_start: 0.8471 (mttt) cc_final: 0.7791 (mppt) REVERT: A 1930 GLU cc_start: 0.7698 (tt0) cc_final: 0.6787 (pm20) REVERT: A 2031 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7692 (mttm) REVERT: A 2068 GLN cc_start: 0.8257 (mt0) cc_final: 0.7952 (mt0) REVERT: A 2199 MET cc_start: 0.6729 (mtm) cc_final: 0.5818 (ttp) REVERT: B 934 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7585 (mp10) REVERT: B 1204 MET cc_start: 0.6894 (ptp) cc_final: 0.6473 (ptp) REVERT: B 1302 GLN cc_start: 0.8510 (tp40) cc_final: 0.7695 (tp-100) REVERT: B 1370 GLU cc_start: 0.7594 (mp0) cc_final: 0.7143 (mp0) REVERT: B 1396 LYS cc_start: 0.8432 (mttp) cc_final: 0.7996 (mttp) REVERT: B 1503 ARG cc_start: 0.6934 (mmt-90) cc_final: 0.6474 (mmp80) REVERT: B 1809 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 1847 LYS cc_start: 0.8481 (mttt) cc_final: 0.7815 (mppt) REVERT: B 1930 GLU cc_start: 0.7828 (tt0) cc_final: 0.6790 (pm20) REVERT: B 2068 GLN cc_start: 0.8212 (mt0) cc_final: 0.7902 (mt0) REVERT: B 2199 MET cc_start: 0.6630 (mtm) cc_final: 0.6194 (ttp) outliers start: 47 outliers final: 26 residues processed: 285 average time/residue: 1.5369 time to fit residues: 496.4779 Evaluate side-chains 270 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1716 SER Chi-restraints excluded: chain B residue 1902 SER Chi-restraints excluded: chain B residue 1939 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 128 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.092836 restraints weight = 90095.364| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.92 r_work: 0.2843 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21058 Z= 0.154 Angle : 0.538 6.051 28542 Z= 0.276 Chirality : 0.042 0.153 3162 Planarity : 0.005 0.053 3672 Dihedral : 6.517 59.108 2976 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.56 % Allowed : 22.21 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.30 (0.17), residues: 2596 helix: 0.76 (0.18), residues: 898 sheet: -0.80 (0.22), residues: 534 loop : -0.54 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1572 TYR 0.023 0.001 TYR B1018 PHE 0.013 0.001 PHE A2171 TRP 0.019 0.001 TRP A1889 HIS 0.006 0.001 HIS A1267 Details of bonding type rmsd covalent geometry : bond 0.00367 (21058) covalent geometry : angle 0.53801 (28542) hydrogen bonds : bond 0.03887 ( 853) hydrogen bonds : angle 4.89169 ( 2495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 908 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7136 (mtm110) REVERT: A 934 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7606 (mp10) REVERT: A 1204 MET cc_start: 0.7050 (ptp) cc_final: 0.6629 (ptp) REVERT: A 1302 GLN cc_start: 0.8517 (tp40) cc_final: 0.7674 (tp-100) REVERT: A 1370 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 1396 LYS cc_start: 0.8368 (mttp) cc_final: 0.7895 (mttp) REVERT: A 1809 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 1847 LYS cc_start: 0.8436 (mttt) cc_final: 0.7782 (mppt) REVERT: A 1930 GLU cc_start: 0.7640 (tt0) cc_final: 0.6776 (pm20) REVERT: A 2068 GLN cc_start: 0.8226 (mt0) cc_final: 0.7910 (mt0) REVERT: A 2199 MET cc_start: 0.6750 (mtm) cc_final: 0.5848 (ttp) REVERT: B 934 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7602 (mp10) REVERT: B 1302 GLN cc_start: 0.8576 (tp40) cc_final: 0.7756 (tp-100) REVERT: B 1370 GLU cc_start: 0.7632 (mp0) cc_final: 0.7152 (mp0) REVERT: B 1396 LYS cc_start: 0.8441 (mttp) cc_final: 0.8072 (mttp) REVERT: B 1503 ARG cc_start: 0.7125 (mmt-90) cc_final: 0.6665 (mmp80) REVERT: B 1809 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 1847 LYS cc_start: 0.8453 (mttt) cc_final: 0.7796 (mppt) REVERT: B 1930 GLU cc_start: 0.7737 (tt0) cc_final: 0.6769 (pm20) REVERT: B 2068 GLN cc_start: 0.8220 (mt0) cc_final: 0.7870 (mt0) REVERT: B 2199 MET cc_start: 0.6625 (mtm) cc_final: 0.6217 (ttp) outliers start: 55 outliers final: 33 residues processed: 293 average time/residue: 1.5075 time to fit residues: 502.0558 Evaluate side-chains 280 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1471 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1902 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1296 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1471 MET Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1716 SER Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1902 SER Chi-restraints excluded: chain B residue 1939 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 231 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.092689 restraints weight = 83863.868| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.97 r_work: 0.2819 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21058 Z= 0.134 Angle : 0.526 5.782 28542 Z= 0.269 Chirality : 0.041 0.149 3162 Planarity : 0.004 0.054 3672 Dihedral : 6.421 58.108 2976 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 2.07 % Allowed : 23.02 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.21 (0.17), residues: 2596 helix: 0.81 (0.18), residues: 906 sheet: -0.75 (0.22), residues: 542 loop : -0.47 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1572 TYR 0.023 0.001 TYR B1018 PHE 0.013 0.001 PHE A2171 TRP 0.019 0.001 TRP A1889 HIS 0.007 0.001 HIS B1455 Details of bonding type rmsd covalent geometry : bond 0.00316 (21058) covalent geometry : angle 0.52562 (28542) hydrogen bonds : bond 0.03701 ( 853) hydrogen bonds : angle 4.78507 ( 2495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 908 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7238 (mtm110) REVERT: A 934 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7774 (mp10) REVERT: A 1204 MET cc_start: 0.7078 (ptp) cc_final: 0.6668 (ptp) REVERT: A 1302 GLN cc_start: 0.8565 (tp40) cc_final: 0.7745 (tp-100) REVERT: A 1396 LYS cc_start: 0.8401 (mttp) cc_final: 0.8069 (mttp) REVERT: A 1809 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 1847 LYS cc_start: 0.8467 (mttt) cc_final: 0.7827 (mppt) REVERT: A 1930 GLU cc_start: 0.7684 (tt0) cc_final: 0.6802 (pm20) REVERT: A 2031 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7916 (mttm) REVERT: A 2068 GLN cc_start: 0.8255 (mt0) cc_final: 0.7931 (mt0) REVERT: A 2199 MET cc_start: 0.6799 (mtm) cc_final: 0.5896 (ttp) REVERT: B 908 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7237 (mtm110) REVERT: B 934 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7767 (mp10) REVERT: B 1302 GLN cc_start: 0.8652 (tp40) cc_final: 0.7817 (tp-100) REVERT: B 1370 GLU cc_start: 0.7600 (mp0) cc_final: 0.7141 (mp0) REVERT: B 1396 LYS cc_start: 0.8456 (mttp) cc_final: 0.8068 (mttp) REVERT: B 1503 ARG cc_start: 0.7022 (mmt-90) cc_final: 0.6576 (mmp80) REVERT: B 1809 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 1847 LYS cc_start: 0.8491 (mttt) cc_final: 0.7865 (mppt) REVERT: B 1930 GLU cc_start: 0.7821 (tt0) cc_final: 0.6803 (pm20) REVERT: B 2068 GLN cc_start: 0.8193 (mt0) cc_final: 0.7853 (mt0) REVERT: B 2199 MET cc_start: 0.6722 (mtm) cc_final: 0.6280 (ttp) outliers start: 44 outliers final: 33 residues processed: 288 average time/residue: 1.5440 time to fit residues: 503.8104 Evaluate side-chains 277 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1545 CYS Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1902 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1296 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1716 SER Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1902 SER Chi-restraints excluded: chain B residue 1939 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2002 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 222 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 257 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.092673 restraints weight = 94969.224| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.02 r_work: 0.2785 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21058 Z= 0.156 Angle : 0.538 5.895 28542 Z= 0.276 Chirality : 0.042 0.152 3162 Planarity : 0.005 0.071 3672 Dihedral : 6.450 57.494 2976 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.93 % Allowed : 23.11 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.23 (0.17), residues: 2596 helix: 0.80 (0.18), residues: 910 sheet: -0.78 (0.22), residues: 534 loop : -0.49 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2165 TYR 0.024 0.001 TYR B1018 PHE 0.013 0.001 PHE A2171 TRP 0.018 0.001 TRP B1889 HIS 0.004 0.001 HIS B1455 Details of bonding type rmsd covalent geometry : bond 0.00373 (21058) covalent geometry : angle 0.53842 (28542) hydrogen bonds : bond 0.03780 ( 853) hydrogen bonds : angle 4.78919 ( 2495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7294 (mt) REVERT: A 934 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7764 (mp10) REVERT: A 1302 GLN cc_start: 0.8591 (tp40) cc_final: 0.7768 (tp-100) REVERT: A 1370 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: A 1396 LYS cc_start: 0.8396 (mttp) cc_final: 0.7992 (mttp) REVERT: A 1809 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 1847 LYS cc_start: 0.8494 (mttt) cc_final: 0.7842 (mppt) REVERT: A 1930 GLU cc_start: 0.7714 (tt0) cc_final: 0.6793 (pm20) REVERT: A 2068 GLN cc_start: 0.8283 (mt0) cc_final: 0.7937 (mt0) REVERT: A 2199 MET cc_start: 0.6856 (mtm) cc_final: 0.5937 (ttp) REVERT: B 908 ARG cc_start: 0.7570 (mtm180) cc_final: 0.7217 (mtm110) REVERT: B 934 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7768 (mp10) REVERT: B 1204 MET cc_start: 0.7084 (ptp) cc_final: 0.6662 (ptp) REVERT: B 1302 GLN cc_start: 0.8621 (tp40) cc_final: 0.7793 (tp-100) REVERT: B 1370 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: B 1396 LYS cc_start: 0.8434 (mttp) cc_final: 0.7991 (mttp) REVERT: B 1503 ARG cc_start: 0.7027 (mmt-90) cc_final: 0.6580 (mmp80) REVERT: B 1617 MET cc_start: 0.8905 (mtm) cc_final: 0.8670 (mtm) REVERT: B 1809 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 1847 LYS cc_start: 0.8509 (mttt) cc_final: 0.7869 (mppt) REVERT: B 1930 GLU cc_start: 0.7844 (tt0) cc_final: 0.6782 (pm20) REVERT: B 2068 GLN cc_start: 0.8200 (mt0) cc_final: 0.7881 (mt0) REVERT: B 2199 MET cc_start: 0.6746 (mtm) cc_final: 0.6293 (ttp) outliers start: 41 outliers final: 31 residues processed: 283 average time/residue: 1.5374 time to fit residues: 491.4469 Evaluate side-chains 285 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1902 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1716 SER Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1902 SER Chi-restraints excluded: chain B residue 1939 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2002 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 256 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1240 HIS B1578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.091866 restraints weight = 85100.534| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.01 r_work: 0.2811 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21058 Z= 0.156 Angle : 0.538 5.875 28542 Z= 0.276 Chirality : 0.042 0.154 3162 Planarity : 0.005 0.060 3672 Dihedral : 6.340 56.856 2974 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.11 % Allowed : 22.98 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.21 (0.17), residues: 2596 helix: 0.84 (0.18), residues: 908 sheet: -0.78 (0.22), residues: 534 loop : -0.49 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2165 TYR 0.023 0.001 TYR B1018 PHE 0.012 0.001 PHE B2171 TRP 0.018 0.001 TRP B1889 HIS 0.006 0.001 HIS B1455 Details of bonding type rmsd covalent geometry : bond 0.00374 (21058) covalent geometry : angle 0.53789 (28542) hydrogen bonds : bond 0.03755 ( 853) hydrogen bonds : angle 4.76997 ( 2495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7283 (mt) REVERT: A 934 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7778 (mp10) REVERT: A 1175 PHE cc_start: 0.7958 (t80) cc_final: 0.7615 (t80) REVERT: A 1302 GLN cc_start: 0.8583 (tp40) cc_final: 0.7769 (tp-100) REVERT: A 1370 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 1396 LYS cc_start: 0.8358 (mttp) cc_final: 0.7897 (mttp) REVERT: A 1809 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 1847 LYS cc_start: 0.8464 (mttt) cc_final: 0.7836 (mppt) REVERT: A 1930 GLU cc_start: 0.7806 (tt0) cc_final: 0.6851 (pm20) REVERT: A 2031 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7788 (mttm) REVERT: A 2068 GLN cc_start: 0.8276 (mt0) cc_final: 0.7965 (mt0) REVERT: A 2199 MET cc_start: 0.6824 (mtm) cc_final: 0.5900 (ttp) REVERT: B 908 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7207 (mtm110) REVERT: B 934 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7774 (mp10) REVERT: B 1204 MET cc_start: 0.7015 (ptp) cc_final: 0.6550 (ptp) REVERT: B 1302 GLN cc_start: 0.8543 (tp40) cc_final: 0.7724 (tp-100) REVERT: B 1370 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: B 1396 LYS cc_start: 0.8416 (mttp) cc_final: 0.7956 (mttp) REVERT: B 1503 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6589 (mmp80) REVERT: B 1617 MET cc_start: 0.8914 (mtm) cc_final: 0.8686 (mtm) REVERT: B 1809 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 1847 LYS cc_start: 0.8491 (mttt) cc_final: 0.7864 (mppt) REVERT: B 1930 GLU cc_start: 0.7827 (tt0) cc_final: 0.6803 (pm20) REVERT: B 2068 GLN cc_start: 0.8196 (mt0) cc_final: 0.7865 (mt0) REVERT: B 2199 MET cc_start: 0.6734 (mtm) cc_final: 0.6293 (ttp) outliers start: 45 outliers final: 32 residues processed: 288 average time/residue: 1.5200 time to fit residues: 494.6177 Evaluate side-chains 282 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1902 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1296 SER Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1545 CYS Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1716 SER Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1902 SER Chi-restraints excluded: chain B residue 1939 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2002 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 248 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093151 restraints weight = 88190.906| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.05 r_work: 0.2829 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21058 Z= 0.112 Angle : 0.519 6.154 28542 Z= 0.264 Chirality : 0.041 0.145 3162 Planarity : 0.004 0.070 3672 Dihedral : 6.206 59.252 2974 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 1.89 % Allowed : 23.25 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.06 (0.17), residues: 2596 helix: 0.98 (0.18), residues: 908 sheet: -0.75 (0.22), residues: 542 loop : -0.39 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2165 TYR 0.021 0.001 TYR B1018 PHE 0.019 0.001 PHE A1417 TRP 0.019 0.001 TRP A1889 HIS 0.006 0.001 HIS B1455 Details of bonding type rmsd covalent geometry : bond 0.00263 (21058) covalent geometry : angle 0.51949 (28542) hydrogen bonds : bond 0.03449 ( 853) hydrogen bonds : angle 4.64431 ( 2495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7695 (mp10) REVERT: A 1175 PHE cc_start: 0.7884 (t80) cc_final: 0.7535 (t80) REVERT: A 1302 GLN cc_start: 0.8557 (tp40) cc_final: 0.7742 (tp-100) REVERT: A 1396 LYS cc_start: 0.8286 (mttp) cc_final: 0.7865 (mttp) REVERT: A 1809 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 1847 LYS cc_start: 0.8474 (mttt) cc_final: 0.7793 (mppt) REVERT: A 1930 GLU cc_start: 0.7824 (tt0) cc_final: 0.6850 (pm20) REVERT: A 1997 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8592 (t) REVERT: A 2031 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7669 (mttm) REVERT: A 2068 GLN cc_start: 0.8233 (mt0) cc_final: 0.7924 (mt0) REVERT: A 2199 MET cc_start: 0.6712 (mtm) cc_final: 0.5777 (ttp) REVERT: B 891 LEU cc_start: 0.7567 (mt) cc_final: 0.7366 (mp) REVERT: B 934 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7697 (mp10) REVERT: B 1204 MET cc_start: 0.6923 (ptp) cc_final: 0.6480 (ptp) REVERT: B 1302 GLN cc_start: 0.8531 (tp40) cc_final: 0.7702 (tp-100) REVERT: B 1370 GLU cc_start: 0.7516 (mp0) cc_final: 0.7042 (mp0) REVERT: B 1396 LYS cc_start: 0.8357 (mttp) cc_final: 0.7876 (mttp) REVERT: B 1503 ARG cc_start: 0.6889 (mmt-90) cc_final: 0.6435 (mmp80) REVERT: B 1617 MET cc_start: 0.8924 (mtm) cc_final: 0.8690 (mtm) REVERT: B 1809 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7501 (mm-30) REVERT: B 1847 LYS cc_start: 0.8498 (mttt) cc_final: 0.7824 (mppt) REVERT: B 1930 GLU cc_start: 0.7851 (tt0) cc_final: 0.6805 (pm20) REVERT: B 2031 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7807 (mttm) REVERT: B 2068 GLN cc_start: 0.8179 (mt0) cc_final: 0.7875 (mt0) REVERT: B 2199 MET cc_start: 0.6665 (mtm) cc_final: 0.6202 (ttp) outliers start: 40 outliers final: 29 residues processed: 283 average time/residue: 1.4825 time to fit residues: 475.0779 Evaluate side-chains 278 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1902 SER Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2002 THR Chi-restraints excluded: chain A residue 2096 LEU Chi-restraints excluded: chain A residue 2105 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1176 SER Chi-restraints excluded: chain B residue 1296 SER Chi-restraints excluded: chain B residue 1443 TYR Chi-restraints excluded: chain B residue 1474 LEU Chi-restraints excluded: chain B residue 1545 CYS Chi-restraints excluded: chain B residue 1602 ARG Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1902 SER Chi-restraints excluded: chain B residue 1939 ARG Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 1996 THR Chi-restraints excluded: chain B residue 2002 THR Chi-restraints excluded: chain B residue 2096 LEU Chi-restraints excluded: chain B residue 2105 LEU Chi-restraints excluded: chain B residue 2124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 196 optimal weight: 0.5980 chunk 134 optimal weight: 0.0070 chunk 82 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 136 optimal weight: 0.0370 chunk 141 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111110 restraints weight = 84399.841| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.84 r_work: 0.2898 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21058 Z= 0.095 Angle : 0.504 6.161 28542 Z= 0.255 Chirality : 0.041 0.153 3162 Planarity : 0.004 0.057 3672 Dihedral : 6.003 58.147 2974 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 1.57 % Allowed : 23.74 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.10 (0.17), residues: 2596 helix: 1.22 (0.18), residues: 906 sheet: -0.74 (0.22), residues: 542 loop : -0.34 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2165 TYR 0.019 0.001 TYR B1018 PHE 0.018 0.001 PHE B1417 TRP 0.019 0.001 TRP A1889 HIS 0.007 0.001 HIS A1455 Details of bonding type rmsd covalent geometry : bond 0.00223 (21058) covalent geometry : angle 0.50407 (28542) hydrogen bonds : bond 0.03203 ( 853) hydrogen bonds : angle 4.48397 ( 2495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15574.78 seconds wall clock time: 263 minutes 44.47 seconds (15824.47 seconds total)