Starting phenix.real_space_refine on Tue May 5 14:47:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ved_64998/05_2026/9ved_64998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ved_64998/05_2026/9ved_64998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ved_64998/05_2026/9ved_64998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ved_64998/05_2026/9ved_64998.map" model { file = "/net/cci-nas-00/data/ceres_data/9ved_64998/05_2026/9ved_64998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ved_64998/05_2026/9ved_64998.cif" } resolution = 3.63 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= 0.009 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 19230 2.51 5 N 4941 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29400 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9652 Classifications: {'peptide': 1223} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 6, 'ARG:plan': 9, 'GLN:plan1': 7, 'GLU:plan': 7, 'HIS:plan': 4, 'TYR:plan': 6, 'TRP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 235 Chain: "C" Number of atoms: 9652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9652 Classifications: {'peptide': 1223} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 6, 'ARG:plan': 9, 'GLN:plan1': 7, 'GLU:plan': 7, 'HIS:plan': 4, 'TYR:plan': 6, 'TRP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 235 Chain: "B" Number of atoms: 9652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9652 Classifications: {'peptide': 1223} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 6, 'ARG:plan': 9, 'GLN:plan1': 7, 'GLU:plan': 7, 'HIS:plan': 4, 'TYR:plan': 6, 'TRP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 235 Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 148 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 148 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 148 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 6.56, per 1000 atoms: 0.22 Number of scatterers: 29400 At special positions: 0 Unit cell: (197.285, 196.23, 155.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 5052 8.00 N 4941 7.00 C 19230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7164 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 12 sheets defined 70.7% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 784 through 813 removed outlier: 5.302A pdb=" N PHE A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 removed outlier: 4.500A pdb=" N THR A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.624A pdb=" N LEU A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 832 " --> pdb=" O MET A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 852 through 868 removed outlier: 3.639A pdb=" N ILE A 859 " --> pdb=" O VAL A 855 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 860 " --> pdb=" O TRP A 856 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 950 removed outlier: 3.576A pdb=" N ALA A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1006 removed outlier: 6.334A pdb=" N PHE A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1023 removed outlier: 4.038A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1050 removed outlier: 3.512A pdb=" N ARG A1031 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1073 through 1080 removed outlier: 3.513A pdb=" N ILE A1077 " --> pdb=" O ASN A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1114 removed outlier: 4.285A pdb=" N ASP A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1159 Processing helix chain 'A' and resid 1161 through 1176 removed outlier: 4.593A pdb=" N VAL A1167 " --> pdb=" O TRP A1163 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1201 removed outlier: 5.990A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A1200 " --> pdb=" O THR A1196 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A1201 " --> pdb=" O THR A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1228 removed outlier: 3.560A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1232 removed outlier: 3.968A pdb=" N CYS A1232 " --> pdb=" O LEU A1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1229 through 1232' Processing helix chain 'A' and resid 1244 through 1250 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 4.113A pdb=" N PHE A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A1299 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1316 removed outlier: 4.128A pdb=" N HIS A1304 " --> pdb=" O HIS A1300 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A1305 " --> pdb=" O TYR A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1365 removed outlier: 3.904A pdb=" N ALA A1321 " --> pdb=" O SER A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1411 through 1416 removed outlier: 3.705A pdb=" N GLU A1416 " --> pdb=" O PHE A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1524 removed outlier: 3.714A pdb=" N ASP A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1546 removed outlier: 3.729A pdb=" N LEU A1540 " --> pdb=" O ALA A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1558 Processing helix chain 'A' and resid 1656 through 1669 removed outlier: 3.671A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A1664 " --> pdb=" O GLU A1660 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A1666 " --> pdb=" O ALA A1662 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A1667 " --> pdb=" O GLU A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1686 Processing helix chain 'A' and resid 1686 through 1701 removed outlier: 3.897A pdb=" N TYR A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1717 Processing helix chain 'A' and resid 1726 through 1749 removed outlier: 3.587A pdb=" N TRP A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A1749 " --> pdb=" O TYR A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1775 Processing helix chain 'A' and resid 1786 through 1803 Processing helix chain 'A' and resid 1958 through 1968 Processing helix chain 'A' and resid 1976 through 1997 Processing helix chain 'A' and resid 2016 through 2041 removed outlier: 4.210A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2064 Processing helix chain 'A' and resid 2064 through 2069 Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2115 through 2128 removed outlier: 4.082A pdb=" N LEU A2119 " --> pdb=" O ASN A2115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A2120 " --> pdb=" O HIS A2116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A2128 " --> pdb=" O GLY A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 removed outlier: 3.508A pdb=" N LEU A2134 " --> pdb=" O PHE A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2175 Processing helix chain 'A' and resid 2184 through 2214 removed outlier: 4.019A pdb=" N ILE A2203 " --> pdb=" O LEU A2199 " (cutoff:3.500A) Proline residue: A2206 - end of helix Processing helix chain 'A' and resid 2252 through 2262 Processing helix chain 'A' and resid 2266 through 2275 removed outlier: 3.617A pdb=" N GLN A2275 " --> pdb=" O GLN A2271 " (cutoff:3.500A) Processing helix chain 'A' and resid 2276 through 2279 removed outlier: 6.322A pdb=" N GLU A2279 " --> pdb=" O TYR A2276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2276 through 2279' Processing helix chain 'A' and resid 2297 through 2310 Processing helix chain 'A' and resid 2326 through 2330 Processing helix chain 'A' and resid 2348 through 2359 Processing helix chain 'A' and resid 2387 through 2391 removed outlier: 3.679A pdb=" N LEU A2390 " --> pdb=" O VAL A2387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2483 Processing helix chain 'A' and resid 2489 through 2493 removed outlier: 3.995A pdb=" N MET A2493 " --> pdb=" O HIS A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2516 Processing helix chain 'A' and resid 2519 through 2533 Processing helix chain 'A' and resid 2536 through 2541 Processing helix chain 'C' and resid 785 through 813 removed outlier: 5.301A pdb=" N PHE C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 824 removed outlier: 4.500A pdb=" N THR C 817 " --> pdb=" O VAL C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 840 removed outlier: 3.624A pdb=" N LEU C 831 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 852 Processing helix chain 'C' and resid 852 through 868 removed outlier: 3.638A pdb=" N ILE C 859 " --> pdb=" O VAL C 855 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 860 " --> pdb=" O TRP C 856 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 950 removed outlier: 3.576A pdb=" N ALA C 938 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1006 removed outlier: 6.332A pdb=" N PHE C 986 " --> pdb=" O ILE C 982 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 991 " --> pdb=" O TYR C 987 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1023 removed outlier: 4.038A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1050 removed outlier: 3.514A pdb=" N ARG C1031 " --> pdb=" O GLU C1027 " (cutoff:3.500A) Proline residue: C1034 - end of helix Processing helix chain 'C' and resid 1073 through 1080 removed outlier: 3.514A pdb=" N ILE C1077 " --> pdb=" O ASN C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1093 through 1114 removed outlier: 4.284A pdb=" N ASP C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1159 Processing helix chain 'C' and resid 1161 through 1176 removed outlier: 4.594A pdb=" N VAL C1167 " --> pdb=" O TRP C1163 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C1176 " --> pdb=" O ALA C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1201 removed outlier: 5.991A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN C1200 " --> pdb=" O THR C1196 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C1201 " --> pdb=" O THR C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1228 removed outlier: 3.562A pdb=" N GLN C1206 " --> pdb=" O ASP C1202 " (cutoff:3.500A) Processing helix chain 'C' and resid 1229 through 1232 removed outlier: 3.968A pdb=" N CYS C1232 " --> pdb=" O LEU C1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1229 through 1232' Processing helix chain 'C' and resid 1244 through 1250 Processing helix chain 'C' and resid 1282 through 1299 removed outlier: 4.112A pdb=" N PHE C1287 " --> pdb=" O ASP C1283 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C1298 " --> pdb=" O ARG C1294 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C1299 " --> pdb=" O ARG C1295 " (cutoff:3.500A) Processing helix chain 'C' and resid 1300 through 1316 removed outlier: 4.128A pdb=" N HIS C1304 " --> pdb=" O HIS C1300 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL C1305 " --> pdb=" O TYR C1301 " (cutoff:3.500A) Processing helix chain 'C' and resid 1317 through 1365 removed outlier: 3.904A pdb=" N ALA C1321 " --> pdb=" O SER C1317 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1408 Processing helix chain 'C' and resid 1411 through 1416 removed outlier: 3.703A pdb=" N GLU C1416 " --> pdb=" O PHE C1413 " (cutoff:3.500A) Processing helix chain 'C' and resid 1510 through 1524 removed outlier: 3.714A pdb=" N ASP C1514 " --> pdb=" O GLN C1510 " (cutoff:3.500A) Processing helix chain 'C' and resid 1524 through 1546 removed outlier: 3.730A pdb=" N LEU C1540 " --> pdb=" O ALA C1536 " (cutoff:3.500A) Processing helix chain 'C' and resid 1553 through 1558 Processing helix chain 'C' and resid 1656 through 1669 removed outlier: 3.672A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C1664 " --> pdb=" O GLU C1660 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C1665 " --> pdb=" O GLU C1661 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C1666 " --> pdb=" O ALA C1662 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C1667 " --> pdb=" O GLU C1663 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1686 Processing helix chain 'C' and resid 1686 through 1701 removed outlier: 3.896A pdb=" N TYR C1692 " --> pdb=" O GLU C1688 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1717 Processing helix chain 'C' and resid 1726 through 1749 removed outlier: 3.586A pdb=" N TRP C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C1749 " --> pdb=" O TYR C1745 " (cutoff:3.500A) Processing helix chain 'C' and resid 1771 through 1775 Processing helix chain 'C' and resid 1786 through 1803 Processing helix chain 'C' and resid 1958 through 1968 Processing helix chain 'C' and resid 1976 through 1997 Processing helix chain 'C' and resid 2016 through 2041 removed outlier: 4.212A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2064 Processing helix chain 'C' and resid 2064 through 2069 Processing helix chain 'C' and resid 2076 through 2100 Processing helix chain 'C' and resid 2115 through 2128 removed outlier: 4.080A pdb=" N LEU C2119 " --> pdb=" O ASN C2115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C2120 " --> pdb=" O HIS C2116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C2128 " --> pdb=" O GLY C2124 " (cutoff:3.500A) Processing helix chain 'C' and resid 2130 through 2142 removed outlier: 3.509A pdb=" N LEU C2134 " --> pdb=" O PHE C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2175 Processing helix chain 'C' and resid 2184 through 2214 removed outlier: 4.019A pdb=" N ILE C2203 " --> pdb=" O LEU C2199 " (cutoff:3.500A) Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2252 through 2262 Processing helix chain 'C' and resid 2266 through 2275 removed outlier: 3.619A pdb=" N GLN C2275 " --> pdb=" O GLN C2271 " (cutoff:3.500A) Processing helix chain 'C' and resid 2276 through 2279 removed outlier: 6.323A pdb=" N GLU C2279 " --> pdb=" O TYR C2276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2276 through 2279' Processing helix chain 'C' and resid 2297 through 2310 Processing helix chain 'C' and resid 2326 through 2330 Processing helix chain 'C' and resid 2348 through 2359 Processing helix chain 'C' and resid 2387 through 2391 removed outlier: 3.680A pdb=" N LEU C2390 " --> pdb=" O VAL C2387 " (cutoff:3.500A) Processing helix chain 'C' and resid 2466 through 2483 Processing helix chain 'C' and resid 2489 through 2493 removed outlier: 3.994A pdb=" N MET C2493 " --> pdb=" O HIS C2490 " (cutoff:3.500A) Processing helix chain 'C' and resid 2500 through 2516 Processing helix chain 'C' and resid 2519 through 2533 Processing helix chain 'C' and resid 2536 through 2541 Processing helix chain 'B' and resid 785 through 813 removed outlier: 5.302A pdb=" N PHE B 810 " --> pdb=" O GLU B 806 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 824 removed outlier: 4.501A pdb=" N THR B 817 " --> pdb=" O VAL B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 840 removed outlier: 3.625A pdb=" N LEU B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 832 " --> pdb=" O MET B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 852 Processing helix chain 'B' and resid 852 through 868 removed outlier: 3.638A pdb=" N ILE B 859 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 860 " --> pdb=" O TRP B 856 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 950 removed outlier: 3.575A pdb=" N ALA B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 1006 removed outlier: 6.333A pdb=" N PHE B 986 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 991 " --> pdb=" O TYR B 987 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1023 removed outlier: 4.039A pdb=" N ARG B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1050 removed outlier: 3.514A pdb=" N ARG B1031 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix Processing helix chain 'B' and resid 1073 through 1080 removed outlier: 3.513A pdb=" N ILE B1077 " --> pdb=" O ASN B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1114 removed outlier: 4.283A pdb=" N ASP B1097 " --> pdb=" O ASN B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1161 through 1176 removed outlier: 4.592A pdb=" N VAL B1167 " --> pdb=" O TRP B1163 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B1176 " --> pdb=" O ALA B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1201 removed outlier: 5.990A pdb=" N THR B1196 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B1200 " --> pdb=" O THR B1196 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B1201 " --> pdb=" O THR B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1228 removed outlier: 3.561A pdb=" N GLN B1206 " --> pdb=" O ASP B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1232 removed outlier: 3.971A pdb=" N CYS B1232 " --> pdb=" O LEU B1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1229 through 1232' Processing helix chain 'B' and resid 1244 through 1250 Processing helix chain 'B' and resid 1282 through 1299 removed outlier: 4.113A pdb=" N PHE B1287 " --> pdb=" O ASP B1283 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B1298 " --> pdb=" O ARG B1294 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B1299 " --> pdb=" O ARG B1295 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1316 removed outlier: 4.129A pdb=" N HIS B1304 " --> pdb=" O HIS B1300 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B1305 " --> pdb=" O TYR B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1365 removed outlier: 3.906A pdb=" N ALA B1321 " --> pdb=" O SER B1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1408 Processing helix chain 'B' and resid 1411 through 1416 removed outlier: 3.704A pdb=" N GLU B1416 " --> pdb=" O PHE B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1510 through 1524 removed outlier: 3.713A pdb=" N ASP B1514 " --> pdb=" O GLN B1510 " (cutoff:3.500A) Processing helix chain 'B' and resid 1524 through 1546 removed outlier: 3.728A pdb=" N LEU B1540 " --> pdb=" O ALA B1536 " (cutoff:3.500A) Processing helix chain 'B' and resid 1553 through 1558 Processing helix chain 'B' and resid 1656 through 1669 removed outlier: 3.673A pdb=" N GLU B1660 " --> pdb=" O ILE B1656 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B1664 " --> pdb=" O GLU B1660 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B1665 " --> pdb=" O GLU B1661 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B1666 " --> pdb=" O ALA B1662 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B1667 " --> pdb=" O GLU B1663 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1686 Processing helix chain 'B' and resid 1686 through 1701 removed outlier: 3.897A pdb=" N TYR B1692 " --> pdb=" O GLU B1688 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1717 Processing helix chain 'B' and resid 1726 through 1749 removed outlier: 3.586A pdb=" N TRP B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B1749 " --> pdb=" O TYR B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1771 through 1775 Processing helix chain 'B' and resid 1786 through 1803 Processing helix chain 'B' and resid 1958 through 1968 Processing helix chain 'B' and resid 1976 through 1997 Processing helix chain 'B' and resid 2016 through 2041 removed outlier: 4.210A pdb=" N PHE B2022 " --> pdb=" O GLN B2018 " (cutoff:3.500A) Processing helix chain 'B' and resid 2042 through 2064 Processing helix chain 'B' and resid 2064 through 2069 Processing helix chain 'B' and resid 2076 through 2100 Processing helix chain 'B' and resid 2115 through 2128 removed outlier: 4.081A pdb=" N LEU B2119 " --> pdb=" O ASN B2115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE B2120 " --> pdb=" O HIS B2116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B2128 " --> pdb=" O GLY B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2142 removed outlier: 3.508A pdb=" N LEU B2134 " --> pdb=" O PHE B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2175 Processing helix chain 'B' and resid 2184 through 2214 removed outlier: 4.019A pdb=" N ILE B2203 " --> pdb=" O LEU B2199 " (cutoff:3.500A) Proline residue: B2206 - end of helix Processing helix chain 'B' and resid 2252 through 2262 Processing helix chain 'B' and resid 2266 through 2275 removed outlier: 3.616A pdb=" N GLN B2275 " --> pdb=" O GLN B2271 " (cutoff:3.500A) Processing helix chain 'B' and resid 2276 through 2279 removed outlier: 6.322A pdb=" N GLU B2279 " --> pdb=" O TYR B2276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2276 through 2279' Processing helix chain 'B' and resid 2297 through 2310 Processing helix chain 'B' and resid 2326 through 2330 Processing helix chain 'B' and resid 2348 through 2359 Processing helix chain 'B' and resid 2387 through 2391 removed outlier: 3.681A pdb=" N LEU B2390 " --> pdb=" O VAL B2387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2483 Processing helix chain 'B' and resid 2489 through 2493 removed outlier: 3.997A pdb=" N MET B2493 " --> pdb=" O HIS B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2500 through 2516 Processing helix chain 'B' and resid 2519 through 2533 Processing helix chain 'B' and resid 2536 through 2541 Processing helix chain 'F' and resid 228 through 244 removed outlier: 3.550A pdb=" N CYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 244 removed outlier: 3.551A pdb=" N CYS D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 244 removed outlier: 3.551A pdb=" N CYS E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2240 through 2243 removed outlier: 4.178A pdb=" N VAL A2226 " --> pdb=" O ALA A2243 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A2321 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A2338 " --> pdb=" O TRP A2321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 3.514A pdb=" N VAL A2249 " --> pdb=" O THR A2283 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A2282 " --> pdb=" O ILE A2448 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A2286 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A2376 " --> pdb=" O PHE A2449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2315 through 2316 Processing sheet with id=AA4, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 5.351A pdb=" N VAL A2367 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A2403 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A2401 " --> pdb=" O PRO A2369 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A2399 " --> pdb=" O LEU A2371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2240 through 2243 removed outlier: 4.179A pdb=" N VAL C2226 " --> pdb=" O ALA C2243 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C2321 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C2338 " --> pdb=" O TRP C2321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 2248 through 2250 removed outlier: 3.515A pdb=" N VAL C2249 " --> pdb=" O THR C2283 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C2282 " --> pdb=" O ILE C2448 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE C2286 " --> pdb=" O LEU C2444 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C2376 " --> pdb=" O PHE C2449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2315 through 2316 Processing sheet with id=AA8, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 5.352A pdb=" N VAL C2367 " --> pdb=" O ILE C2403 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE C2403 " --> pdb=" O VAL C2367 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL C2401 " --> pdb=" O PRO C2369 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C2399 " --> pdb=" O LEU C2371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2240 through 2243 removed outlier: 4.180A pdb=" N VAL B2226 " --> pdb=" O ALA B2243 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B2321 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B2338 " --> pdb=" O TRP B2321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 3.515A pdb=" N VAL B2249 " --> pdb=" O THR B2283 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B2282 " --> pdb=" O ILE B2448 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B2286 " --> pdb=" O LEU B2444 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B2376 " --> pdb=" O PHE B2449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2315 through 2316 Processing sheet with id=AB3, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 5.351A pdb=" N VAL B2367 " --> pdb=" O ILE B2403 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B2403 " --> pdb=" O VAL B2367 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B2401 " --> pdb=" O PRO B2369 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU B2399 " --> pdb=" O LEU B2371 " (cutoff:3.500A) 1900 hydrogen bonds defined for protein. 5601 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: 5.85 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5652 1.32 - 1.45: 7422 1.45 - 1.57: 16737 1.57 - 1.69: 0 1.69 - 1.81: 261 Bond restraints: 30072 Sorted by residual: bond pdb=" CA TYR C2533 " pdb=" C TYR C2533 " ideal model delta sigma weight residual 1.518 1.383 0.135 4.01e-02 6.22e+02 1.14e+01 bond pdb=" CA TYR A2533 " pdb=" C TYR A2533 " ideal model delta sigma weight residual 1.518 1.383 0.135 4.01e-02 6.22e+02 1.14e+01 bond pdb=" CA TYR B2533 " pdb=" C TYR B2533 " ideal model delta sigma weight residual 1.518 1.384 0.134 4.01e-02 6.22e+02 1.12e+01 bond pdb=" CB MET C2539 " pdb=" CG MET C2539 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.07e+00 bond pdb=" CB ASN C2161 " pdb=" CG ASN C2161 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 6.96e+00 ... (remaining 30067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 38843 2.09 - 4.19: 1611 4.19 - 6.28: 262 6.28 - 8.38: 63 8.38 - 10.47: 15 Bond angle restraints: 40794 Sorted by residual: angle pdb=" C PHE A1751 " pdb=" N PHE A1752 " pdb=" CA PHE A1752 " ideal model delta sigma weight residual 120.49 113.61 6.88 1.42e+00 4.96e-01 2.34e+01 angle pdb=" C PHE C1751 " pdb=" N PHE C1752 " pdb=" CA PHE C1752 " ideal model delta sigma weight residual 120.49 113.65 6.84 1.42e+00 4.96e-01 2.32e+01 angle pdb=" C PHE B1751 " pdb=" N PHE B1752 " pdb=" CA PHE B1752 " ideal model delta sigma weight residual 120.49 113.67 6.82 1.42e+00 4.96e-01 2.30e+01 angle pdb=" CA TRP C1033 " pdb=" CB TRP C1033 " pdb=" CG TRP C1033 " ideal model delta sigma weight residual 113.60 105.10 8.50 1.90e+00 2.77e-01 2.00e+01 angle pdb=" CA TRP A1033 " pdb=" CB TRP A1033 " pdb=" CG TRP A1033 " ideal model delta sigma weight residual 113.60 105.11 8.49 1.90e+00 2.77e-01 1.99e+01 ... (remaining 40789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16001 17.99 - 35.98: 1518 35.98 - 53.97: 184 53.97 - 71.97: 42 71.97 - 89.96: 45 Dihedral angle restraints: 17790 sinusoidal: 6810 harmonic: 10980 Sorted by residual: dihedral pdb=" CA ILE C1179 " pdb=" C ILE C1179 " pdb=" N PHE C1180 " pdb=" CA PHE C1180 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ILE B1179 " pdb=" C ILE B1179 " pdb=" N PHE B1180 " pdb=" CA PHE B1180 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ILE A1179 " pdb=" C ILE A1179 " pdb=" N PHE A1180 " pdb=" CA PHE A1180 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 17787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4072 0.077 - 0.153: 558 0.153 - 0.230: 50 0.230 - 0.306: 0 0.306 - 0.383: 3 Chirality restraints: 4683 Sorted by residual: chirality pdb=" CA TYR C2533 " pdb=" N TYR C2533 " pdb=" C TYR C2533 " pdb=" CB TYR C2533 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA TYR A2533 " pdb=" N TYR A2533 " pdb=" C TYR A2533 " pdb=" CB TYR A2533 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA TYR B2533 " pdb=" N TYR B2533 " pdb=" C TYR B2533 " pdb=" CB TYR B2533 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 4680 not shown) Planarity restraints: 5085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B2381 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO B2382 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B2382 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B2382 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C2381 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO C2382 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C2382 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C2382 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2381 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A2382 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A2382 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A2382 " -0.037 5.00e-02 4.00e+02 ... (remaining 5082 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 213 2.52 - 3.11: 24001 3.11 - 3.71: 45812 3.71 - 4.30: 59958 4.30 - 4.90: 98568 Nonbonded interactions: 228552 Sorted by model distance: nonbonded pdb=" OH TYR C1412 " pdb=" OE1 GLU B2537 " model vdw 1.919 3.040 nonbonded pdb=" OE1 GLN A2018 " pdb=" OG SER C2211 " model vdw 2.015 3.040 nonbonded pdb=" OE1 GLU A2537 " pdb=" OH TYR B1412 " model vdw 2.024 3.040 nonbonded pdb=" O ASN C1142 " pdb=" NH1 ARG C1147 " model vdw 2.085 3.120 nonbonded pdb=" O ASN A1142 " pdb=" NH1 ARG A1147 " model vdw 2.085 3.120 ... (remaining 228547 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 26.390 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.012 0.135 30072 Z= 0.496 Angle : 1.006 10.470 40794 Z= 0.551 Chirality : 0.053 0.383 4683 Planarity : 0.006 0.067 5085 Dihedral : 14.667 89.956 10626 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3636 helix: 0.45 (0.10), residues: 2433 sheet: -2.28 (0.31), residues: 210 loop : -2.24 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B2502 TYR 0.030 0.003 TYR A1081 PHE 0.024 0.003 PHE B2120 TRP 0.044 0.003 TRP B1016 HIS 0.012 0.002 HIS B2058 Details of bonding type rmsd covalent geometry : bond 0.01166 (30072) covalent geometry : angle 1.00643 (40794) hydrogen bonds : bond 0.13756 ( 1900) hydrogen bonds : angle 6.07316 ( 5601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1998 PHE cc_start: 0.4144 (m-80) cc_final: 0.3731 (m-80) REVERT: A 2038 TYR cc_start: 0.9113 (t80) cc_final: 0.8766 (t80) REVERT: C 986 PHE cc_start: 0.6695 (m-10) cc_final: 0.6156 (t80) REVERT: C 1153 LEU cc_start: 0.8433 (mm) cc_final: 0.7618 (tp) REVERT: C 1323 TYR cc_start: 0.6896 (t80) cc_final: 0.6657 (t80) REVERT: C 1998 PHE cc_start: 0.4454 (m-80) cc_final: 0.4169 (m-80) REVERT: C 2473 ILE cc_start: 0.9165 (tp) cc_final: 0.8810 (tp) REVERT: B 986 PHE cc_start: 0.6694 (m-10) cc_final: 0.6236 (t80) REVERT: B 1153 LEU cc_start: 0.8299 (mm) cc_final: 0.7742 (tp) REVERT: B 1998 PHE cc_start: 0.4305 (m-80) cc_final: 0.4059 (m-80) REVERT: B 2262 GLN cc_start: 0.6500 (tm-30) cc_final: 0.6282 (tm-30) REVERT: B 2263 PHE cc_start: 0.8217 (m-80) cc_final: 0.7275 (m-80) REVERT: B 2304 MET cc_start: 0.8274 (ttp) cc_final: 0.8000 (ttp) REVERT: B 2493 MET cc_start: 0.9609 (ptm) cc_final: 0.9344 (ptm) REVERT: B 2495 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7673 (mt-10) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1527 time to fit residues: 111.3331 Evaluate side-chains 321 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 80.0000 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 HIS A1655 HIS A1967 HIS A2075 GLN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1526 HIS C1967 HIS C2075 GLN C2244 GLN C2285 GLN C2490 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 HIS B1967 HIS B2075 GLN ** B2244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133858 restraints weight = 48210.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127619 restraints weight = 60964.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125280 restraints weight = 60254.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125790 restraints weight = 52624.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125246 restraints weight = 39960.013| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30072 Z= 0.166 Angle : 0.664 10.845 40794 Z= 0.341 Chirality : 0.042 0.212 4683 Planarity : 0.005 0.047 5085 Dihedral : 5.342 59.114 4023 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.50 % Allowed : 9.35 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3636 helix: 1.20 (0.10), residues: 2475 sheet: -2.24 (0.30), residues: 246 loop : -1.89 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1664 TYR 0.020 0.002 TYR B1301 PHE 0.023 0.002 PHE C2251 TRP 0.027 0.002 TRP A1996 HIS 0.006 0.001 HIS C1699 Details of bonding type rmsd covalent geometry : bond 0.00384 (30072) covalent geometry : angle 0.66357 (40794) hydrogen bonds : bond 0.04156 ( 1900) hydrogen bonds : angle 4.46860 ( 5601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 401 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1982 LEU cc_start: 0.8692 (tp) cc_final: 0.8344 (tt) REVERT: A 1998 PHE cc_start: 0.4053 (m-80) cc_final: 0.3661 (m-80) REVERT: A 2031 MET cc_start: 0.7631 (mtt) cc_final: 0.7355 (mtt) REVERT: C 1791 MET cc_start: 0.8144 (mmm) cc_final: 0.7906 (mmm) REVERT: C 1998 PHE cc_start: 0.4591 (m-80) cc_final: 0.4192 (m-80) REVERT: B 1009 MET cc_start: 0.4957 (tpp) cc_final: 0.4701 (tpp) REVERT: B 1153 LEU cc_start: 0.8354 (mm) cc_final: 0.7757 (tt) REVERT: B 1998 PHE cc_start: 0.4516 (m-80) cc_final: 0.4183 (m-80) REVERT: B 2018 GLN cc_start: 0.7864 (mm110) cc_final: 0.6303 (tt0) REVERT: B 2263 PHE cc_start: 0.8171 (m-80) cc_final: 0.7029 (m-80) REVERT: B 2493 MET cc_start: 0.9596 (ptm) cc_final: 0.9237 (ptm) outliers start: 45 outliers final: 25 residues processed: 425 average time/residue: 0.1579 time to fit residues: 113.6387 Evaluate side-chains 350 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2437 CYS Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2357 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1526 HIS Chi-restraints excluded: chain B residue 2437 CYS Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain F residue 226 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 220 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 334 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 345 optimal weight: 3.9990 chunk 113 optimal weight: 40.0000 chunk 131 optimal weight: 50.0000 chunk 126 optimal weight: 40.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1225 ASN C1748 GLN C1967 HIS ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1967 HIS B2244 GLN B2262 GLN ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.129474 restraints weight = 48626.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122135 restraints weight = 62529.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119319 restraints weight = 65511.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119312 restraints weight = 60255.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118738 restraints weight = 48943.241| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30072 Z= 0.241 Angle : 0.696 9.589 40794 Z= 0.358 Chirality : 0.044 0.312 4683 Planarity : 0.005 0.049 5085 Dihedral : 5.201 56.819 4023 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.36 % Allowed : 14.27 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3636 helix: 1.34 (0.10), residues: 2475 sheet: -2.04 (0.30), residues: 246 loop : -1.85 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2361 TYR 0.027 0.002 TYR B1977 PHE 0.048 0.002 PHE A1039 TRP 0.033 0.002 TRP A1996 HIS 0.011 0.002 HIS B1526 Details of bonding type rmsd covalent geometry : bond 0.00580 (30072) covalent geometry : angle 0.69575 (40794) hydrogen bonds : bond 0.04331 ( 1900) hydrogen bonds : angle 4.33228 ( 5601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 368 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1145 HIS cc_start: 0.7130 (m-70) cc_final: 0.6855 (m-70) REVERT: A 1998 PHE cc_start: 0.4240 (m-80) cc_final: 0.3845 (m-80) REVERT: A 2031 MET cc_start: 0.7714 (mtt) cc_final: 0.7463 (mtt) REVERT: A 2485 PHE cc_start: 0.8733 (m-10) cc_final: 0.8501 (m-80) REVERT: C 1998 PHE cc_start: 0.4277 (m-80) cc_final: 0.3954 (m-80) REVERT: C 2020 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7019 (m-10) REVERT: C 2072 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6561 (ttt) REVERT: B 1209 LEU cc_start: 0.7129 (tp) cc_final: 0.6864 (tt) REVERT: B 1998 PHE cc_start: 0.4265 (m-80) cc_final: 0.4031 (m-80) REVERT: B 2020 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: B 2467 VAL cc_start: 0.8636 (t) cc_final: 0.8304 (t) REVERT: B 2493 MET cc_start: 0.9574 (ptm) cc_final: 0.9219 (ptm) REVERT: B 2513 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9179 (t) outliers start: 71 outliers final: 53 residues processed: 411 average time/residue: 0.1545 time to fit residues: 109.0289 Evaluate side-chains 394 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2437 CYS Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1219 THR Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1967 HIS Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2357 LEU Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2467 VAL Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1246 ILE Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1777 GLU Chi-restraints excluded: chain B residue 1967 HIS Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2437 CYS Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain B residue 2513 VAL Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 125 optimal weight: 50.0000 chunk 182 optimal weight: 0.8980 chunk 7 optimal weight: 50.0000 chunk 34 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 1 optimal weight: 50.0000 chunk 248 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN A2389 GLN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1526 HIS C1967 HIS ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2262 GLN C2391 GLN B1047 GLN B1142 ASN B1225 ASN B1967 HIS ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128589 restraints weight = 47921.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122927 restraints weight = 63754.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120962 restraints weight = 59887.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121401 restraints weight = 48752.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121641 restraints weight = 38551.996| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30072 Z= 0.179 Angle : 0.635 10.017 40794 Z= 0.325 Chirality : 0.042 0.334 4683 Planarity : 0.004 0.050 5085 Dihedral : 4.963 51.936 4023 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.26 % Allowed : 15.74 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3636 helix: 1.55 (0.10), residues: 2472 sheet: -1.89 (0.30), residues: 246 loop : -1.79 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B2361 TYR 0.019 0.001 TYR A1046 PHE 0.024 0.001 PHE B1961 TRP 0.035 0.002 TRP A1996 HIS 0.020 0.002 HIS B1304 Details of bonding type rmsd covalent geometry : bond 0.00428 (30072) covalent geometry : angle 0.63529 (40794) hydrogen bonds : bond 0.03978 ( 1900) hydrogen bonds : angle 4.12732 ( 5601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 369 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1145 HIS cc_start: 0.7075 (m-70) cc_final: 0.6855 (m-70) REVERT: A 1322 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 1737 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7427 (t) REVERT: A 1998 PHE cc_start: 0.4235 (m-80) cc_final: 0.3847 (m-80) REVERT: A 2020 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: C 1791 MET cc_start: 0.8198 (mmm) cc_final: 0.7994 (mmm) REVERT: C 1998 PHE cc_start: 0.4214 (m-80) cc_final: 0.3904 (m-80) REVERT: C 2072 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6568 (ttt) REVERT: C 2251 PHE cc_start: 0.8098 (m-10) cc_final: 0.7767 (m-10) REVERT: C 2262 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: C 2467 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8215 (t) REVERT: B 1209 LEU cc_start: 0.7222 (tp) cc_final: 0.6870 (tt) REVERT: B 1998 PHE cc_start: 0.4624 (m-80) cc_final: 0.4333 (m-80) REVERT: B 2020 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: B 2467 VAL cc_start: 0.8511 (t) cc_final: 0.8134 (t) REVERT: B 2493 MET cc_start: 0.9550 (ptm) cc_final: 0.9293 (ptm) outliers start: 98 outliers final: 63 residues processed: 438 average time/residue: 0.1499 time to fit residues: 113.4627 Evaluate side-chains 414 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2309 TYR Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1967 HIS Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2262 GLN Chi-restraints excluded: chain C residue 2357 LEU Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2467 VAL Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1165 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1225 ASN Chi-restraints excluded: chain B residue 1246 ILE Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1526 HIS Chi-restraints excluded: chain B residue 1737 THR Chi-restraints excluded: chain B residue 1777 GLU Chi-restraints excluded: chain B residue 1967 HIS Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 0.0670 chunk 326 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 chunk 264 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 339 optimal weight: 9.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1748 GLN C1047 GLN C1225 ASN C1967 HIS ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN B1225 ASN B1967 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.159693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127875 restraints weight = 48424.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125495 restraints weight = 71928.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122293 restraints weight = 54267.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122200 restraints weight = 50675.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122511 restraints weight = 44796.987| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30072 Z= 0.147 Angle : 0.615 12.956 40794 Z= 0.311 Chirality : 0.041 0.286 4683 Planarity : 0.004 0.050 5085 Dihedral : 4.763 46.801 4023 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.33 % Allowed : 16.77 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3636 helix: 1.69 (0.10), residues: 2478 sheet: -1.85 (0.29), residues: 261 loop : -1.75 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2361 TYR 0.020 0.001 TYR A1046 PHE 0.020 0.001 PHE B 985 TRP 0.039 0.002 TRP A1996 HIS 0.012 0.001 HIS B1304 Details of bonding type rmsd covalent geometry : bond 0.00341 (30072) covalent geometry : angle 0.61479 (40794) hydrogen bonds : bond 0.03738 ( 1900) hydrogen bonds : angle 3.99718 ( 5601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 378 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1998 PHE cc_start: 0.4105 (m-80) cc_final: 0.3750 (m-80) REVERT: A 2020 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: C 2020 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: C 2072 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6793 (ttt) REVERT: C 2492 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9082 (tt) REVERT: B 1209 LEU cc_start: 0.7295 (tp) cc_final: 0.6946 (tt) REVERT: B 1327 ASN cc_start: 0.8025 (t0) cc_final: 0.7746 (t0) REVERT: B 1349 MET cc_start: 0.8091 (tpp) cc_final: 0.7875 (tpp) REVERT: B 1998 PHE cc_start: 0.4582 (m-80) cc_final: 0.4293 (m-80) REVERT: B 2020 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: B 2153 MET cc_start: 0.8281 (mmm) cc_final: 0.7847 (mmm) REVERT: B 2493 MET cc_start: 0.9555 (ptm) cc_final: 0.9270 (ptm) REVERT: B 2513 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9279 (t) outliers start: 100 outliers final: 61 residues processed: 448 average time/residue: 0.1508 time to fit residues: 117.1759 Evaluate side-chains 420 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TYR Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1777 GLU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1165 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1225 ASN Chi-restraints excluded: chain B residue 1246 ILE Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1314 LEU Chi-restraints excluded: chain B residue 1737 THR Chi-restraints excluded: chain B residue 1777 GLU Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2410 VAL Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2513 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 242 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 ASN ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1225 ASN ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN B1225 ASN B1526 HIS B1967 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129540 restraints weight = 48106.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124950 restraints weight = 66319.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122085 restraints weight = 63317.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122522 restraints weight = 56978.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122808 restraints weight = 40787.955| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30072 Z= 0.162 Angle : 0.630 11.436 40794 Z= 0.317 Chirality : 0.041 0.277 4683 Planarity : 0.004 0.050 5085 Dihedral : 4.686 44.223 4023 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.59 % Allowed : 17.76 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3636 helix: 1.72 (0.10), residues: 2484 sheet: -1.71 (0.31), residues: 246 loop : -1.66 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2361 TYR 0.020 0.001 TYR A1046 PHE 0.048 0.001 PHE A1039 TRP 0.050 0.002 TRP A1996 HIS 0.022 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00384 (30072) covalent geometry : angle 0.62970 (40794) hydrogen bonds : bond 0.03736 ( 1900) hydrogen bonds : angle 3.95328 ( 5601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 368 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1998 PHE cc_start: 0.4189 (m-80) cc_final: 0.3841 (m-80) REVERT: A 2020 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6124 (m-80) REVERT: C 1143 PHE cc_start: 0.5925 (m-10) cc_final: 0.5706 (m-10) REVERT: C 2020 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: C 2072 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6576 (ttt) REVERT: C 2492 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9046 (tt) REVERT: B 1100 LEU cc_start: 0.7670 (tt) cc_final: 0.7438 (tt) REVERT: B 1209 LEU cc_start: 0.7277 (tp) cc_final: 0.6894 (tt) REVERT: B 1327 ASN cc_start: 0.8028 (t0) cc_final: 0.7748 (t0) REVERT: B 1998 PHE cc_start: 0.4512 (m-80) cc_final: 0.4274 (m-80) REVERT: B 2020 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: B 2263 PHE cc_start: 0.8194 (m-80) cc_final: 0.7679 (m-80) REVERT: B 2493 MET cc_start: 0.9502 (ptm) cc_final: 0.9246 (ptm) REVERT: B 2513 VAL cc_start: 0.9490 (OUTLIER) cc_final: 0.9276 (t) outliers start: 108 outliers final: 77 residues processed: 445 average time/residue: 0.1478 time to fit residues: 114.3100 Evaluate side-chains 435 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 352 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TYR Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1777 GLU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2349 THR Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2437 CYS Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2197 LEU Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain B residue 1165 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1225 ASN Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1526 HIS Chi-restraints excluded: chain B residue 1737 THR Chi-restraints excluded: chain B residue 1777 GLU Chi-restraints excluded: chain B residue 1967 HIS Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2410 VAL Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2437 CYS Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2513 VAL Chi-restraints excluded: chain B residue 2539 MET Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 353 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 155 optimal weight: 0.0070 chunk 76 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 ASN C1225 ASN ** C1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN B1225 ASN B1526 HIS ** B1748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1963 HIS B1967 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.161671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132206 restraints weight = 48550.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127098 restraints weight = 61267.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125843 restraints weight = 55319.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126246 restraints weight = 45155.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126396 restraints weight = 37595.682| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30072 Z= 0.121 Angle : 0.599 12.073 40794 Z= 0.300 Chirality : 0.040 0.294 4683 Planarity : 0.004 0.050 5085 Dihedral : 4.502 36.267 4023 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.59 % Allowed : 18.80 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3636 helix: 1.83 (0.10), residues: 2487 sheet: -1.70 (0.30), residues: 258 loop : -1.60 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2361 TYR 0.022 0.001 TYR A1046 PHE 0.022 0.001 PHE B1736 TRP 0.055 0.002 TRP C1996 HIS 0.017 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00273 (30072) covalent geometry : angle 0.59926 (40794) hydrogen bonds : bond 0.03497 ( 1900) hydrogen bonds : angle 3.85163 ( 5601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 382 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 PHE cc_start: 0.6921 (m-80) cc_final: 0.6032 (m-80) REVERT: A 1998 PHE cc_start: 0.4086 (m-80) cc_final: 0.3832 (m-80) REVERT: A 2020 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: A 2513 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9130 (t) REVERT: C 1009 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4553 (tpp) REVERT: C 1099 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6567 (tt) REVERT: C 1800 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8229 (tt) REVERT: C 2018 GLN cc_start: 0.7799 (mm110) cc_final: 0.6277 (tt0) REVERT: C 2072 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6993 (ttt) REVERT: C 2391 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: C 2492 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9029 (tt) REVERT: B 1100 LEU cc_start: 0.7756 (tt) cc_final: 0.7473 (tt) REVERT: B 1209 LEU cc_start: 0.7244 (tp) cc_final: 0.6866 (tt) REVERT: B 1327 ASN cc_start: 0.7997 (t0) cc_final: 0.7744 (t0) REVERT: B 1800 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8190 (tt) REVERT: B 2018 GLN cc_start: 0.7671 (mm-40) cc_final: 0.6365 (tt0) REVERT: B 2263 PHE cc_start: 0.8101 (m-80) cc_final: 0.7626 (m-80) REVERT: B 2304 MET cc_start: 0.7934 (ttp) cc_final: 0.7711 (ttp) REVERT: B 2493 MET cc_start: 0.9480 (ptm) cc_final: 0.9203 (ptm) outliers start: 108 outliers final: 67 residues processed: 453 average time/residue: 0.1466 time to fit residues: 114.6170 Evaluate side-chains 437 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 361 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TYR Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1777 GLU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2349 THR Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1800 LEU Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2197 LEU Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1225 ASN Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1314 LEU Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2039 LEU Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2410 VAL Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2539 MET Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 212 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 chunk 248 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 323 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 131 optimal weight: 50.0000 chunk 237 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1225 ASN ** C1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN B1293 GLN B1967 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132200 restraints weight = 48556.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122555 restraints weight = 58520.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121321 restraints weight = 62906.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122137 restraints weight = 53943.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122263 restraints weight = 41295.338| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30072 Z= 0.168 Angle : 0.635 13.077 40794 Z= 0.317 Chirality : 0.041 0.256 4683 Planarity : 0.004 0.067 5085 Dihedral : 4.550 38.246 4023 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.43 % Allowed : 19.83 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3636 helix: 1.79 (0.10), residues: 2490 sheet: -1.54 (0.32), residues: 243 loop : -1.55 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2361 TYR 0.025 0.001 TYR A1977 PHE 0.021 0.001 PHE C1995 TRP 0.049 0.002 TRP C1996 HIS 0.014 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00400 (30072) covalent geometry : angle 0.63492 (40794) hydrogen bonds : bond 0.03677 ( 1900) hydrogen bonds : angle 3.88698 ( 5601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 367 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 PHE cc_start: 0.6870 (m-80) cc_final: 0.6129 (m-80) REVERT: A 1977 TYR cc_start: 0.8932 (t80) cc_final: 0.8708 (t80) REVERT: A 1998 PHE cc_start: 0.4091 (m-80) cc_final: 0.3771 (m-80) REVERT: A 2018 GLN cc_start: 0.7859 (mm110) cc_final: 0.6222 (tt0) REVERT: A 2020 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: C 1009 MET cc_start: 0.5084 (mmp) cc_final: 0.4592 (tpp) REVERT: C 2018 GLN cc_start: 0.7902 (mm110) cc_final: 0.6306 (tt0) REVERT: C 2072 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6799 (ttt) REVERT: C 2391 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: C 2492 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9059 (tt) REVERT: B 1100 LEU cc_start: 0.7873 (tt) cc_final: 0.7533 (tt) REVERT: B 1209 LEU cc_start: 0.7390 (tp) cc_final: 0.6966 (tt) REVERT: B 1327 ASN cc_start: 0.8026 (t0) cc_final: 0.7733 (t0) REVERT: B 2018 GLN cc_start: 0.7694 (mm-40) cc_final: 0.6354 (tt0) REVERT: B 2020 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: B 2263 PHE cc_start: 0.8141 (m-80) cc_final: 0.7632 (m-80) REVERT: B 2304 MET cc_start: 0.8018 (ttp) cc_final: 0.7751 (ttp) REVERT: B 2493 MET cc_start: 0.9480 (ptm) cc_final: 0.9247 (ptm) outliers start: 103 outliers final: 83 residues processed: 438 average time/residue: 0.1478 time to fit residues: 112.0432 Evaluate side-chains 451 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 363 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TYR Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1777 GLU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2069 THR Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2349 THR Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2437 CYS Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 997 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1735 VAL Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2197 LEU Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1165 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1222 ILE Chi-restraints excluded: chain B residue 1225 ASN Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1314 LEU Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1526 HIS Chi-restraints excluded: chain B residue 1737 THR Chi-restraints excluded: chain B residue 1777 GLU Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2410 VAL Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain B residue 2513 VAL Chi-restraints excluded: chain B residue 2539 MET Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 147 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 130 optimal weight: 50.0000 chunk 54 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 301 optimal weight: 0.9990 chunk 360 optimal weight: 0.3980 chunk 294 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 256 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1526 HIS ** A2116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1225 ASN ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133088 restraints weight = 48986.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129115 restraints weight = 63898.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127122 restraints weight = 53539.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127430 restraints weight = 49155.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127552 restraints weight = 39545.087| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30072 Z= 0.130 Angle : 0.611 11.961 40794 Z= 0.304 Chirality : 0.040 0.263 4683 Planarity : 0.004 0.052 5085 Dihedral : 4.390 32.595 4023 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.36 % Allowed : 20.53 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.14), residues: 3636 helix: 1.90 (0.10), residues: 2490 sheet: -1.66 (0.31), residues: 240 loop : -1.48 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2361 TYR 0.023 0.001 TYR A1046 PHE 0.023 0.001 PHE B 985 TRP 0.056 0.002 TRP A1996 HIS 0.012 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00298 (30072) covalent geometry : angle 0.61072 (40794) hydrogen bonds : bond 0.03439 ( 1900) hydrogen bonds : angle 3.79017 ( 5601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 376 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 PHE cc_start: 0.6649 (m-80) cc_final: 0.6111 (m-80) REVERT: A 1977 TYR cc_start: 0.8881 (t80) cc_final: 0.8653 (t80) REVERT: A 1998 PHE cc_start: 0.4007 (m-80) cc_final: 0.3731 (m-80) REVERT: A 2020 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: C 2031 MET cc_start: 0.8222 (mmt) cc_final: 0.7613 (mmt) REVERT: C 2072 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6670 (ttt) REVERT: C 2391 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: C 2442 ASN cc_start: 0.8111 (p0) cc_final: 0.7667 (p0) REVERT: C 2492 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 1100 LEU cc_start: 0.7775 (tt) cc_final: 0.7477 (tt) REVERT: B 1209 LEU cc_start: 0.7326 (tp) cc_final: 0.6903 (tt) REVERT: B 1327 ASN cc_start: 0.7939 (t0) cc_final: 0.7699 (t0) REVERT: B 1800 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 2018 GLN cc_start: 0.7526 (mm-40) cc_final: 0.6261 (tt0) REVERT: B 2263 PHE cc_start: 0.7978 (m-80) cc_final: 0.7567 (m-80) REVERT: B 2304 MET cc_start: 0.7922 (ttp) cc_final: 0.7662 (ttp) REVERT: B 2493 MET cc_start: 0.9526 (ptm) cc_final: 0.9274 (ptm) outliers start: 101 outliers final: 78 residues processed: 446 average time/residue: 0.1548 time to fit residues: 118.8597 Evaluate side-chains 439 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 356 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TYR Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1777 GLU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2069 THR Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2349 THR Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2461 LEU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 997 MET Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1050 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1225 ASN Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1735 VAL Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2197 LEU Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1222 ILE Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1314 LEU Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1526 HIS Chi-restraints excluded: chain B residue 1735 VAL Chi-restraints excluded: chain B residue 1737 THR Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2539 MET Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 151 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 368 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 347 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1526 HIS ** A2116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1225 ASN ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2322 ASN C2391 GLN B1967 HIS ** B2116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134615 restraints weight = 48719.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127362 restraints weight = 62556.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125343 restraints weight = 60502.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125981 restraints weight = 49661.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125972 restraints weight = 38390.016| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30072 Z= 0.137 Angle : 0.628 16.236 40794 Z= 0.312 Chirality : 0.040 0.265 4683 Planarity : 0.004 0.050 5085 Dihedral : 4.381 31.421 4023 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.99 % Allowed : 20.83 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3636 helix: 1.93 (0.10), residues: 2493 sheet: -1.67 (0.31), residues: 240 loop : -1.48 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1664 TYR 0.026 0.001 TYR A1046 PHE 0.020 0.001 PHE C1736 TRP 0.051 0.002 TRP A1996 HIS 0.011 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00318 (30072) covalent geometry : angle 0.62844 (40794) hydrogen bonds : bond 0.03459 ( 1900) hydrogen bonds : angle 3.79983 ( 5601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 365 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 PHE cc_start: 0.6712 (m-80) cc_final: 0.6201 (m-80) REVERT: A 2020 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: A 2485 PHE cc_start: 0.7974 (m-10) cc_final: 0.7246 (m-10) REVERT: C 2031 MET cc_start: 0.8243 (mmt) cc_final: 0.7660 (mmt) REVERT: C 2072 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6657 (ttt) REVERT: C 2442 ASN cc_start: 0.8118 (p0) cc_final: 0.7693 (p0) REVERT: C 2492 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 1100 LEU cc_start: 0.7717 (tt) cc_final: 0.7431 (tt) REVERT: B 1209 LEU cc_start: 0.7341 (tp) cc_final: 0.6921 (tt) REVERT: B 1327 ASN cc_start: 0.7960 (t0) cc_final: 0.7710 (t0) REVERT: B 1800 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8145 (tt) REVERT: B 2018 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6266 (tt0) REVERT: B 2263 PHE cc_start: 0.7997 (m-80) cc_final: 0.7514 (m-80) REVERT: B 2304 MET cc_start: 0.7966 (ttp) cc_final: 0.7722 (ttp) outliers start: 90 outliers final: 78 residues processed: 425 average time/residue: 0.1524 time to fit residues: 112.1631 Evaluate side-chains 438 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 356 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1184 TYR Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1526 HIS Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1777 GLU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2069 THR Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2349 THR Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2437 CYS Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2461 LEU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2197 LEU Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2391 GLN Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1222 ILE Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1314 LEU Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1526 HIS Chi-restraints excluded: chain B residue 1735 VAL Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1967 HIS Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2197 LEU Chi-restraints excluded: chain B residue 2287 GLU Chi-restraints excluded: chain B residue 2349 THR Chi-restraints excluded: chain B residue 2434 LEU Chi-restraints excluded: chain B residue 2464 TYR Chi-restraints excluded: chain B residue 2513 VAL Chi-restraints excluded: chain B residue 2539 MET Chi-restraints excluded: chain F residue 226 CYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 195 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 220 optimal weight: 0.0870 chunk 356 optimal weight: 0.4980 chunk 228 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 92 optimal weight: 0.0050 chunk 209 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1526 HIS ** A2116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1225 ASN ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN B1967 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136697 restraints weight = 49303.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128780 restraints weight = 61847.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126633 restraints weight = 65414.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127659 restraints weight = 52818.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127790 restraints weight = 39830.784| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30072 Z= 0.116 Angle : 0.611 13.353 40794 Z= 0.304 Chirality : 0.040 0.270 4683 Planarity : 0.004 0.050 5085 Dihedral : 4.280 26.423 4023 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.76 % Allowed : 21.29 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3636 helix: 2.00 (0.10), residues: 2499 sheet: -1.65 (0.31), residues: 240 loop : -1.40 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1664 TYR 0.042 0.001 TYR A1977 PHE 0.050 0.001 PHE B2485 TRP 0.043 0.002 TRP A1996 HIS 0.015 0.001 HIS B1967 Details of bonding type rmsd covalent geometry : bond 0.00255 (30072) covalent geometry : angle 0.61055 (40794) hydrogen bonds : bond 0.03307 ( 1900) hydrogen bonds : angle 3.73698 ( 5601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4600.69 seconds wall clock time: 80 minutes 14.05 seconds (4814.05 seconds total)