Starting phenix.real_space_refine on Tue Sep 15 06:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b3r_7042/09_2026/6b3r_7042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b3r_7042/09_2026/6b3r_7042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b3r_7042/09_2026/6b3r_7042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b3r_7042/09_2026/6b3r_7042.map" model { file = "/net/cci-nas-00/data/ceres_data/6b3r_7042/09_2026/6b3r_7042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b3r_7042/09_2026/6b3r_7042.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 210 5.16 5 C 23361 2.51 5 N 6060 2.21 5 O 6087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35718 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1502, 11826 Classifications: {'peptide': 1502} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1433} Chain breaks: 11 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 608 Unresolved non-hydrogen angles: 803 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'TYR:plan': 12, 'TRP:plan': 5, 'PHE:plan': 16, 'GLN:plan1': 8, 'ARG:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 350 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Restraints were copied for chains: C, E, D, F Time building chain proxies: 21.37, per 1000 atoms: 0.60 Number of scatterers: 35718 At special positions: 0 Unit cell: (204.1, 214.5, 153.4, 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 210 16.00 O 6087 8.00 N 6060 7.00 C 23361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 881 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C 881 " - pdb=" SG CYS C1059 " distance=2.03 Simple disulfide: pdb=" SG CYS E 881 " - pdb=" SG CYS E1059 " distance=2.03 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: 2.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 18 sheets defined 64.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.752A pdb=" N PHE A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 625 removed outlier: 3.889A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.659A pdb=" N THR A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 684 through 706 Proline residue: A 693 - end of helix removed outlier: 3.810A pdb=" N PHE A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.776A pdb=" N GLN A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 805 Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 829 through 840 Processing helix chain 'A' and resid 845 through 866 removed outlier: 3.516A pdb=" N CYS A 851 " --> pdb=" O PRO A 847 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 4.078A pdb=" N SER A 899 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 949 removed outlier: 3.637A pdb=" N TYR A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 972 Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 989 through 1005 removed outlier: 3.521A pdb=" N ILE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1022 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1032 through 1050 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.881A pdb=" N ALA A1069 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1094 through 1116 removed outlier: 4.050A pdb=" N GLN A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1161 Processing helix chain 'A' and resid 1162 through 1175 removed outlier: 3.521A pdb=" N LEU A1166 " --> pdb=" O PHE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 5.715A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1228 Processing helix chain 'A' and resid 1229 through 1232 removed outlier: 3.613A 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 1245 through 1250 removed outlier: 3.806A pdb=" N PHE A1249 " --> pdb=" O VAL A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1267 removed outlier: 4.098A pdb=" N THR A1266 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A1267 " --> pdb=" O MET A1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1263 through 1267' Processing helix chain 'A' and resid 1279 through 1298 removed outlier: 3.590A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1315 removed outlier: 3.559A pdb=" N LEU A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A1311 " --> pdb=" O ALA A1307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A1312 " --> pdb=" O ASP A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1365 Processing helix chain 'A' and resid 1494 through 1499 Processing helix chain 'A' and resid 1499 through 1504 Processing helix chain 'A' and resid 1506 through 1524 Processing helix chain 'A' and resid 1524 through 1546 removed outlier: 4.609A pdb=" N MET A1530 " --> pdb=" O HIS A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 removed outlier: 3.877A pdb=" N GLN A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A1560 " --> pdb=" O LEU A1556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A1561 " --> pdb=" O ASP A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1570 removed outlier: 4.238A pdb=" N SER A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A1570 " --> pdb=" O ALA A1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1565 through 1570' Processing helix chain 'A' and resid 1656 through 1667 removed outlier: 3.585A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1686 Processing helix chain 'A' and resid 1687 through 1702 removed outlier: 3.746A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 removed outlier: 3.522A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1746 removed outlier: 3.901A pdb=" N TRP A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1755 Processing helix chain 'A' and resid 1756 through 1763 Processing helix chain 'A' and resid 1769 through 1775 Processing helix chain 'A' and resid 1785 through 1803 Processing helix chain 'A' and resid 1955 through 1967 removed outlier: 4.279A pdb=" N PHE A1961 " --> pdb=" O PRO A1957 " (cutoff:3.500A) Processing helix chain 'A' and resid 1976 through 1995 Processing helix chain 'A' and resid 2016 through 2041 removed outlier: 3.775A pdb=" N PHE A2020 " --> pdb=" O VAL A2016 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A2021 " --> pdb=" O PRO A2017 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2063 removed outlier: 3.790A pdb=" N PHE A2062 " --> pdb=" O HIS A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2098 Processing helix chain 'A' and resid 2115 through 2128 removed outlier: 3.830A pdb=" N VAL A2128 " --> pdb=" O GLY A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2143 Processing helix chain 'A' and resid 2148 through 2175 Processing helix chain 'A' and resid 2186 through 2205 removed outlier: 3.717A pdb=" N GLY A2193 " --> pdb=" O TYR A2189 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A2194 " --> pdb=" O GLY A2190 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2212 Processing helix chain 'A' and resid 2252 through 2263 removed outlier: 3.522A pdb=" N TYR A2256 " --> pdb=" O THR A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2266 through 2275 removed outlier: 3.557A pdb=" N MET A2270 " --> pdb=" O TYR A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2310 Processing helix chain 'A' and resid 2348 through 2360 Processing helix chain 'A' and resid 2466 through 2485 removed outlier: 4.026A pdb=" N PHE A2484 " --> pdb=" O PHE A2480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A2485 " --> pdb=" O VAL A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2491 through 2496 Processing helix chain 'A' and resid 2500 through 2517 Processing helix chain 'A' and resid 2518 through 2533 removed outlier: 3.595A pdb=" N GLU A2522 " --> pdb=" O GLU A2518 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.752A pdb=" N PHE C 594 " --> pdb=" O CYS C 590 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 625 removed outlier: 3.890A pdb=" N LEU C 613 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 652 removed outlier: 3.659A pdb=" N THR C 652 " --> pdb=" O ILE C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 664 Processing helix chain 'C' and resid 684 through 706 Proline residue: C 693 - end of helix removed outlier: 3.810A pdb=" N PHE C 696 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 698 " --> pdb=" O GLY C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.776A pdb=" N GLN C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 805 Processing helix chain 'C' and resid 809 through 824 Processing helix chain 'C' and resid 829 through 840 Processing helix chain 'C' and resid 845 through 866 removed outlier: 3.516A pdb=" N CYS C 851 " --> pdb=" O PRO C 847 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS C 858 " --> pdb=" O THR C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 4.078A pdb=" N SER C 899 " --> pdb=" O ILE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 949 removed outlier: 3.639A pdb=" N TYR C 941 " --> pdb=" O GLU C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 972 Processing helix chain 'C' and resid 973 through 984 Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 989 through 1005 removed outlier: 3.521A pdb=" N ILE C 993 " --> pdb=" O PHE C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1032 through 1050 Processing helix chain 'C' and resid 1066 through 1070 removed outlier: 3.882A pdb=" N ALA C1069 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1080 Processing helix chain 'C' and resid 1094 through 1116 removed outlier: 4.050A pdb=" N GLN C1109 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C1115 " --> pdb=" O PHE C1111 " (cutoff:3.500A) Processing helix chain 'C' and resid 1149 through 1161 Processing helix chain 'C' and resid 1162 through 1175 removed outlier: 3.520A pdb=" N LEU C1166 " --> pdb=" O PHE C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1199 removed outlier: 5.715A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1228 Processing helix chain 'C' and resid 1229 through 1232 removed outlier: 3.614A 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 1245 through 1250 removed outlier: 3.805A pdb=" N PHE C1249 " --> pdb=" O VAL C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1263 through 1267 removed outlier: 4.099A pdb=" N THR C1266 " --> pdb=" O GLU C1263 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C1267 " --> pdb=" O MET C1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1263 through 1267' Processing helix chain 'C' and resid 1279 through 1298 removed outlier: 3.590A pdb=" N ASP C1283 " --> pdb=" O GLY C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1315 removed outlier: 3.558A pdb=" N LEU C1303 " --> pdb=" O SER C1299 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C1307 " --> pdb=" O LEU C1303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C1311 " --> pdb=" O ALA C1307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C1312 " --> pdb=" O ASP C1308 " (cutoff:3.500A) Processing helix chain 'C' and resid 1315 through 1365 Processing helix chain 'C' and resid 1494 through 1499 Processing helix chain 'C' and resid 1499 through 1504 Processing helix chain 'C' and resid 1506 through 1524 Processing helix chain 'C' and resid 1524 through 1546 removed outlier: 4.609A pdb=" N MET C1530 " --> pdb=" O HIS C1526 " (cutoff:3.500A) Processing helix chain 'C' and resid 1554 through 1563 removed outlier: 3.877A pdb=" N GLN C1558 " --> pdb=" O GLY C1554 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1559 " --> pdb=" O VAL C1555 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR C1560 " --> pdb=" O LEU C1556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL C1561 " --> pdb=" O ASP C1557 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1570 removed outlier: 4.238A pdb=" N SER C1569 " --> pdb=" O GLU C1565 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY C1570 " --> pdb=" O ALA C1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1565 through 1570' Processing helix chain 'C' and resid 1656 through 1667 removed outlier: 3.585A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) Processing helix chain 'C' and resid 1673 through 1686 Processing helix chain 'C' and resid 1687 through 1702 removed outlier: 3.746A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 removed outlier: 3.522A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1746 removed outlier: 3.901A pdb=" N TRP C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1752 through 1755 Processing helix chain 'C' and resid 1756 through 1763 Processing helix chain 'C' and resid 1769 through 1775 Processing helix chain 'C' and resid 1785 through 1803 Processing helix chain 'C' and resid 1955 through 1967 removed outlier: 4.280A pdb=" N PHE C1961 " --> pdb=" O PRO C1957 " (cutoff:3.500A) Processing helix chain 'C' and resid 1976 through 1995 Processing helix chain 'C' and resid 2016 through 2041 removed outlier: 3.775A pdb=" N PHE C2020 " --> pdb=" O VAL C2016 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C2021 " --> pdb=" O PRO C2017 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2063 removed outlier: 3.790A pdb=" N PHE C2062 " --> pdb=" O HIS C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2098 Processing helix chain 'C' and resid 2115 through 2128 removed outlier: 3.830A pdb=" N VAL C2128 " --> pdb=" O GLY C2124 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2143 Processing helix chain 'C' and resid 2148 through 2175 Processing helix chain 'C' and resid 2186 through 2205 removed outlier: 3.717A pdb=" N GLY C2193 " --> pdb=" O TYR C2189 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C2194 " --> pdb=" O GLY C2190 " (cutoff:3.500A) Processing helix chain 'C' and resid 2205 through 2212 Processing helix chain 'C' and resid 2252 through 2263 removed outlier: 3.521A pdb=" N TYR C2256 " --> pdb=" O THR C2252 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2275 removed outlier: 3.558A pdb=" N MET C2270 " --> pdb=" O TYR C2266 " (cutoff:3.500A) Processing helix chain 'C' and resid 2297 through 2310 Processing helix chain 'C' and resid 2348 through 2360 Processing helix chain 'C' and resid 2466 through 2485 removed outlier: 4.026A pdb=" N PHE C2484 " --> pdb=" O PHE C2480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C2485 " --> pdb=" O VAL C2481 " (cutoff:3.500A) Processing helix chain 'C' and resid 2491 through 2496 Processing helix chain 'C' and resid 2500 through 2517 Processing helix chain 'C' and resid 2518 through 2533 removed outlier: 3.596A pdb=" N GLU C2522 " --> pdb=" O GLU C2518 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2543 Processing helix chain 'E' and resid 587 through 599 removed outlier: 3.753A pdb=" N PHE E 594 " --> pdb=" O CYS E 590 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 625 removed outlier: 3.890A pdb=" N LEU E 613 " --> pdb=" O VAL E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 652 removed outlier: 3.660A pdb=" N THR E 652 " --> pdb=" O ILE E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 664 Processing helix chain 'E' and resid 684 through 706 Proline residue: E 693 - end of helix removed outlier: 3.810A pdb=" N PHE E 696 " --> pdb=" O ILE E 692 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 698 " --> pdb=" O GLY E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 removed outlier: 3.776A pdb=" N GLN E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 805 Processing helix chain 'E' and resid 809 through 824 Processing helix chain 'E' and resid 829 through 840 Processing helix chain 'E' and resid 845 through 866 removed outlier: 3.516A pdb=" N CYS E 851 " --> pdb=" O PRO E 847 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS E 858 " --> pdb=" O THR E 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 899 removed outlier: 4.078A pdb=" N SER E 899 " --> pdb=" O ILE E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 949 removed outlier: 3.638A pdb=" N TYR E 941 " --> pdb=" O GLU E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 968 through 972 Processing helix chain 'E' and resid 973 through 984 Processing helix chain 'E' and resid 984 through 989 Processing helix chain 'E' and resid 989 through 1005 removed outlier: 3.521A pdb=" N ILE E 993 " --> pdb=" O PHE E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1022 Processing helix chain 'E' and resid 1025 through 1031 Processing helix chain 'E' and resid 1032 through 1050 Processing helix chain 'E' and resid 1066 through 1070 removed outlier: 3.882A pdb=" N ALA E1069 " --> pdb=" O TRP E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1075 through 1080 Processing helix chain 'E' and resid 1094 through 1116 removed outlier: 4.050A pdb=" N GLN E1109 " --> pdb=" O SER E1105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU E1114 " --> pdb=" O VAL E1110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG E1115 " --> pdb=" O PHE E1111 " (cutoff:3.500A) Processing helix chain 'E' and resid 1149 through 1161 Processing helix chain 'E' and resid 1162 through 1175 removed outlier: 3.519A pdb=" N LEU E1166 " --> pdb=" O PHE E1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1199 removed outlier: 5.716A pdb=" N THR E1196 " --> pdb=" O LEU E1192 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR E1197 " --> pdb=" O LEU E1193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1205 through 1228 Processing helix chain 'E' and resid 1229 through 1232 removed outlier: 3.613A pdb=" N CYS E1232 " --> pdb=" O LEU E1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1229 through 1232' Processing helix chain 'E' and resid 1245 through 1250 removed outlier: 3.806A pdb=" N PHE E1249 " --> pdb=" O VAL E1245 " (cutoff:3.500A) Processing helix chain 'E' and resid 1263 through 1267 removed outlier: 4.099A pdb=" N THR E1266 " --> pdb=" O GLU E1263 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG E1267 " --> pdb=" O MET E1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1263 through 1267' Processing helix chain 'E' and resid 1279 through 1298 removed outlier: 3.591A pdb=" N ASP E1283 " --> pdb=" O GLY E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1299 through 1315 removed outlier: 3.558A pdb=" N LEU E1303 " --> pdb=" O SER E1299 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E1307 " --> pdb=" O LEU E1303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA E1311 " --> pdb=" O ALA E1307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E1312 " --> pdb=" O ASP E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1315 through 1365 Processing helix chain 'E' and resid 1494 through 1499 Processing helix chain 'E' and resid 1499 through 1504 Processing helix chain 'E' and resid 1506 through 1524 Processing helix chain 'E' and resid 1524 through 1546 removed outlier: 4.609A pdb=" N MET E1530 " --> pdb=" O HIS E1526 " (cutoff:3.500A) Processing helix chain 'E' and resid 1554 through 1563 removed outlier: 3.877A pdb=" N GLN E1558 " --> pdb=" O GLY E1554 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E1559 " --> pdb=" O VAL E1555 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR E1560 " --> pdb=" O LEU E1556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL E1561 " --> pdb=" O ASP E1557 " (cutoff:3.500A) Processing helix chain 'E' and resid 1565 through 1570 removed outlier: 4.238A pdb=" N SER E1569 " --> pdb=" O GLU E1565 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY E1570 " --> pdb=" O ALA E1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1565 through 1570' Processing helix chain 'E' and resid 1656 through 1667 removed outlier: 3.586A pdb=" N GLU E1660 " --> pdb=" O ILE E1656 " (cutoff:3.500A) Processing helix chain 'E' and resid 1673 through 1686 Processing helix chain 'E' and resid 1687 through 1702 removed outlier: 3.747A pdb=" N HIS E1699 " --> pdb=" O ILE E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1708 through 1718 removed outlier: 3.522A pdb=" N VAL E1712 " --> pdb=" O LEU E1708 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E1713 " --> pdb=" O VAL E1709 " (cutoff:3.500A) Processing helix chain 'E' and resid 1726 through 1746 removed outlier: 3.900A pdb=" N TRP E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1752 through 1755 Processing helix chain 'E' and resid 1756 through 1763 Processing helix chain 'E' and resid 1769 through 1775 Processing helix chain 'E' and resid 1785 through 1803 Processing helix chain 'E' and resid 1955 through 1967 removed outlier: 4.280A pdb=" N PHE E1961 " --> pdb=" O PRO E1957 " (cutoff:3.500A) Processing helix chain 'E' and resid 1976 through 1995 Processing helix chain 'E' and resid 2016 through 2041 removed outlier: 3.775A pdb=" N PHE E2020 " --> pdb=" O VAL E2016 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E2021 " --> pdb=" O PRO E2017 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE E2022 " --> pdb=" O GLN E2018 " (cutoff:3.500A) Processing helix chain 'E' and resid 2042 through 2063 removed outlier: 3.791A pdb=" N PHE E2062 " --> pdb=" O HIS E2058 " (cutoff:3.500A) Processing helix chain 'E' and resid 2076 through 2098 Processing helix chain 'E' and resid 2115 through 2128 removed outlier: 3.830A pdb=" N VAL E2128 " --> pdb=" O GLY E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2131 through 2143 Processing helix chain 'E' and resid 2148 through 2175 Processing helix chain 'E' and resid 2186 through 2205 removed outlier: 3.717A pdb=" N GLY E2193 " --> pdb=" O TYR E2189 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E2194 " --> pdb=" O GLY E2190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2205 through 2212 Processing helix chain 'E' and resid 2252 through 2263 removed outlier: 3.522A pdb=" N TYR E2256 " --> pdb=" O THR E2252 " (cutoff:3.500A) Processing helix chain 'E' and resid 2266 through 2275 removed outlier: 3.557A pdb=" N MET E2270 " --> pdb=" O TYR E2266 " (cutoff:3.500A) Processing helix chain 'E' and resid 2297 through 2310 Processing helix chain 'E' and resid 2348 through 2360 Processing helix chain 'E' and resid 2466 through 2485 removed outlier: 4.027A pdb=" N PHE E2484 " --> pdb=" O PHE E2480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E2485 " --> pdb=" O VAL E2481 " (cutoff:3.500A) Processing helix chain 'E' and resid 2491 through 2496 Processing helix chain 'E' and resid 2500 through 2517 Processing helix chain 'E' and resid 2518 through 2533 removed outlier: 3.595A pdb=" N GLU E2522 " --> pdb=" O GLU E2518 " (cutoff:3.500A) Processing helix chain 'E' and resid 2535 through 2543 Processing sheet with id=AA1, first strand: chain 'A' and resid 2219 through 2220 removed outlier: 4.124A pdb=" N VAL A2219 " --> pdb=" O VAL A2453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2229 through 2231 removed outlier: 6.402A pdb=" N LEU A2230 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2281 through 2282 Processing sheet with id=AA4, first strand: chain 'A' and resid 2286 through 2287 Processing sheet with id=AA5, first strand: chain 'A' and resid 2315 through 2317 Processing sheet with id=AA6, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 5.604A pdb=" N VAL A2367 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE A2403 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A2401 " --> pdb=" O PRO A2369 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU A2399 " --> pdb=" O LEU A2371 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A2406 " --> pdb=" O TRP A2429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2219 through 2220 removed outlier: 4.125A pdb=" N VAL C2219 " --> pdb=" O VAL C2453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2229 through 2231 removed outlier: 6.401A pdb=" N LEU C2230 " --> pdb=" O LEU C2238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2281 through 2282 Processing sheet with id=AB1, first strand: chain 'C' and resid 2286 through 2287 Processing sheet with id=AB2, first strand: chain 'C' and resid 2315 through 2317 Processing sheet with id=AB3, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 5.604A pdb=" N VAL C2367 " --> pdb=" O ILE C2403 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE C2403 " --> pdb=" O VAL C2367 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL C2401 " --> pdb=" O PRO C2369 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU C2399 " --> pdb=" O LEU C2371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C2406 " --> pdb=" O TRP C2429 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 2219 through 2220 removed outlier: 4.124A pdb=" N VAL E2219 " --> pdb=" O VAL E2453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 2229 through 2231 removed outlier: 6.402A pdb=" N LEU E2230 " --> pdb=" O LEU E2238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 2281 through 2282 Processing sheet with id=AB7, first strand: chain 'E' and resid 2286 through 2287 Processing sheet with id=AB8, first strand: chain 'E' and resid 2315 through 2317 Processing sheet with id=AB9, first strand: chain 'E' and resid 2366 through 2372 removed outlier: 5.605A pdb=" N VAL E2367 " --> pdb=" O ILE E2403 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE E2403 " --> pdb=" O VAL E2367 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL E2401 " --> pdb=" O PRO E2369 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E2399 " --> pdb=" O LEU E2371 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E2406 " --> pdb=" O TRP E2429 " (cutoff:3.500A) 2028 hydrogen bonds defined for protein. 6003 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: 7.46 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11094 1.34 - 1.46: 8886 1.46 - 1.58: 16284 1.58 - 1.71: 0 1.71 - 1.83: 324 Bond restraints: 36588 Sorted by residual: bond pdb=" CG1 ILE A2162 " pdb=" CD1 ILE A2162 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.34e+00 bond pdb=" CG1 ILE E2162 " pdb=" CD1 ILE E2162 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.32e+00 bond pdb=" CG1 ILE C2162 " pdb=" CD1 ILE C2162 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.30e+00 bond pdb=" C PHE A1751 " pdb=" N PHE A1752 " ideal model delta sigma weight residual 1.331 1.293 0.038 2.07e-02 2.33e+03 3.34e+00 bond pdb=" C PHE E1751 " pdb=" N PHE E1752 " ideal model delta sigma weight residual 1.331 1.293 0.038 2.07e-02 2.33e+03 3.34e+00 ... (remaining 36583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 48341 2.69 - 5.38: 1115 5.38 - 8.06: 239 8.06 - 10.75: 39 10.75 - 13.44: 12 Bond angle restraints: 49746 Sorted by residual: angle pdb=" C VAL A 827 " pdb=" N MET A 828 " pdb=" CA MET A 828 " ideal model delta sigma weight residual 126.32 134.08 -7.76 1.74e+00 3.30e-01 1.99e+01 angle pdb=" C VAL E 827 " pdb=" N MET E 828 " pdb=" CA MET E 828 " ideal model delta sigma weight residual 126.32 134.00 -7.68 1.74e+00 3.30e-01 1.95e+01 angle pdb=" C VAL C 827 " pdb=" N MET C 828 " pdb=" CA MET C 828 " ideal model delta sigma weight residual 126.32 133.98 -7.66 1.74e+00 3.30e-01 1.94e+01 angle pdb=" N PHE E2205 " pdb=" CA PHE E2205 " pdb=" C PHE E2205 " ideal model delta sigma weight residual 109.81 119.29 -9.48 2.21e+00 2.05e-01 1.84e+01 angle pdb=" N PHE C2205 " pdb=" CA PHE C2205 " pdb=" C PHE C2205 " ideal model delta sigma weight residual 109.81 119.26 -9.45 2.21e+00 2.05e-01 1.83e+01 ... (remaining 49741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 20426 15.62 - 31.24: 1033 31.24 - 46.86: 165 46.86 - 62.47: 6 62.47 - 78.09: 21 Dihedral angle restraints: 21651 sinusoidal: 8229 harmonic: 13422 Sorted by residual: dihedral pdb=" CA TRP E1506 " pdb=" C TRP E1506 " pdb=" N VAL E1507 " pdb=" CA VAL E1507 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP C1506 " pdb=" C TRP C1506 " pdb=" N VAL C1507 " pdb=" CA VAL C1507 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP A1506 " pdb=" C TRP A1506 " pdb=" N VAL A1507 " pdb=" CA VAL A1507 " ideal model delta harmonic sigma weight residual -180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 21648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3898 0.054 - 0.109: 1415 0.109 - 0.163: 288 0.163 - 0.218: 54 0.218 - 0.272: 12 Chirality restraints: 5667 Sorted by residual: chirality pdb=" CA PHE E2205 " pdb=" N PHE E2205 " pdb=" C PHE E2205 " pdb=" CB PHE E2205 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PHE A2205 " pdb=" N PHE A2205 " pdb=" C PHE A2205 " pdb=" CB PHE A2205 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA PHE C2205 " pdb=" N PHE C2205 " pdb=" C PHE C2205 " pdb=" CB PHE C2205 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5664 not shown) Planarity restraints: 6246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C2455 " -0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO C2456 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C2456 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C2456 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A2455 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A2456 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A2456 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A2456 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E2455 " 0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO E2456 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E2456 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E2456 " 0.057 5.00e-02 4.00e+02 ... (remaining 6243 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7665 2.78 - 3.31: 33127 3.31 - 3.84: 58159 3.84 - 4.37: 66494 4.37 - 4.90: 111107 Nonbonded interactions: 276552 Sorted by model distance: nonbonded pdb=" OG SER C2535 " pdb=" OG1 THR C2538 " model vdw 2.247 3.040 nonbonded pdb=" OG SER A2535 " pdb=" OG1 THR A2538 " model vdw 2.247 3.040 nonbonded pdb=" OG SER E2535 " pdb=" OG1 THR E2538 " model vdw 2.247 3.040 nonbonded pdb=" O LEU C1161 " pdb=" NE2 GLN C1293 " model vdw 2.292 3.120 nonbonded pdb=" O LEU A1161 " pdb=" NE2 GLN A1293 " model vdw 2.292 3.120 ... (remaining 276547 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 5.430 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 46.980 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 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 : 0.006 0.090 36591 Z= 0.269 Angle : 1.042 13.441 49752 Z= 0.526 Chirality : 0.058 0.272 5667 Planarity : 0.007 0.093 6246 Dihedral : 10.173 78.092 12912 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.25 % Allowed : 4.59 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -4.41 (0.09), residues: 4434 helix: -2.45 (0.07), residues: 2586 sheet: -3.56 (0.29), residues: 168 loop : -3.48 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 846 TYR 0.029 0.003 TYR C1184 PHE 0.031 0.003 PHE E2205 TRP 0.037 0.004 TRP A2542 HIS 0.012 0.002 HIS A2340 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.27 (36588) covalent geometry : angle 1.04227 / 0.53 (49746) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 0.92474 / 0.49 ( 6) hydrogen bonds : bond 0.14896 / 10.11 ( 2028) hydrogen bonds : angle 7.05207 / 4.94 ( 6003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1051 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 ARG cc_start: 0.6083 (mtt180) cc_final: 0.5802 (ptt-90) REVERT: A 858 CYS cc_start: 0.8729 (m) cc_final: 0.8432 (m) REVERT: A 870 LYS cc_start: 0.2274 (mttt) cc_final: 0.2013 (mptt) REVERT: A 910 ASN cc_start: 0.7957 (t0) cc_final: 0.7532 (m-40) REVERT: A 975 LEU cc_start: 0.7678 (tm) cc_final: 0.7467 (mm) REVERT: A 1054 MET cc_start: 0.4192 (mmm) cc_final: 0.3756 (mpp) REVERT: A 1093 ASN cc_start: 0.7360 (m110) cc_final: 0.7108 (m-40) REVERT: A 1320 PHE cc_start: 0.7556 (t80) cc_final: 0.7299 (t80) REVERT: A 1342 LEU cc_start: 0.8826 (mt) cc_final: 0.8584 (tp) REVERT: A 1348 GLN cc_start: 0.8123 (mt0) cc_final: 0.7282 (mt0) REVERT: A 1349 MET cc_start: 0.8509 (mmm) cc_final: 0.8030 (mmm) REVERT: A 1495 MET cc_start: 0.3677 (ptt) cc_final: 0.2792 (ptm) REVERT: A 1544 GLU cc_start: 0.7635 (tt0) cc_final: 0.7167 (tm-30) REVERT: A 1716 LEU cc_start: 0.7738 (mt) cc_final: 0.7497 (mp) REVERT: A 1740 MET cc_start: 0.7978 (tpt) cc_final: 0.6361 (ttm) REVERT: A 1755 ASN cc_start: 0.5017 (m-40) cc_final: 0.4520 (m-40) REVERT: A 1791 MET cc_start: 0.6486 (ptp) cc_final: 0.6030 (ptm) REVERT: A 1952 GLN cc_start: 0.1783 (pt0) cc_final: 0.1309 (mp10) REVERT: A 1980 MET cc_start: 0.6350 (mtp) cc_final: 0.6119 (mtp) REVERT: A 1984 ASP cc_start: 0.7677 (m-30) cc_final: 0.7127 (m-30) REVERT: A 1996 TRP cc_start: 0.4566 (t-100) cc_final: 0.4221 (t-100) REVERT: A 2062 PHE cc_start: 0.6664 (m-80) cc_final: 0.6008 (m-80) REVERT: A 2191 MET cc_start: 0.5081 (ptt) cc_final: 0.4093 (ttm) REVERT: A 2222 GLN cc_start: 0.6020 (mt0) cc_final: 0.5599 (pp30) REVERT: A 2231 LYS cc_start: 0.7926 (mttt) cc_final: 0.7542 (mtmm) REVERT: A 2276 TYR cc_start: 0.6652 (m-80) cc_final: 0.6304 (m-10) REVERT: A 2285 GLN cc_start: 0.6290 (mt0) cc_final: 0.6055 (mm110) REVERT: A 2314 ASP cc_start: 0.7692 (m-30) cc_final: 0.7350 (p0) REVERT: A 2323 PHE cc_start: 0.6832 (m-80) cc_final: 0.6331 (m-80) REVERT: A 2333 VAL cc_start: 0.6156 (t) cc_final: 0.5771 (p) REVERT: A 2352 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7353 (tpm170) REVERT: A 2353 GLN cc_start: 0.7638 (mt0) cc_final: 0.7392 (tt0) REVERT: A 2356 GLN cc_start: 0.7473 (mt0) cc_final: 0.7180 (mt0) REVERT: A 2365 SER cc_start: 0.8469 (p) cc_final: 0.8158 (m) REVERT: A 2430 TRP cc_start: 0.5754 (m100) cc_final: 0.5157 (m100) REVERT: A 2434 LEU cc_start: 0.6610 (mt) cc_final: 0.6277 (mt) REVERT: A 2451 ASP cc_start: 0.5684 (m-30) cc_final: 0.5138 (t70) REVERT: A 2485 PHE cc_start: 0.6442 (m-10) cc_final: 0.6133 (m-10) REVERT: A 2492 ILE cc_start: 0.7849 (mt) cc_final: 0.7556 (mt) REVERT: A 2505 LYS cc_start: 0.7389 (mttt) cc_final: 0.7181 (mtpp) REVERT: A 2520 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 860 ILE cc_start: 0.2684 (mt) cc_final: 0.2204 (mt) REVERT: C 946 HIS cc_start: -0.2913 (m90) cc_final: -0.3468 (m170) REVERT: C 1031 ARG cc_start: 0.3468 (mtt180) cc_final: 0.3178 (ptm160) REVERT: C 1094 LEU cc_start: 0.2455 (tp) cc_final: 0.2170 (mp) REVERT: C 1210 TRP cc_start: 0.3676 (t-100) cc_final: 0.3284 (t-100) REVERT: C 1261 PRO cc_start: 0.4263 (Cg_endo) cc_final: 0.3759 (Cg_exo) REVERT: C 1347 ARG cc_start: 0.6159 (mtt180) cc_final: 0.5671 (ttp80) REVERT: C 1495 MET cc_start: 0.2876 (ptt) cc_final: 0.2527 (mmp) REVERT: C 1668 GLN cc_start: 0.5242 (mp-120) cc_final: 0.4927 (pt0) REVERT: C 1695 ILE cc_start: 0.3907 (mt) cc_final: 0.3383 (tt) REVERT: C 1740 MET cc_start: 0.2909 (tpt) cc_final: 0.2698 (mmm) REVERT: C 1976 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (m) REVERT: C 1977 TYR cc_start: 0.7659 (t80) cc_final: 0.7315 (t80) REVERT: C 1980 MET cc_start: 0.6562 (mtp) cc_final: 0.6327 (mtp) REVERT: C 1984 ASP cc_start: 0.7934 (m-30) cc_final: 0.7713 (m-30) REVERT: C 2083 TYR cc_start: 0.6016 (t80) cc_final: 0.5663 (t80) REVERT: C 2120 PHE cc_start: 0.7982 (m-80) cc_final: 0.7349 (m-80) REVERT: C 2197 LEU cc_start: 0.8633 (tm) cc_final: 0.8343 (mp) REVERT: C 2257 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6958 (mm-30) REVERT: C 2268 LEU cc_start: 0.8092 (mt) cc_final: 0.7742 (mt) REVERT: C 2324 GLN cc_start: 0.6299 (mt0) cc_final: 0.5071 (tp40) REVERT: C 2356 GLN cc_start: 0.6432 (mt0) cc_final: 0.6050 (mt0) REVERT: C 2357 LEU cc_start: 0.7282 (mt) cc_final: 0.6991 (mt) REVERT: C 2385 ASN cc_start: 0.6747 (m-40) cc_final: 0.5826 (m-40) REVERT: C 2387 VAL cc_start: 0.5067 (t) cc_final: 0.4483 (m) REVERT: C 2391 GLN cc_start: 0.6475 (mt0) cc_final: 0.6005 (mp-120) REVERT: C 2395 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6836 (tp30) REVERT: C 2431 VAL cc_start: 0.7198 (t) cc_final: 0.6073 (t) REVERT: C 2443 LEU cc_start: 0.7642 (mt) cc_final: 0.7382 (mp) REVERT: C 2499 CYS cc_start: 0.7109 (m) cc_final: 0.5783 (m) REVERT: C 2528 LYS cc_start: 0.6741 (mtpm) cc_final: 0.6280 (tptt) REVERT: C 2539 MET cc_start: 0.7589 (tpp) cc_final: 0.6764 (tpp) REVERT: C 2541 LYS cc_start: 0.5098 (mttt) cc_final: 0.4398 (tttm) REVERT: E 782 ARG cc_start: 0.1643 (mtt180) cc_final: 0.1329 (mtp-110) REVERT: E 843 PRO cc_start: 0.3729 (Cg_endo) cc_final: 0.3196 (Cg_exo) REVERT: E 925 GLN cc_start: -0.0011 (mt0) cc_final: -0.0271 (pp30) REVERT: E 1038 LEU cc_start: 0.1423 (mt) cc_final: 0.1215 (tt) REVERT: E 1147 ARG cc_start: 0.3143 (ptt-90) cc_final: 0.2814 (ptp90) REVERT: E 1264 MET cc_start: 0.1089 (ptm) cc_final: 0.0247 (ttm) REVERT: E 1358 LYS cc_start: 0.8033 (mttt) cc_final: 0.7707 (ttmm) REVERT: E 1502 MET cc_start: 0.1164 (tpt) cc_final: 0.0829 (ptm) REVERT: E 1731 MET cc_start: 0.4282 (mmm) cc_final: 0.3925 (mtm) REVERT: E 1774 LEU cc_start: 0.3101 (tt) cc_final: 0.2733 (mm) REVERT: E 1791 MET cc_start: 0.4398 (ptp) cc_final: 0.4101 (ppp) REVERT: E 1980 MET cc_start: 0.6004 (mtp) cc_final: 0.5560 (mpp) REVERT: E 1996 TRP cc_start: 0.3200 (t-100) cc_final: 0.2513 (m-10) REVERT: E 2133 GLU cc_start: 0.7105 (mp0) cc_final: 0.6459 (mp0) REVERT: E 2134 LEU cc_start: 0.7529 (mt) cc_final: 0.7230 (mt) REVERT: E 2170 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6990 (mm-30) REVERT: E 2182 LYS cc_start: 0.7858 (tttt) cc_final: 0.6974 (pttp) REVERT: E 2230 LEU cc_start: 0.8043 (mt) cc_final: 0.7780 (tp) REVERT: E 2256 TYR cc_start: 0.4812 (m-80) cc_final: 0.4459 (t80) REVERT: E 2258 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7026 (mm-30) REVERT: E 2270 MET cc_start: 0.5052 (mmm) cc_final: 0.4174 (mtp) REVERT: E 2279 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6142 (mm-30) REVERT: E 2287 GLU cc_start: 0.5017 (mt-10) cc_final: 0.4531 (tt0) REVERT: E 2304 MET cc_start: 0.6095 (mmm) cc_final: 0.5663 (ttt) REVERT: E 2341 THR cc_start: 0.4483 (p) cc_final: 0.4195 (m) REVERT: E 2375 TYR cc_start: 0.4630 (m-80) cc_final: 0.4342 (m-80) REVERT: E 2390 LEU cc_start: 0.4135 (mt) cc_final: 0.3741 (mt) REVERT: E 2520 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7599 (pt0) REVERT: E 2523 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 2528 LYS cc_start: 0.6937 (mtpm) cc_final: 0.6585 (tptt) REVERT: E 2545 GLU cc_start: 0.7716 (tt0) cc_final: 0.7500 (tp30) outliers start: 9 outliers final: 2 residues processed: 1057 average time/residue: 0.2502 time to fit residues: 418.4028 Evaluate side-chains 612 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 609 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1976 VAL Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain E residue 2500 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 7.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 808 HIS ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 GLN A1145 HIS A1200 GLN A1206 GLN A1510 GLN A1543 GLN A2118 ASN A2177 GLN A2244 GLN A2262 GLN C 798 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 HIS C1138 ASN C1293 GLN C1503 GLN C1543 GLN C1698 ASN ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2435 GLN E 798 GLN E1013 HIS E1047 GLN E1120 GLN ** E1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2050 GLN E2096 GLN E2116 HIS E2181 GLN E2261 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.230924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.227089 restraints weight = 63051.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.226921 restraints weight = 119061.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.226516 restraints weight = 115746.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.226059 restraints weight = 119792.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.225693 restraints weight = 130213.039| |-----------------------------------------------------------------------------| r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5283 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36591 Z= 0.150 Angle : 0.724 11.759 49752 Z= 0.362 Chirality : 0.045 0.266 5667 Planarity : 0.006 0.063 6246 Dihedral : 5.917 52.448 4944 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.99 % Favored : 92.99 % Rotamer: Outliers : 3.17 % Allowed : 10.77 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.12), residues: 4434 helix: -0.38 (0.09), residues: 2676 sheet: -2.74 (0.32), residues: 174 loop : -3.18 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1347 TYR 0.023 0.002 TYR C 923 PHE 0.022 0.002 PHE C1729 TRP 0.020 0.002 TRP C2542 HIS 0.009 0.001 HIS A1145 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (36588) covalent geometry : angle 0.72322 / 0.36 (49746) SS BOND : bond 0.00522 / 0.25 ( 3) SS BOND : angle 2.37891 / 1.37 ( 6) hydrogen bonds : bond 0.04744 / 3.24 ( 2028) hydrogen bonds : angle 5.06419 / 3.52 ( 6003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 701 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 824 GLU cc_start: 0.6350 (tp30) cc_final: 0.6142 (tp30) REVERT: A 854 THR cc_start: 0.8308 (p) cc_final: 0.7088 (t) REVERT: A 885 PHE cc_start: 0.5513 (p90) cc_final: 0.5285 (p90) REVERT: A 1060 ILE cc_start: 0.6912 (tp) cc_final: 0.6252 (mm) REVERT: A 1177 ILE cc_start: 0.8318 (mt) cc_final: 0.8104 (mt) REVERT: A 1530 MET cc_start: 0.7759 (ptm) cc_final: 0.7369 (ttp) REVERT: A 1716 LEU cc_start: 0.9415 (mt) cc_final: 0.9173 (mp) REVERT: A 1745 TYR cc_start: 0.8242 (t80) cc_final: 0.7626 (t80) REVERT: A 1980 MET cc_start: 0.8488 (mtp) cc_final: 0.8225 (mtp) REVERT: A 1984 ASP cc_start: 0.7770 (m-30) cc_final: 0.7466 (m-30) REVERT: A 2062 PHE cc_start: 0.7085 (m-80) cc_final: 0.6752 (m-80) REVERT: A 2303 GLN cc_start: 0.5739 (OUTLIER) cc_final: 0.5421 (mp10) REVERT: A 2340 HIS cc_start: 0.4675 (t-90) cc_final: 0.4289 (t70) REVERT: A 2430 TRP cc_start: 0.6411 (m100) cc_final: 0.6066 (m100) REVERT: A 2495 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 2506 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8053 (tt) REVERT: C 865 MET cc_start: 0.3707 (mmt) cc_final: 0.3386 (mmm) REVERT: C 1005 ARG cc_start: 0.3180 (mmm-85) cc_final: 0.1339 (mmm-85) REVERT: C 1058 LEU cc_start: 0.3089 (mm) cc_final: 0.2759 (mt) REVERT: C 1238 MET cc_start: 0.1467 (ptp) cc_final: -0.0209 (tpp) REVERT: C 1717 TRP cc_start: 0.2319 (t60) cc_final: 0.1940 (t-100) REVERT: C 2035 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7392 (mmt180) REVERT: C 2052 VAL cc_start: 0.6727 (p) cc_final: 0.6442 (p) REVERT: C 2058 HIS cc_start: 0.5192 (m90) cc_final: 0.4801 (m-70) REVERT: C 2149 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7680 (tp) REVERT: C 2153 MET cc_start: 0.7960 (mmt) cc_final: 0.7745 (mtm) REVERT: C 2541 LYS cc_start: 0.6756 (mttt) cc_final: 0.6197 (tttm) REVERT: E 782 ARG cc_start: 0.4188 (mtt180) cc_final: 0.3436 (mtp-110) REVERT: E 997 MET cc_start: 0.4710 (ptt) cc_final: 0.3550 (ptm) REVERT: E 1731 MET cc_start: 0.4184 (mmm) cc_final: 0.3558 (mtm) REVERT: E 2429 TRP cc_start: 0.5225 (m-90) cc_final: 0.4541 (m-90) outliers start: 114 outliers final: 47 residues processed: 779 average time/residue: 0.2286 time to fit residues: 291.3952 Evaluate side-chains 585 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 535 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1525 LYS Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2303 GLN Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2295 ARG Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 1661 GLU Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2149 LEU Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2247 SER Chi-restraints excluded: chain E residue 2248 ILE Chi-restraints excluded: chain E residue 2309 TYR Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2540 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 420 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 169 optimal weight: 0.0470 chunk 120 optimal weight: 10.0000 chunk 400 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 927 HIS ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 GLN A1225 ASN A1315 GLN A1510 GLN A1655 HIS ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN A2118 ASN A2244 GLN A2285 GLN A2353 GLN C 910 ASN ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2050 GLN C2181 GLN C2356 GLN E 808 HIS E1200 GLN ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2018 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.228786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.224757 restraints weight = 62444.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.224558 restraints weight = 130094.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.224069 restraints weight = 120541.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.223675 restraints weight = 124949.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.223287 restraints weight = 126346.241| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36591 Z= 0.140 Angle : 0.683 14.071 49752 Z= 0.337 Chirality : 0.044 0.279 5667 Planarity : 0.005 0.066 6246 Dihedral : 5.422 41.613 4942 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.88 % Favored : 93.10 % Rotamer: Outliers : 3.92 % Allowed : 12.77 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.33 (0.12), residues: 4434 helix: 0.38 (0.10), residues: 2709 sheet: -2.58 (0.30), residues: 198 loop : -3.00 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2295 TYR 0.019 0.001 TYR A1970 PHE 0.022 0.002 PHE C2163 TRP 0.028 0.002 TRP A1754 HIS 0.016 0.001 HIS C2116 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (36588) covalent geometry : angle 0.68168 / 0.34 (49746) SS BOND : bond 0.02099 / 1.07 ( 3) SS BOND : angle 3.48136 / 1.93 ( 6) hydrogen bonds : bond 0.04204 / 2.89 ( 2028) hydrogen bonds : angle 4.73662 / 3.30 ( 6003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 589 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 THR cc_start: 0.7747 (p) cc_final: 0.7410 (t) REVERT: A 1084 ASP cc_start: 0.5539 (m-30) cc_final: 0.5015 (m-30) REVERT: A 1142 ASN cc_start: 0.6287 (t0) cc_final: 0.5852 (t0) REVERT: A 1495 MET cc_start: 0.5429 (ptt) cc_final: 0.5217 (ptm) REVERT: A 1530 MET cc_start: 0.7663 (ptm) cc_final: 0.7260 (ttp) REVERT: A 1655 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5432 (t70) REVERT: A 1745 TYR cc_start: 0.8370 (t80) cc_final: 0.7886 (t80) REVERT: A 1755 ASN cc_start: 0.4572 (m-40) cc_final: 0.4078 (m-40) REVERT: A 1980 MET cc_start: 0.8418 (mtp) cc_final: 0.8143 (mtm) REVERT: A 1984 ASP cc_start: 0.7667 (m-30) cc_final: 0.7386 (m-30) REVERT: A 2062 PHE cc_start: 0.7189 (m-80) cc_final: 0.6834 (m-80) REVERT: A 2270 MET cc_start: 0.4196 (mmt) cc_final: 0.3971 (mmt) REVERT: A 2340 HIS cc_start: 0.4326 (t-90) cc_final: 0.3993 (t70) REVERT: C 794 LEU cc_start: 0.1591 (OUTLIER) cc_final: 0.0790 (mp) REVERT: C 1005 ARG cc_start: 0.3004 (mmm-85) cc_final: 0.1273 (mmm-85) REVERT: C 1152 MET cc_start: 0.5152 (tmm) cc_final: 0.2136 (mtm) REVERT: C 1153 LEU cc_start: 0.2025 (OUTLIER) cc_final: 0.1494 (tp) REVERT: C 1215 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4703 (mp) REVERT: C 1238 MET cc_start: 0.1374 (ptp) cc_final: -0.0260 (tpp) REVERT: C 1704 SER cc_start: 0.6776 (p) cc_final: 0.6323 (m) REVERT: C 1717 TRP cc_start: 0.2475 (t60) cc_final: 0.2042 (t-100) REVERT: C 2035 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7505 (mmt180) REVERT: C 2149 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 2206 PRO cc_start: 0.5886 (Cg_endo) cc_final: 0.5446 (Cg_endo) REVERT: C 2391 GLN cc_start: 0.6745 (mp10) cc_final: 0.6228 (mp-120) REVERT: E 782 ARG cc_start: 0.4449 (mtt180) cc_final: 0.3408 (mtp-110) REVERT: E 856 TRP cc_start: 0.4906 (m100) cc_final: 0.4171 (m-90) REVERT: E 1530 MET cc_start: 0.1957 (ptt) cc_final: 0.1264 (ptp) REVERT: E 2321 TRP cc_start: 0.5847 (m-10) cc_final: 0.5426 (m-90) REVERT: E 2375 TYR cc_start: 0.3906 (m-80) cc_final: 0.3646 (m-80) REVERT: E 2429 TRP cc_start: 0.5280 (m-90) cc_final: 0.4617 (m-90) REVERT: E 2485 PHE cc_start: 0.7952 (m-10) cc_final: 0.7219 (m-80) outliers start: 141 outliers final: 67 residues processed: 693 average time/residue: 0.2094 time to fit residues: 244.6414 Evaluate side-chains 583 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 511 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1952 GLN Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2118 ASN Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2244 GLN Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1695 ILE Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2119 LEU Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2183 LYS Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain E residue 997 MET Chi-restraints excluded: chain E residue 1182 LEU Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2171 THR Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2432 ILE Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 246 optimal weight: 0.0370 chunk 107 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 403 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 164 optimal weight: 8.9990 chunk 374 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 446 optimal weight: 0.5980 chunk 445 optimal weight: 0.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1324 ASN A1344 GLN A1527 HIS A1655 HIS ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 GLN A2285 GLN A2353 GLN C 808 HIS C 927 HIS C1963 HIS E1304 HIS ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.227687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.223629 restraints weight = 62212.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.223274 restraints weight = 131510.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.222645 restraints weight = 139422.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222270 restraints weight = 128237.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.221818 restraints weight = 128192.411| |-----------------------------------------------------------------------------| r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5408 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36591 Z= 0.130 Angle : 0.668 14.044 49752 Z= 0.326 Chirality : 0.043 0.230 5667 Planarity : 0.004 0.070 6246 Dihedral : 5.165 40.174 4942 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.05 % Rotamer: Outliers : 3.70 % Allowed : 14.16 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 (0.13), residues: 4434 helix: 0.75 (0.10), residues: 2712 sheet: -2.33 (0.32), residues: 198 loop : -2.90 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1347 TYR 0.016 0.001 TYR A1970 PHE 0.023 0.001 PHE E2205 TRP 0.036 0.002 TRP A1754 HIS 0.019 0.001 HIS A1655 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (36588) covalent geometry : angle 0.66735 / 0.33 (49746) SS BOND : bond 0.00281 / 0.14 ( 3) SS BOND : angle 1.88725 / 1.08 ( 6) hydrogen bonds : bond 0.03934 / 2.71 ( 2028) hydrogen bonds : angle 4.59120 / 3.21 ( 6003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 568 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7466 (tp-100) REVERT: A 844 ARG cc_start: 0.5144 (ptt-90) cc_final: 0.4530 (ppt170) REVERT: A 1084 ASP cc_start: 0.5520 (m-30) cc_final: 0.5058 (m-30) REVERT: A 1545 LEU cc_start: 0.7671 (mm) cc_final: 0.7449 (mm) REVERT: A 1745 TYR cc_start: 0.8470 (t80) cc_final: 0.8075 (t80) REVERT: A 1755 ASN cc_start: 0.3949 (m-40) cc_final: 0.3576 (m-40) REVERT: A 1980 MET cc_start: 0.8333 (mtp) cc_final: 0.8042 (mtm) REVERT: A 2062 PHE cc_start: 0.7068 (m-80) cc_final: 0.6677 (m-80) REVERT: A 2161 ASN cc_start: 0.8504 (t0) cc_final: 0.8052 (t0) REVERT: A 2506 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8166 (tt) REVERT: C 794 LEU cc_start: 0.1526 (OUTLIER) cc_final: 0.0770 (mp) REVERT: C 1005 ARG cc_start: 0.2781 (mmm-85) cc_final: 0.0946 (mmm-85) REVERT: C 1153 LEU cc_start: 0.2008 (OUTLIER) cc_final: 0.1582 (tp) REVERT: C 1215 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4775 (mp) REVERT: C 1238 MET cc_start: 0.1903 (OUTLIER) cc_final: 0.0370 (tpp) REVERT: C 1704 SER cc_start: 0.6692 (p) cc_final: 0.6307 (m) REVERT: C 1717 TRP cc_start: 0.2509 (t60) cc_final: 0.2015 (t-100) REVERT: C 2035 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7662 (mmt180) REVERT: C 2052 VAL cc_start: 0.6707 (p) cc_final: 0.6446 (p) REVERT: C 2149 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8274 (tp) REVERT: C 2206 PRO cc_start: 0.5716 (Cg_endo) cc_final: 0.5300 (Cg_endo) REVERT: C 2391 GLN cc_start: 0.6643 (mp10) cc_final: 0.6147 (mp-120) REVERT: C 2531 PHE cc_start: 0.8527 (t80) cc_final: 0.8244 (t80) REVERT: E 782 ARG cc_start: 0.4318 (mtt180) cc_final: 0.3254 (mtp-110) REVERT: E 856 TRP cc_start: 0.4945 (m100) cc_final: 0.4011 (m-90) REVERT: E 997 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.4196 (ptm) REVERT: E 1152 MET cc_start: 0.5521 (ppp) cc_final: 0.5307 (ppp) REVERT: E 1530 MET cc_start: 0.2001 (ptt) cc_final: 0.1241 (ptp) REVERT: E 1791 MET cc_start: 0.3047 (ptp) cc_final: 0.2448 (ppp) REVERT: E 1805 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4672 (tt) REVERT: E 2098 ARG cc_start: 0.6446 (ptt-90) cc_final: 0.5941 (mtm110) REVERT: E 2149 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8720 (tp) REVERT: E 2194 LEU cc_start: 0.8884 (tp) cc_final: 0.8670 (tt) REVERT: E 2216 VAL cc_start: 0.3676 (OUTLIER) cc_final: 0.3356 (t) REVERT: E 2293 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7399 (mp) REVERT: E 2321 TRP cc_start: 0.5959 (m-10) cc_final: 0.5479 (m-90) REVERT: E 2375 TYR cc_start: 0.3763 (m-80) cc_final: 0.3347 (m-80) REVERT: E 2485 PHE cc_start: 0.7854 (m-10) cc_final: 0.7343 (m-80) outliers start: 133 outliers final: 67 residues processed: 665 average time/residue: 0.2129 time to fit residues: 239.7840 Evaluate side-chains 588 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 510 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2183 LYS Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 997 MET Chi-restraints excluded: chain E residue 1182 LEU Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1661 GLU Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1788 VAL Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 2149 LEU Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2216 VAL Chi-restraints excluded: chain E residue 2293 LEU Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 413 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 321 optimal weight: 0.6980 chunk 404 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1324 ASN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 GLN C 910 ASN C 927 HIS C1304 HIS E1107 GLN E1206 GLN ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2027 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.227445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.223439 restraints weight = 61951.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.223228 restraints weight = 129982.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.222618 restraints weight = 121642.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.222211 restraints weight = 126607.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.221796 restraints weight = 122278.729| |-----------------------------------------------------------------------------| r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36591 Z= 0.128 Angle : 0.660 13.402 49752 Z= 0.320 Chirality : 0.043 0.230 5667 Planarity : 0.004 0.049 6246 Dihedral : 4.976 38.971 4942 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.61 % Favored : 93.37 % Rotamer: Outliers : 3.53 % Allowed : 15.39 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.62 (0.13), residues: 4434 helix: 0.96 (0.10), residues: 2715 sheet: -1.96 (0.34), residues: 192 loop : -2.81 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1724 TYR 0.040 0.001 TYR C1977 PHE 0.023 0.001 PHE C1143 TRP 0.037 0.001 TRP A1754 HIS 0.020 0.001 HIS A1655 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (36588) covalent geometry : angle 0.65947 / 0.32 (49746) SS BOND : bond 0.00251 / 0.13 ( 3) SS BOND : angle 1.21494 / 0.71 ( 6) hydrogen bonds : bond 0.03829 / 2.63 ( 2028) hydrogen bonds : angle 4.49746 / 3.15 ( 6003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 551 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7507 (tp-100) REVERT: A 844 ARG cc_start: 0.5236 (ptt-90) cc_final: 0.4696 (ppt170) REVERT: A 1054 MET cc_start: 0.5778 (mpp) cc_final: 0.5543 (mpp) REVERT: A 1084 ASP cc_start: 0.5511 (m-30) cc_final: 0.5036 (m-30) REVERT: A 1209 LEU cc_start: 0.8470 (tt) cc_final: 0.8241 (tp) REVERT: A 1545 LEU cc_start: 0.7688 (mm) cc_final: 0.7474 (mm) REVERT: A 1745 TYR cc_start: 0.8480 (t80) cc_final: 0.8134 (t80) REVERT: A 1755 ASN cc_start: 0.4159 (m-40) cc_final: 0.3820 (m-40) REVERT: A 2053 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9004 (tp) REVERT: A 2062 PHE cc_start: 0.7060 (m-80) cc_final: 0.6658 (m-80) REVERT: A 2118 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7959 (t0) REVERT: A 2506 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 794 LEU cc_start: 0.1538 (OUTLIER) cc_final: 0.0766 (mp) REVERT: C 1005 ARG cc_start: 0.2669 (mmm-85) cc_final: 0.0783 (mmm-85) REVERT: C 1152 MET cc_start: 0.4865 (tmm) cc_final: 0.1944 (mtm) REVERT: C 1153 LEU cc_start: 0.1828 (OUTLIER) cc_final: 0.1584 (tp) REVERT: C 1215 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4440 (mp) REVERT: C 1238 MET cc_start: 0.1848 (ptp) cc_final: 0.0357 (tpp) REVERT: C 1323 TYR cc_start: 0.3820 (m-80) cc_final: 0.2864 (m-80) REVERT: C 1704 SER cc_start: 0.6837 (p) cc_final: 0.6428 (m) REVERT: C 1717 TRP cc_start: 0.2520 (t60) cc_final: 0.1947 (t-100) REVERT: C 2035 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7719 (mmt180) REVERT: C 2149 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8477 (tp) REVERT: C 2206 PRO cc_start: 0.5769 (Cg_endo) cc_final: 0.5409 (Cg_endo) REVERT: C 2270 MET cc_start: 0.5246 (mmm) cc_final: 0.4773 (mpp) REVERT: C 2391 GLN cc_start: 0.6660 (mp10) cc_final: 0.6105 (mp-120) REVERT: C 2475 LEU cc_start: 0.7783 (mt) cc_final: 0.7201 (tp) REVERT: C 2531 PHE cc_start: 0.8540 (t80) cc_final: 0.8234 (t80) REVERT: E 782 ARG cc_start: 0.4275 (mtt180) cc_final: 0.3204 (mtp-110) REVERT: E 856 TRP cc_start: 0.4934 (m100) cc_final: 0.3973 (m-90) REVERT: E 997 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.3602 (ptm) REVERT: E 1152 MET cc_start: 0.5772 (ppp) cc_final: 0.5465 (ppp) REVERT: E 1530 MET cc_start: 0.2060 (ptt) cc_final: 0.1323 (ptp) REVERT: E 1791 MET cc_start: 0.2942 (ptp) cc_final: 0.2057 (ppp) REVERT: E 1805 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4727 (tt) REVERT: E 2098 ARG cc_start: 0.6597 (ptt-90) cc_final: 0.5863 (ttp-110) REVERT: E 2149 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8914 (tp) REVERT: E 2194 LEU cc_start: 0.8910 (tp) cc_final: 0.8701 (tt) REVERT: E 2216 VAL cc_start: 0.3343 (OUTLIER) cc_final: 0.3026 (t) REVERT: E 2321 TRP cc_start: 0.5928 (m-10) cc_final: 0.5482 (m-90) REVERT: E 2375 TYR cc_start: 0.3836 (m-80) cc_final: 0.3509 (m-80) REVERT: E 2479 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7952 (tptt) REVERT: E 2485 PHE cc_start: 0.8006 (m-10) cc_final: 0.7313 (m-80) outliers start: 127 outliers final: 79 residues processed: 644 average time/residue: 0.2027 time to fit residues: 221.9775 Evaluate side-chains 600 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 509 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2118 ASN Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1695 ILE Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2153 MET Chi-restraints excluded: chain C residue 2183 LYS Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 997 MET Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1101 LEU Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1788 VAL Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 1976 VAL Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2065 LEU Chi-restraints excluded: chain E residue 2149 LEU Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2216 VAL Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2432 ILE Chi-restraints excluded: chain E residue 2479 LYS Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2540 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 312 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 397 optimal weight: 7.9990 chunk 420 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 368 optimal weight: 5.9990 chunk 350 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN A1225 ASN A1324 ASN A1510 GLN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 GLN A2370 HIS C 798 GLN C 927 HIS C2322 ASN ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2018 GLN E2303 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.219414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.215131 restraints weight = 61545.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.214362 restraints weight = 147437.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.211817 restraints weight = 148843.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.209001 restraints weight = 136391.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.207382 restraints weight = 111167.298| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 36591 Z= 0.237 Angle : 0.791 11.677 49752 Z= 0.394 Chirality : 0.048 0.332 5667 Planarity : 0.006 0.066 6246 Dihedral : 5.404 37.281 4942 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.07 % Favored : 91.90 % Rotamer: Outliers : 4.17 % Allowed : 15.53 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.02 (0.12), residues: 4434 helix: 0.62 (0.10), residues: 2718 sheet: -2.11 (0.36), residues: 174 loop : -2.92 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1528 TYR 0.023 0.002 TYR E1359 PHE 0.030 0.003 PHE A1747 TRP 0.040 0.003 TRP A1754 HIS 0.008 0.001 HIS A1796 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (36588) covalent geometry : angle 0.79106 / 0.39 (49746) SS BOND : bond 0.00103 / 0.05 ( 3) SS BOND : angle 1.17625 / 0.69 ( 6) hydrogen bonds : bond 0.04559 / 3.17 ( 2028) hydrogen bonds : angle 4.86173 / 3.41 ( 6003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 512 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 812 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 845 PHE cc_start: 0.7472 (t80) cc_final: 0.7190 (t80) REVERT: A 1054 MET cc_start: 0.6514 (mpp) cc_final: 0.5775 (mmt) REVERT: A 1060 ILE cc_start: 0.7175 (tp) cc_final: 0.6896 (mm) REVERT: A 1244 TRP cc_start: 0.6174 (t-100) cc_final: 0.5052 (m-90) REVERT: A 2047 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.8900 (mp) REVERT: A 2447 VAL cc_start: 0.6491 (t) cc_final: 0.6276 (t) REVERT: A 2485 PHE cc_start: 0.7999 (m-10) cc_final: 0.7754 (m-10) REVERT: A 2506 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8449 (tt) REVERT: C 794 LEU cc_start: 0.1589 (OUTLIER) cc_final: 0.0635 (mp) REVERT: C 1005 ARG cc_start: 0.2516 (mmm-85) cc_final: 0.0727 (mmm-85) REVERT: C 1153 LEU cc_start: 0.1752 (OUTLIER) cc_final: 0.1376 (tp) REVERT: C 1215 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4707 (mp) REVERT: C 1238 MET cc_start: 0.1658 (OUTLIER) cc_final: 0.0326 (tpp) REVERT: C 1265 MET cc_start: 0.3768 (OUTLIER) cc_final: 0.3453 (ptp) REVERT: C 1704 SER cc_start: 0.7019 (p) cc_final: 0.6728 (m) REVERT: C 2033 ILE cc_start: 0.8424 (mt) cc_final: 0.8115 (mm) REVERT: C 2035 ARG cc_start: 0.8294 (mmm160) cc_final: 0.8039 (mmt180) REVERT: C 2206 PRO cc_start: 0.6021 (Cg_exo) cc_final: 0.5673 (Cg_endo) REVERT: E 782 ARG cc_start: 0.4486 (mtt180) cc_final: 0.2959 (mtp-110) REVERT: E 1054 MET cc_start: 0.4748 (ptp) cc_final: 0.4518 (ptp) REVERT: E 1530 MET cc_start: 0.2245 (ptt) cc_final: 0.1296 (ptp) REVERT: E 1805 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4916 (tt) REVERT: E 2098 ARG cc_start: 0.6741 (ptt-90) cc_final: 0.6133 (ttp-110) REVERT: E 2216 VAL cc_start: 0.3903 (OUTLIER) cc_final: 0.3597 (t) REVERT: E 2230 LEU cc_start: 0.7105 (mm) cc_final: 0.6876 (mm) REVERT: E 2321 TRP cc_start: 0.6384 (m-10) cc_final: 0.5740 (m-90) REVERT: E 2429 TRP cc_start: 0.5477 (m-90) cc_final: 0.4603 (m-90) REVERT: E 2446 MET cc_start: 0.6318 (tpp) cc_final: 0.5973 (tpp) REVERT: E 2479 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (tptt) outliers start: 150 outliers final: 95 residues processed: 618 average time/residue: 0.1961 time to fit residues: 206.9553 Evaluate side-chains 563 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 457 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1093 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1032 LEU Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1265 MET Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2183 LYS Chi-restraints excluded: chain C residue 2203 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2364 GLN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2474 VAL Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2542 TRP Chi-restraints excluded: chain E residue 1038 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1788 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 1976 VAL Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2103 THR Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2216 VAL Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2347 ASN Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2441 CYS Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2479 LYS Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2525 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 402 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 231 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN A1510 GLN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 GLN A2324 GLN C 927 HIS C1493 HIS ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 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 = 0.4581 r_free = 0.4581 target = 0.223865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.219734 restraints weight = 62069.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.219319 restraints weight = 137148.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.218551 restraints weight = 132515.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.210576 restraints weight = 141738.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.206687 restraints weight = 126276.162| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36591 Z= 0.127 Angle : 0.674 14.818 49752 Z= 0.326 Chirality : 0.043 0.232 5667 Planarity : 0.004 0.052 6246 Dihedral : 4.986 43.753 4942 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 3.06 % Allowed : 17.14 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.58 (0.13), residues: 4434 helix: 0.99 (0.10), residues: 2733 sheet: -1.89 (0.34), residues: 192 loop : -2.86 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1347 TYR 0.019 0.001 TYR E1359 PHE 0.027 0.001 PHE E2323 TRP 0.029 0.002 TRP A1119 HIS 0.009 0.001 HIS C2116 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (36588) covalent geometry : angle 0.67399 / 0.33 (49746) SS BOND : bond 0.00161 / 0.08 ( 3) SS BOND : angle 0.91985 / 0.54 ( 6) hydrogen bonds : bond 0.03782 / 2.60 ( 2028) hydrogen bonds : angle 4.52450 / 3.17 ( 6003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 524 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 GLN cc_start: 0.8000 (tp40) cc_final: 0.7335 (tp-100) REVERT: A 1054 MET cc_start: 0.6207 (mpp) cc_final: 0.5334 (mmt) REVERT: A 1060 ILE cc_start: 0.7555 (tp) cc_final: 0.7219 (mm) REVERT: A 1244 TRP cc_start: 0.6268 (t-100) cc_final: 0.5156 (m-90) REVERT: A 1745 TYR cc_start: 0.8574 (t80) cc_final: 0.8317 (t80) REVERT: A 2062 PHE cc_start: 0.7090 (m-80) cc_final: 0.6871 (m-80) REVERT: A 2129 PRO cc_start: 0.7387 (Cg_endo) cc_final: 0.7151 (Cg_exo) REVERT: A 2506 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 794 LEU cc_start: 0.1023 (OUTLIER) cc_final: 0.0538 (mp) REVERT: C 1005 ARG cc_start: 0.2069 (mmm-85) cc_final: 0.0182 (mmm-85) REVERT: C 1152 MET cc_start: 0.4909 (tmm) cc_final: 0.2200 (mtm) REVERT: C 1215 LEU cc_start: 0.5071 (OUTLIER) cc_final: 0.4670 (mp) REVERT: C 1238 MET cc_start: 0.1878 (OUTLIER) cc_final: 0.0493 (tpp) REVERT: C 1265 MET cc_start: 0.3099 (mtm) cc_final: 0.2836 (ptp) REVERT: C 1323 TYR cc_start: 0.4020 (m-80) cc_final: 0.3247 (m-80) REVERT: C 1704 SER cc_start: 0.7070 (p) cc_final: 0.6731 (m) REVERT: C 2127 LEU cc_start: 0.7565 (tt) cc_final: 0.7347 (tt) REVERT: C 2206 PRO cc_start: 0.5210 (Cg_exo) cc_final: 0.4854 (Cg_endo) REVERT: C 2391 GLN cc_start: 0.6844 (mp10) cc_final: 0.6343 (mp-120) REVERT: E 782 ARG cc_start: 0.4357 (mtt180) cc_final: 0.2931 (mtp-110) REVERT: E 1054 MET cc_start: 0.4537 (ptp) cc_final: 0.4268 (ptp) REVERT: E 1170 PHE cc_start: 0.1217 (OUTLIER) cc_final: 0.0697 (m-80) REVERT: E 1188 CYS cc_start: 0.0860 (OUTLIER) cc_final: 0.0319 (t) REVERT: E 1265 MET cc_start: 0.2314 (tpt) cc_final: 0.1451 (mtp) REVERT: E 1331 ILE cc_start: 0.5713 (OUTLIER) cc_final: 0.5142 (tp) REVERT: E 1530 MET cc_start: 0.2413 (ptt) cc_final: 0.1680 (ptp) REVERT: E 2098 ARG cc_start: 0.6467 (ptt-90) cc_final: 0.6059 (ttp-110) REVERT: E 2101 TYR cc_start: 0.5501 (m-80) cc_final: 0.5150 (m-10) REVERT: E 2241 MET cc_start: 0.5732 (mmm) cc_final: 0.5410 (mmm) REVERT: E 2321 TRP cc_start: 0.5946 (m-10) cc_final: 0.5472 (m-90) REVERT: E 2429 TRP cc_start: 0.5454 (m-90) cc_final: 0.4760 (m-90) REVERT: E 2539 MET cc_start: 0.7832 (mtp) cc_final: 0.7511 (mtp) outliers start: 110 outliers final: 67 residues processed: 605 average time/residue: 0.2064 time to fit residues: 212.4967 Evaluate side-chains 553 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 479 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2153 MET Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2542 TRP Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1170 PHE Chi-restraints excluded: chain E residue 1188 CYS Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1331 ILE Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2326 ASP Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 368 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 365 optimal weight: 9.9990 chunk 418 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 927 HIS C1093 ASN ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.220810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.216751 restraints weight = 61517.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.216372 restraints weight = 140164.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.215570 restraints weight = 130540.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.208643 restraints weight = 132761.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.205072 restraints weight = 122077.203| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36591 Z= 0.173 Angle : 0.723 14.937 49752 Z= 0.354 Chirality : 0.045 0.297 5667 Planarity : 0.005 0.052 6246 Dihedral : 5.056 43.534 4942 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.67 % Favored : 92.31 % Rotamer: Outliers : 2.95 % Allowed : 18.14 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.59 (0.13), residues: 4434 helix: 1.00 (0.10), residues: 2706 sheet: -1.86 (0.34), residues: 198 loop : -2.84 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1761 TYR 0.028 0.002 TYR E2375 PHE 0.027 0.002 PHE A1098 TRP 0.053 0.002 TRP C2429 HIS 0.008 0.001 HIS C2116 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (36588) covalent geometry : angle 0.72295 / 0.35 (49746) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 1.13222 / 0.66 ( 6) hydrogen bonds : bond 0.04058 / 2.82 ( 2028) hydrogen bonds : angle 4.65208 / 3.26 ( 6003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 500 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1054 MET cc_start: 0.6120 (mpp) cc_final: 0.5717 (mmt) REVERT: A 1244 TRP cc_start: 0.6347 (t-100) cc_final: 0.5092 (m-90) REVERT: A 2047 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 2506 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8427 (tt) REVERT: C 794 LEU cc_start: 0.1109 (OUTLIER) cc_final: 0.0579 (mp) REVERT: C 1005 ARG cc_start: 0.1968 (mmm-85) cc_final: 0.0193 (mmm-85) REVERT: C 1215 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4719 (mp) REVERT: C 1323 TYR cc_start: 0.3816 (m-80) cc_final: 0.3218 (m-80) REVERT: C 1747 PHE cc_start: 0.3401 (m-10) cc_final: 0.3064 (m-80) REVERT: C 2206 PRO cc_start: 0.5364 (Cg_exo) cc_final: 0.5012 (Cg_endo) REVERT: C 2239 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5794 (m-80) REVERT: C 2296 ILE cc_start: 0.6251 (pt) cc_final: 0.6044 (pt) REVERT: E 782 ARG cc_start: 0.4353 (mtt180) cc_final: 0.2830 (mtp-110) REVERT: E 1054 MET cc_start: 0.4897 (ptp) cc_final: 0.4620 (ptp) REVERT: E 1170 PHE cc_start: 0.1409 (OUTLIER) cc_final: 0.0959 (m-80) REVERT: E 1188 CYS cc_start: 0.1224 (OUTLIER) cc_final: 0.0613 (t) REVERT: E 1265 MET cc_start: 0.2345 (tpt) cc_final: 0.1552 (mtp) REVERT: E 1331 ILE cc_start: 0.5781 (OUTLIER) cc_final: 0.5130 (tp) REVERT: E 1530 MET cc_start: 0.2531 (ptt) cc_final: 0.1703 (ptp) REVERT: E 2031 MET cc_start: 0.6480 (mmm) cc_final: 0.5925 (mmm) REVERT: E 2098 ARG cc_start: 0.6664 (ptt-90) cc_final: 0.6245 (ttp-110) REVERT: E 2241 MET cc_start: 0.5779 (mmm) cc_final: 0.5418 (mmm) REVERT: E 2270 MET cc_start: 0.4308 (OUTLIER) cc_final: 0.3520 (mtp) REVERT: E 2321 TRP cc_start: 0.6139 (m-10) cc_final: 0.4872 (m100) REVERT: E 2429 TRP cc_start: 0.5396 (m-90) cc_final: 0.4619 (m-90) REVERT: E 2431 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7326 (p) outliers start: 106 outliers final: 80 residues processed: 573 average time/residue: 0.1991 time to fit residues: 194.2644 Evaluate side-chains 555 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 465 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain A residue 2467 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1032 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2364 GLN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2542 TRP Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1166 LEU Chi-restraints excluded: chain E residue 1170 PHE Chi-restraints excluded: chain E residue 1188 CYS Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1331 ILE Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 265 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 208 optimal weight: 0.3980 chunk 422 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 444 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 chunk 290 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 GLN C 927 HIS C1304 HIS ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 HIS ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.218199 restraints weight = 61569.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.217632 restraints weight = 144225.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.216904 restraints weight = 135491.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.210265 restraints weight = 133012.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.206508 restraints weight = 109289.680| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36591 Z= 0.141 Angle : 0.693 14.716 49752 Z= 0.337 Chirality : 0.044 0.282 5667 Planarity : 0.004 0.054 6246 Dihedral : 4.928 44.705 4942 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.70 % Favored : 93.28 % Rotamer: Outliers : 2.81 % Allowed : 18.59 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.48 (0.13), residues: 4434 helix: 1.05 (0.10), residues: 2742 sheet: -1.78 (0.35), residues: 198 loop : -2.82 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1121 TYR 0.031 0.001 TYR E1359 PHE 0.027 0.002 PHE C1143 TRP 0.044 0.002 TRP C2429 HIS 0.011 0.001 HIS C2116 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (36588) covalent geometry : angle 0.69291 / 0.34 (49746) SS BOND : bond 0.00170 / 0.09 ( 3) SS BOND : angle 1.03300 / 0.60 ( 6) hydrogen bonds : bond 0.03801 / 2.62 ( 2028) hydrogen bonds : angle 4.54545 / 3.19 ( 6003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 497 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1054 MET cc_start: 0.6113 (mpp) cc_final: 0.5539 (mmt) REVERT: A 1244 TRP cc_start: 0.6319 (t-100) cc_final: 0.5202 (m-90) REVERT: A 2270 MET cc_start: 0.4587 (mmt) cc_final: 0.4286 (mmt) REVERT: A 2285 GLN cc_start: 0.6343 (mm-40) cc_final: 0.6038 (mm110) REVERT: A 2506 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8362 (tt) REVERT: A 2539 MET cc_start: 0.9028 (tpp) cc_final: 0.8742 (ttp) REVERT: C 794 LEU cc_start: 0.0879 (OUTLIER) cc_final: 0.0412 (mp) REVERT: C 1005 ARG cc_start: 0.1971 (mmm-85) cc_final: 0.0153 (mmm-85) REVERT: C 1025 ARG cc_start: 0.4765 (mtm-85) cc_final: 0.4099 (mmm-85) REVERT: C 1215 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4770 (mp) REVERT: C 1323 TYR cc_start: 0.3768 (m-80) cc_final: 0.3176 (m-80) REVERT: C 1747 PHE cc_start: 0.3493 (m-10) cc_final: 0.3161 (m-80) REVERT: C 2206 PRO cc_start: 0.5189 (Cg_exo) cc_final: 0.4890 (Cg_endo) REVERT: C 2239 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5679 (m-80) REVERT: C 2296 ILE cc_start: 0.6187 (pt) cc_final: 0.5959 (pt) REVERT: C 2537 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8695 (mm-30) REVERT: E 782 ARG cc_start: 0.4318 (mtt180) cc_final: 0.2812 (mtp-110) REVERT: E 1054 MET cc_start: 0.4765 (ptp) cc_final: 0.4502 (ptp) REVERT: E 1170 PHE cc_start: 0.1459 (OUTLIER) cc_final: 0.0949 (m-80) REVERT: E 1188 CYS cc_start: 0.1201 (OUTLIER) cc_final: 0.0571 (t) REVERT: E 1265 MET cc_start: 0.2545 (tpt) cc_final: 0.1560 (mtp) REVERT: E 1296 ILE cc_start: 0.5163 (mm) cc_final: 0.4914 (mm) REVERT: E 1331 ILE cc_start: 0.5762 (OUTLIER) cc_final: 0.5135 (tp) REVERT: E 1530 MET cc_start: 0.2506 (ptt) cc_final: 0.1750 (ptp) REVERT: E 2031 MET cc_start: 0.6390 (mmm) cc_final: 0.5972 (mmm) REVERT: E 2098 ARG cc_start: 0.6699 (ptt-90) cc_final: 0.6352 (ttp-110) REVERT: E 2241 MET cc_start: 0.6063 (mmm) cc_final: 0.5723 (mmm) REVERT: E 2270 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4077 (mtp) REVERT: E 2321 TRP cc_start: 0.6063 (m-10) cc_final: 0.5402 (m-90) REVERT: E 2429 TRP cc_start: 0.5270 (m-90) cc_final: 0.4466 (m-90) REVERT: E 2431 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7298 (p) outliers start: 101 outliers final: 80 residues processed: 574 average time/residue: 0.2111 time to fit residues: 205.2948 Evaluate side-chains 562 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 472 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain A residue 2467 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 1032 LEU Chi-restraints excluded: chain C residue 1215 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2200 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2364 GLN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2537 GLU Chi-restraints excluded: chain C residue 2542 TRP Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1170 PHE Chi-restraints excluded: chain E residue 1188 CYS Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1331 ILE Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1533 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1788 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2326 ASP Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 440 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 373 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 144 optimal weight: 0.4980 chunk 297 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1324 ASN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2337 ASN C 927 HIS C1004 GLN C1304 HIS ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2116 HIS E 927 HIS E1145 HIS ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.223842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.219734 restraints weight = 61990.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.219530 restraints weight = 137790.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.218950 restraints weight = 129936.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.218465 restraints weight = 131220.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.218103 restraints weight = 122986.327| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36591 Z= 0.126 Angle : 0.680 15.019 49752 Z= 0.330 Chirality : 0.043 0.290 5667 Planarity : 0.004 0.052 6246 Dihedral : 4.742 45.248 4942 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.72 % Favored : 93.26 % Rotamer: Outliers : 2.50 % Allowed : 18.75 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.28 (0.13), residues: 4434 helix: 1.21 (0.10), residues: 2748 sheet: -1.60 (0.36), residues: 192 loop : -2.74 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2406 TYR 0.025 0.001 TYR E1359 PHE 0.027 0.001 PHE E 800 TRP 0.033 0.002 TRP E1016 HIS 0.010 0.001 HIS C2116 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (36588) covalent geometry : angle 0.68016 / 0.33 (49746) SS BOND : bond 0.00181 / 0.09 ( 3) SS BOND : angle 1.07565 / 0.62 ( 6) hydrogen bonds : bond 0.03621 / 2.50 ( 2028) hydrogen bonds : angle 4.43370 / 3.11 ( 6003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 524 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 PHE cc_start: 0.8140 (t80) cc_final: 0.7795 (t80) REVERT: A 1244 TRP cc_start: 0.6241 (t-100) cc_final: 0.5230 (m-90) REVERT: A 1320 PHE cc_start: 0.8007 (t80) cc_final: 0.7730 (t80) REVERT: A 2062 PHE cc_start: 0.7111 (m-80) cc_final: 0.6824 (m-80) REVERT: A 2506 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8348 (tt) REVERT: A 2539 MET cc_start: 0.8934 (tpp) cc_final: 0.8670 (ttp) REVERT: C 794 LEU cc_start: 0.1035 (OUTLIER) cc_final: 0.0782 (mp) REVERT: C 1005 ARG cc_start: 0.2670 (mmm-85) cc_final: 0.0908 (mmm-85) REVERT: C 1025 ARG cc_start: 0.4419 (mtm-85) cc_final: 0.4107 (mmm-85) REVERT: C 1323 TYR cc_start: 0.3510 (m-80) cc_final: 0.3186 (m-80) REVERT: C 2206 PRO cc_start: 0.5491 (Cg_exo) cc_final: 0.5271 (Cg_endo) REVERT: C 2239 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5931 (m-80) REVERT: C 2296 ILE cc_start: 0.6001 (pt) cc_final: 0.5783 (pt) REVERT: C 2391 GLN cc_start: 0.6608 (mp10) cc_final: 0.6145 (mp-120) REVERT: E 782 ARG cc_start: 0.4511 (mtt180) cc_final: 0.3012 (mtp-110) REVERT: E 856 TRP cc_start: 0.4770 (m100) cc_final: 0.3402 (m-90) REVERT: E 997 MET cc_start: 0.3961 (mmt) cc_final: 0.0975 (ptm) REVERT: E 1054 MET cc_start: 0.5216 (ptp) cc_final: 0.4993 (ptp) REVERT: E 1170 PHE cc_start: 0.1102 (OUTLIER) cc_final: 0.0564 (m-80) REVERT: E 1188 CYS cc_start: 0.1863 (OUTLIER) cc_final: 0.1140 (t) REVERT: E 1265 MET cc_start: 0.2404 (tpt) cc_final: 0.1215 (mtp) REVERT: E 1296 ILE cc_start: 0.4436 (mm) cc_final: 0.4207 (mm) REVERT: E 1791 MET cc_start: 0.4085 (mpp) cc_final: 0.3752 (mpp) REVERT: E 2031 MET cc_start: 0.6154 (mmm) cc_final: 0.5759 (mmm) REVERT: E 2098 ARG cc_start: 0.6591 (ptt-90) cc_final: 0.6158 (ttp-110) REVERT: E 2241 MET cc_start: 0.5908 (mmm) cc_final: 0.5565 (mmm) REVERT: E 2321 TRP cc_start: 0.5924 (m-10) cc_final: 0.5263 (m-90) REVERT: E 2429 TRP cc_start: 0.5250 (m-90) cc_final: 0.4580 (m-90) REVERT: E 2431 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7302 (p) outliers start: 90 outliers final: 67 residues processed: 594 average time/residue: 0.2129 time to fit residues: 214.4810 Evaluate side-chains 555 residues out of total 4041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 482 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 1032 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2364 GLN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2542 TRP Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1170 PHE Chi-restraints excluded: chain E residue 1188 CYS Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2326 ASP Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 124 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 408 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 chunk 35 optimal weight: 0.7980 chunk 361 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 GLN C 927 HIS ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS E1361 GLN E1526 HIS ** E1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.223071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218998 restraints weight = 61337.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.218632 restraints weight = 131247.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.217957 restraints weight = 134340.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.217568 restraints weight = 127086.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.217144 restraints weight = 116689.064| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36591 Z= 0.136 Angle : 0.693 14.556 49752 Z= 0.337 Chirality : 0.044 0.285 5667 Planarity : 0.004 0.054 6246 Dihedral : 4.729 44.746 4942 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.53 % Allowed : 18.84 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.25 (0.13), residues: 4434 helix: 1.23 (0.10), residues: 2742 sheet: -1.62 (0.34), residues: 210 loop : -2.74 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1724 TYR 0.029 0.001 TYR E1359 PHE 0.028 0.002 PHE A1098 TRP 0.037 0.002 TRP C2429 HIS 0.009 0.001 HIS E1304 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (36588) covalent geometry : angle 0.69317 / 0.34 (49746) SS BOND : bond 0.00150 / 0.08 ( 3) SS BOND : angle 0.91201 / 0.53 ( 6) hydrogen bonds : bond 0.03662 / 2.53 ( 2028) hydrogen bonds : angle 4.44083 / 3.12 ( 6003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6255.55 seconds wall clock time: 109 minutes 6.13 seconds (6546.13 seconds total)