Starting phenix.real_space_refine on Fri Oct 30 23:44:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r90_4764/10_2026/6r90_4764.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r90_4764/10_2026/6r90_4764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r90_4764/10_2026/6r90_4764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r90_4764/10_2026/6r90_4764.map" model { file = "/net/cci-nas-00/data/ceres_data/6r90_4764/10_2026/6r90_4764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r90_4764/10_2026/6r90_4764.cif" } resolution = 4.5 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= -0.003 sd= 0.767 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 66 5.16 5 C 12543 2.51 5 N 3818 2.21 5 O 4553 1.98 5 H 18818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40086 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1614 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1269 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1730 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1457 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1681 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1456 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1663 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1446 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4581 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 12898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12898 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5680 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 22, 'TRANS': 342} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.19, per 1000 atoms: 0.13 Number of scatterers: 40086 At special positions: 0 Unit cell: (152.22, 173.72, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 288 15.00 O 4553 8.00 N 3818 7.00 C 12543 6.00 H 18818 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 942.9 milliseconds 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 35 sheets defined 34.5% alpha, 26.0% beta 143 base pairs and 232 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.611A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.547A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.692A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.609A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.640A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.505A pdb=" N ALA D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.681A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.896A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.533A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.206A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 250 through 256 removed outlier: 3.510A pdb=" N ILE K 253 " --> pdb=" O PRO K 250 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER K 256 " --> pdb=" O ILE K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 755 through 759 Processing helix chain 'K' and resid 768 through 772 removed outlier: 4.127A pdb=" N PHE K 771 " --> pdb=" O SER K 768 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER K 772 " --> pdb=" O LYS K 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 768 through 772' Processing helix chain 'K' and resid 985 through 990 Processing helix chain 'K' and resid 1044 through 1060 Processing helix chain 'K' and resid 1069 through 1075 Processing helix chain 'K' and resid 1091 through 1096 Processing helix chain 'K' and resid 1097 through 1100 Processing helix chain 'K' and resid 1101 through 1109 Processing helix chain 'K' and resid 1125 through 1138 removed outlier: 3.586A pdb=" N ARG K1138 " --> pdb=" O GLU K1134 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 79 Processing helix chain 'L' and resid 82 through 99 removed outlier: 3.784A pdb=" N VAL L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.782A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.714A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.610A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.638A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.963A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 1004 through 1009 removed outlier: 3.866A pdb=" N VAL K1006 " --> pdb=" O GLY K1031 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER K1027 " --> pdb=" O VAL K1040 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL K1040 " --> pdb=" O SER K1027 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU K1029 " --> pdb=" O GLY K1038 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY K1038 " --> pdb=" O LEU K1029 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR K 3 " --> pdb=" O LEU K1043 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 17 through 21 removed outlier: 6.150A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 61 through 67 removed outlier: 4.194A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 121 through 124 Processing sheet with id=AB6, first strand: chain 'K' and resid 163 through 169 removed outlier: 4.354A pdb=" N HIS K 163 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL K 181 " --> pdb=" O ILE K 165 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL K 167 " --> pdb=" O CYS K 179 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS K 179 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE K 169 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR K 177 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 163 through 169 removed outlier: 4.354A pdb=" N HIS K 163 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL K 181 " --> pdb=" O ILE K 165 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL K 167 " --> pdb=" O CYS K 179 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS K 179 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE K 169 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR K 177 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 218 through 221 Processing sheet with id=AB9, first strand: chain 'K' and resid 258 through 263 removed outlier: 4.206A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU K 280 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU K 304 " --> pdb=" O LEU K 280 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N MET K 282 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL K 302 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU K 284 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU K 300 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU K 286 " --> pdb=" O LYS K 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 313 through 318 removed outlier: 6.770A pdb=" N VAL K 321 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER K 331 " --> pdb=" O THR K 352 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR K 352 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU K 333 " --> pdb=" O MET K 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 361 through 365 removed outlier: 3.998A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.711A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.711A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER K 764 " --> pdb=" O GLN K 806 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 811 through 820 removed outlier: 5.441A pdb=" N ALA K 813 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA K 834 " --> pdb=" O ALA K 813 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR K 827 " --> pdb=" O TYR K 853 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR K 853 " --> pdb=" O THR K 827 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 870 through 876 removed outlier: 3.778A pdb=" N SER K 872 " --> pdb=" O SER K 883 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL K 888 " --> pdb=" O ASN K 904 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN K 904 " --> pdb=" O VAL K 888 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU K 890 " --> pdb=" O GLU K 902 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 911 through 917 removed outlier: 6.618A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 954 through 961 removed outlier: 3.884A pdb=" N ALA K 956 " --> pdb=" O ALA K 968 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN K 964 " --> pdb=" O LEU K 960 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 1076 through 1077 Processing sheet with id=AD1, first strand: chain 'K' and resid 1113 through 1114 Processing sheet with id=AD2, first strand: chain 'L' and resid 106 through 109 Processing sheet with id=AD3, first strand: chain 'L' and resid 114 through 119 removed outlier: 6.741A pdb=" N GLY L 130 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU L 117 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA L 128 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TRP L 119 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR L 126 " --> pdb=" O TRP L 119 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 159 through 161 removed outlier: 6.640A pdb=" N SER L 175 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 204 through 210 removed outlier: 6.205A pdb=" N GLY L 219 " --> pdb=" O CYS L 205 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU L 207 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL L 217 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL L 209 " --> pdb=" O MET L 215 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET L 215 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 247 through 250 removed outlier: 3.628A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 291 through 296 removed outlier: 3.612A pdb=" N ALA L 293 " --> pdb=" O THR L 306 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 343 through 344 removed outlier: 3.742A pdb=" N CYS L 384 " --> pdb=" O VAL L 374 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 688 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 232 stacking parallelities Total time for adding SS restraints: 9.61 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18776 1.03 - 1.22: 152 1.22 - 1.42: 9568 1.42 - 1.62: 12481 1.62 - 1.82: 107 Bond restraints: 41084 Sorted by residual: bond pdb=" P 3DR J 93 " pdb=" O5' 3DR J 93 " ideal model delta sigma weight residual 1.720 1.592 0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1' DT J 89 " pdb=" N1 DT J 89 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" C1' DT J 70 " pdb=" N1 DT J 70 " ideal model delta sigma weight residual 1.468 1.555 -0.087 1.40e-02 5.10e+03 3.86e+01 bond pdb=" C5' 3DR J 94 " pdb="H5'' 3DR J 94 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C1' 3DR J 93 " pdb="H1'2 3DR J 93 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.54e+01 ... (remaining 41079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.13: 74383 7.13 - 14.27: 13 14.27 - 21.40: 0 21.40 - 28.53: 3 28.53 - 35.67: 3 Bond angle restraints: 74402 Sorted by residual: angle pdb=" CB CYS L 66 " pdb=" CA CYS L 66 " pdb=" HA CYS L 66 " ideal model delta sigma weight residual 109.00 73.33 35.67 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C CYS L 66 " pdb=" CA CYS L 66 " pdb=" HA CYS L 66 " ideal model delta sigma weight residual 109.00 74.85 34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N CYS L 66 " pdb=" CA CYS L 66 " pdb=" HA CYS L 66 " ideal model delta sigma weight residual 110.00 76.13 33.87 3.00e+00 1.11e-01 1.27e+02 angle pdb=" CD2 LEU L 63 " pdb=" CG LEU L 63 " pdb=" HG LEU L 63 " ideal model delta sigma weight residual 108.00 83.69 24.31 3.00e+00 1.11e-01 6.57e+01 angle pdb=" CB LEU L 63 " pdb=" CG LEU L 63 " pdb=" HG LEU L 63 " ideal model delta sigma weight residual 109.00 85.37 23.63 3.00e+00 1.11e-01 6.20e+01 ... (remaining 74397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 16290 34.73 - 69.46: 1864 69.46 - 104.19: 46 104.19 - 138.92: 5 138.92 - 173.66: 7 Dihedral angle restraints: 18212 sinusoidal: 11795 harmonic: 6417 Sorted by residual: dihedral pdb=" CA ILE K 884 " pdb=" C ILE K 884 " pdb=" N ASN K 885 " pdb=" CA ASN K 885 " ideal model delta harmonic sigma weight residual -180.00 -148.14 -31.86 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA ARG K 928 " pdb=" C ARG K 928 " pdb=" N SER K 929 " pdb=" CA SER K 929 " ideal model delta harmonic sigma weight residual -180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ARG K 847 " pdb=" C ARG K 847 " pdb=" N ILE K 848 " pdb=" CA ILE K 848 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 18209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 3541 0.340 - 0.680: 1 0.680 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.699: 1 Chirality restraints: 3543 Sorted by residual: chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" CA CYS L 66 " pdb=" N CYS L 66 " pdb=" C CYS L 66 " pdb=" CB CYS L 66 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' DA J 61 " pdb=" C4' DA J 61 " pdb=" O3' DA J 61 " pdb=" C2' DA J 61 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.66e-01 ... (remaining 3540 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 382 " -0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C PHE K 382 " 0.090 2.00e-02 2.50e+03 pdb=" O PHE K 382 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS K 383 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 381 " 0.025 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C ALA K 381 " -0.089 2.00e-02 2.50e+03 pdb=" O ALA K 381 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE K 382 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 146 " 0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO L 147 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO L 147 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 147 " 0.044 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 4116 2.24 - 2.83: 83234 2.83 - 3.42: 101269 3.42 - 4.01: 146370 4.01 - 4.60: 214548 Nonbonded interactions: 549537 Sorted by model distance: nonbonded pdb=" OD1 ASN K 36 " pdb=" HZ2 LYS K 60 " model vdw 1.652 2.450 nonbonded pdb=" O ARG L 113 " pdb=" H LYS L 132 " model vdw 1.653 2.450 nonbonded pdb=" HE ARG E 70 " pdb=" OD1 ASN F 26 " model vdw 1.657 2.450 nonbonded pdb=" O LEU E 104 " pdb=" HG1 THR E 108 " model vdw 1.657 2.450 nonbonded pdb=" O HIS F 76 " pdb="HH12 ARG H 93 " model vdw 1.660 2.450 ... (remaining 549532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 27 through 102)) } ncs_group { reference = (chain 'C' and ((resid 16 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 17 through 76 or (resid 77 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA or nam \ e HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid 78 through 11 \ 9)) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 34 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 35 through 124) \ ) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) } 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: 1.930 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: 0.080 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 39.420 Find NCS groups from input model: 0.270 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: 0.020 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.008 0.128 22266 Z= 0.601 Angle : 0.984 12.058 31343 Z= 0.764 Chirality : 0.065 1.699 3543 Planarity : 0.006 0.081 2998 Dihedral : 22.948 173.656 9132 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.07 % Favored : 96.62 % Rotamer: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.17), residues: 1922 helix: 0.56 (0.18), residues: 638 sheet: -0.72 (0.23), residues: 465 loop : -1.77 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 313 TYR 0.024 0.002 TYR K 245 PHE 0.033 0.003 PHE K 382 TRP 0.020 0.003 TRP K 207 HIS 0.006 0.001 HIS L 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.60 (22266) covalent geometry : angle 0.98373 / 0.76 (31343) hydrogen bonds : bond 0.13422 / 9.20 ( 1081) hydrogen bonds : angle 5.74629 / 4.24 ( 2788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 585 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8243 (mm-30) REVERT: A 53 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8376 (mtt90) REVERT: A 57 LYS cc_start: 0.9420 (tttt) cc_final: 0.9018 (tppt) REVERT: A 62 LEU cc_start: 0.9698 (mt) cc_final: 0.9445 (mt) REVERT: A 70 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7929 (mtm110) REVERT: A 74 GLU cc_start: 0.8425 (tt0) cc_final: 0.8170 (tt0) REVERT: A 106 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7793 (tp30) REVERT: B 38 LEU cc_start: 0.9385 (mt) cc_final: 0.9042 (mt) REVERT: B 46 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7424 (mtt90) REVERT: B 99 TYR cc_start: 0.8632 (m-10) cc_final: 0.8392 (m-10) REVERT: C 40 TYR cc_start: 0.8573 (m-80) cc_final: 0.8042 (m-10) REVERT: C 96 LYS cc_start: 0.8832 (tptt) cc_final: 0.8240 (ttmm) REVERT: C 111 ASN cc_start: 0.8947 (t0) cc_final: 0.8732 (t0) REVERT: D 44 LYS cc_start: 0.8882 (mttt) cc_final: 0.8491 (mtmt) REVERT: D 96 GLN cc_start: 0.9053 (tt0) cc_final: 0.8806 (tt0) REVERT: D 100 ARG cc_start: 0.8660 (mtt90) cc_final: 0.8240 (tpp80) REVERT: D 109 LYS cc_start: 0.9180 (mttt) cc_final: 0.8608 (mmmt) REVERT: D 116 THR cc_start: 0.9143 (m) cc_final: 0.8929 (p) REVERT: E 50 ARG cc_start: 0.8735 (ttp-170) cc_final: 0.8404 (ttm-80) REVERT: E 61 LEU cc_start: 0.9180 (mt) cc_final: 0.8892 (mt) REVERT: E 98 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7878 (pp20) REVERT: E 110 LEU cc_start: 0.9485 (mt) cc_final: 0.9249 (tp) REVERT: F 60 LYS cc_start: 0.7780 (tttt) cc_final: 0.7555 (ttmm) REVERT: F 89 TYR cc_start: 0.8681 (m-10) cc_final: 0.8476 (m-80) REVERT: G 39 ASN cc_start: 0.8811 (m110) cc_final: 0.8569 (p0) REVERT: G 63 ILE cc_start: 0.9127 (mt) cc_final: 0.8913 (tp) REVERT: H 94 GLU cc_start: 0.8990 (mp0) cc_final: 0.8489 (mp0) REVERT: H 97 THR cc_start: 0.9456 (m) cc_final: 0.9238 (p) REVERT: H 101 LEU cc_start: 0.9164 (mt) cc_final: 0.8534 (mt) REVERT: H 117 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8424 (ttpt) REVERT: K 87 CYS cc_start: 0.6383 (p) cc_final: 0.6123 (m) REVERT: K 152 LEU cc_start: 0.8616 (mt) cc_final: 0.8228 (mt) REVERT: K 166 ASP cc_start: 0.7317 (m-30) cc_final: 0.6785 (m-30) REVERT: K 194 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7861 (tm-30) REVERT: K 203 ASN cc_start: 0.7238 (m110) cc_final: 0.6389 (m110) REVERT: K 217 SER cc_start: 0.7990 (p) cc_final: 0.7715 (t) REVERT: K 234 GLN cc_start: 0.8645 (tp40) cc_final: 0.8075 (tt0) REVERT: K 235 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8186 (tm-30) REVERT: K 330 ASP cc_start: 0.3658 (m-30) cc_final: 0.3268 (m-30) REVERT: K 378 CYS cc_start: 0.7740 (m) cc_final: 0.7417 (m) REVERT: K 379 SER cc_start: 0.7821 (t) cc_final: 0.7030 (p) REVERT: K 755 SER cc_start: 0.7966 (p) cc_final: 0.7664 (m) REVERT: K 787 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6560 (mt-10) REVERT: K 969 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8308 (tm-30) REVERT: K 1014 MET cc_start: 0.2502 (tpp) cc_final: 0.1535 (pmm) REVERT: K 1030 PHE cc_start: 0.7555 (p90) cc_final: 0.7355 (p90) REVERT: K 1097 PHE cc_start: 0.7839 (t80) cc_final: 0.7570 (t80) REVERT: K 1102 ARG cc_start: 0.9049 (ttt90) cc_final: 0.8261 (mpt180) REVERT: K 1105 MET cc_start: 0.6986 (mtt) cc_final: 0.6353 (mtt) REVERT: L 88 GLN cc_start: 0.8506 (mt0) cc_final: 0.8079 (tt0) REVERT: L 123 HIS cc_start: 0.8188 (t-90) cc_final: 0.6938 (t-90) REVERT: L 240 MET cc_start: 0.7828 (mtt) cc_final: 0.7625 (mtt) REVERT: L 373 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5694 (t70) REVERT: L 388 ASP cc_start: 0.7156 (t70) cc_final: 0.6946 (t0) REVERT: L 398 ASN cc_start: 0.7137 (t0) cc_final: 0.6652 (t0) outliers start: 4 outliers final: 2 residues processed: 587 average time/residue: 0.3858 time to fit residues: 330.3805 Evaluate side-chains 447 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 444 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN C 105 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 743 GLN K 859 GLN K 904 ASN K1016 ASN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1055 GLN K1111 ASN L 91 GLN L 92 GLN L 170 ASN L 319 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.147543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.121580 restraints weight = 125137.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127325 restraints weight = 53127.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130813 restraints weight = 28304.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.132997 restraints weight = 18236.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.134343 restraints weight = 13576.134| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 22266 Z= 0.252 Angle : 0.773 11.434 31343 Z= 0.467 Chirality : 0.056 1.687 3543 Planarity : 0.006 0.072 2998 Dihedral : 26.534 175.291 5386 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 1922 helix: 0.75 (0.20), residues: 649 sheet: -0.71 (0.24), residues: 431 loop : -1.72 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 369 TYR 0.016 0.002 TYR H 41 PHE 0.029 0.002 PHE A 68 TRP 0.013 0.002 TRP K1073 HIS 0.007 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.25 (22266) covalent geometry : angle 0.77312 / 0.47 (31343) hydrogen bonds : bond 0.07148 / 4.83 ( 1081) hydrogen bonds : angle 5.46955 / 4.00 ( 2788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8361 (mm-30) REVERT: A 57 LYS cc_start: 0.9480 (tttt) cc_final: 0.9154 (tppt) REVERT: A 62 LEU cc_start: 0.9567 (mt) cc_final: 0.9102 (mt) REVERT: A 70 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7755 (mtm110) REVERT: A 98 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7753 (mm-30) REVERT: A 106 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8074 (tp30) REVERT: B 41 ARG cc_start: 0.8745 (ttm170) cc_final: 0.8523 (mtp-110) REVERT: B 99 TYR cc_start: 0.8589 (m-10) cc_final: 0.8248 (m-10) REVERT: C 39 ASN cc_start: 0.8300 (m110) cc_final: 0.8088 (m-40) REVERT: C 96 LYS cc_start: 0.8974 (tptt) cc_final: 0.8454 (ttmm) REVERT: D 44 LYS cc_start: 0.8970 (mttt) cc_final: 0.8687 (mmmm) REVERT: D 100 ARG cc_start: 0.8586 (mtt90) cc_final: 0.8260 (tpp80) REVERT: D 109 LYS cc_start: 0.9211 (mttt) cc_final: 0.8634 (tppt) REVERT: E 50 ARG cc_start: 0.8829 (ttp-170) cc_final: 0.8401 (ttm-80) REVERT: E 61 LEU cc_start: 0.9277 (mt) cc_final: 0.8959 (mt) REVERT: E 98 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7661 (pp20) REVERT: E 100 TYR cc_start: 0.9141 (t80) cc_final: 0.8773 (t80) REVERT: F 75 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8539 (tt0) REVERT: H 94 GLU cc_start: 0.9227 (mp0) cc_final: 0.8829 (mp0) REVERT: H 117 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8523 (ttpt) REVERT: K 16 ASN cc_start: 0.7784 (m110) cc_final: 0.7365 (t0) REVERT: K 35 LYS cc_start: 0.8448 (mttt) cc_final: 0.7990 (mttp) REVERT: K 36 ASN cc_start: 0.8445 (t0) cc_final: 0.7876 (t0) REVERT: K 57 MET cc_start: 0.3370 (tpp) cc_final: 0.3063 (tpp) REVERT: K 152 LEU cc_start: 0.8785 (mt) cc_final: 0.8414 (mt) REVERT: K 235 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8031 (tm-30) REVERT: K 327 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8271 (ttp80) REVERT: K 1030 PHE cc_start: 0.7898 (p90) cc_final: 0.7632 (p90) REVERT: K 1069 GLU cc_start: 0.6701 (tp30) cc_final: 0.6471 (tp30) REVERT: K 1102 ARG cc_start: 0.9138 (ttt90) cc_final: 0.8283 (mpt180) REVERT: K 1105 MET cc_start: 0.6992 (mtt) cc_final: 0.6359 (mtt) REVERT: L 88 GLN cc_start: 0.8470 (mt0) cc_final: 0.8103 (tt0) REVERT: L 123 HIS cc_start: 0.8335 (t-90) cc_final: 0.7405 (t-90) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.3715 time to fit residues: 274.7116 Evaluate side-chains 423 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [7, 17, 192, 181, 31, 91, 149, 138, 46, 1, 160] chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 39 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.118695 restraints weight = 125149.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124376 restraints weight = 53299.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127862 restraints weight = 28547.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130059 restraints weight = 18474.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131403 restraints weight = 13774.129| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 22266 Z= 0.253 Angle : 0.736 11.233 31343 Z= 0.450 Chirality : 0.054 1.672 3543 Planarity : 0.006 0.114 2998 Dihedral : 26.467 173.382 5386 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.17 % Rotamer: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.07 (0.18), residues: 1922 helix: 0.65 (0.20), residues: 647 sheet: -0.78 (0.24), residues: 439 loop : -1.75 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 327 TYR 0.016 0.002 TYR H 41 PHE 0.019 0.002 PHE L 257 TRP 0.010 0.002 TRP L 83 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.25 (22266) covalent geometry : angle 0.73618 / 0.45 (31343) hydrogen bonds : bond 0.06667 / 4.49 ( 1081) hydrogen bonds : angle 5.36810 / 3.91 ( 2788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8425 (mm-30) REVERT: A 54 ARG cc_start: 0.8596 (tpt90) cc_final: 0.8208 (tpp-160) REVERT: A 57 LYS cc_start: 0.9458 (tttt) cc_final: 0.9113 (tppt) REVERT: A 61 LEU cc_start: 0.9163 (mt) cc_final: 0.8782 (mt) REVERT: A 62 LEU cc_start: 0.9598 (mt) cc_final: 0.9351 (mt) REVERT: A 70 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7708 (mtm110) REVERT: A 106 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8103 (tp30) REVERT: B 53 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7642 (tm-30) REVERT: B 99 TYR cc_start: 0.8658 (m-10) cc_final: 0.8305 (m-10) REVERT: C 37 LYS cc_start: 0.9223 (ttmm) cc_final: 0.8849 (ttmm) REVERT: C 39 ASN cc_start: 0.8716 (m-40) cc_final: 0.8273 (m-40) REVERT: C 42 GLU cc_start: 0.8247 (mp0) cc_final: 0.7692 (mp0) REVERT: C 96 LYS cc_start: 0.9015 (tptt) cc_final: 0.8516 (ttmm) REVERT: D 44 LYS cc_start: 0.9012 (mttt) cc_final: 0.8791 (mtmt) REVERT: D 52 ASP cc_start: 0.8882 (p0) cc_final: 0.8642 (p0) REVERT: D 96 GLN cc_start: 0.9260 (tt0) cc_final: 0.8563 (tp40) REVERT: D 100 ARG cc_start: 0.8695 (mtt90) cc_final: 0.8371 (tpp80) REVERT: D 109 LYS cc_start: 0.9131 (mttt) cc_final: 0.8565 (tppp) REVERT: E 50 ARG cc_start: 0.8952 (ttp-170) cc_final: 0.8327 (ttm-80) REVERT: E 61 LEU cc_start: 0.9341 (mt) cc_final: 0.9040 (mt) REVERT: E 98 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7742 (pp20) REVERT: E 100 TYR cc_start: 0.9205 (t80) cc_final: 0.8835 (t80) REVERT: H 94 GLU cc_start: 0.9235 (mp0) cc_final: 0.8929 (mp0) REVERT: H 106 GLU cc_start: 0.8900 (mp0) cc_final: 0.8650 (mp0) REVERT: H 117 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8464 (ttpt) REVERT: K 16 ASN cc_start: 0.7868 (m110) cc_final: 0.7497 (t0) REVERT: K 35 LYS cc_start: 0.8532 (mttt) cc_final: 0.8234 (mttt) REVERT: K 36 ASN cc_start: 0.8544 (t0) cc_final: 0.8086 (t0) REVERT: K 47 GLU cc_start: 0.7951 (tp30) cc_final: 0.7506 (pm20) REVERT: K 124 ILE cc_start: 0.8380 (mt) cc_final: 0.8112 (tt) REVERT: K 152 LEU cc_start: 0.8815 (mt) cc_final: 0.8582 (mp) REVERT: K 215 GLU cc_start: 0.9013 (tp30) cc_final: 0.8562 (tp30) REVERT: K 235 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8012 (tm-30) REVERT: K 787 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6442 (mt-10) REVERT: K 824 ASP cc_start: 0.8070 (t0) cc_final: 0.7687 (t0) REVERT: K 842 GLU cc_start: 0.5660 (mm-30) cc_final: 0.4903 (mp0) REVERT: K 1030 PHE cc_start: 0.7884 (p90) cc_final: 0.7583 (p90) REVERT: K 1069 GLU cc_start: 0.6822 (tp30) cc_final: 0.6515 (tp30) REVERT: K 1102 ARG cc_start: 0.9141 (ttt90) cc_final: 0.8281 (mpt180) REVERT: K 1105 MET cc_start: 0.7043 (mtt) cc_final: 0.6382 (mtt) REVERT: L 88 GLN cc_start: 0.8510 (mt0) cc_final: 0.8139 (tt0) REVERT: L 123 HIS cc_start: 0.8736 (t-90) cc_final: 0.7621 (t-90) REVERT: L 358 ASP cc_start: 0.8287 (t70) cc_final: 0.8085 (t0) REVERT: L 405 ASP cc_start: 0.7379 (p0) cc_final: 0.7114 (p0) outliers start: 1 outliers final: 0 residues processed: 485 average time/residue: 0.3636 time to fit residues: 262.3000 Evaluate side-chains 421 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [35, 22, 205, 54, 196, 114, 118, 0, 194, 169, 212] chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 212 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 993 GLN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.145421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118640 restraints weight = 124585.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124662 restraints weight = 51862.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.128296 restraints weight = 27336.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.130593 restraints weight = 17414.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.132005 restraints weight = 12844.771| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22266 Z= 0.206 Angle : 0.692 11.267 31343 Z= 0.422 Chirality : 0.053 1.673 3543 Planarity : 0.005 0.073 2998 Dihedral : 26.447 173.800 5386 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 0.06 % Allowed : 1.32 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.97 (0.18), residues: 1922 helix: 0.86 (0.20), residues: 649 sheet: -0.73 (0.25), residues: 427 loop : -1.80 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 80 TYR 0.014 0.002 TYR H 41 PHE 0.017 0.002 PHE L 257 TRP 0.008 0.002 TRP L 203 HIS 0.008 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.21 (22266) covalent geometry : angle 0.69250 / 0.42 (31343) hydrogen bonds : bond 0.05997 / 4.05 ( 1081) hydrogen bonds : angle 5.09826 / 3.71 ( 2788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8525 (mm-30) REVERT: A 54 ARG cc_start: 0.8650 (tpt90) cc_final: 0.8141 (tpp-160) REVERT: A 70 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7770 (mtm110) REVERT: A 97 CYS cc_start: 0.9009 (m) cc_final: 0.8746 (m) REVERT: A 98 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7732 (mm-30) REVERT: A 106 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8107 (tp30) REVERT: B 99 TYR cc_start: 0.8675 (m-10) cc_final: 0.8332 (m-10) REVERT: C 37 LYS cc_start: 0.9264 (ttmm) cc_final: 0.8925 (ttmm) REVERT: C 39 ASN cc_start: 0.8741 (m-40) cc_final: 0.8292 (m-40) REVERT: C 42 GLU cc_start: 0.8325 (mp0) cc_final: 0.7686 (mp0) REVERT: C 96 LYS cc_start: 0.9025 (tptt) cc_final: 0.8495 (ttmm) REVERT: D 44 LYS cc_start: 0.9029 (mttt) cc_final: 0.8642 (mmmm) REVERT: D 52 ASP cc_start: 0.8918 (p0) cc_final: 0.8696 (p0) REVERT: D 96 GLN cc_start: 0.9241 (tt0) cc_final: 0.8551 (tp40) REVERT: D 100 ARG cc_start: 0.8728 (mtt90) cc_final: 0.8443 (tpp80) REVERT: D 109 LYS cc_start: 0.9111 (mttt) cc_final: 0.8552 (tppp) REVERT: E 50 ARG cc_start: 0.8980 (ttp-170) cc_final: 0.8293 (ttm-80) REVERT: E 61 LEU cc_start: 0.9361 (mt) cc_final: 0.9026 (mt) REVERT: E 86 GLN cc_start: 0.6976 (mt0) cc_final: 0.6758 (mm110) REVERT: E 98 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7798 (pp20) REVERT: E 100 TYR cc_start: 0.9222 (t80) cc_final: 0.8840 (t80) REVERT: F 85 MET cc_start: 0.8128 (mmp) cc_final: 0.7805 (mmp) REVERT: G 52 LEU cc_start: 0.9592 (mt) cc_final: 0.9359 (mm) REVERT: H 94 GLU cc_start: 0.9331 (mp0) cc_final: 0.9014 (mp0) REVERT: H 106 GLU cc_start: 0.8873 (mp0) cc_final: 0.8616 (mp0) REVERT: H 117 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8435 (ttpt) REVERT: K 16 ASN cc_start: 0.7631 (m110) cc_final: 0.7315 (t0) REVERT: K 35 LYS cc_start: 0.8490 (mttt) cc_final: 0.8176 (mttt) REVERT: K 36 ASN cc_start: 0.8567 (t0) cc_final: 0.8056 (t0) REVERT: K 47 GLU cc_start: 0.7975 (tp30) cc_final: 0.7505 (pm20) REVERT: K 124 ILE cc_start: 0.8399 (mt) cc_final: 0.8150 (tt) REVERT: K 152 LEU cc_start: 0.8755 (mt) cc_final: 0.8502 (mp) REVERT: K 158 ARG cc_start: 0.6979 (ttt180) cc_final: 0.6369 (ttm170) REVERT: K 215 GLU cc_start: 0.9031 (tp30) cc_final: 0.8563 (tp30) REVERT: K 235 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7992 (tm-30) REVERT: K 787 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6390 (mt-10) REVERT: K 824 ASP cc_start: 0.8082 (t0) cc_final: 0.7677 (t0) REVERT: K 930 VAL cc_start: 0.5103 (p) cc_final: 0.4902 (m) REVERT: K 1007 PHE cc_start: 0.7520 (m-80) cc_final: 0.7299 (m-10) REVERT: K 1030 PHE cc_start: 0.7926 (p90) cc_final: 0.7592 (p90) REVERT: K 1069 GLU cc_start: 0.6843 (tp30) cc_final: 0.6540 (tp30) REVERT: K 1102 ARG cc_start: 0.9150 (ttt90) cc_final: 0.8282 (mpt180) REVERT: K 1105 MET cc_start: 0.7113 (mtt) cc_final: 0.6391 (mtt) REVERT: L 88 GLN cc_start: 0.8508 (mt0) cc_final: 0.8149 (tt0) REVERT: L 208 ASP cc_start: 0.7266 (t70) cc_final: 0.7063 (t0) REVERT: L 394 ILE cc_start: 0.9019 (mt) cc_final: 0.8690 (mt) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.3498 time to fit residues: 248.5961 Evaluate side-chains 426 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [114, 88, 214, 11, 136, 30, 85, 75, 53, 173, 157] chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 743 GLN ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112210 restraints weight = 127502.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117595 restraints weight = 54475.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.120912 restraints weight = 29387.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122954 restraints weight = 19132.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.124195 restraints weight = 14434.668| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 22266 Z= 0.341 Angle : 0.817 11.236 31343 Z= 0.489 Chirality : 0.055 1.675 3543 Planarity : 0.006 0.074 2998 Dihedral : 26.521 173.465 5386 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.77 % Rotamer: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.89 (0.18), residues: 1922 helix: -0.32 (0.18), residues: 646 sheet: -1.05 (0.24), residues: 451 loop : -2.08 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 332 TYR 0.024 0.002 TYR G 51 PHE 0.028 0.002 PHE F 101 TRP 0.019 0.003 TRP K1047 HIS 0.009 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.34 (22266) covalent geometry : angle 0.81650 / 0.49 (31343) hydrogen bonds : bond 0.07475 / 5.00 ( 1081) hydrogen bonds : angle 5.83988 / 4.24 ( 2788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8635 (mm-30) REVERT: A 54 ARG cc_start: 0.8670 (tpt90) cc_final: 0.8154 (tpp-160) REVERT: A 70 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7863 (mtm110) REVERT: A 97 CYS cc_start: 0.9144 (m) cc_final: 0.7916 (t) REVERT: A 98 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7929 (mm-30) REVERT: A 106 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8074 (tp30) REVERT: B 53 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7949 (tm-30) REVERT: C 37 LYS cc_start: 0.9377 (ttmm) cc_final: 0.8701 (tppt) REVERT: C 39 ASN cc_start: 0.8885 (m-40) cc_final: 0.8516 (m-40) REVERT: C 42 GLU cc_start: 0.8261 (mp0) cc_final: 0.7724 (mp0) REVERT: C 92 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7743 (tp30) REVERT: C 96 LYS cc_start: 0.9085 (tptt) cc_final: 0.8623 (ttmm) REVERT: D 44 LYS cc_start: 0.9126 (mttt) cc_final: 0.8752 (mmmm) REVERT: D 64 ASN cc_start: 0.9133 (m-40) cc_final: 0.8878 (m-40) REVERT: D 100 ARG cc_start: 0.8851 (mtt90) cc_final: 0.8430 (tpp80) REVERT: D 109 LYS cc_start: 0.9157 (mttt) cc_final: 0.8719 (tppt) REVERT: E 61 LEU cc_start: 0.9347 (mt) cc_final: 0.9121 (mt) REVERT: E 98 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7842 (pp20) REVERT: F 85 MET cc_start: 0.8248 (mmp) cc_final: 0.8010 (mmp) REVERT: G 84 LEU cc_start: 0.9079 (mt) cc_final: 0.8875 (mm) REVERT: H 63 MET cc_start: 0.8982 (mmm) cc_final: 0.8302 (mmm) REVERT: H 106 GLU cc_start: 0.8884 (mp0) cc_final: 0.8592 (mp0) REVERT: H 117 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8487 (ttpt) REVERT: K 16 ASN cc_start: 0.7823 (m110) cc_final: 0.7230 (t0) REVERT: K 36 ASN cc_start: 0.8617 (t0) cc_final: 0.8090 (t0) REVERT: K 47 GLU cc_start: 0.7907 (tp30) cc_final: 0.7529 (pm20) REVERT: K 124 ILE cc_start: 0.8423 (mt) cc_final: 0.8148 (tt) REVERT: K 152 LEU cc_start: 0.8809 (mt) cc_final: 0.8603 (mp) REVERT: K 193 TYR cc_start: 0.5407 (m-80) cc_final: 0.5119 (m-80) REVERT: K 215 GLU cc_start: 0.9023 (tp30) cc_final: 0.8677 (tp30) REVERT: K 235 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8087 (tm-30) REVERT: K 1007 PHE cc_start: 0.7654 (m-80) cc_final: 0.7365 (m-10) REVERT: K 1030 PHE cc_start: 0.8112 (p90) cc_final: 0.7770 (p90) REVERT: K 1047 TRP cc_start: 0.7738 (t-100) cc_final: 0.7399 (t-100) REVERT: K 1102 ARG cc_start: 0.9149 (ttt90) cc_final: 0.8445 (mpt180) REVERT: L 88 GLN cc_start: 0.8537 (mt0) cc_final: 0.8199 (tt0) REVERT: L 119 TRP cc_start: 0.7943 (m100) cc_final: 0.6959 (m100) REVERT: L 360 ASN cc_start: 0.9360 (m110) cc_final: 0.9139 (p0) REVERT: L 409 SER cc_start: 0.7777 (m) cc_final: 0.7471 (m) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.3589 time to fit residues: 255.1705 Evaluate side-chains 417 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [63, 87, 107, 102, 1, 157, 120, 121, 49, 210, 172] chunk 63 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN D 48 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.142827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115922 restraints weight = 125256.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.121875 restraints weight = 51840.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125531 restraints weight = 27326.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127812 restraints weight = 17459.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129181 restraints weight = 12931.455| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22266 Z= 0.186 Angle : 0.685 11.196 31343 Z= 0.415 Chirality : 0.053 1.660 3543 Planarity : 0.005 0.085 2998 Dihedral : 26.525 173.109 5386 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 0.06 % Allowed : 0.96 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.34 (0.18), residues: 1922 helix: 0.52 (0.19), residues: 650 sheet: -1.00 (0.24), residues: 439 loop : -1.96 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 369 TYR 0.017 0.002 TYR K 58 PHE 0.016 0.002 PHE L 141 TRP 0.008 0.002 TRP L 119 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.19 (22266) covalent geometry : angle 0.68543 / 0.42 (31343) hydrogen bonds : bond 0.05795 / 3.91 ( 1081) hydrogen bonds : angle 5.02988 / 3.66 ( 2788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8556 (mm-30) REVERT: A 54 ARG cc_start: 0.8666 (tpt90) cc_final: 0.7942 (tpp-160) REVERT: A 57 LYS cc_start: 0.9381 (ttmm) cc_final: 0.9167 (tppt) REVERT: A 62 LEU cc_start: 0.9455 (mt) cc_final: 0.9194 (mt) REVERT: A 70 ARG cc_start: 0.8190 (mtm110) cc_final: 0.7795 (mtm110) REVERT: A 97 CYS cc_start: 0.9051 (m) cc_final: 0.7860 (t) REVERT: A 98 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7929 (mm-30) REVERT: A 106 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8039 (tp30) REVERT: B 37 ARG cc_start: 0.8982 (mtm-85) cc_final: 0.8556 (mtm180) REVERT: B 53 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7780 (tm-30) REVERT: C 37 LYS cc_start: 0.9316 (ttmm) cc_final: 0.9052 (ttmm) REVERT: C 39 ASN cc_start: 0.8658 (m-40) cc_final: 0.8306 (m-40) REVERT: C 42 GLU cc_start: 0.8271 (mp0) cc_final: 0.7676 (mp0) REVERT: C 96 LYS cc_start: 0.9000 (tptt) cc_final: 0.8441 (ttmm) REVERT: D 44 LYS cc_start: 0.9034 (mttt) cc_final: 0.8681 (mmmm) REVERT: D 64 ASN cc_start: 0.9054 (m-40) cc_final: 0.8845 (m-40) REVERT: D 87 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8132 (mmt90) REVERT: D 100 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8424 (tpp80) REVERT: D 109 LYS cc_start: 0.9128 (mttt) cc_final: 0.8602 (tppp) REVERT: E 61 LEU cc_start: 0.9398 (mt) cc_final: 0.9117 (mt) REVERT: E 97 CYS cc_start: 0.8893 (m) cc_final: 0.8450 (t) REVERT: E 98 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7756 (pp20) REVERT: F 85 MET cc_start: 0.8197 (mmp) cc_final: 0.7898 (mmp) REVERT: H 106 GLU cc_start: 0.8884 (mp0) cc_final: 0.8593 (mp0) REVERT: H 117 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8365 (ttpt) REVERT: K 16 ASN cc_start: 0.7626 (m110) cc_final: 0.7311 (t0) REVERT: K 35 LYS cc_start: 0.8457 (mttt) cc_final: 0.8026 (mttp) REVERT: K 36 ASN cc_start: 0.8624 (t0) cc_final: 0.8091 (t0) REVERT: K 47 GLU cc_start: 0.7895 (tp30) cc_final: 0.7553 (pm20) REVERT: K 124 ILE cc_start: 0.8427 (mt) cc_final: 0.8147 (tt) REVERT: K 152 LEU cc_start: 0.8731 (mt) cc_final: 0.8501 (mp) REVERT: K 193 TYR cc_start: 0.5205 (m-80) cc_final: 0.4970 (m-80) REVERT: K 215 GLU cc_start: 0.9053 (tp30) cc_final: 0.8580 (tp30) REVERT: K 235 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8078 (tm-30) REVERT: K 930 VAL cc_start: 0.5546 (p) cc_final: 0.5340 (m) REVERT: K 1007 PHE cc_start: 0.7621 (m-80) cc_final: 0.7417 (m-10) REVERT: K 1030 PHE cc_start: 0.8122 (p90) cc_final: 0.7683 (p90) REVERT: K 1102 ARG cc_start: 0.9157 (ttt90) cc_final: 0.8432 (mpt180) REVERT: L 88 GLN cc_start: 0.8539 (mt0) cc_final: 0.8159 (tt0) REVERT: L 119 TRP cc_start: 0.7910 (m100) cc_final: 0.7016 (m100) REVERT: L 361 PHE cc_start: 0.8783 (t80) cc_final: 0.8351 (t80) REVERT: L 409 SER cc_start: 0.7808 (m) cc_final: 0.7521 (m) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.3447 time to fit residues: 245.4308 Evaluate side-chains 418 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [18, 196, 24, 182, 41, 64, 106, 11, 200, 209, 145] chunk 18 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.138624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112554 restraints weight = 126338.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.118068 restraints weight = 53764.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.121488 restraints weight = 28886.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123576 restraints weight = 18735.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124908 restraints weight = 14070.593| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 22266 Z= 0.274 Angle : 0.749 11.049 31343 Z= 0.449 Chirality : 0.054 1.663 3543 Planarity : 0.006 0.112 2998 Dihedral : 26.564 172.813 5386 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.66 % Favored : 93.18 % Rotamer: Outliers : 0.06 % Allowed : 1.08 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.63 (0.18), residues: 1922 helix: 0.18 (0.19), residues: 649 sheet: -1.14 (0.24), residues: 444 loop : -2.03 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 82 TYR 0.036 0.002 TYR D 41 PHE 0.021 0.002 PHE F 101 TRP 0.008 0.002 TRP K 207 HIS 0.008 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.27 (22266) covalent geometry : angle 0.74899 / 0.45 (31343) hydrogen bonds : bond 0.06409 / 4.30 ( 1081) hydrogen bonds : angle 5.42707 / 3.94 ( 2788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8534 (mm-30) REVERT: A 54 ARG cc_start: 0.8642 (tpt90) cc_final: 0.8213 (tpp-160) REVERT: A 57 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9223 (tppt) REVERT: A 62 LEU cc_start: 0.9496 (mt) cc_final: 0.9211 (mt) REVERT: A 70 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7843 (mtm110) REVERT: A 97 CYS cc_start: 0.9114 (m) cc_final: 0.7964 (t) REVERT: A 98 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7948 (mm-30) REVERT: A 106 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8086 (tp30) REVERT: B 37 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8624 (mtm180) REVERT: B 53 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7883 (tm-30) REVERT: C 37 LYS cc_start: 0.9369 (ttmm) cc_final: 0.8698 (tppt) REVERT: C 39 ASN cc_start: 0.8768 (m-40) cc_final: 0.8433 (m-40) REVERT: C 42 GLU cc_start: 0.8222 (mp0) cc_final: 0.7701 (mp0) REVERT: C 92 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7601 (tp30) REVERT: C 96 LYS cc_start: 0.9028 (tptt) cc_final: 0.8776 (tppt) REVERT: D 44 LYS cc_start: 0.9094 (mttt) cc_final: 0.8733 (mmmm) REVERT: D 100 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8508 (tpp80) REVERT: D 109 LYS cc_start: 0.9137 (mttt) cc_final: 0.8628 (tppp) REVERT: E 61 LEU cc_start: 0.9349 (mt) cc_final: 0.9107 (mt) REVERT: E 97 CYS cc_start: 0.8805 (m) cc_final: 0.8417 (t) REVERT: E 98 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7895 (pp20) REVERT: F 85 MET cc_start: 0.8248 (mmp) cc_final: 0.7952 (mmp) REVERT: H 48 GLN cc_start: 0.7757 (tt0) cc_final: 0.7382 (tm-30) REVERT: H 106 GLU cc_start: 0.8856 (mp0) cc_final: 0.8570 (mp0) REVERT: H 117 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8422 (ttpt) REVERT: K 35 LYS cc_start: 0.8570 (mttt) cc_final: 0.8238 (mttt) REVERT: K 36 ASN cc_start: 0.8620 (t0) cc_final: 0.8118 (t0) REVERT: K 47 GLU cc_start: 0.7841 (tp30) cc_final: 0.7579 (pm20) REVERT: K 124 ILE cc_start: 0.8403 (mt) cc_final: 0.8141 (tt) REVERT: K 152 LEU cc_start: 0.8754 (mt) cc_final: 0.8538 (mp) REVERT: K 193 TYR cc_start: 0.5246 (m-80) cc_final: 0.4990 (m-80) REVERT: K 215 GLU cc_start: 0.9021 (tp30) cc_final: 0.8670 (tp30) REVERT: K 235 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8138 (tm-30) REVERT: K 330 ASP cc_start: 0.4405 (m-30) cc_final: 0.4113 (m-30) REVERT: K 722 ARG cc_start: 0.7828 (mmt90) cc_final: 0.7414 (tpp80) REVERT: K 879 LYS cc_start: 0.8376 (mttt) cc_final: 0.8052 (mmtt) REVERT: K 1030 PHE cc_start: 0.8205 (p90) cc_final: 0.7753 (p90) REVERT: K 1102 ARG cc_start: 0.9140 (ttt90) cc_final: 0.8449 (mpt180) REVERT: L 88 GLN cc_start: 0.8528 (mt0) cc_final: 0.8148 (tt0) REVERT: L 268 LYS cc_start: 0.7385 (mttt) cc_final: 0.6862 (mttt) REVERT: L 304 LEU cc_start: 0.9390 (tt) cc_final: 0.9164 (tp) REVERT: L 382 MET cc_start: 0.7415 (mtt) cc_final: 0.6985 (mtt) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.3491 time to fit residues: 248.8606 Evaluate side-chains 420 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [162, 154, 102, 130, 9, 129, 136, 44, 24, 206, 204] chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 113 GLN K 93 GLN ** K 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 845 GLN ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.140721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114396 restraints weight = 124915.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.120034 restraints weight = 53092.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123489 restraints weight = 28451.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125643 restraints weight = 18436.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127012 restraints weight = 13795.593| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22266 Z= 0.202 Angle : 0.691 10.975 31343 Z= 0.418 Chirality : 0.053 1.634 3543 Planarity : 0.005 0.117 2998 Dihedral : 26.605 172.659 5386 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 0.06 % Allowed : 0.78 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.42 (0.18), residues: 1922 helix: 0.51 (0.19), residues: 648 sheet: -1.11 (0.24), residues: 440 loop : -2.00 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 369 TYR 0.019 0.002 TYR D 41 PHE 0.015 0.002 PHE L 141 TRP 0.025 0.002 TRP L 270 HIS 0.008 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.20 (22266) covalent geometry : angle 0.69115 / 0.42 (31343) hydrogen bonds : bond 0.05709 / 3.84 ( 1081) hydrogen bonds : angle 5.05734 / 3.68 ( 2788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 469 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8519 (mm-30) REVERT: A 57 LYS cc_start: 0.9458 (ttmm) cc_final: 0.9211 (tppt) REVERT: A 62 LEU cc_start: 0.9449 (mt) cc_final: 0.9193 (mt) REVERT: A 70 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7758 (mtm110) REVERT: A 98 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7858 (mm-30) REVERT: A 106 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8050 (tp30) REVERT: B 37 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8587 (mtm180) REVERT: B 53 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7857 (tm-30) REVERT: C 37 LYS cc_start: 0.9349 (ttmm) cc_final: 0.8689 (tppt) REVERT: C 39 ASN cc_start: 0.8659 (m-40) cc_final: 0.8377 (m-40) REVERT: C 42 GLU cc_start: 0.8189 (mp0) cc_final: 0.7680 (mp0) REVERT: C 96 LYS cc_start: 0.8994 (tptt) cc_final: 0.8688 (tppt) REVERT: D 44 LYS cc_start: 0.9077 (mttt) cc_final: 0.8712 (mmmm) REVERT: D 100 ARG cc_start: 0.8752 (mtt90) cc_final: 0.8529 (tpp80) REVERT: D 109 LYS cc_start: 0.9123 (mttt) cc_final: 0.8602 (tppp) REVERT: E 61 LEU cc_start: 0.9444 (mt) cc_final: 0.9149 (mt) REVERT: E 97 CYS cc_start: 0.8874 (m) cc_final: 0.8378 (t) REVERT: E 98 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7800 (pp20) REVERT: F 85 MET cc_start: 0.8178 (mmp) cc_final: 0.7854 (mmp) REVERT: H 48 GLN cc_start: 0.7799 (tt0) cc_final: 0.7441 (tm-30) REVERT: H 106 GLU cc_start: 0.8818 (mp0) cc_final: 0.8552 (mp0) REVERT: H 117 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8374 (ttpt) REVERT: K 4 ASN cc_start: 0.8220 (m-40) cc_final: 0.7861 (m-40) REVERT: K 152 LEU cc_start: 0.8744 (mt) cc_final: 0.8442 (mt) REVERT: K 193 TYR cc_start: 0.5223 (m-80) cc_final: 0.4960 (m-80) REVERT: K 215 GLU cc_start: 0.9002 (tp30) cc_final: 0.8598 (tp30) REVERT: K 235 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8442 (tm-30) REVERT: K 330 ASP cc_start: 0.4440 (m-30) cc_final: 0.4122 (m-30) REVERT: K 879 LYS cc_start: 0.8358 (mttt) cc_final: 0.8045 (mmtt) REVERT: K 926 LEU cc_start: 0.7848 (tp) cc_final: 0.7592 (tp) REVERT: K 1030 PHE cc_start: 0.8180 (p90) cc_final: 0.7702 (p90) REVERT: K 1057 ARG cc_start: 0.6707 (mtt180) cc_final: 0.6374 (mtt180) REVERT: K 1102 ARG cc_start: 0.9141 (ttt90) cc_final: 0.8400 (mpt180) REVERT: L 88 GLN cc_start: 0.8515 (mt0) cc_final: 0.8174 (tt0) REVERT: L 101 TYR cc_start: 0.8019 (m-10) cc_final: 0.7646 (m-10) REVERT: L 119 TRP cc_start: 0.7886 (m100) cc_final: 0.7167 (m100) REVERT: L 281 PHE cc_start: 0.7966 (p90) cc_final: 0.7410 (p90) REVERT: L 304 LEU cc_start: 0.9400 (tt) cc_final: 0.9125 (tp) REVERT: L 358 ASP cc_start: 0.8462 (t0) cc_final: 0.8167 (t0) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.3548 time to fit residues: 249.5198 Evaluate side-chains 415 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [95, 51, 183, 78, 109, 186, 71, 216, 214, 157, 46] chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 255 GLN ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.141277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114605 restraints weight = 120630.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120486 restraints weight = 50003.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.124089 restraints weight = 26271.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.126305 restraints weight = 16708.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127691 restraints weight = 12339.232| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22266 Z= 0.179 Angle : 0.672 10.759 31343 Z= 0.404 Chirality : 0.052 1.625 3543 Planarity : 0.005 0.078 2998 Dihedral : 26.612 172.456 5386 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.16 (0.19), residues: 1922 helix: 0.81 (0.20), residues: 650 sheet: -1.07 (0.25), residues: 437 loop : -1.86 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 80 TYR 0.024 0.002 TYR K 136 PHE 0.028 0.002 PHE E 105 TRP 0.011 0.002 TRP L 270 HIS 0.008 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 (22266) covalent geometry : angle 0.67201 / 0.40 (31343) hydrogen bonds : bond 0.05340 / 3.59 ( 1081) hydrogen bonds : angle 4.82480 / 3.51 ( 2788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8559 (mm-30) REVERT: A 57 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9189 (tppt) REVERT: A 62 LEU cc_start: 0.9457 (mt) cc_final: 0.9173 (mt) REVERT: A 70 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7747 (mtm110) REVERT: A 98 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7890 (mm-30) REVERT: A 106 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8042 (tp30) REVERT: B 53 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7824 (tm-30) REVERT: B 85 MET cc_start: 0.7408 (mmm) cc_final: 0.7180 (mmm) REVERT: C 37 LYS cc_start: 0.9308 (ttmm) cc_final: 0.8650 (tppt) REVERT: C 39 ASN cc_start: 0.8593 (m-40) cc_final: 0.8353 (m-40) REVERT: C 42 GLU cc_start: 0.8258 (mp0) cc_final: 0.7715 (mp0) REVERT: C 96 LYS cc_start: 0.8979 (tptt) cc_final: 0.8520 (ttmm) REVERT: D 44 LYS cc_start: 0.9012 (mttt) cc_final: 0.8676 (mmmm) REVERT: D 100 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8425 (tpp80) REVERT: D 109 LYS cc_start: 0.9130 (mttt) cc_final: 0.8592 (tppp) REVERT: E 61 LEU cc_start: 0.9414 (mt) cc_final: 0.9116 (mt) REVERT: E 97 CYS cc_start: 0.8883 (m) cc_final: 0.8433 (t) REVERT: E 98 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7928 (pp20) REVERT: F 85 MET cc_start: 0.8214 (mmp) cc_final: 0.7873 (mmp) REVERT: G 75 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8945 (tppt) REVERT: H 48 GLN cc_start: 0.7841 (tt0) cc_final: 0.7507 (tm-30) REVERT: H 63 MET cc_start: 0.8913 (mmm) cc_final: 0.8303 (mmm) REVERT: H 106 GLU cc_start: 0.8839 (mp0) cc_final: 0.8578 (mp0) REVERT: H 117 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8336 (ttpt) REVERT: K 16 ASN cc_start: 0.7996 (t0) cc_final: 0.7719 (t0) REVERT: K 152 LEU cc_start: 0.8718 (mt) cc_final: 0.8403 (mt) REVERT: K 193 TYR cc_start: 0.5021 (m-80) cc_final: 0.4757 (m-80) REVERT: K 215 GLU cc_start: 0.9035 (tp30) cc_final: 0.8597 (tp30) REVERT: K 235 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8423 (tm-30) REVERT: K 330 ASP cc_start: 0.4447 (m-30) cc_final: 0.4077 (m-30) REVERT: K 879 LYS cc_start: 0.8341 (mttt) cc_final: 0.8040 (mmtt) REVERT: K 1030 PHE cc_start: 0.8164 (p90) cc_final: 0.7795 (p90) REVERT: K 1057 ARG cc_start: 0.6760 (mtt180) cc_final: 0.6442 (mtt180) REVERT: K 1102 ARG cc_start: 0.9145 (ttt90) cc_final: 0.8397 (mpt180) REVERT: L 88 GLN cc_start: 0.8499 (mt0) cc_final: 0.8149 (tt0) REVERT: L 101 TYR cc_start: 0.8104 (m-10) cc_final: 0.7783 (m-10) REVERT: L 119 TRP cc_start: 0.8017 (m100) cc_final: 0.7193 (m100) REVERT: L 177 MET cc_start: 0.8116 (tpp) cc_final: 0.7847 (tpp) REVERT: L 304 LEU cc_start: 0.9414 (tt) cc_final: 0.9141 (tp) REVERT: L 332 ARG cc_start: 0.7921 (ptm160) cc_final: 0.7671 (ptm160) REVERT: L 358 ASP cc_start: 0.8492 (t0) cc_final: 0.8207 (t0) REVERT: L 399 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7136 (mm-30) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 0.3423 time to fit residues: 243.4057 Evaluate side-chains 418 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [111, 204, 102, 125, 73, 66, 187, 78, 195, 188, 142] chunk 111 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115804 restraints weight = 119926.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121748 restraints weight = 49472.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125396 restraints weight = 25977.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.127609 restraints weight = 16459.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129038 restraints weight = 12145.730| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22266 Z= 0.163 Angle : 0.661 10.677 31343 Z= 0.397 Chirality : 0.052 1.593 3543 Planarity : 0.006 0.144 2998 Dihedral : 26.623 172.644 5386 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.95 (0.19), residues: 1922 helix: 1.05 (0.20), residues: 649 sheet: -0.99 (0.24), residues: 437 loop : -1.79 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 80 TYR 0.017 0.001 TYR D 41 PHE 0.025 0.001 PHE K 169 TRP 0.012 0.002 TRP L 270 HIS 0.023 0.001 HIS L 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (22266) covalent geometry : angle 0.66066 / 0.40 (31343) hydrogen bonds : bond 0.05130 / 3.45 ( 1081) hydrogen bonds : angle 4.65840 / 3.38 ( 2788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8552 (mm-30) REVERT: A 57 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9179 (tppt) REVERT: A 62 LEU cc_start: 0.9447 (mt) cc_final: 0.9131 (mt) REVERT: A 70 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7727 (mtm110) REVERT: A 86 GLN cc_start: 0.7823 (mt0) cc_final: 0.7580 (mt0) REVERT: A 98 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7702 (mm-30) REVERT: A 106 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8020 (tp30) REVERT: B 37 ARG cc_start: 0.8915 (mtm-85) cc_final: 0.8540 (mtm180) REVERT: B 53 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8166 (tp30) REVERT: C 37 LYS cc_start: 0.9292 (ttmm) cc_final: 0.8641 (tppt) REVERT: C 39 ASN cc_start: 0.8540 (m-40) cc_final: 0.8304 (m-40) REVERT: C 42 GLU cc_start: 0.8274 (mp0) cc_final: 0.7731 (mp0) REVERT: C 96 LYS cc_start: 0.8988 (tptt) cc_final: 0.8522 (ttmm) REVERT: D 44 LYS cc_start: 0.8965 (mttt) cc_final: 0.8624 (mmmm) REVERT: D 109 LYS cc_start: 0.9129 (mttt) cc_final: 0.8545 (tppp) REVERT: E 61 LEU cc_start: 0.9403 (mt) cc_final: 0.9084 (mt) REVERT: E 97 CYS cc_start: 0.8834 (m) cc_final: 0.8357 (t) REVERT: E 98 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7896 (pp20) REVERT: F 85 MET cc_start: 0.8167 (mmp) cc_final: 0.7843 (mmp) REVERT: G 75 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8943 (tppt) REVERT: H 48 GLN cc_start: 0.7793 (tt0) cc_final: 0.7490 (tm-30) REVERT: H 63 MET cc_start: 0.8886 (mmm) cc_final: 0.8259 (mmm) REVERT: H 109 LYS cc_start: 0.9292 (mttt) cc_final: 0.8991 (mmtm) REVERT: H 117 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8318 (ttpt) REVERT: K 16 ASN cc_start: 0.7948 (t0) cc_final: 0.7680 (t0) REVERT: K 152 LEU cc_start: 0.8668 (mt) cc_final: 0.8366 (mt) REVERT: K 193 TYR cc_start: 0.4955 (m-80) cc_final: 0.4670 (m-80) REVERT: K 215 GLU cc_start: 0.9039 (tp30) cc_final: 0.8592 (tp30) REVERT: K 235 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8409 (tm-30) REVERT: K 330 ASP cc_start: 0.4399 (m-30) cc_final: 0.4016 (m-30) REVERT: K 343 GLN cc_start: 0.8877 (tp40) cc_final: 0.8159 (tm-30) REVERT: K 879 LYS cc_start: 0.8325 (mttt) cc_final: 0.7953 (mmtt) REVERT: K 949 PHE cc_start: 0.7277 (p90) cc_final: 0.7015 (p90) REVERT: K 1057 ARG cc_start: 0.6728 (mtt180) cc_final: 0.6445 (mtt180) REVERT: K 1102 ARG cc_start: 0.9142 (ttt90) cc_final: 0.8401 (mpt180) REVERT: L 88 GLN cc_start: 0.8483 (mt0) cc_final: 0.8142 (tt0) REVERT: L 101 TYR cc_start: 0.8079 (m-10) cc_final: 0.7809 (m-10) REVERT: L 119 TRP cc_start: 0.7962 (m100) cc_final: 0.7197 (m100) REVERT: L 177 MET cc_start: 0.8189 (tpp) cc_final: 0.7916 (tpp) REVERT: L 304 LEU cc_start: 0.9395 (tt) cc_final: 0.9115 (tp) REVERT: L 399 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7066 (mm-30) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.3546 time to fit residues: 256.1244 Evaluate side-chains 423 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: [145, 127, 117, 185, 89, 43, 52, 156, 132, 93, 74] chunk 145 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 43 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.142058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115177 restraints weight = 124808.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121210 restraints weight = 51237.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.124877 restraints weight = 26766.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.127171 restraints weight = 17021.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.128562 restraints weight = 12524.557| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22266 Z= 0.183 Angle : 0.671 10.754 31343 Z= 0.401 Chirality : 0.052 1.616 3543 Planarity : 0.005 0.074 2998 Dihedral : 26.632 172.713 5386 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.30 % Favored : 93.60 % Rotamer: Outliers : 0.06 % Allowed : 0.30 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1922 helix: 0.93 (0.20), residues: 655 sheet: -1.10 (0.24), residues: 455 loop : -1.77 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 80 TYR 0.017 0.002 TYR K 136 PHE 0.024 0.002 PHE K1088 TRP 0.012 0.002 TRP L 270 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (22266) covalent geometry : angle 0.67148 / 0.40 (31343) hydrogen bonds : bond 0.05214 / 3.51 ( 1081) hydrogen bonds : angle 4.74726 / 3.44 ( 2788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7471.91 seconds wall clock time: 127 minutes 46.73 seconds (7666.73 seconds total)