Starting phenix.real_space_refine on Sat Sep 12 14:09:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z3l_6879/09_2026/5z3l_6879.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z3l_6879/09_2026/5z3l_6879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5z3l_6879/09_2026/5z3l_6879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z3l_6879/09_2026/5z3l_6879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5z3l_6879/09_2026/5z3l_6879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z3l_6879/09_2026/5z3l_6879.map" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 29 5.16 5 C 9670 2.51 5 N 3091 2.21 5 O 3701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16783 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 4772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4772 Classifications: {'peptide': 581} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 564} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.89, per 1000 atoms: 0.23 Number of scatterers: 16783 At special positions: 0 Unit cell: (145.2, 126.72, 129.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 292 15.00 O 3701 8.00 N 3091 7.00 C 9670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 569.9 milliseconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 63.5% alpha, 2.2% beta 118 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.619A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.752A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.376A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.422A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.631A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.704A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.866A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.926A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.699A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.619A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.753A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.586A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.721A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.538A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.704A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.866A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.925A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.699A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 674 through 683 removed outlier: 4.464A pdb=" N THR O 680 " --> pdb=" O ASP O 676 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS O 681 " --> pdb=" O THR O 677 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU O 682 " --> pdb=" O ARG O 678 " (cutoff:3.500A) Processing helix chain 'O' and resid 683 through 689 removed outlier: 4.399A pdb=" N ASN O 687 " --> pdb=" O LEU O 683 " (cutoff:3.500A) Processing helix chain 'O' and resid 744 through 750 removed outlier: 3.547A pdb=" N ALA O 748 " --> pdb=" O TYR O 744 " (cutoff:3.500A) Processing helix chain 'O' and resid 768 through 785 removed outlier: 4.492A pdb=" N ASN O 784 " --> pdb=" O SER O 780 " (cutoff:3.500A) Processing helix chain 'O' and resid 797 through 810 removed outlier: 3.687A pdb=" N LEU O 805 " --> pdb=" O GLN O 801 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU O 806 " --> pdb=" O THR O 802 " (cutoff:3.500A) Processing helix chain 'O' and resid 827 through 838 removed outlier: 3.772A pdb=" N PHE O 835 " --> pdb=" O TRP O 831 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA O 836 " --> pdb=" O SER O 832 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS O 837 " --> pdb=" O SER O 833 " (cutoff:3.500A) Processing helix chain 'O' and resid 850 through 863 removed outlier: 4.080A pdb=" N LYS O 857 " --> pdb=" O GLU O 853 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS O 860 " --> pdb=" O ALA O 856 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG O 862 " --> pdb=" O GLN O 858 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA O 863 " --> pdb=" O ALA O 859 " (cutoff:3.500A) Processing helix chain 'O' and resid 879 through 886 removed outlier: 3.804A pdb=" N LYS O 885 " --> pdb=" O ALA O 881 " (cutoff:3.500A) Processing helix chain 'O' and resid 904 through 913 removed outlier: 3.550A pdb=" N LEU O 910 " --> pdb=" O LEU O 906 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN O 911 " --> pdb=" O SER O 907 " (cutoff:3.500A) Processing helix chain 'O' and resid 944 through 958 removed outlier: 3.892A pdb=" N SER O 948 " --> pdb=" O LYS O 944 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL O 949 " --> pdb=" O ILE O 945 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS O 950 " --> pdb=" O PHE O 946 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER O 951 " --> pdb=" O ASN O 947 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE O 952 " --> pdb=" O SER O 948 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU O 954 " --> pdb=" O LYS O 950 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TRP O 955 " --> pdb=" O SER O 951 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR O 958 " --> pdb=" O GLU O 954 " (cutoff:3.500A) Processing helix chain 'O' and resid 968 through 973 Processing helix chain 'O' and resid 975 through 987 removed outlier: 3.578A pdb=" N LEU O 987 " --> pdb=" O LEU O 983 " (cutoff:3.500A) Processing helix chain 'O' and resid 995 through 999 Processing helix chain 'O' and resid 1020 through 1031 removed outlier: 3.800A pdb=" N GLN O1024 " --> pdb=" O GLN O1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O1030 " --> pdb=" O MET O1026 " (cutoff:3.500A) Processing helix chain 'O' and resid 1055 through 1061 removed outlier: 4.032A pdb=" N ASN O1060 " --> pdb=" O LYS O1056 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS O1061 " --> pdb=" O LYS O1057 " (cutoff:3.500A) Processing helix chain 'O' and resid 1068 through 1073 removed outlier: 3.713A pdb=" N ILE O1072 " --> pdb=" O VAL O1068 " (cutoff:3.500A) Processing helix chain 'O' and resid 1082 through 1085 removed outlier: 3.706A pdb=" N VAL O1085 " --> pdb=" O ILE O1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1082 through 1085' Processing helix chain 'O' and resid 1086 through 1091 removed outlier: 4.199A pdb=" N LEU O1091 " --> pdb=" O GLY O1087 " (cutoff:3.500A) Processing helix chain 'O' and resid 1091 through 1103 removed outlier: 3.976A pdb=" N ILE O1095 " --> pdb=" O LEU O1091 " (cutoff:3.500A) Proline residue: O1097 - end of helix removed outlier: 3.521A pdb=" N LYS O1100 " --> pdb=" O LEU O1096 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA O1101 " --> pdb=" O PRO O1097 " (cutoff:3.500A) Processing helix chain 'O' and resid 1113 through 1127 removed outlier: 4.050A pdb=" N ASP O1117 " --> pdb=" O THR O1113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR O1125 " --> pdb=" O ASP O1121 " (cutoff:3.500A) Processing helix chain 'O' and resid 1134 through 1138 removed outlier: 3.520A pdb=" N THR O1137 " --> pdb=" O ASP O1134 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS O1138 " --> pdb=" O GLY O1135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1134 through 1138' Processing helix chain 'O' and resid 1139 through 1150 removed outlier: 4.494A pdb=" N SER O1143 " --> pdb=" O SER O1139 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU O1144 " --> pdb=" O ASP O1140 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU O1146 " --> pdb=" O ARG O1142 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG O1147 " --> pdb=" O SER O1143 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU O1148 " --> pdb=" O GLU O1144 " (cutoff:3.500A) Processing helix chain 'O' and resid 1187 through 1198 removed outlier: 3.832A pdb=" N GLN O1194 " --> pdb=" O ASP O1190 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP O1195 " --> pdb=" O LEU O1191 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA O1197 " --> pdb=" O ALA O1193 " (cutoff:3.500A) Processing helix chain 'O' and resid 1217 through 1226 removed outlier: 3.741A pdb=" N ILE O1221 " --> pdb=" O VAL O1217 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU O1223 " --> pdb=" O GLU O1219 " (cutoff:3.500A) Processing helix chain 'O' and resid 1229 through 1231 No H-bonds generated for 'chain 'O' and resid 1229 through 1231' Processing helix chain 'O' and resid 1232 through 1243 removed outlier: 4.094A pdb=" N LYS O1240 " --> pdb=" O ILE O1236 " (cutoff:3.500A) Processing helix chain 'O' and resid 1246 through 1250 removed outlier: 3.660A pdb=" N GLN O1250 " --> pdb=" O SER O1247 " (cutoff:3.500A) Processing helix chain 'O' and resid 1253 through 1259 removed outlier: 4.073A pdb=" N LEU O1257 " --> pdb=" O LEU O1253 " (cutoff:3.500A) Processing helix chain 'O' and resid 1261 through 1269 removed outlier: 3.913A pdb=" N ARG O1265 " --> pdb=" O GLU O1261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS O1266 " --> pdb=" O GLU O1262 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1287 removed outlier: 3.793A pdb=" N GLU O1285 " --> pdb=" O SER O1281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE O1286 " --> pdb=" O GLU O1282 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1307 removed outlier: 3.570A pdb=" N THR O1298 " --> pdb=" O MET O1294 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS O1306 " --> pdb=" O GLU O1302 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS O1307 " --> pdb=" O ASP O1303 " (cutoff:3.500A) Processing helix chain 'O' and resid 1338 through 1343 Processing helix chain 'O' and resid 1344 through 1347 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 5.774A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.761A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'O' and resid 789 through 790 removed outlier: 3.995A pdb=" N LEU O 790 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL O 869 " --> pdb=" O TYR O 819 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 1130 through 1131 removed outlier: 7.266A pdb=" N LEU O1131 " --> pdb=" O ILE O1160 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N SER O1162 " --> pdb=" O LEU O1131 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE O1109 " --> pdb=" O ILE O1179 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3802 1.34 - 1.45: 4752 1.45 - 1.57: 8477 1.57 - 1.69: 582 1.69 - 1.81: 53 Bond restraints: 17666 Sorted by residual: bond pdb=" C3' DG J 56 " pdb=" C2' DG J 56 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C3' DC I 56 " pdb=" C2' DC I 56 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.51e+00 bond pdb=" C3' DG I 76 " pdb=" C2' DG I 76 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.36e+00 bond pdb=" C3' DT I 112 " pdb=" C2' DT I 112 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.26e+00 ... (remaining 17661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24140 1.88 - 3.77: 886 3.77 - 5.65: 51 5.65 - 7.53: 12 7.53 - 9.42: 6 Bond angle restraints: 25095 Sorted by residual: angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.25 109.96 -6.71 1.05e+00 9.07e-01 4.09e+01 angle pdb=" O4' DA I 135 " pdb=" C1' DA I 135 " pdb=" N9 DA I 135 " ideal model delta sigma weight residual 108.00 111.40 -3.40 7.00e-01 2.04e+00 2.36e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 57 " pdb=" C4 DT J 57 " pdb=" O4 DT J 57 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 143 " pdb=" C4 DT J 143 " pdb=" O4 DT J 143 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 25090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 8647 35.71 - 71.41: 1261 71.41 - 107.12: 20 107.12 - 142.83: 5 142.83 - 178.54: 8 Dihedral angle restraints: 9941 sinusoidal: 6007 harmonic: 3934 Sorted by residual: dihedral pdb=" CA PHE O1110 " pdb=" C PHE O1110 " pdb=" N GLN O1111 " pdb=" CA GLN O1111 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N THR B 96 " pdb=" CA THR B 96 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 41.46 178.54 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 9938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2049 0.042 - 0.084: 630 0.084 - 0.126: 153 0.126 - 0.168: 19 0.168 - 0.210: 9 Chirality restraints: 2860 Sorted by residual: chirality pdb=" CG LEU O1145 " pdb=" CB LEU O1145 " pdb=" CD1 LEU O1145 " pdb=" CD2 LEU O1145 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU O1170 " pdb=" CB LEU O1170 " pdb=" CD1 LEU O1170 " pdb=" CD2 LEU O1170 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2857 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO H 100 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL O1064 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C VAL O1064 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL O1064 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE O1065 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO D 100 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.024 5.00e-02 4.00e+02 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1352 2.74 - 3.28: 16390 3.28 - 3.82: 31004 3.82 - 4.36: 36260 4.36 - 4.90: 53153 Nonbonded interactions: 138159 Sorted by model distance: nonbonded pdb=" OH TYR H 39 " pdb=" OP2 DG I 22 " model vdw 2.197 3.040 nonbonded pdb=" O VAL H 108 " pdb=" OG1 THR H 112 " model vdw 2.237 3.040 nonbonded pdb=" O VAL D 108 " pdb=" OG1 THR D 112 " model vdw 2.238 3.040 nonbonded pdb=" O ALA O 791 " pdb=" NH1 ARG O 993 " model vdw 2.239 3.120 nonbonded pdb=" O2 DC I 140 " pdb=" N2 DG J 8 " model vdw 2.262 3.120 ... (remaining 138154 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17666 Z= 0.418 Angle : 0.735 9.418 25095 Z= 0.606 Chirality : 0.044 0.210 2860 Planarity : 0.004 0.044 2168 Dihedral : 24.561 178.537 7385 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.95 % Favored : 89.98 % Rotamer: Outliers : 0.35 % Allowed : 1.31 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -3.74 (0.19), residues: 1317 helix: -2.88 (0.14), residues: 718 sheet: -2.02 (0.58), residues: 63 loop : -1.67 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.018 0.001 TYR O 914 PHE 0.020 0.002 PHE O1065 TRP 0.015 0.001 TRP O1083 HIS 0.004 0.001 HIS O 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.42 (17666) covalent geometry : angle 0.73509 / 0.61 (25095) hydrogen bonds : bond 0.15287 / 10.13 ( 828) hydrogen bonds : angle 8.10095 / 5.89 ( 2159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 510 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8478 (tt0) cc_final: 0.7660 (tm-30) REVERT: A 107 THR cc_start: 0.9525 (m) cc_final: 0.9265 (t) REVERT: A 123 ASP cc_start: 0.8072 (p0) cc_final: 0.7351 (m-30) REVERT: B 25 ASN cc_start: 0.7849 (t0) cc_final: 0.7566 (t0) REVERT: C 92 GLU cc_start: 0.7134 (pt0) cc_final: 0.6806 (tt0) REVERT: D 95 VAL cc_start: 0.9196 (p) cc_final: 0.8883 (p) REVERT: D 103 LEU cc_start: 0.8666 (tp) cc_final: 0.7788 (tp) REVERT: E 60 LEU cc_start: 0.7656 (tp) cc_final: 0.7393 (tt) REVERT: E 105 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7580 (tm-30) REVERT: E 113 HIS cc_start: 0.8197 (t70) cc_final: 0.6314 (t70) REVERT: E 125 GLN cc_start: 0.8444 (pt0) cc_final: 0.7270 (tm-30) REVERT: F 68 ASP cc_start: 0.8897 (m-30) cc_final: 0.8153 (m-30) REVERT: F 74 GLU cc_start: 0.8543 (tp30) cc_final: 0.8297 (tm-30) REVERT: F 88 TYR cc_start: 0.7953 (m-10) cc_final: 0.7040 (m-10) REVERT: G 56 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8797 (mm-30) REVERT: G 68 ASN cc_start: 0.8403 (m-40) cc_final: 0.7703 (m110) REVERT: G 78 ILE cc_start: 0.8575 (pt) cc_final: 0.8360 (pt) REVERT: G 113 SER cc_start: 0.9371 (m) cc_final: 0.9129 (p) REVERT: H 56 MET cc_start: 0.8825 (tpp) cc_final: 0.8585 (tpt) REVERT: H 90 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8221 (mm-30) REVERT: H 102 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6935 (tp30) REVERT: H 105 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8497 (mmtm) REVERT: H 109 SER cc_start: 0.9040 (m) cc_final: 0.8803 (p) REVERT: O 838 TRP cc_start: 0.7272 (m100) cc_final: 0.6842 (m100) REVERT: O 852 ASN cc_start: 0.9103 (m-40) cc_final: 0.8597 (p0) REVERT: O 894 ASP cc_start: 0.8484 (t70) cc_final: 0.8150 (t70) REVERT: O 908 LEU cc_start: 0.9278 (mp) cc_final: 0.9054 (mm) REVERT: O 912 THR cc_start: 0.9013 (m) cc_final: 0.8729 (p) REVERT: O 1058 ILE cc_start: 0.8738 (pt) cc_final: 0.8290 (tt) REVERT: O 1067 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7274 (tt0) REVERT: O 1116 MET cc_start: 0.8354 (mtp) cc_final: 0.7899 (tmm) REVERT: O 1140 ASP cc_start: 0.8691 (t0) cc_final: 0.7587 (m-30) REVERT: O 1223 GLU cc_start: 0.8896 (mp0) cc_final: 0.8686 (pp20) REVERT: O 1294 MET cc_start: 0.7474 (mmm) cc_final: 0.7249 (mmm) outliers start: 4 outliers final: 1 residues processed: 513 average time/residue: 0.1750 time to fit residues: 123.3143 Evaluate side-chains 296 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN A 108 ASN B 18 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 60 ASN D 92 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 94 ASN H 92 GLN O 784 ASN O 785 HIS ** O 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1049 ASN ** O1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1104 HIS O1111 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.100027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077012 restraints weight = 72815.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.078730 restraints weight = 41352.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079915 restraints weight = 28257.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.080720 restraints weight = 22147.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.081205 restraints weight = 19105.876| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17666 Z= 0.188 Angle : 0.726 12.633 25095 Z= 0.401 Chirality : 0.046 0.347 2860 Planarity : 0.006 0.050 2168 Dihedral : 29.821 179.811 4672 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.35 % Allowed : 3.83 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.20), residues: 1317 helix: -1.63 (0.16), residues: 751 sheet: -1.59 (0.66), residues: 50 loop : -1.71 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O1268 TYR 0.024 0.002 TYR C 39 PHE 0.022 0.003 PHE O 782 TRP 0.021 0.003 TRP O 888 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (17666) covalent geometry : angle 0.72611 / 0.40 (25095) hydrogen bonds : bond 0.05475 / 3.65 ( 828) hydrogen bonds : angle 5.34361 / 3.87 ( 2159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 352 time to evaluate : 0.472 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: A 93 GLN cc_start: 0.8904 (tt0) cc_final: 0.8059 (tm-30) REVERT: A 94 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 106 ASP cc_start: 0.8716 (m-30) cc_final: 0.8406 (m-30) REVERT: A 130 ILE cc_start: 0.8837 (tp) cc_final: 0.8535 (tp) REVERT: B 49 LEU cc_start: 0.7665 (mp) cc_final: 0.7427 (mp) REVERT: B 75 HIS cc_start: 0.7746 (t-90) cc_final: 0.7503 (t-90) REVERT: B 85 ASP cc_start: 0.8428 (m-30) cc_final: 0.8223 (m-30) REVERT: D 32 GLU cc_start: 0.8083 (pp20) cc_final: 0.7882 (pp20) REVERT: D 46 HIS cc_start: 0.8921 (m-70) cc_final: 0.8642 (m170) REVERT: D 68 GLU cc_start: 0.8202 (tp30) cc_final: 0.7923 (tp30) REVERT: D 83 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.6875 (mmm160) REVERT: D 89 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7825 (tpp80) REVERT: D 103 LEU cc_start: 0.8955 (tp) cc_final: 0.8353 (tp) REVERT: D 105 LYS cc_start: 0.7318 (ttpp) cc_final: 0.7108 (mtmt) REVERT: E 60 LEU cc_start: 0.7921 (tp) cc_final: 0.7642 (tt) REVERT: E 61 LEU cc_start: 0.7781 (tp) cc_final: 0.7289 (tp) REVERT: E 64 LYS cc_start: 0.9038 (mppt) cc_final: 0.8805 (mmtp) REVERT: E 106 ASP cc_start: 0.8912 (m-30) cc_final: 0.8464 (m-30) REVERT: E 122 LYS cc_start: 0.8840 (ptmt) cc_final: 0.8632 (ptpp) REVERT: E 125 GLN cc_start: 0.8518 (pt0) cc_final: 0.7624 (tm-30) REVERT: F 60 VAL cc_start: 0.9144 (p) cc_final: 0.8823 (t) REVERT: F 68 ASP cc_start: 0.8198 (m-30) cc_final: 0.7807 (m-30) REVERT: F 74 GLU cc_start: 0.8574 (tp30) cc_final: 0.8167 (tm-30) REVERT: G 56 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8646 (mm-30) REVERT: G 64 GLU cc_start: 0.8788 (pp20) cc_final: 0.8266 (tm-30) REVERT: G 92 GLU cc_start: 0.8620 (pp20) cc_final: 0.8407 (pp20) REVERT: H 39 TYR cc_start: 0.7986 (t80) cc_final: 0.7573 (t80) REVERT: H 44 GLN cc_start: 0.8917 (tt0) cc_final: 0.8603 (tm-30) REVERT: H 56 MET cc_start: 0.8692 (tpp) cc_final: 0.8377 (tpt) REVERT: H 77 LEU cc_start: 0.8889 (tp) cc_final: 0.8584 (tp) REVERT: H 90 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8432 (tp30) REVERT: H 109 SER cc_start: 0.9197 (m) cc_final: 0.8830 (p) REVERT: O 778 MET cc_start: 0.9012 (mmp) cc_final: 0.8767 (mmm) REVERT: O 838 TRP cc_start: 0.7383 (m100) cc_final: 0.7177 (m100) REVERT: O 852 ASN cc_start: 0.9015 (m-40) cc_final: 0.8649 (p0) REVERT: O 894 ASP cc_start: 0.8325 (t70) cc_final: 0.7987 (t70) REVERT: O 920 LEU cc_start: 0.8883 (mm) cc_final: 0.8679 (mm) REVERT: O 1107 LEU cc_start: 0.8909 (mt) cc_final: 0.8524 (mp) REVERT: O 1116 MET cc_start: 0.8733 (mtp) cc_final: 0.7953 (tmm) REVERT: O 1140 ASP cc_start: 0.8077 (t0) cc_final: 0.7314 (m-30) outliers start: 4 outliers final: 0 residues processed: 353 average time/residue: 0.1458 time to fit residues: 75.5864 Evaluate side-chains 260 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 145 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS C 38 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 890 HIS ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1050 ASN ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.098591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074796 restraints weight = 72586.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076525 restraints weight = 40978.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.077719 restraints weight = 27972.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.078548 restraints weight = 21918.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078943 restraints weight = 18938.435| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17666 Z= 0.164 Angle : 0.670 8.114 25095 Z= 0.376 Chirality : 0.045 0.350 2860 Planarity : 0.005 0.055 2168 Dihedral : 29.893 178.461 4672 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.21), residues: 1317 helix: -0.94 (0.17), residues: 757 sheet: -1.30 (0.68), residues: 51 loop : -1.76 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O1132 TYR 0.041 0.002 TYR H 80 PHE 0.026 0.002 PHE O1241 TRP 0.013 0.002 TRP O1083 HIS 0.024 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (17666) covalent geometry : angle 0.66953 / 0.38 (25095) hydrogen bonds : bond 0.04871 / 3.21 ( 828) hydrogen bonds : angle 4.79187 / 3.46 ( 2159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.490 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: A 86 SER cc_start: 0.9102 (m) cc_final: 0.8666 (t) REVERT: A 93 GLN cc_start: 0.8932 (tt0) cc_final: 0.7982 (tm-30) REVERT: A 94 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 123 ASP cc_start: 0.7511 (m-30) cc_final: 0.7180 (t70) REVERT: A 130 ILE cc_start: 0.8800 (tp) cc_final: 0.8518 (tp) REVERT: B 16 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7161 (pttm) REVERT: B 85 ASP cc_start: 0.8650 (m-30) cc_final: 0.8375 (m-30) REVERT: B 96 THR cc_start: 0.8246 (m) cc_final: 0.7985 (m) REVERT: C 39 TYR cc_start: 0.8292 (m-80) cc_final: 0.7873 (m-80) REVERT: D 46 HIS cc_start: 0.9018 (m-70) cc_final: 0.8769 (m-70) REVERT: D 103 LEU cc_start: 0.8738 (tp) cc_final: 0.8269 (tp) REVERT: D 105 LYS cc_start: 0.7415 (ttpp) cc_final: 0.7193 (mtmt) REVERT: E 64 LYS cc_start: 0.9104 (mppt) cc_final: 0.8886 (mmtp) REVERT: E 90 MET cc_start: 0.7830 (mmp) cc_final: 0.7406 (mmp) REVERT: F 68 ASP cc_start: 0.8066 (m-30) cc_final: 0.7613 (m-30) REVERT: F 74 GLU cc_start: 0.8583 (tp30) cc_final: 0.8092 (tm-30) REVERT: F 84 MET cc_start: 0.8297 (mmp) cc_final: 0.7834 (mmt) REVERT: F 88 TYR cc_start: 0.8348 (m-80) cc_final: 0.7888 (m-80) REVERT: G 56 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8530 (mm-30) REVERT: G 57 TYR cc_start: 0.8229 (t80) cc_final: 0.7564 (t80) REVERT: G 64 GLU cc_start: 0.8825 (pp20) cc_final: 0.8524 (tm-30) REVERT: G 68 ASN cc_start: 0.8765 (m-40) cc_final: 0.8249 (m-40) REVERT: G 72 ASP cc_start: 0.8696 (t70) cc_final: 0.8485 (t70) REVERT: H 39 TYR cc_start: 0.7917 (t80) cc_final: 0.7509 (t80) REVERT: H 44 GLN cc_start: 0.8934 (tt0) cc_final: 0.8659 (tm-30) REVERT: H 59 MET cc_start: 0.8876 (ttm) cc_final: 0.8605 (tpp) REVERT: H 77 LEU cc_start: 0.8968 (tp) cc_final: 0.8670 (tp) REVERT: H 90 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8419 (tp30) REVERT: H 109 SER cc_start: 0.9332 (m) cc_final: 0.8965 (p) REVERT: O 852 ASN cc_start: 0.9033 (m-40) cc_final: 0.8652 (p0) REVERT: O 1058 ILE cc_start: 0.8347 (mp) cc_final: 0.7917 (tt) REVERT: O 1116 MET cc_start: 0.8776 (mtp) cc_final: 0.7491 (tmm) REVERT: O 1161 LEU cc_start: 0.8581 (mt) cc_final: 0.8380 (mp) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.1363 time to fit residues: 65.7189 Evaluate side-chains 243 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 134 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 84 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 68 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 785 HIS ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1192 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.096358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.071952 restraints weight = 74655.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073441 restraints weight = 45136.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074567 restraints weight = 32342.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075324 restraints weight = 26247.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.075649 restraints weight = 23167.333| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17666 Z= 0.172 Angle : 0.674 9.349 25095 Z= 0.376 Chirality : 0.045 0.354 2860 Planarity : 0.005 0.046 2168 Dihedral : 29.989 176.130 4672 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.54 (0.22), residues: 1317 helix: -0.52 (0.18), residues: 753 sheet: -0.70 (0.73), residues: 51 loop : -1.69 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 17 TYR 0.020 0.002 TYR F 88 PHE 0.029 0.002 PHE O1241 TRP 0.012 0.002 TRP O1083 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (17666) covalent geometry : angle 0.67361 / 0.38 (25095) hydrogen bonds : bond 0.04826 / 3.18 ( 828) hydrogen bonds : angle 4.54427 / 3.25 ( 2159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9213 (m) cc_final: 0.8941 (t) REVERT: A 93 GLN cc_start: 0.9034 (tt0) cc_final: 0.8204 (tm-30) REVERT: A 94 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 123 ASP cc_start: 0.8049 (m-30) cc_final: 0.7287 (t70) REVERT: A 130 ILE cc_start: 0.8923 (tp) cc_final: 0.8645 (tp) REVERT: B 53 GLU cc_start: 0.8145 (tp30) cc_final: 0.7812 (tp30) REVERT: B 96 THR cc_start: 0.8510 (m) cc_final: 0.8179 (m) REVERT: C 39 TYR cc_start: 0.8130 (m-80) cc_final: 0.7865 (m-80) REVERT: C 57 TYR cc_start: 0.8987 (t80) cc_final: 0.8651 (t80) REVERT: C 68 ASN cc_start: 0.9416 (m-40) cc_final: 0.9214 (m110) REVERT: D 46 HIS cc_start: 0.9056 (m-70) cc_final: 0.8797 (m-70) REVERT: D 65 ASP cc_start: 0.8950 (t0) cc_final: 0.8616 (t0) REVERT: D 83 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.7126 (mmm160) REVERT: D 105 LYS cc_start: 0.7637 (ttpp) cc_final: 0.7249 (mtmt) REVERT: F 68 ASP cc_start: 0.8158 (m-30) cc_final: 0.7758 (m-30) REVERT: F 74 GLU cc_start: 0.8571 (tp30) cc_final: 0.8215 (tm-30) REVERT: F 84 MET cc_start: 0.8180 (mmp) cc_final: 0.7644 (mmp) REVERT: F 88 TYR cc_start: 0.8405 (m-80) cc_final: 0.7607 (m-10) REVERT: G 59 THR cc_start: 0.9154 (m) cc_final: 0.8789 (p) REVERT: G 64 GLU cc_start: 0.8861 (pp20) cc_final: 0.8578 (tm-30) REVERT: G 68 ASN cc_start: 0.8813 (m-40) cc_final: 0.8480 (m-40) REVERT: H 65 ASP cc_start: 0.7855 (p0) cc_final: 0.7469 (p0) REVERT: H 90 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8479 (tp30) REVERT: H 109 SER cc_start: 0.9325 (m) cc_final: 0.8995 (p) REVERT: O 831 TRP cc_start: 0.7943 (m100) cc_final: 0.6993 (m100) REVERT: O 838 TRP cc_start: 0.7622 (m100) cc_final: 0.7416 (m100) REVERT: O 852 ASN cc_start: 0.9035 (m-40) cc_final: 0.8608 (p0) REVERT: O 885 LYS cc_start: 0.6222 (mtmm) cc_final: 0.5679 (mptt) REVERT: O 894 ASP cc_start: 0.8472 (t70) cc_final: 0.8242 (t70) REVERT: O 1058 ILE cc_start: 0.8425 (mp) cc_final: 0.8107 (tt) REVERT: O 1119 MET cc_start: 0.8294 (tmm) cc_final: 0.8077 (tmm) REVERT: O 1139 SER cc_start: 0.6892 (t) cc_final: 0.6635 (p) REVERT: O 1140 ASP cc_start: 0.8279 (t0) cc_final: 0.7452 (m-30) REVERT: O 1161 LEU cc_start: 0.8554 (mt) cc_final: 0.8331 (mp) REVERT: O 1294 MET cc_start: 0.7119 (mmm) cc_final: 0.6586 (mmm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1390 time to fit residues: 63.5805 Evaluate side-chains 238 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 76 optimal weight: 40.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 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 = 0.3811 r_free = 0.3811 target = 0.095086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070509 restraints weight = 72297.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072221 restraints weight = 40587.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073344 restraints weight = 27569.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074153 restraints weight = 21700.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074505 restraints weight = 18854.677| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17666 Z= 0.160 Angle : 0.665 8.719 25095 Z= 0.368 Chirality : 0.045 0.363 2860 Planarity : 0.005 0.051 2168 Dihedral : 30.049 179.527 4672 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.26 (0.22), residues: 1317 helix: -0.24 (0.19), residues: 754 sheet: -0.67 (0.74), residues: 51 loop : -1.66 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 71 TYR 0.017 0.002 TYR H 80 PHE 0.026 0.002 PHE O1241 TRP 0.008 0.002 TRP O 888 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (17666) covalent geometry : angle 0.66481 / 0.37 (25095) hydrogen bonds : bond 0.04561 / 3.01 ( 828) hydrogen bonds : angle 4.42397 / 3.17 ( 2159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: A 86 SER cc_start: 0.9308 (m) cc_final: 0.8972 (t) REVERT: A 93 GLN cc_start: 0.9100 (tt0) cc_final: 0.8376 (tm-30) REVERT: A 94 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 123 ASP cc_start: 0.7830 (m-30) cc_final: 0.7121 (t70) REVERT: B 16 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7341 (pttm) REVERT: B 53 GLU cc_start: 0.8298 (tp30) cc_final: 0.8062 (tp30) REVERT: B 85 ASP cc_start: 0.8930 (m-30) cc_final: 0.8627 (m-30) REVERT: B 96 THR cc_start: 0.8484 (m) cc_final: 0.8247 (m) REVERT: C 35 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7992 (ttp-110) REVERT: C 68 ASN cc_start: 0.9467 (m-40) cc_final: 0.9236 (m110) REVERT: C 93 LEU cc_start: 0.9017 (tp) cc_final: 0.8569 (tp) REVERT: D 46 HIS cc_start: 0.9063 (m-70) cc_final: 0.8785 (m-70) REVERT: D 65 ASP cc_start: 0.9085 (t0) cc_final: 0.8676 (t0) REVERT: D 83 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.7132 (mmm160) REVERT: D 93 THR cc_start: 0.9409 (p) cc_final: 0.9200 (t) REVERT: D 98 LEU cc_start: 0.9223 (tp) cc_final: 0.8866 (tt) REVERT: D 105 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7357 (mtmt) REVERT: E 67 PHE cc_start: 0.9327 (t80) cc_final: 0.8618 (t80) REVERT: E 71 VAL cc_start: 0.9088 (t) cc_final: 0.8815 (t) REVERT: F 74 GLU cc_start: 0.8653 (tp30) cc_final: 0.8328 (tm-30) REVERT: F 84 MET cc_start: 0.8263 (mmp) cc_final: 0.7803 (mmp) REVERT: F 88 TYR cc_start: 0.8567 (m-80) cc_final: 0.7788 (m-10) REVERT: F 91 LYS cc_start: 0.9422 (tttm) cc_final: 0.9006 (ttpt) REVERT: G 56 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8446 (mm-30) REVERT: G 57 TYR cc_start: 0.8662 (t80) cc_final: 0.8049 (t80) REVERT: G 59 THR cc_start: 0.9219 (m) cc_final: 0.8932 (p) REVERT: G 64 GLU cc_start: 0.8645 (pp20) cc_final: 0.8195 (tm-30) REVERT: H 44 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8374 (tm-30) REVERT: H 56 MET cc_start: 0.9030 (tpp) cc_final: 0.8811 (tpt) REVERT: H 109 SER cc_start: 0.9333 (m) cc_final: 0.9044 (p) REVERT: O 831 TRP cc_start: 0.7987 (m100) cc_final: 0.6939 (m100) REVERT: O 852 ASN cc_start: 0.9079 (m-40) cc_final: 0.8632 (p0) REVERT: O 894 ASP cc_start: 0.8475 (t70) cc_final: 0.8071 (t0) REVERT: O 978 LEU cc_start: 0.6258 (tp) cc_final: 0.6034 (tp) REVERT: O 1058 ILE cc_start: 0.8394 (mp) cc_final: 0.8094 (tt) REVERT: O 1119 MET cc_start: 0.8390 (tmm) cc_final: 0.8106 (tmm) REVERT: O 1139 SER cc_start: 0.6938 (t) cc_final: 0.6708 (p) REVERT: O 1140 ASP cc_start: 0.8324 (t0) cc_final: 0.7450 (m-30) REVERT: O 1161 LEU cc_start: 0.8536 (mt) cc_final: 0.8297 (mp) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.1313 time to fit residues: 59.9046 Evaluate side-chains 236 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 1 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 147 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068939 restraints weight = 72579.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070580 restraints weight = 40914.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071729 restraints weight = 27992.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072509 restraints weight = 22128.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072811 restraints weight = 19290.280| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17666 Z= 0.172 Angle : 0.676 9.170 25095 Z= 0.374 Chirality : 0.045 0.363 2860 Planarity : 0.005 0.049 2168 Dihedral : 30.058 176.468 4672 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.22 (0.22), residues: 1317 helix: -0.19 (0.18), residues: 768 sheet: -0.66 (0.74), residues: 51 loop : -1.71 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 128 TYR 0.022 0.002 TYR C 39 PHE 0.025 0.002 PHE O1241 TRP 0.012 0.002 TRP O 838 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (17666) covalent geometry : angle 0.67616 / 0.37 (25095) hydrogen bonds : bond 0.04658 / 3.09 ( 828) hydrogen bonds : angle 4.40183 / 3.15 ( 2159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9203 (tt0) cc_final: 0.8412 (tm-30) REVERT: A 94 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 123 ASP cc_start: 0.8055 (m-30) cc_final: 0.7656 (t70) REVERT: B 16 LYS cc_start: 0.7667 (tmtt) cc_final: 0.7197 (pttm) REVERT: B 53 GLU cc_start: 0.8306 (tp30) cc_final: 0.8055 (tp30) REVERT: B 96 THR cc_start: 0.8553 (m) cc_final: 0.8328 (m) REVERT: C 35 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8116 (ttm110) REVERT: C 84 GLN cc_start: 0.8215 (mt0) cc_final: 0.7950 (mt0) REVERT: C 93 LEU cc_start: 0.8940 (tp) cc_final: 0.8546 (tp) REVERT: D 46 HIS cc_start: 0.9089 (m-70) cc_final: 0.8811 (m-70) REVERT: D 65 ASP cc_start: 0.9082 (t0) cc_final: 0.8719 (t0) REVERT: D 83 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.7164 (mmm160) REVERT: D 98 LEU cc_start: 0.9284 (tp) cc_final: 0.8876 (tt) REVERT: D 105 LYS cc_start: 0.7702 (ttpp) cc_final: 0.7254 (mtmt) REVERT: E 60 LEU cc_start: 0.7991 (tp) cc_final: 0.7782 (tp) REVERT: E 67 PHE cc_start: 0.9310 (t80) cc_final: 0.8473 (t80) REVERT: E 70 LEU cc_start: 0.9580 (tp) cc_final: 0.9372 (tp) REVERT: E 71 VAL cc_start: 0.9164 (t) cc_final: 0.8851 (t) REVERT: E 89 VAL cc_start: 0.8839 (t) cc_final: 0.8570 (t) REVERT: E 105 GLU cc_start: 0.8811 (tt0) cc_final: 0.8313 (tm-30) REVERT: E 120 MET cc_start: 0.8499 (mmm) cc_final: 0.8159 (mmm) REVERT: F 74 GLU cc_start: 0.8676 (tp30) cc_final: 0.8339 (tm-30) REVERT: F 91 LYS cc_start: 0.9406 (tttm) cc_final: 0.9080 (ttpt) REVERT: G 56 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8819 (mm-30) REVERT: G 57 TYR cc_start: 0.8436 (t80) cc_final: 0.8190 (t80) REVERT: G 59 THR cc_start: 0.9208 (m) cc_final: 0.8902 (p) REVERT: G 64 GLU cc_start: 0.8707 (pp20) cc_final: 0.8327 (tm-30) REVERT: G 68 ASN cc_start: 0.8880 (m-40) cc_final: 0.8348 (m110) REVERT: G 112 GLN cc_start: 0.7985 (mm110) cc_final: 0.7703 (mm-40) REVERT: H 31 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7909 (mmtm) REVERT: H 44 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8388 (tm-30) REVERT: H 56 MET cc_start: 0.9121 (tpp) cc_final: 0.8803 (tpt) REVERT: H 109 SER cc_start: 0.9380 (m) cc_final: 0.9124 (p) REVERT: O 794 MET cc_start: 0.7350 (tmm) cc_final: 0.6933 (mpp) REVERT: O 831 TRP cc_start: 0.8040 (m100) cc_final: 0.7207 (m100) REVERT: O 852 ASN cc_start: 0.9070 (m-40) cc_final: 0.8629 (p0) REVERT: O 894 ASP cc_start: 0.8507 (t70) cc_final: 0.7379 (p0) REVERT: O 1058 ILE cc_start: 0.8434 (mp) cc_final: 0.8060 (tt) REVERT: O 1119 MET cc_start: 0.8203 (tmm) cc_final: 0.7998 (tmm) REVERT: O 1139 SER cc_start: 0.6946 (t) cc_final: 0.6612 (p) REVERT: O 1140 ASP cc_start: 0.8309 (t0) cc_final: 0.7485 (m-30) REVERT: O 1142 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8327 (mtt90) REVERT: O 1294 MET cc_start: 0.7336 (mmm) cc_final: 0.6782 (mmm) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1394 time to fit residues: 62.6422 Evaluate side-chains 239 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 40.0000 chunk 96 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 68 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1050 ASN O1071 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.094335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069448 restraints weight = 73367.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070964 restraints weight = 43636.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072053 restraints weight = 30866.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072677 restraints weight = 24996.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.072859 restraints weight = 22218.443| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17666 Z= 0.138 Angle : 0.657 8.372 25095 Z= 0.363 Chirality : 0.045 0.368 2860 Planarity : 0.005 0.076 2168 Dihedral : 30.040 176.658 4672 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.17 % Allowed : 1.91 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1317 helix: -0.06 (0.18), residues: 773 sheet: -0.66 (0.73), residues: 51 loop : -1.72 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.019 0.002 TYR D 39 PHE 0.027 0.002 PHE O1159 TRP 0.019 0.002 TRP O1083 HIS 0.010 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (17666) covalent geometry : angle 0.65652 / 0.36 (25095) hydrogen bonds : bond 0.04385 / 2.92 ( 828) hydrogen bonds : angle 4.31303 / 3.11 ( 2159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: A 74 ILE cc_start: 0.9464 (tp) cc_final: 0.9245 (tp) REVERT: A 123 ASP cc_start: 0.7960 (m-30) cc_final: 0.7148 (t70) REVERT: B 16 LYS cc_start: 0.7639 (tmtt) cc_final: 0.7139 (pttm) REVERT: B 53 GLU cc_start: 0.8121 (tp30) cc_final: 0.7890 (tp30) REVERT: B 96 THR cc_start: 0.8415 (m) cc_final: 0.8185 (m) REVERT: C 35 ARG cc_start: 0.8290 (ttm110) cc_final: 0.8087 (ttp-110) REVERT: C 39 TYR cc_start: 0.8234 (m-80) cc_final: 0.8020 (m-80) REVERT: C 61 GLU cc_start: 0.8536 (pp20) cc_final: 0.8224 (tm-30) REVERT: D 46 HIS cc_start: 0.9056 (m-70) cc_final: 0.8815 (m-70) REVERT: D 65 ASP cc_start: 0.9062 (t0) cc_final: 0.8694 (t0) REVERT: D 68 GLU cc_start: 0.8192 (tp30) cc_final: 0.7887 (tp30) REVERT: D 83 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.7100 (mmm160) REVERT: D 98 LEU cc_start: 0.9323 (tp) cc_final: 0.9072 (tt) REVERT: E 67 PHE cc_start: 0.9234 (t80) cc_final: 0.8506 (t80) REVERT: E 71 VAL cc_start: 0.9174 (t) cc_final: 0.8747 (t) REVERT: E 89 VAL cc_start: 0.8938 (t) cc_final: 0.8506 (p) REVERT: E 105 GLU cc_start: 0.8768 (tt0) cc_final: 0.8323 (tm-30) REVERT: F 74 GLU cc_start: 0.8500 (tp30) cc_final: 0.8260 (tm-30) REVERT: F 84 MET cc_start: 0.7913 (mmp) cc_final: 0.7571 (mmp) REVERT: F 91 LYS cc_start: 0.9360 (tttm) cc_final: 0.9047 (ttpt) REVERT: G 56 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8804 (mm-30) REVERT: G 64 GLU cc_start: 0.8584 (pp20) cc_final: 0.8146 (tm-30) REVERT: G 112 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7558 (mm-40) REVERT: H 39 TYR cc_start: 0.7913 (t80) cc_final: 0.7697 (t80) REVERT: H 44 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8238 (tm-30) REVERT: H 56 MET cc_start: 0.9061 (tpp) cc_final: 0.8795 (tpt) REVERT: H 109 SER cc_start: 0.9439 (m) cc_final: 0.9077 (p) REVERT: O 794 MET cc_start: 0.7312 (tmm) cc_final: 0.6959 (mpp) REVERT: O 831 TRP cc_start: 0.8124 (m100) cc_final: 0.7369 (m100) REVERT: O 852 ASN cc_start: 0.9014 (m-40) cc_final: 0.8588 (p0) REVERT: O 888 TRP cc_start: 0.6720 (m100) cc_final: 0.6396 (m-10) REVERT: O 891 MET cc_start: 0.9157 (tmm) cc_final: 0.8811 (tmm) REVERT: O 894 ASP cc_start: 0.8415 (t70) cc_final: 0.7517 (p0) REVERT: O 978 LEU cc_start: 0.6230 (tp) cc_final: 0.6002 (tp) REVERT: O 1015 MET cc_start: 0.5664 (mmp) cc_final: 0.5373 (mmp) REVERT: O 1058 ILE cc_start: 0.8368 (mp) cc_final: 0.8014 (tt) REVERT: O 1139 SER cc_start: 0.6851 (t) cc_final: 0.6557 (p) REVERT: O 1140 ASP cc_start: 0.8195 (t0) cc_final: 0.7434 (m-30) REVERT: O 1294 MET cc_start: 0.7326 (mmm) cc_final: 0.6788 (mmm) outliers start: 2 outliers final: 0 residues processed: 288 average time/residue: 0.1304 time to fit residues: 57.0091 Evaluate side-chains 238 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 149 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 50.0000 chunk 137 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 106 HIS E 113 HIS ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1198 HIS ** 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 = 0.3732 r_free = 0.3732 target = 0.090883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065837 restraints weight = 72422.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067464 restraints weight = 40832.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068594 restraints weight = 28092.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069294 restraints weight = 22248.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069716 restraints weight = 19433.360| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17666 Z= 0.207 Angle : 0.728 10.220 25095 Z= 0.400 Chirality : 0.046 0.367 2860 Planarity : 0.005 0.056 2168 Dihedral : 30.127 173.581 4672 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.14 (0.22), residues: 1317 helix: -0.16 (0.18), residues: 768 sheet: -0.80 (0.64), residues: 62 loop : -1.59 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG D 76 TYR 0.030 0.003 TYR D 80 PHE 0.024 0.002 PHE O1241 TRP 0.009 0.002 TRP O1083 HIS 0.013 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (17666) covalent geometry : angle 0.72794 / 0.40 (25095) hydrogen bonds : bond 0.05290 / 3.52 ( 828) hydrogen bonds : angle 4.46024 / 3.18 ( 2159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9595 (tp) cc_final: 0.9379 (tp) REVERT: A 123 ASP cc_start: 0.8280 (m-30) cc_final: 0.7755 (t70) REVERT: B 16 LYS cc_start: 0.7626 (tmtt) cc_final: 0.7191 (pttm) REVERT: C 35 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8105 (ttp-110) REVERT: C 39 TYR cc_start: 0.8302 (m-80) cc_final: 0.8032 (m-80) REVERT: C 61 GLU cc_start: 0.8671 (pp20) cc_final: 0.8243 (tm-30) REVERT: D 46 HIS cc_start: 0.9195 (m-70) cc_final: 0.8832 (m-70) REVERT: D 65 ASP cc_start: 0.9235 (t0) cc_final: 0.8820 (t0) REVERT: D 68 GLU cc_start: 0.8307 (tp30) cc_final: 0.7986 (tp30) REVERT: D 83 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.7741 (mtm-85) REVERT: D 98 LEU cc_start: 0.9365 (tp) cc_final: 0.9130 (tt) REVERT: E 67 PHE cc_start: 0.9321 (t80) cc_final: 0.8556 (t80) REVERT: E 71 VAL cc_start: 0.9446 (t) cc_final: 0.9112 (t) REVERT: E 83 ARG cc_start: 0.7463 (mmt-90) cc_final: 0.6496 (mmp80) REVERT: E 105 GLU cc_start: 0.8923 (tt0) cc_final: 0.8349 (tm-30) REVERT: F 45 ARG cc_start: 0.6915 (tpt90) cc_final: 0.6353 (tpp80) REVERT: F 74 GLU cc_start: 0.8598 (tp30) cc_final: 0.8387 (tm-30) REVERT: F 84 MET cc_start: 0.8251 (mmp) cc_final: 0.7948 (mmp) REVERT: F 91 LYS cc_start: 0.9345 (tttm) cc_final: 0.8975 (ttpt) REVERT: G 56 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8648 (mm-30) REVERT: G 64 GLU cc_start: 0.8796 (pp20) cc_final: 0.8379 (tm-30) REVERT: G 112 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7775 (mm-40) REVERT: H 44 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8144 (tm-30) REVERT: H 54 LYS cc_start: 0.9301 (mmmt) cc_final: 0.8778 (mmtp) REVERT: H 56 MET cc_start: 0.9213 (tpp) cc_final: 0.8890 (tpt) REVERT: H 59 MET cc_start: 0.8858 (ttm) cc_final: 0.8519 (tpp) REVERT: H 109 SER cc_start: 0.9495 (m) cc_final: 0.9225 (p) REVERT: O 752 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7589 (tptt) REVERT: O 794 MET cc_start: 0.7477 (tmm) cc_final: 0.7142 (mpp) REVERT: O 831 TRP cc_start: 0.8381 (m100) cc_final: 0.7668 (m100) REVERT: O 852 ASN cc_start: 0.9049 (m-40) cc_final: 0.8618 (p0) REVERT: O 894 ASP cc_start: 0.8535 (t70) cc_final: 0.7684 (p0) REVERT: O 1015 MET cc_start: 0.5684 (mmp) cc_final: 0.5405 (mmp) REVERT: O 1058 ILE cc_start: 0.8638 (mp) cc_final: 0.8322 (tt) REVERT: O 1139 SER cc_start: 0.6964 (t) cc_final: 0.6651 (p) REVERT: O 1140 ASP cc_start: 0.8297 (t0) cc_final: 0.7505 (m-30) REVERT: O 1142 ARG cc_start: 0.8852 (mtt180) cc_final: 0.7692 (mtt90) REVERT: O 1294 MET cc_start: 0.7381 (mmm) cc_final: 0.6869 (mmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1458 time to fit residues: 60.7917 Evaluate side-chains 229 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 40.0000 chunk 116 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** 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 = 0.3774 r_free = 0.3774 target = 0.092961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068186 restraints weight = 73514.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069738 restraints weight = 42950.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070871 restraints weight = 30270.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071577 restraints weight = 24369.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071987 restraints weight = 21489.404| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17666 Z= 0.139 Angle : 0.686 10.370 25095 Z= 0.373 Chirality : 0.045 0.382 2860 Planarity : 0.005 0.063 2168 Dihedral : 30.093 176.067 4672 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.01 (0.22), residues: 1317 helix: -0.06 (0.18), residues: 781 sheet: -0.68 (0.65), residues: 62 loop : -1.59 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 53 TYR 0.035 0.002 TYR G 57 PHE 0.024 0.002 PHE O1241 TRP 0.015 0.002 TRP O 831 HIS 0.011 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (17666) covalent geometry : angle 0.68567 / 0.37 (25095) hydrogen bonds : bond 0.04470 / 2.98 ( 828) hydrogen bonds : angle 4.25584 / 3.06 ( 2159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9552 (tp) cc_final: 0.9341 (tp) REVERT: A 123 ASP cc_start: 0.8180 (m-30) cc_final: 0.7268 (t70) REVERT: B 16 LYS cc_start: 0.7609 (tmtt) cc_final: 0.7193 (pttm) REVERT: C 61 GLU cc_start: 0.8620 (pp20) cc_final: 0.8293 (tm-30) REVERT: C 64 GLU cc_start: 0.8428 (tt0) cc_final: 0.7914 (tt0) REVERT: D 46 HIS cc_start: 0.9079 (m-70) cc_final: 0.8845 (m-70) REVERT: D 65 ASP cc_start: 0.9216 (t0) cc_final: 0.8789 (t0) REVERT: D 68 GLU cc_start: 0.8150 (tp30) cc_final: 0.7755 (tp30) REVERT: D 80 TYR cc_start: 0.8214 (m-10) cc_final: 0.7676 (m-80) REVERT: D 83 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.7739 (mtm-85) REVERT: D 98 LEU cc_start: 0.9318 (tp) cc_final: 0.9014 (tt) REVERT: E 67 PHE cc_start: 0.9258 (t80) cc_final: 0.8476 (t80) REVERT: E 71 VAL cc_start: 0.9348 (t) cc_final: 0.8978 (t) REVERT: E 83 ARG cc_start: 0.7463 (mmt-90) cc_final: 0.6373 (mmp80) REVERT: E 105 GLU cc_start: 0.8841 (tt0) cc_final: 0.8287 (tm-30) REVERT: E 120 MET cc_start: 0.8483 (mmp) cc_final: 0.7685 (mmp) REVERT: F 45 ARG cc_start: 0.6647 (tpt90) cc_final: 0.6149 (mmm-85) REVERT: F 74 GLU cc_start: 0.8592 (tp30) cc_final: 0.8318 (tm-30) REVERT: F 84 MET cc_start: 0.8214 (mmp) cc_final: 0.7847 (mmp) REVERT: F 91 LYS cc_start: 0.9293 (tttm) cc_final: 0.8995 (ttpt) REVERT: G 56 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8633 (mm-30) REVERT: G 64 GLU cc_start: 0.8862 (pp20) cc_final: 0.8317 (tm-30) REVERT: G 92 GLU cc_start: 0.8150 (pp20) cc_final: 0.7937 (pm20) REVERT: G 112 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7734 (mm-40) REVERT: H 44 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8112 (tm-30) REVERT: H 54 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8731 (mmtp) REVERT: H 56 MET cc_start: 0.9182 (tpp) cc_final: 0.8877 (tpt) REVERT: H 59 MET cc_start: 0.8893 (ttm) cc_final: 0.8562 (tpp) REVERT: H 109 SER cc_start: 0.9411 (m) cc_final: 0.9205 (p) REVERT: O 752 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7634 (tptt) REVERT: O 794 MET cc_start: 0.7345 (tmm) cc_final: 0.7093 (mpp) REVERT: O 831 TRP cc_start: 0.8232 (m100) cc_final: 0.7537 (m100) REVERT: O 852 ASN cc_start: 0.9045 (m-40) cc_final: 0.8620 (p0) REVERT: O 888 TRP cc_start: 0.6636 (m100) cc_final: 0.6218 (m-10) REVERT: O 891 MET cc_start: 0.9074 (tmm) cc_final: 0.8736 (tmm) REVERT: O 894 ASP cc_start: 0.8462 (t70) cc_final: 0.7465 (p0) REVERT: O 978 LEU cc_start: 0.6212 (tp) cc_final: 0.5993 (tp) REVERT: O 1015 MET cc_start: 0.6001 (mmp) cc_final: 0.5796 (mmp) REVERT: O 1058 ILE cc_start: 0.8531 (mp) cc_final: 0.8258 (tt) REVERT: O 1139 SER cc_start: 0.6877 (t) cc_final: 0.6563 (p) REVERT: O 1140 ASP cc_start: 0.8181 (t0) cc_final: 0.7497 (m-30) REVERT: O 1142 ARG cc_start: 0.8811 (mtt180) cc_final: 0.7581 (mtt90) REVERT: O 1162 SER cc_start: 0.9113 (t) cc_final: 0.8862 (p) REVERT: O 1294 MET cc_start: 0.7343 (mmm) cc_final: 0.6836 (mmm) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1321 time to fit residues: 57.7119 Evaluate side-chains 237 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.0570 chunk 96 optimal weight: 30.0000 chunk 139 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 135 optimal weight: 0.0980 chunk 152 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 68 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 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 = 0.3785 r_free = 0.3785 target = 0.093461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068294 restraints weight = 72705.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069811 restraints weight = 42927.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070913 restraints weight = 30409.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071610 restraints weight = 24613.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071901 restraints weight = 21775.296| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17666 Z= 0.139 Angle : 0.678 9.951 25095 Z= 0.370 Chirality : 0.044 0.368 2860 Planarity : 0.004 0.052 2168 Dihedral : 30.077 176.280 4672 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1317 helix: 0.02 (0.18), residues: 777 sheet: -0.44 (0.65), residues: 62 loop : -1.52 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 53 TYR 0.034 0.002 TYR D 37 PHE 0.024 0.002 PHE O1241 TRP 0.015 0.002 TRP O1083 HIS 0.009 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (17666) covalent geometry : angle 0.67828 / 0.37 (25095) hydrogen bonds : bond 0.04345 / 2.88 ( 828) hydrogen bonds : angle 4.19406 / 3.01 ( 2159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 108 ASN cc_start: 0.9541 (OUTLIER) cc_final: 0.9240 (t0) REVERT: A 123 ASP cc_start: 0.8212 (m-30) cc_final: 0.7128 (t70) REVERT: B 16 LYS cc_start: 0.7589 (tmtt) cc_final: 0.6999 (pttm) REVERT: D 32 GLU cc_start: 0.8386 (pp20) cc_final: 0.8182 (pp20) REVERT: D 46 HIS cc_start: 0.9107 (m-70) cc_final: 0.8825 (m-70) REVERT: D 65 ASP cc_start: 0.9199 (t0) cc_final: 0.8738 (t0) REVERT: D 83 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.7701 (mtm-85) REVERT: D 98 LEU cc_start: 0.9287 (tp) cc_final: 0.9041 (tt) REVERT: E 67 PHE cc_start: 0.9275 (t80) cc_final: 0.8495 (t80) REVERT: E 71 VAL cc_start: 0.9303 (t) cc_final: 0.8978 (t) REVERT: E 83 ARG cc_start: 0.7482 (mmt-90) cc_final: 0.6376 (mmp80) REVERT: E 105 GLU cc_start: 0.8890 (tt0) cc_final: 0.8262 (tm-30) REVERT: E 120 MET cc_start: 0.8480 (mmp) cc_final: 0.7564 (mmm) REVERT: F 45 ARG cc_start: 0.6662 (tpt90) cc_final: 0.6181 (mmm-85) REVERT: F 74 GLU cc_start: 0.8648 (tp30) cc_final: 0.8379 (tm-30) REVERT: F 84 MET cc_start: 0.8359 (mmp) cc_final: 0.8123 (mmp) REVERT: F 88 TYR cc_start: 0.8884 (m-80) cc_final: 0.8387 (m-80) REVERT: F 91 LYS cc_start: 0.9322 (tttm) cc_final: 0.8961 (ttpt) REVERT: G 56 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8562 (mm-30) REVERT: G 64 GLU cc_start: 0.8775 (pp20) cc_final: 0.8411 (tm-30) REVERT: G 92 GLU cc_start: 0.8288 (pp20) cc_final: 0.7673 (pm20) REVERT: G 112 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7735 (mm110) REVERT: H 44 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8132 (tm-30) REVERT: H 54 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8698 (mmtp) REVERT: H 56 MET cc_start: 0.9187 (tpp) cc_final: 0.8847 (tpp) REVERT: H 59 MET cc_start: 0.8831 (ttm) cc_final: 0.8492 (tpp) REVERT: H 108 VAL cc_start: 0.9167 (t) cc_final: 0.8902 (t) REVERT: H 109 SER cc_start: 0.9397 (m) cc_final: 0.9160 (p) REVERT: O 794 MET cc_start: 0.7317 (tmm) cc_final: 0.7054 (mpp) REVERT: O 831 TRP cc_start: 0.8313 (m100) cc_final: 0.7615 (m100) REVERT: O 852 ASN cc_start: 0.9103 (m-40) cc_final: 0.8677 (p0) REVERT: O 888 TRP cc_start: 0.6669 (m100) cc_final: 0.6267 (m-10) REVERT: O 891 MET cc_start: 0.9080 (tmm) cc_final: 0.8717 (tmm) REVERT: O 894 ASP cc_start: 0.8461 (t70) cc_final: 0.7445 (p0) REVERT: O 978 LEU cc_start: 0.6154 (tp) cc_final: 0.5945 (tp) REVERT: O 1015 MET cc_start: 0.6031 (mmp) cc_final: 0.5801 (mmp) REVERT: O 1058 ILE cc_start: 0.8486 (mp) cc_final: 0.8214 (tt) REVERT: O 1139 SER cc_start: 0.6895 (t) cc_final: 0.6578 (p) REVERT: O 1140 ASP cc_start: 0.8174 (t0) cc_final: 0.7505 (m-30) REVERT: O 1294 MET cc_start: 0.7375 (mmm) cc_final: 0.6947 (mmm) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.1263 time to fit residues: 55.3248 Evaluate side-chains 235 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 73 optimal weight: 40.0000 chunk 70 optimal weight: 0.0270 chunk 89 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** 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 = 0.3782 r_free = 0.3782 target = 0.093357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068147 restraints weight = 73151.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069629 restraints weight = 43231.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070696 restraints weight = 30628.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071397 restraints weight = 24856.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071660 restraints weight = 21997.058| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17666 Z= 0.139 Angle : 0.679 9.740 25095 Z= 0.370 Chirality : 0.044 0.373 2860 Planarity : 0.005 0.054 2168 Dihedral : 30.074 176.324 4672 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.88 (0.23), residues: 1317 helix: 0.03 (0.18), residues: 775 sheet: -0.28 (0.65), residues: 62 loop : -1.52 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 53 TYR 0.031 0.002 TYR O1029 PHE 0.032 0.002 PHE B 100 TRP 0.014 0.002 TRP O1083 HIS 0.013 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (17666) covalent geometry : angle 0.67911 / 0.37 (25095) hydrogen bonds : bond 0.04383 / 2.91 ( 828) hydrogen bonds : angle 4.19804 / 3.01 ( 2159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.54 seconds wall clock time: 54 minutes 54.38 seconds (3294.38 seconds total)