Starting phenix.real_space_refine on Fri Sep 27 14:58:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3l_6879/09_2024/5z3l_6879.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3l_6879/09_2024/5z3l_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3l_6879/09_2024/5z3l_6879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3l_6879/09_2024/5z3l_6879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3l_6879/09_2024/5z3l_6879.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3l_6879/09_2024/5z3l_6879.cif" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.65, per 1000 atoms: 0.57 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: 4.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 6.73 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: 8.10 Time building geometry restraints manager: 5.38 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' DA J 14 " pdb=" O3' DA J 14 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" C3' DA J 71 " pdb=" O3' DA J 71 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" C3' DG I 40 " pdb=" O3' DG I 40 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 17661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24572 1.88 - 3.77: 463 3.77 - 5.65: 42 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=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.06e+00 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.77e+00 angle pdb=" C ILE O 815 " pdb=" N ARG O 816 " pdb=" CA ARG O 816 " ideal model delta sigma weight residual 121.54 127.06 -5.52 1.91e+00 2.74e-01 8.36e+00 angle pdb=" C3' DG I 128 " pdb=" C2' DG I 128 " pdb=" C1' DG I 128 " ideal model delta sigma weight residual 101.60 97.28 4.32 1.50e+00 4.44e-01 8.28e+00 ... (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: 2309 0.042 - 0.084: 426 0.084 - 0.126: 102 0.126 - 0.168: 15 0.168 - 0.210: 8 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: 0.230 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.670 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.003 0.046 17666 Z= 0.147 Angle : 0.606 9.418 25095 Z= 0.348 Chirality : 0.037 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP O1083 HIS 0.004 0.001 HIS O 749 PHE 0.020 0.002 PHE O1065 TYR 0.018 0.001 TYR O 914 ARG 0.005 0.000 ARG B 95 *********************** 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 fitting. rotamer outliers: 4 poor density : 510 time to evaluate : 1.574 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: 0.7649 (tm-30) REVERT: A 107 THR cc_start: 0.9525 (m) cc_final: 0.9264 (t) REVERT: A 123 ASP cc_start: 0.8072 (p0) cc_final: 0.7347 (m-30) REVERT: B 25 ASN cc_start: 0.7849 (t0) cc_final: 0.7132 (t0) REVERT: C 92 GLU cc_start: 0.7134 (pt0) cc_final: 0.6809 (tt0) REVERT: D 95 VAL cc_start: 0.9196 (p) cc_final: 0.8885 (p) REVERT: D 103 LEU cc_start: 0.8666 (tp) cc_final: 0.7792 (tp) REVERT: E 60 LEU cc_start: 0.7656 (tp) cc_final: 0.7379 (tt) REVERT: E 81 ASP cc_start: 0.7757 (p0) cc_final: 0.7536 (p0) REVERT: E 105 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7577 (tm-30) REVERT: E 113 HIS cc_start: 0.8197 (t70) cc_final: 0.6321 (t70) REVERT: E 125 GLN cc_start: 0.8444 (pt0) cc_final: 0.7274 (tm-30) REVERT: F 68 ASP cc_start: 0.8897 (m-30) cc_final: 0.8155 (m-30) REVERT: F 74 GLU cc_start: 0.8543 (tp30) cc_final: 0.8294 (tm-30) REVERT: F 79 LYS cc_start: 0.8420 (mmtp) cc_final: 0.8020 (ttpt) REVERT: F 88 TYR cc_start: 0.7953 (m-10) cc_final: 0.7041 (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: 0.9131 (p) REVERT: H 56 MET cc_start: 0.8825 (tpp) cc_final: 0.8584 (tpt) REVERT: H 90 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8221 (mm-30) REVERT: H 102 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6939 (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: 0.8802 (p) REVERT: O 838 TRP cc_start: 0.7272 (m100) cc_final: 0.6844 (m100) REVERT: O 852 ASN cc_start: 0.9103 (m-40) cc_final: 0.8595 (p0) REVERT: O 894 ASP cc_start: 0.8484 (t70) cc_final: 0.8151 (t70) REVERT: O 908 LEU cc_start: 0.9278 (mp) cc_final: 0.9058 (mm) REVERT: O 912 THR cc_start: 0.9013 (m) cc_final: 0.8731 (p) REVERT: O 1058 ILE cc_start: 0.8738 (pt) cc_final: 0.8285 (tt) REVERT: O 1067 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7276 (tt0) REVERT: O 1116 MET cc_start: 0.8354 (mtp) cc_final: 0.7903 (tmm) REVERT: O 1140 ASP cc_start: 0.8691 (t0) cc_final: 0.7590 (m-30) REVERT: O 1223 GLU cc_start: 0.8896 (mp0) cc_final: 0.8685 (pp20) REVERT: O 1294 MET cc_start: 0.7474 (mmm) cc_final: 0.7243 (mmm) outliers start: 4 outliers final: 1 residues processed: 513 average time/residue: 0.3861 time to fit residues: 267.4262 Evaluate side-chains 295 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 25 ASN C 68 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 784 ASN ** O 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 897 HIS O 929 ASN ** O1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1104 HIS O1111 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17666 Z= 0.276 Angle : 0.684 9.009 25095 Z= 0.380 Chirality : 0.041 0.175 2860 Planarity : 0.006 0.050 2168 Dihedral : 29.665 179.189 4672 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.20), residues: 1317 helix: -1.19 (0.17), residues: 757 sheet: -1.77 (0.63), residues: 57 loop : -1.88 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP O 888 HIS 0.015 0.002 HIS B 75 PHE 0.030 0.003 PHE O1241 TYR 0.018 0.003 TYR C 39 ARG 0.007 0.001 ARG D 76 *********************** 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 352 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 1.557 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 93 GLN cc_start: 0.9307 (tt0) cc_final: 0.8499 (tm-30) REVERT: B 96 THR cc_start: 0.8895 (m) cc_final: 0.8643 (m) REVERT: C 61 GLU cc_start: 0.8934 (pp20) cc_final: 0.8399 (tm-30) REVERT: C 93 LEU cc_start: 0.8904 (tp) cc_final: 0.8615 (tp) REVERT: D 46 HIS cc_start: 0.9085 (m-70) cc_final: 0.8708 (m170) REVERT: D 82 LYS cc_start: 0.9656 (mtmm) cc_final: 0.9391 (mtmm) REVERT: D 98 LEU cc_start: 0.9200 (tp) cc_final: 0.8825 (tt) REVERT: D 103 LEU cc_start: 0.8971 (tp) cc_final: 0.8521 (tp) REVERT: D 105 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7441 (mtmt) REVERT: E 53 ARG cc_start: 0.7242 (tmm160) cc_final: 0.7039 (ttp80) REVERT: E 67 PHE cc_start: 0.8791 (t80) cc_final: 0.8543 (t80) REVERT: E 106 ASP cc_start: 0.8985 (m-30) cc_final: 0.8631 (m-30) REVERT: F 50 ILE cc_start: 0.7980 (mm) cc_final: 0.7778 (mm) REVERT: F 74 GLU cc_start: 0.8703 (tp30) cc_final: 0.8356 (tm-30) REVERT: F 84 MET cc_start: 0.8586 (mmp) cc_final: 0.8255 (mmp) REVERT: G 42 ARG cc_start: 0.8680 (ttt90) cc_final: 0.8456 (ttp-170) REVERT: G 56 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8888 (mm-30) REVERT: G 59 THR cc_start: 0.9110 (m) cc_final: 0.8812 (p) REVERT: G 64 GLU cc_start: 0.9336 (pp20) cc_final: 0.8808 (tm-30) REVERT: G 92 GLU cc_start: 0.9305 (pp20) cc_final: 0.8288 (pm20) REVERT: H 39 TYR cc_start: 0.8204 (t80) cc_final: 0.7878 (t80) REVERT: H 54 LYS cc_start: 0.8728 (mmpt) cc_final: 0.8472 (mmmm) REVERT: H 90 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8927 (mm-30) REVERT: H 105 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8619 (mmtm) REVERT: H 109 SER cc_start: 0.9391 (m) cc_final: 0.9134 (p) REVERT: O 745 TYR cc_start: 0.5388 (OUTLIER) cc_final: 0.5145 (m-10) REVERT: O 852 ASN cc_start: 0.9273 (m-40) cc_final: 0.8892 (p0) REVERT: O 879 GLU cc_start: 0.7451 (pt0) cc_final: 0.6848 (pt0) REVERT: O 891 MET cc_start: 0.9263 (tmm) cc_final: 0.8980 (tmm) REVERT: O 1116 MET cc_start: 0.8678 (mtp) cc_final: 0.7843 (tmm) REVERT: O 1294 MET cc_start: 0.7268 (mmm) cc_final: 0.7013 (mmm) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.3170 time to fit residues: 160.4523 Evaluate side-chains 242 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN C 68 ASN D 92 GLN F 27 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1054 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17666 Z= 0.282 Angle : 0.684 8.608 25095 Z= 0.381 Chirality : 0.041 0.195 2860 Planarity : 0.005 0.053 2168 Dihedral : 29.823 179.255 4672 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1317 helix: -0.36 (0.18), residues: 774 sheet: -1.27 (0.57), residues: 67 loop : -1.77 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O 888 HIS 0.013 0.002 HIS B 75 PHE 0.025 0.002 PHE O1241 TYR 0.021 0.002 TYR B 88 ARG 0.008 0.001 ARG G 71 *********************** 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 313 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9483 (tt0) cc_final: 0.8735 (tm-30) REVERT: B 16 LYS cc_start: 0.7859 (tmtt) cc_final: 0.7323 (pttm) REVERT: B 88 TYR cc_start: 0.9036 (m-10) cc_final: 0.8330 (m-10) REVERT: C 35 ARG cc_start: 0.8481 (ttm110) cc_final: 0.8213 (ttp-110) REVERT: C 41 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 61 GLU cc_start: 0.8962 (pp20) cc_final: 0.8575 (tm-30) REVERT: C 65 LEU cc_start: 0.9233 (mt) cc_final: 0.8993 (mp) REVERT: D 32 GLU cc_start: 0.8530 (pp20) cc_final: 0.8325 (pp20) REVERT: D 75 SER cc_start: 0.9593 (p) cc_final: 0.9198 (m) REVERT: D 80 TYR cc_start: 0.8390 (m-10) cc_final: 0.7666 (m-80) REVERT: D 98 LEU cc_start: 0.9350 (tp) cc_final: 0.9081 (tt) REVERT: E 106 ASP cc_start: 0.8779 (m-30) cc_final: 0.8409 (m-30) REVERT: E 133 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7195 (mt-10) REVERT: F 40 ARG cc_start: 0.8516 (ttm170) cc_final: 0.8230 (ttm170) REVERT: F 59 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8757 (ttmm) REVERT: F 84 MET cc_start: 0.8485 (mmp) cc_final: 0.8085 (mmp) REVERT: F 91 LYS cc_start: 0.9277 (tttt) cc_final: 0.9044 (ttpt) REVERT: G 64 GLU cc_start: 0.9165 (pp20) cc_final: 0.8563 (tm-30) REVERT: G 68 ASN cc_start: 0.8317 (m-40) cc_final: 0.7917 (m110) REVERT: G 92 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8509 (pm20) REVERT: G 112 GLN cc_start: 0.7785 (mm110) cc_final: 0.7564 (mm110) REVERT: H 39 TYR cc_start: 0.8355 (t80) cc_final: 0.7948 (t80) REVERT: H 44 GLN cc_start: 0.9319 (tt0) cc_final: 0.8938 (tm-30) REVERT: H 56 MET cc_start: 0.9142 (tpt) cc_final: 0.8885 (tpp) REVERT: H 65 ASP cc_start: 0.8471 (p0) cc_final: 0.8228 (p0) REVERT: O 794 MET cc_start: 0.8013 (tmm) cc_final: 0.7627 (tmm) REVERT: O 831 TRP cc_start: 0.8319 (m100) cc_final: 0.7541 (m100) REVERT: O 852 ASN cc_start: 0.9251 (m-40) cc_final: 0.8852 (p0) REVERT: O 888 TRP cc_start: 0.6876 (m100) cc_final: 0.6567 (m100) REVERT: O 891 MET cc_start: 0.9329 (tmm) cc_final: 0.8999 (tmm) REVERT: O 894 ASP cc_start: 0.8677 (t70) cc_final: 0.7906 (p0) REVERT: O 1116 MET cc_start: 0.8793 (mtp) cc_final: 0.7623 (tmm) REVERT: O 1122 PHE cc_start: 0.8295 (t80) cc_final: 0.7976 (t80) REVERT: O 1140 ASP cc_start: 0.8627 (t0) cc_final: 0.8135 (m-30) REVERT: O 1142 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8331 (mtt180) REVERT: O 1144 GLU cc_start: 0.8941 (pt0) cc_final: 0.8489 (pp20) REVERT: O 1346 TYR cc_start: 0.2937 (m-80) cc_final: 0.1960 (t80) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.3126 time to fit residues: 141.8200 Evaluate side-chains 245 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 68 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1186 ASN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17666 Z= 0.270 Angle : 0.673 9.778 25095 Z= 0.376 Chirality : 0.041 0.164 2860 Planarity : 0.005 0.058 2168 Dihedral : 29.942 176.253 4672 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1317 helix: -0.04 (0.19), residues: 781 sheet: -0.95 (0.64), residues: 63 loop : -1.66 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 935 HIS 0.013 0.002 HIS B 75 PHE 0.024 0.002 PHE O1241 TYR 0.018 0.002 TYR C 57 ARG 0.004 0.001 ARG E 69 *********************** 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 300 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9477 (tt0) cc_final: 0.8781 (tm-30) REVERT: A 94 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 16 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7270 (pttm) REVERT: B 79 LYS cc_start: 0.7920 (pttm) cc_final: 0.7506 (ttmt) REVERT: C 35 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8239 (ttp-110) REVERT: C 61 GLU cc_start: 0.8827 (pp20) cc_final: 0.8505 (tm-30) REVERT: C 65 LEU cc_start: 0.9233 (mt) cc_final: 0.8931 (mp) REVERT: C 84 GLN cc_start: 0.9237 (mm110) cc_final: 0.8927 (mt0) REVERT: C 91 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8476 (mt-10) REVERT: D 46 HIS cc_start: 0.9260 (m90) cc_final: 0.8998 (m90) REVERT: D 65 ASP cc_start: 0.9401 (t0) cc_final: 0.9199 (t0) REVERT: E 67 PHE cc_start: 0.8657 (t80) cc_final: 0.8339 (t80) REVERT: E 77 ASP cc_start: 0.9078 (t70) cc_final: 0.8748 (m-30) REVERT: E 83 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.6779 (mmp80) REVERT: E 133 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7689 (mt-10) REVERT: F 50 ILE cc_start: 0.8191 (mm) cc_final: 0.7944 (mm) REVERT: F 84 MET cc_start: 0.8492 (mmp) cc_final: 0.8165 (mmp) REVERT: G 42 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8420 (ttm170) REVERT: G 56 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9153 (mm-30) REVERT: G 57 TYR cc_start: 0.8984 (t80) cc_final: 0.8574 (t80) REVERT: G 64 GLU cc_start: 0.9065 (pp20) cc_final: 0.8191 (tm-30) REVERT: G 68 ASN cc_start: 0.8275 (m-40) cc_final: 0.6908 (m110) REVERT: G 92 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8887 (tm-30) REVERT: G 111 ILE cc_start: 0.7967 (mp) cc_final: 0.7746 (mt) REVERT: H 44 GLN cc_start: 0.9262 (tt0) cc_final: 0.8841 (tm-30) REVERT: H 54 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8519 (mmtp) REVERT: H 56 MET cc_start: 0.9223 (tpt) cc_final: 0.8867 (tpp) REVERT: O 810 TYR cc_start: 0.8033 (t80) cc_final: 0.7782 (t80) REVERT: O 823 VAL cc_start: 0.8850 (m) cc_final: 0.7749 (t) REVERT: O 831 TRP cc_start: 0.8482 (m100) cc_final: 0.7710 (m100) REVERT: O 852 ASN cc_start: 0.9288 (m-40) cc_final: 0.8894 (p0) REVERT: O 858 GLN cc_start: 0.9307 (tp-100) cc_final: 0.9091 (tp-100) REVERT: O 888 TRP cc_start: 0.6736 (m100) cc_final: 0.6519 (m100) REVERT: O 891 MET cc_start: 0.9367 (tmm) cc_final: 0.9084 (tmm) REVERT: O 894 ASP cc_start: 0.8785 (t70) cc_final: 0.7932 (p0) REVERT: O 899 MET cc_start: 0.6561 (tpp) cc_final: 0.6102 (ttt) REVERT: O 1058 ILE cc_start: 0.8844 (mp) cc_final: 0.8621 (tt) REVERT: O 1116 MET cc_start: 0.8817 (mtp) cc_final: 0.7656 (tmm) REVERT: O 1248 GLU cc_start: 0.8308 (pm20) cc_final: 0.7870 (mp0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3229 time to fit residues: 138.1309 Evaluate side-chains 234 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 0.0570 overall best weight: 4.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 68 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17666 Z= 0.295 Angle : 0.694 9.866 25095 Z= 0.387 Chirality : 0.041 0.223 2860 Planarity : 0.005 0.065 2168 Dihedral : 30.110 177.595 4672 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1317 helix: 0.18 (0.19), residues: 772 sheet: -0.79 (0.65), residues: 63 loop : -1.45 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O1083 HIS 0.016 0.002 HIS B 75 PHE 0.022 0.002 PHE O1241 TYR 0.020 0.002 TYR C 39 ARG 0.005 0.001 ARG G 71 *********************** 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 276 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9500 (tt0) cc_final: 0.8804 (tm-30) REVERT: B 16 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7057 (pttm) REVERT: C 57 TYR cc_start: 0.9194 (t80) cc_final: 0.8307 (t80) REVERT: C 91 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8576 (mt-10) REVERT: D 46 HIS cc_start: 0.9210 (m90) cc_final: 0.8918 (m90) REVERT: D 65 ASP cc_start: 0.9517 (t0) cc_final: 0.9298 (t0) REVERT: D 76 ARG cc_start: 0.9305 (ptm160) cc_final: 0.8682 (tmm-80) REVERT: D 80 TYR cc_start: 0.8535 (m-10) cc_final: 0.7814 (m-80) REVERT: D 90 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9101 (mm-30) REVERT: E 67 PHE cc_start: 0.8616 (t80) cc_final: 0.8336 (t80) REVERT: E 77 ASP cc_start: 0.9269 (t70) cc_final: 0.9064 (m-30) REVERT: E 105 GLU cc_start: 0.8928 (tt0) cc_final: 0.8167 (tm-30) REVERT: F 24 ASP cc_start: 0.7306 (t0) cc_final: 0.6281 (m-30) REVERT: F 44 LYS cc_start: 0.8267 (mttm) cc_final: 0.8062 (mttm) REVERT: F 50 ILE cc_start: 0.8516 (mm) cc_final: 0.8306 (mm) REVERT: F 79 LYS cc_start: 0.9354 (mmtt) cc_final: 0.9000 (mtmt) REVERT: F 84 MET cc_start: 0.8463 (mmp) cc_final: 0.8155 (mmp) REVERT: F 91 LYS cc_start: 0.9204 (tttm) cc_final: 0.8989 (ttpt) REVERT: G 42 ARG cc_start: 0.8743 (ttt90) cc_final: 0.8393 (ttm170) REVERT: G 56 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9159 (mm-30) REVERT: G 57 TYR cc_start: 0.8958 (t80) cc_final: 0.8742 (t80) REVERT: G 61 GLU cc_start: 0.7922 (tt0) cc_final: 0.7559 (tt0) REVERT: G 64 GLU cc_start: 0.9251 (pp20) cc_final: 0.8583 (tm-30) REVERT: G 68 ASN cc_start: 0.8632 (m-40) cc_final: 0.7928 (m110) REVERT: G 112 GLN cc_start: 0.8416 (mm110) cc_final: 0.8155 (mm110) REVERT: H 54 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8591 (mmmm) REVERT: H 56 MET cc_start: 0.9278 (tpt) cc_final: 0.9026 (tpp) REVERT: H 119 THR cc_start: 0.9096 (m) cc_final: 0.8856 (t) REVERT: O 810 TYR cc_start: 0.8206 (t80) cc_final: 0.7903 (t80) REVERT: O 823 VAL cc_start: 0.8925 (m) cc_final: 0.8474 (t) REVERT: O 831 TRP cc_start: 0.8608 (m100) cc_final: 0.7954 (m100) REVERT: O 852 ASN cc_start: 0.9291 (m-40) cc_final: 0.8903 (p0) REVERT: O 891 MET cc_start: 0.9341 (tmm) cc_final: 0.9066 (tmm) REVERT: O 894 ASP cc_start: 0.8696 (t70) cc_final: 0.8441 (t70) REVERT: O 1116 MET cc_start: 0.8866 (mtp) cc_final: 0.7735 (tmm) REVERT: O 1142 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8236 (mtt180) REVERT: O 1248 GLU cc_start: 0.8323 (pm20) cc_final: 0.7808 (mp0) REVERT: O 1294 MET cc_start: 0.7495 (mmm) cc_final: 0.7018 (mmm) REVERT: O 1346 TYR cc_start: 0.4025 (m-10) cc_final: 0.3493 (m-80) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2986 time to fit residues: 120.9419 Evaluate side-chains 225 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 0.0370 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 858 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17666 Z= 0.222 Angle : 0.647 9.778 25095 Z= 0.361 Chirality : 0.039 0.180 2860 Planarity : 0.004 0.064 2168 Dihedral : 30.105 174.312 4672 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1317 helix: 0.40 (0.19), residues: 764 sheet: -0.63 (0.65), residues: 63 loop : -1.24 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O1083 HIS 0.012 0.001 HIS B 75 PHE 0.020 0.002 PHE O1241 TYR 0.024 0.002 TYR O1029 ARG 0.005 0.000 ARG F 92 *********************** 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 295 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9438 (tt0) cc_final: 0.8664 (tm-30) REVERT: B 16 LYS cc_start: 0.7799 (tmtt) cc_final: 0.6932 (pttt) REVERT: B 88 TYR cc_start: 0.9005 (m-10) cc_final: 0.8421 (m-10) REVERT: C 91 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8786 (mt-10) REVERT: D 46 HIS cc_start: 0.9232 (m90) cc_final: 0.9030 (m-70) REVERT: D 65 ASP cc_start: 0.9370 (t0) cc_final: 0.9148 (t0) REVERT: D 76 ARG cc_start: 0.9262 (ptm160) cc_final: 0.8718 (tmm-80) REVERT: D 80 TYR cc_start: 0.8450 (m-10) cc_final: 0.7606 (m-80) REVERT: E 67 PHE cc_start: 0.8561 (t80) cc_final: 0.8325 (t80) REVERT: E 77 ASP cc_start: 0.9314 (t70) cc_final: 0.9103 (m-30) REVERT: E 105 GLU cc_start: 0.8939 (tt0) cc_final: 0.8373 (tm-30) REVERT: F 24 ASP cc_start: 0.7214 (t0) cc_final: 0.6402 (m-30) REVERT: F 50 ILE cc_start: 0.8360 (mm) cc_final: 0.8128 (mm) REVERT: F 79 LYS cc_start: 0.9387 (mmtt) cc_final: 0.9033 (mtmt) REVERT: F 84 MET cc_start: 0.8441 (mmp) cc_final: 0.8175 (mmp) REVERT: F 88 TYR cc_start: 0.8474 (m-10) cc_final: 0.7960 (m-10) REVERT: G 56 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9059 (mm-30) REVERT: G 57 TYR cc_start: 0.8917 (t80) cc_final: 0.8708 (t80) REVERT: G 61 GLU cc_start: 0.7915 (tt0) cc_final: 0.7624 (tt0) REVERT: G 112 GLN cc_start: 0.8406 (mm110) cc_final: 0.8182 (mm110) REVERT: H 56 MET cc_start: 0.9172 (tpt) cc_final: 0.8950 (tpp) REVERT: H 76 ARG cc_start: 0.8885 (ptp-170) cc_final: 0.8530 (ptp-170) REVERT: H 119 THR cc_start: 0.9165 (m) cc_final: 0.8957 (t) REVERT: O 752 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7315 (mmmt) REVERT: O 810 TYR cc_start: 0.8162 (t80) cc_final: 0.7859 (t80) REVERT: O 823 VAL cc_start: 0.8950 (m) cc_final: 0.8509 (t) REVERT: O 831 TRP cc_start: 0.8504 (m100) cc_final: 0.7852 (m100) REVERT: O 852 ASN cc_start: 0.9257 (m-40) cc_final: 0.8857 (p0) REVERT: O 888 TRP cc_start: 0.6944 (m100) cc_final: 0.6613 (m100) REVERT: O 891 MET cc_start: 0.9395 (tmm) cc_final: 0.9107 (tmm) REVERT: O 894 ASP cc_start: 0.8514 (t70) cc_final: 0.8135 (t70) REVERT: O 1108 ILE cc_start: 0.8770 (tt) cc_final: 0.8544 (mp) REVERT: O 1112 MET cc_start: 0.8708 (mmt) cc_final: 0.8406 (mmm) REVERT: O 1116 MET cc_start: 0.8902 (mtp) cc_final: 0.7874 (tmm) REVERT: O 1142 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8230 (mtt180) REVERT: O 1248 GLU cc_start: 0.8423 (pm20) cc_final: 0.7900 (mp0) REVERT: O 1346 TYR cc_start: 0.4340 (m-10) cc_final: 0.4032 (m-80) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.3083 time to fit residues: 131.3742 Evaluate side-chains 229 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 chunk 128 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17666 Z= 0.360 Angle : 0.757 9.736 25095 Z= 0.417 Chirality : 0.044 0.278 2860 Planarity : 0.005 0.067 2168 Dihedral : 30.318 177.765 4672 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1317 helix: 0.27 (0.19), residues: 759 sheet: -1.15 (0.61), residues: 68 loop : -1.39 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O1083 HIS 0.018 0.002 HIS B 75 PHE 0.021 0.003 PHE A 84 TYR 0.026 0.002 TYR C 57 ARG 0.008 0.001 ARG G 42 *********************** 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 278 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8339 (tp) cc_final: 0.8110 (tp) REVERT: A 93 GLN cc_start: 0.9490 (tt0) cc_final: 0.8793 (tm-30) REVERT: B 16 LYS cc_start: 0.7774 (tmtt) cc_final: 0.6898 (pttt) REVERT: B 84 MET cc_start: 0.9123 (tpp) cc_final: 0.8634 (mmm) REVERT: C 35 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8164 (ttm110) REVERT: C 56 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8597 (tm-30) REVERT: C 91 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8827 (mt-10) REVERT: D 80 TYR cc_start: 0.8448 (m-10) cc_final: 0.7933 (m-10) REVERT: E 46 VAL cc_start: 0.8973 (t) cc_final: 0.8317 (t) REVERT: E 77 ASP cc_start: 0.9394 (t70) cc_final: 0.9172 (m-30) REVERT: E 105 GLU cc_start: 0.8978 (tt0) cc_final: 0.8266 (tm-30) REVERT: F 24 ASP cc_start: 0.7240 (t0) cc_final: 0.6035 (m-30) REVERT: F 44 LYS cc_start: 0.8457 (mttm) cc_final: 0.8101 (mttm) REVERT: F 79 LYS cc_start: 0.9463 (mmtt) cc_final: 0.9046 (mtmt) REVERT: F 91 LYS cc_start: 0.9202 (tttm) cc_final: 0.8990 (ttpt) REVERT: G 56 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9148 (mm-30) REVERT: G 64 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8965 (tm-30) REVERT: G 92 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8792 (tm-30) REVERT: H 54 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8612 (mmtp) REVERT: H 76 ARG cc_start: 0.8988 (ptp-170) cc_final: 0.8724 (ptp-170) REVERT: O 745 TYR cc_start: 0.6016 (m-10) cc_final: 0.5389 (t80) REVERT: O 752 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7338 (tptt) REVERT: O 810 TYR cc_start: 0.8345 (t80) cc_final: 0.7981 (t80) REVERT: O 831 TRP cc_start: 0.8733 (m100) cc_final: 0.8125 (m100) REVERT: O 834 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7745 (mm-30) REVERT: O 852 ASN cc_start: 0.9325 (m-40) cc_final: 0.8940 (p0) REVERT: O 888 TRP cc_start: 0.7067 (m100) cc_final: 0.6676 (m100) REVERT: O 891 MET cc_start: 0.9392 (tmm) cc_final: 0.9068 (tmm) REVERT: O 894 ASP cc_start: 0.8463 (t70) cc_final: 0.8061 (p0) REVERT: O 903 GLN cc_start: 0.8180 (pm20) cc_final: 0.7931 (pm20) REVERT: O 1112 MET cc_start: 0.8765 (mmt) cc_final: 0.8496 (mmm) REVERT: O 1116 MET cc_start: 0.8843 (mtp) cc_final: 0.7828 (tmm) REVERT: O 1142 ARG cc_start: 0.8595 (mtt180) cc_final: 0.8285 (mtt180) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3263 time to fit residues: 134.9206 Evaluate side-chains 220 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1192 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17666 Z= 0.271 Angle : 0.697 10.507 25095 Z= 0.386 Chirality : 0.041 0.236 2860 Planarity : 0.005 0.058 2168 Dihedral : 30.285 174.759 4672 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1317 helix: 0.45 (0.19), residues: 749 sheet: -1.04 (0.60), residues: 74 loop : -1.19 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O1083 HIS 0.010 0.001 HIS B 75 PHE 0.031 0.002 PHE E 67 TYR 0.016 0.002 TYR C 39 ARG 0.010 0.001 ARG G 42 *********************** 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 271 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8251 (tp) cc_final: 0.7956 (tp) REVERT: A 93 GLN cc_start: 0.9450 (tt0) cc_final: 0.8650 (tm-30) REVERT: B 16 LYS cc_start: 0.7898 (tmtt) cc_final: 0.6857 (pttt) REVERT: B 84 MET cc_start: 0.8964 (tpp) cc_final: 0.8678 (mmm) REVERT: C 35 ARG cc_start: 0.8793 (mtm-85) cc_final: 0.8552 (ttm110) REVERT: C 41 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 56 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8614 (tm-30) REVERT: D 73 GLU cc_start: 0.8955 (tp30) cc_final: 0.8727 (tp30) REVERT: D 76 ARG cc_start: 0.9344 (ptm160) cc_final: 0.8765 (tmm-80) REVERT: D 80 TYR cc_start: 0.8419 (m-10) cc_final: 0.7608 (m-80) REVERT: E 46 VAL cc_start: 0.8845 (t) cc_final: 0.8239 (t) REVERT: E 67 PHE cc_start: 0.8421 (t80) cc_final: 0.8216 (t80) REVERT: E 77 ASP cc_start: 0.9380 (t70) cc_final: 0.9122 (m-30) REVERT: E 105 GLU cc_start: 0.9012 (tt0) cc_final: 0.8258 (tm-30) REVERT: E 120 MET cc_start: 0.9172 (mmm) cc_final: 0.8866 (mmm) REVERT: F 24 ASP cc_start: 0.7392 (t0) cc_final: 0.6770 (m-30) REVERT: F 68 ASP cc_start: 0.8598 (m-30) cc_final: 0.8155 (m-30) REVERT: F 79 LYS cc_start: 0.9486 (mmtt) cc_final: 0.9044 (mtmt) REVERT: F 84 MET cc_start: 0.8565 (mmp) cc_final: 0.8242 (mmp) REVERT: G 61 GLU cc_start: 0.8023 (tt0) cc_final: 0.7803 (tt0) REVERT: G 64 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8915 (tm-30) REVERT: G 92 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8396 (pm20) REVERT: H 54 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8494 (mmtp) REVERT: O 745 TYR cc_start: 0.5975 (m-10) cc_final: 0.5389 (t80) REVERT: O 752 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7394 (tptt) REVERT: O 810 TYR cc_start: 0.8278 (t80) cc_final: 0.7922 (t80) REVERT: O 823 VAL cc_start: 0.9041 (m) cc_final: 0.7773 (t) REVERT: O 831 TRP cc_start: 0.8689 (m100) cc_final: 0.7890 (m100) REVERT: O 852 ASN cc_start: 0.9309 (m-40) cc_final: 0.8929 (p0) REVERT: O 888 TRP cc_start: 0.7068 (m100) cc_final: 0.6615 (m100) REVERT: O 891 MET cc_start: 0.9435 (tmm) cc_final: 0.9174 (tmm) REVERT: O 894 ASP cc_start: 0.8500 (t70) cc_final: 0.7847 (p0) REVERT: O 903 GLN cc_start: 0.8086 (pm20) cc_final: 0.7817 (pm20) REVERT: O 1112 MET cc_start: 0.8752 (mmt) cc_final: 0.8450 (mmm) REVERT: O 1116 MET cc_start: 0.8813 (mtp) cc_final: 0.7849 (tmm) REVERT: O 1294 MET cc_start: 0.7047 (mmm) cc_final: 0.6585 (mmm) REVERT: O 1346 TYR cc_start: 0.4106 (m-10) cc_final: 0.3866 (m-80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2835 time to fit residues: 114.6516 Evaluate side-chains 221 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 141 optimal weight: 0.0470 chunk 85 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 overall best weight: 2.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN E 93 GLN O 939 ASN ** O1050 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17666 Z= 0.227 Angle : 0.675 10.744 25095 Z= 0.373 Chirality : 0.040 0.200 2860 Planarity : 0.004 0.067 2168 Dihedral : 30.218 173.674 4672 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1317 helix: 0.63 (0.19), residues: 747 sheet: -0.75 (0.62), residues: 74 loop : -1.11 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O1083 HIS 0.014 0.002 HIS G 82 PHE 0.023 0.002 PHE B 100 TYR 0.030 0.002 TYR G 57 ARG 0.007 0.000 ARG F 45 *********************** 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 278 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LYS cc_start: 0.7921 (tmtt) cc_final: 0.6815 (pttt) REVERT: B 79 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8458 (tttt) REVERT: C 35 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8479 (ttm110) REVERT: C 41 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8178 (tm-30) REVERT: C 56 GLU cc_start: 0.9433 (mm-30) cc_final: 0.8647 (tm-30) REVERT: C 99 ARG cc_start: 0.9087 (tpt-90) cc_final: 0.8771 (mmm160) REVERT: D 65 ASP cc_start: 0.9414 (t0) cc_final: 0.9207 (t0) REVERT: D 73 GLU cc_start: 0.8935 (tp30) cc_final: 0.8706 (tp30) REVERT: D 76 ARG cc_start: 0.9283 (ptm160) cc_final: 0.8730 (tmm-80) REVERT: D 80 TYR cc_start: 0.8366 (m-10) cc_final: 0.7559 (m-80) REVERT: E 50 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8092 (mm-30) REVERT: E 105 GLU cc_start: 0.8936 (tt0) cc_final: 0.8409 (tm-30) REVERT: E 120 MET cc_start: 0.9176 (mmm) cc_final: 0.8909 (mmm) REVERT: F 24 ASP cc_start: 0.7322 (t0) cc_final: 0.6843 (m-30) REVERT: F 79 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9052 (mtmt) REVERT: F 84 MET cc_start: 0.8619 (mmp) cc_final: 0.8305 (mmp) REVERT: G 64 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8883 (tm-30) REVERT: G 92 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8657 (tm-30) REVERT: H 44 GLN cc_start: 0.9292 (tt0) cc_final: 0.8860 (tm-30) REVERT: H 54 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8544 (mmtp) REVERT: O 745 TYR cc_start: 0.5710 (m-10) cc_final: 0.5032 (t80) REVERT: O 810 TYR cc_start: 0.8272 (t80) cc_final: 0.7893 (t80) REVERT: O 823 VAL cc_start: 0.8999 (m) cc_final: 0.8567 (t) REVERT: O 831 TRP cc_start: 0.8679 (m100) cc_final: 0.8304 (m100) REVERT: O 888 TRP cc_start: 0.7229 (m100) cc_final: 0.6729 (m100) REVERT: O 894 ASP cc_start: 0.8431 (t70) cc_final: 0.8187 (t70) REVERT: O 903 GLN cc_start: 0.8038 (pm20) cc_final: 0.7803 (pm20) REVERT: O 1112 MET cc_start: 0.8709 (mmt) cc_final: 0.8409 (mmm) REVERT: O 1116 MET cc_start: 0.8797 (mtp) cc_final: 0.7824 (tmm) REVERT: O 1294 MET cc_start: 0.6835 (mmm) cc_final: 0.6424 (mmm) REVERT: O 1346 TYR cc_start: 0.3803 (m-10) cc_final: 0.3583 (m-80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2764 time to fit residues: 114.9108 Evaluate side-chains 227 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 93 GLN ** O1050 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17666 Z= 0.260 Angle : 0.700 10.269 25095 Z= 0.384 Chirality : 0.041 0.206 2860 Planarity : 0.004 0.064 2168 Dihedral : 30.221 173.874 4672 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1317 helix: 0.56 (0.19), residues: 750 sheet: -0.74 (0.61), residues: 74 loop : -1.12 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O1083 HIS 0.010 0.001 HIS B 75 PHE 0.020 0.002 PHE O1241 TYR 0.027 0.002 TYR G 57 ARG 0.006 0.001 ARG G 42 ********************** 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 269 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9371 (tt0) cc_final: 0.9078 (tt0) REVERT: B 16 LYS cc_start: 0.7925 (tmtt) cc_final: 0.6820 (pttt) REVERT: B 84 MET cc_start: 0.8942 (tpp) cc_final: 0.8688 (mmm) REVERT: C 35 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8370 (ttm110) REVERT: C 41 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 99 ARG cc_start: 0.9114 (tpt-90) cc_final: 0.8773 (mmm160) REVERT: D 34 TYR cc_start: 0.8107 (m-10) cc_final: 0.7726 (m-10) REVERT: D 73 GLU cc_start: 0.8944 (tp30) cc_final: 0.8695 (tp30) REVERT: D 76 ARG cc_start: 0.9244 (ptm160) cc_final: 0.8697 (tmm-80) REVERT: D 80 TYR cc_start: 0.8333 (m-10) cc_final: 0.7615 (m-80) REVERT: E 50 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8027 (mm-30) REVERT: E 105 GLU cc_start: 0.8983 (tt0) cc_final: 0.8410 (tm-30) REVERT: F 24 ASP cc_start: 0.7315 (t0) cc_final: 0.6813 (m-30) REVERT: F 68 ASP cc_start: 0.8577 (m-30) cc_final: 0.8210 (m-30) REVERT: F 79 LYS cc_start: 0.9496 (mmtt) cc_final: 0.9054 (mtmt) REVERT: F 84 MET cc_start: 0.8581 (mmp) cc_final: 0.8341 (mmp) REVERT: G 64 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8908 (tm-30) REVERT: G 92 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8754 (pm20) REVERT: H 54 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8476 (mmtp) REVERT: O 745 TYR cc_start: 0.5677 (m-10) cc_final: 0.4928 (t80) REVERT: O 810 TYR cc_start: 0.8324 (t80) cc_final: 0.7955 (t80) REVERT: O 823 VAL cc_start: 0.9018 (m) cc_final: 0.8552 (t) REVERT: O 831 TRP cc_start: 0.8548 (m100) cc_final: 0.7880 (m100) REVERT: O 888 TRP cc_start: 0.7260 (m100) cc_final: 0.6756 (m100) REVERT: O 894 ASP cc_start: 0.8255 (t70) cc_final: 0.8018 (t70) REVERT: O 903 GLN cc_start: 0.8115 (pm20) cc_final: 0.7847 (pm20) REVERT: O 1112 MET cc_start: 0.8727 (mmt) cc_final: 0.8488 (mmm) REVERT: O 1116 MET cc_start: 0.8832 (mtp) cc_final: 0.7827 (tmm) REVERT: O 1294 MET cc_start: 0.6657 (mmm) cc_final: 0.6306 (mmm) REVERT: O 1346 TYR cc_start: 0.3861 (m-10) cc_final: 0.3617 (m-80) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2879 time to fit residues: 115.8586 Evaluate side-chains 225 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.0470 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** O1050 ASN ** 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 = 0.3646 r_free = 0.3646 target = 0.086374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061222 restraints weight = 75038.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062577 restraints weight = 43564.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063553 restraints weight = 31080.526| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.7724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17666 Z= 0.237 Angle : 0.684 10.099 25095 Z= 0.376 Chirality : 0.040 0.188 2860 Planarity : 0.004 0.059 2168 Dihedral : 30.202 172.938 4672 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1317 helix: 0.59 (0.19), residues: 748 sheet: -0.66 (0.63), residues: 68 loop : -1.10 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O1083 HIS 0.010 0.001 HIS B 75 PHE 0.021 0.002 PHE B 100 TYR 0.022 0.002 TYR G 57 ARG 0.011 0.001 ARG F 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.09 seconds wall clock time: 58 minutes 37.92 seconds (3517.92 seconds total)