Starting phenix.real_space_refine on Sat Sep 12 15:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.map" model { file = "/net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z3o_6880/09_2026/5z3o_6880.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 29 5.16 5 C 9675 2.51 5 N 3095 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16802 Number of models: 1 Model: "" Number of chains: 12 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: 4763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4763 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 563} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.33, per 1000 atoms: 0.20 Number of scatterers: 16802 At special positions: 0 Unit cell: (149.16, 117.48, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 294 15.00 Mg 1 11.99 O 3708 8.00 N 3095 7.00 C 9675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 574.5 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 8 sheets defined 64.6% alpha, 3.0% beta 114 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.502A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.625A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.513A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.659A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.797A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.571A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.704A 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 removed outlier: 3.746A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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: 3.745A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.589A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 4.006A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.502A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.625A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.514A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.653A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.630A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.705A 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 removed outlier: 3.747A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) 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: 3.746A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.588A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.007A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 683 Processing helix chain 'O' and resid 683 through 690 removed outlier: 4.427A pdb=" N ASN O 687 " --> pdb=" O LEU O 683 " (cutoff:3.500A) Processing helix chain 'O' and resid 745 through 750 Processing helix chain 'O' and resid 768 through 784 removed outlier: 3.640A pdb=" N ASN O 784 " --> pdb=" O SER O 780 " (cutoff:3.500A) Processing helix chain 'O' and resid 797 through 812 Processing helix chain 'O' and resid 824 through 838 removed outlier: 4.241A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA O 836 " --> pdb=" O SER O 832 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS O 837 " --> pdb=" O SER O 833 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 863 removed outlier: 3.984A pdb=" N ALA O 856 " --> pdb=" O ASN O 852 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS O 857 " --> pdb=" O GLU O 853 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA O 863 " --> pdb=" O ALA O 859 " (cutoff:3.500A) Processing helix chain 'O' and resid 873 through 879 removed outlier: 3.885A pdb=" N ILE O 877 " --> pdb=" O PHE O 873 " (cutoff:3.500A) Processing helix chain 'O' and resid 879 through 886 Processing helix chain 'O' and resid 895 through 900 Processing helix chain 'O' and resid 904 through 912 Processing helix chain 'O' and resid 942 through 958 removed outlier: 4.237A pdb=" N ASN O 947 " --> pdb=" O PRO O 943 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS O 950 " --> pdb=" O PHE O 946 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER O 951 " --> pdb=" O ASN O 947 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE O 952 " --> pdb=" O SER O 948 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP O 953 " --> pdb=" O VAL O 949 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU O 954 " --> pdb=" O LYS O 950 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP O 955 " --> pdb=" O SER O 951 " (cutoff:3.500A) Processing helix chain 'O' and resid 968 through 973 Processing helix chain 'O' and resid 976 through 987 removed outlier: 3.771A 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: 3.780A pdb=" N GLN O1024 " --> pdb=" O GLN O1020 " (cutoff:3.500A) Processing helix chain 'O' and resid 1049 through 1059 removed outlier: 4.055A pdb=" N LEU O1055 " --> pdb=" O GLN O1051 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) Processing helix chain 'O' and resid 1068 through 1073 Processing helix chain 'O' and resid 1082 through 1085 removed outlier: 3.571A 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 1103 removed outlier: 3.729A pdb=" N GLU O1090 " --> pdb=" O ALA O1086 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU O1091 " --> pdb=" O GLY O1087 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU O1092 " --> pdb=" O LYS O1088 " (cutoff:3.500A) Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1113 through 1126 Processing helix chain 'O' and resid 1139 through 1150 removed outlier: 3.918A pdb=" N LEU O1146 " --> pdb=" O ARG O1142 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG O1147 " --> pdb=" O SER O1143 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O1148 " --> pdb=" O GLU O1144 " (cutoff:3.500A) Processing helix chain 'O' and resid 1187 through 1199 removed outlier: 4.469A pdb=" N ASP O1195 " --> pdb=" O LEU O1191 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA O1197 " --> pdb=" O ALA O1193 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG O1199 " --> pdb=" O ASP O1195 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1226 removed outlier: 4.227A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) Processing helix chain 'O' and resid 1227 through 1231 removed outlier: 4.012A pdb=" N ILE O1231 " --> pdb=" O LYS O1228 " (cutoff:3.500A) Processing helix chain 'O' and resid 1232 through 1241 removed outlier: 4.154A pdb=" N LYS O1240 " --> pdb=" O ILE O1236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE O1241 " --> pdb=" O GLN O1237 " (cutoff:3.500A) Processing helix chain 'O' and resid 1246 through 1250 removed outlier: 3.935A pdb=" N GLN O1250 " --> pdb=" O SER O1247 " (cutoff:3.500A) Processing helix chain 'O' and resid 1251 through 1263 removed outlier: 4.221A pdb=" N ALA O1260 " --> pdb=" O SER O1256 " (cutoff:3.500A) Processing helix chain 'O' and resid 1264 through 1268 Processing helix chain 'O' and resid 1279 through 1286 Processing helix chain 'O' and resid 1290 through 1307 removed outlier: 3.625A pdb=" N VAL O1296 " --> pdb=" O GLU O1292 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS O1306 " --> pdb=" O GLU O1302 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS O1307 " --> pdb=" O ASP O1303 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1341 removed outlier: 3.622A pdb=" N GLU O1341 " --> pdb=" O ARG O1337 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1337 through 1341' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.606A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.607A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.269A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.852A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 788 through 790 removed outlier: 3.922A pdb=" N GLY O 788 " --> pdb=" O ARG O 919 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE O 921 " --> pdb=" O GLY O 788 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU O 790 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 922 " --> pdb=" O ILE O 893 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 1130 through 1131 removed outlier: 6.810A pdb=" N LEU O1131 " --> pdb=" O ILE O1160 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N SER O1162 " --> pdb=" O LEU O1131 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 297 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3371 1.33 - 1.45: 5070 1.45 - 1.57: 8607 1.57 - 1.69: 585 1.69 - 1.81: 53 Bond restraints: 17686 Sorted by residual: bond pdb=" C3' DC I 125 " pdb=" C2' DC I 125 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DA J 14 " pdb=" C2' DA J 14 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG I 55 " pdb=" C2' DG I 55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG I 146 " pdb=" C2' DG I 146 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.89e+00 bond pdb=" C3' DA J 10 " pdb=" C2' DA J 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.67e+00 ... (remaining 17681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 24300 2.05 - 4.09: 774 4.09 - 6.14: 43 6.14 - 8.19: 9 8.19 - 10.24: 2 Bond angle restraints: 25128 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 103.25 110.03 -6.78 1.05e+00 9.07e-01 4.17e+01 angle pdb=" O4' DA J 59 " pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.61e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I 87 " pdb=" C4 DT I 87 " pdb=" O4 DT I 87 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 89 " pdb=" C4 DT I 89 " pdb=" O4 DT I 89 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 25123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 8659 35.72 - 71.44: 1259 71.44 - 107.16: 20 107.16 - 142.88: 2 142.88 - 178.60: 7 Dihedral angle restraints: 9947 sinusoidal: 6016 harmonic: 3931 Sorted by residual: dihedral pdb=" CA PRO O 932 " pdb=" C PRO O 932 " pdb=" N GLU O 933 " pdb=" CA GLU O 933 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA HIS O 913 " pdb=" C HIS O 913 " pdb=" N TYR O 914 " pdb=" CA TYR O 914 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU O1258 " pdb=" C LEU O1258 " pdb=" N ASP O1259 " pdb=" CA ASP O1259 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 9944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2240 0.051 - 0.102: 529 0.102 - 0.153: 80 0.153 - 0.204: 11 0.204 - 0.255: 3 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CG LEU O1258 " pdb=" CB LEU O1258 " pdb=" CD1 LEU O1258 " pdb=" CD2 LEU O1258 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU O1222 " pdb=" CB LEU O1222 " pdb=" CD1 LEU O1222 " pdb=" CD2 LEU O1222 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+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 1.13e+00 ... (remaining 2860 not shown) Planarity restraints: 2167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.027 2.00e-02 2.50e+03 1.36e-02 5.06e+00 pdb=" N9 DA I 39 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.025 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO E 121 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 121 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.027 5.00e-02 4.00e+02 ... (remaining 2164 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 295 2.62 - 3.19: 14733 3.19 - 3.76: 29374 3.76 - 4.33: 38774 4.33 - 4.90: 56567 Nonbonded interactions: 139743 Sorted by model distance: nonbonded pdb=" O1B ADP O1501 " pdb="MG MG O1502 " model vdw 2.055 2.170 nonbonded pdb=" O1A ADP O1501 " pdb="MG MG O1502 " model vdw 2.065 2.170 nonbonded pdb=" O ALA O 748 " pdb=" ND2 ASN O 784 " model vdw 2.205 3.120 nonbonded pdb=" OP1 DA I 97 " pdb=" ND2 ASN O1186 " model vdw 2.230 3.120 nonbonded pdb=" O LEU O 971 " pdb=" OG1 THR O 976 " model vdw 2.236 3.040 ... (remaining 139738 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17686 Z= 0.424 Angle : 0.761 10.236 25128 Z= 0.616 Chirality : 0.045 0.255 2863 Planarity : 0.004 0.048 2167 Dihedral : 24.397 178.604 7393 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 0.44 % Allowed : 1.74 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.19), residues: 1316 helix: -2.37 (0.15), residues: 742 sheet: -2.49 (0.55), residues: 65 loop : -2.07 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 919 TYR 0.018 0.002 TYR F 98 PHE 0.022 0.002 PHE O1241 TRP 0.014 0.001 TRP O1083 HIS 0.004 0.001 HIS O 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.42 (17686) covalent geometry : angle 0.76065 / 0.62 (25128) hydrogen bonds : bond 0.10872 / 6.53 ( 854) hydrogen bonds : angle 8.10821 / 5.79 ( 2241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 454 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8859 (pt0) cc_final: 0.8505 (mm-30) REVERT: B 82 THR cc_start: 0.9479 (p) cc_final: 0.9205 (p) REVERT: D 51 ILE cc_start: 0.8053 (tt) cc_final: 0.7817 (tt) REVERT: E 60 LEU cc_start: 0.8606 (tp) cc_final: 0.7927 (tp) REVERT: F 80 THR cc_start: 0.9092 (m) cc_final: 0.8891 (p) REVERT: G 90 ASP cc_start: 0.8364 (t0) cc_final: 0.8114 (t0) REVERT: O 806 LEU cc_start: 0.8832 (mt) cc_final: 0.8631 (mt) REVERT: O 891 MET cc_start: 0.6384 (ptp) cc_final: 0.6107 (ptp) REVERT: O 895 GLU cc_start: 0.7322 (tp30) cc_final: 0.7101 (tp30) REVERT: O 1184 ASP cc_start: 0.7979 (m-30) cc_final: 0.6867 (m-30) REVERT: O 1188 HIS cc_start: 0.7937 (p-80) cc_final: 0.7448 (p-80) REVERT: O 1222 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8474 (tm) outliers start: 5 outliers final: 3 residues processed: 457 average time/residue: 0.1648 time to fit residues: 104.7182 Evaluate side-chains 245 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 241 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS B 25 ASN C 73 ASN E 68 GLN E 125 GLN G 73 ASN H 92 GLN ** O 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 801 GLN O 897 HIS ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1104 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.096781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068514 restraints weight = 61028.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070133 restraints weight = 32201.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071148 restraints weight = 22503.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071713 restraints weight = 18645.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.071956 restraints weight = 17003.807| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 17686 Z= 0.262 Angle : 0.807 9.521 25128 Z= 0.433 Chirality : 0.048 0.367 2863 Planarity : 0.006 0.062 2167 Dihedral : 29.823 178.719 4690 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.53 % Allowed : 12.71 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1316 helix: -0.64 (0.18), residues: 762 sheet: -1.92 (0.64), residues: 64 loop : -1.73 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 77 TYR 0.025 0.003 TYR B 98 PHE 0.027 0.003 PHE O 946 TRP 0.012 0.003 TRP O1185 HIS 0.010 0.002 HIS O 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.26 (17686) covalent geometry : angle 0.80723 / 0.43 (25128) hydrogen bonds : bond 0.05232 / 3.47 ( 854) hydrogen bonds : angle 5.25758 / 3.80 ( 2241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.509 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: B 64 ASN cc_start: 0.8645 (m-40) cc_final: 0.8267 (m110) REVERT: B 74 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 61 GLU cc_start: 0.7505 (tp30) cc_final: 0.7263 (tp30) REVERT: C 64 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: C 73 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8135 (t0) REVERT: C 77 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.6599 (mmt90) REVERT: E 122 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8641 (ptpp) REVERT: F 88 TYR cc_start: 0.8744 (m-10) cc_final: 0.8422 (m-80) REVERT: G 42 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7907 (mtp85) REVERT: G 95 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8446 (mtpp) REVERT: H 59 MET cc_start: 0.8698 (tpp) cc_final: 0.8398 (tpp) REVERT: H 80 TYR cc_start: 0.7785 (m-10) cc_final: 0.7474 (m-10) REVERT: O 891 MET cc_start: 0.6193 (ptp) cc_final: 0.5990 (ptp) REVERT: O 1184 ASP cc_start: 0.7564 (m-30) cc_final: 0.7191 (m-30) REVERT: O 1294 MET cc_start: 0.8602 (mmm) cc_final: 0.8359 (mmm) outliers start: 52 outliers final: 35 residues processed: 282 average time/residue: 0.1373 time to fit residues: 56.5699 Evaluate side-chains 249 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 789 ILE Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 918 TYR Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 110 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN G 38 ASN G 73 ASN H 46 HIS ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.069813 restraints weight = 61406.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071520 restraints weight = 30848.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072566 restraints weight = 21033.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073160 restraints weight = 17244.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073377 restraints weight = 15663.375| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17686 Z= 0.159 Angle : 0.690 9.461 25128 Z= 0.377 Chirality : 0.045 0.378 2863 Planarity : 0.005 0.052 2167 Dihedral : 29.835 179.016 4686 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.09 % Allowed : 15.49 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1316 helix: 0.04 (0.19), residues: 756 sheet: -1.44 (0.66), residues: 64 loop : -1.61 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 63 TYR 0.024 0.002 TYR B 98 PHE 0.022 0.002 PHE O 946 TRP 0.009 0.002 TRP O1083 HIS 0.006 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (17686) covalent geometry : angle 0.68995 / 0.38 (25128) hydrogen bonds : bond 0.04451 / 3.00 ( 854) hydrogen bonds : angle 4.68079 / 3.40 ( 2241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7510 (tp30) cc_final: 0.7263 (tp30) REVERT: B 64 ASN cc_start: 0.8526 (m-40) cc_final: 0.8019 (m110) REVERT: B 74 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 64 GLU cc_start: 0.8456 (tt0) cc_final: 0.8009 (pt0) REVERT: C 75 LYS cc_start: 0.9050 (mptt) cc_final: 0.8666 (mmmt) REVERT: C 77 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.6460 (mmt90) REVERT: D 44 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8599 (tm-30) REVERT: E 122 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8624 (ptpp) REVERT: F 63 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8010 (mt-10) REVERT: F 88 TYR cc_start: 0.8624 (m-10) cc_final: 0.8302 (m-80) REVERT: G 95 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8420 (mtpp) REVERT: H 80 TYR cc_start: 0.7819 (m-10) cc_final: 0.7486 (m-10) REVERT: H 102 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7824 (tm-30) REVERT: O 899 MET cc_start: 0.8856 (tmm) cc_final: 0.8609 (tmm) REVERT: O 1053 MET cc_start: 0.8531 (ppp) cc_final: 0.7962 (ppp) REVERT: O 1184 ASP cc_start: 0.7432 (m-30) cc_final: 0.7232 (m-30) outliers start: 47 outliers final: 29 residues processed: 265 average time/residue: 0.1360 time to fit residues: 53.3576 Evaluate side-chains 239 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain O residue 766 THR Chi-restraints excluded: chain O residue 789 ILE Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1059 CYS Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN O 749 HIS ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.096591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068424 restraints weight = 60876.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070113 restraints weight = 30706.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071156 restraints weight = 20981.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071668 restraints weight = 17250.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072001 restraints weight = 15768.608| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17686 Z= 0.168 Angle : 0.682 9.718 25128 Z= 0.371 Chirality : 0.044 0.376 2863 Planarity : 0.005 0.053 2167 Dihedral : 29.895 179.154 4686 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 4.79 % Allowed : 15.32 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1316 helix: 0.34 (0.19), residues: 762 sheet: -1.37 (0.66), residues: 64 loop : -1.51 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 982 TYR 0.023 0.002 TYR B 98 PHE 0.019 0.002 PHE O1063 TRP 0.012 0.002 TRP O1083 HIS 0.011 0.001 HIS O 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (17686) covalent geometry : angle 0.68237 / 0.37 (25128) hydrogen bonds : bond 0.04372 / 2.96 ( 854) hydrogen bonds : angle 4.39085 / 3.20 ( 2241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASN cc_start: 0.8593 (m-40) cc_final: 0.8083 (m110) REVERT: B 74 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 84 MET cc_start: 0.8426 (mmm) cc_final: 0.7970 (mmm) REVERT: B 91 LYS cc_start: 0.8714 (tttt) cc_final: 0.8511 (tttm) REVERT: C 64 GLU cc_start: 0.8471 (tt0) cc_final: 0.8059 (pt0) REVERT: C 72 ASP cc_start: 0.8090 (m-30) cc_final: 0.7829 (m-30) REVERT: C 75 LYS cc_start: 0.9024 (mptt) cc_final: 0.8750 (mmmt) REVERT: C 77 ARG cc_start: 0.7465 (mtt-85) cc_final: 0.6388 (mmt90) REVERT: D 44 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 73 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8449 (tp30) REVERT: E 122 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8646 (ptpp) REVERT: F 25 ASN cc_start: 0.6023 (OUTLIER) cc_final: 0.5572 (m-40) REVERT: F 74 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 88 TYR cc_start: 0.8685 (m-10) cc_final: 0.8338 (m-80) REVERT: G 36 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8611 (mmtp) REVERT: G 95 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8373 (mtpp) REVERT: H 39 TYR cc_start: 0.8100 (t80) cc_final: 0.7640 (t80) REVERT: H 59 MET cc_start: 0.8849 (tpp) cc_final: 0.8374 (tpp) REVERT: H 80 TYR cc_start: 0.7952 (m-10) cc_final: 0.7662 (m-10) REVERT: H 102 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7728 (tm-30) REVERT: O 790 LEU cc_start: 0.8966 (tp) cc_final: 0.8655 (tt) outliers start: 55 outliers final: 37 residues processed: 251 average time/residue: 0.1287 time to fit residues: 48.5049 Evaluate side-chains 242 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 890 HIS Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1059 CYS Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN O 783 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.095429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067141 restraints weight = 60239.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068800 restraints weight = 30334.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.069835 restraints weight = 20794.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070404 restraints weight = 17093.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070630 restraints weight = 15534.048| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17686 Z= 0.184 Angle : 0.702 11.855 25128 Z= 0.376 Chirality : 0.045 0.383 2863 Planarity : 0.005 0.056 2167 Dihedral : 29.965 179.420 4686 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 4.96 % Allowed : 15.93 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1316 helix: 0.67 (0.19), residues: 755 sheet: -1.67 (0.61), residues: 70 loop : -1.40 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 96 TYR 0.023 0.002 TYR C 57 PHE 0.020 0.002 PHE O1063 TRP 0.011 0.002 TRP O1185 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (17686) covalent geometry : angle 0.70212 / 0.38 (25128) hydrogen bonds : bond 0.04452 / 3.01 ( 854) hydrogen bonds : angle 4.24898 / 3.10 ( 2241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASN cc_start: 0.8606 (m-40) cc_final: 0.8068 (m110) REVERT: B 74 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 84 MET cc_start: 0.8397 (mmm) cc_final: 0.8164 (mmm) REVERT: B 91 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8549 (tttm) REVERT: C 27 VAL cc_start: 0.9291 (t) cc_final: 0.9070 (p) REVERT: C 64 GLU cc_start: 0.8494 (tt0) cc_final: 0.8109 (pt0) REVERT: C 72 ASP cc_start: 0.8149 (m-30) cc_final: 0.7790 (m-30) REVERT: C 73 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7365 (t0) REVERT: C 75 LYS cc_start: 0.9048 (mptt) cc_final: 0.8378 (mptt) REVERT: C 77 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.7157 (mtt-85) REVERT: C 91 GLU cc_start: 0.7600 (pt0) cc_final: 0.7370 (pt0) REVERT: D 44 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8580 (tm-30) REVERT: E 60 LEU cc_start: 0.8407 (tp) cc_final: 0.8182 (tt) REVERT: E 122 LYS cc_start: 0.8997 (ptmt) cc_final: 0.8732 (ptpp) REVERT: F 25 ASN cc_start: 0.6113 (OUTLIER) cc_final: 0.5694 (m-40) REVERT: F 88 TYR cc_start: 0.8652 (m-10) cc_final: 0.8306 (m-80) REVERT: G 36 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8690 (mmtp) REVERT: G 38 ASN cc_start: 0.8898 (p0) cc_final: 0.8681 (p0) REVERT: G 95 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8442 (mtpp) REVERT: H 39 TYR cc_start: 0.8109 (t80) cc_final: 0.7654 (t80) REVERT: H 80 TYR cc_start: 0.7999 (m-10) cc_final: 0.7638 (m-10) REVERT: H 102 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7670 (tm-30) REVERT: O 790 LEU cc_start: 0.8782 (tp) cc_final: 0.8459 (tt) REVERT: O 1031 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.4520 (mmt90) REVERT: O 1053 MET cc_start: 0.8522 (ppp) cc_final: 0.8018 (ppp) REVERT: O 1055 LEU cc_start: 0.8207 (mt) cc_final: 0.7953 (mt) REVERT: O 1300 MET cc_start: 0.6221 (ttp) cc_final: 0.5477 (ptm) outliers start: 57 outliers final: 41 residues processed: 250 average time/residue: 0.1343 time to fit residues: 49.3992 Evaluate side-chains 247 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain O residue 766 THR Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 882 LEU Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1031 ARG Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 71 optimal weight: 0.8980 chunk 149 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 124 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.096565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068703 restraints weight = 60701.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070358 restraints weight = 30544.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071412 restraints weight = 20857.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071988 restraints weight = 17158.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072229 restraints weight = 15615.411| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17686 Z= 0.139 Angle : 0.653 9.062 25128 Z= 0.358 Chirality : 0.043 0.380 2863 Planarity : 0.004 0.054 2167 Dihedral : 29.860 178.416 4686 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.32 % Favored : 94.53 % Rotamer: Outliers : 3.66 % Allowed : 17.67 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1316 helix: 0.79 (0.19), residues: 760 sheet: -1.69 (0.62), residues: 70 loop : -1.36 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O1299 TYR 0.032 0.002 TYR C 57 PHE 0.022 0.002 PHE O1063 TRP 0.016 0.002 TRP O 777 HIS 0.005 0.001 HIS O 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (17686) covalent geometry : angle 0.65336 / 0.36 (25128) hydrogen bonds : bond 0.04076 / 2.76 ( 854) hydrogen bonds : angle 4.10984 / 2.99 ( 2241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: B 53 GLU cc_start: 0.7687 (tp30) cc_final: 0.7435 (tp30) REVERT: B 64 ASN cc_start: 0.8550 (m-40) cc_final: 0.8001 (m110) REVERT: B 74 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 91 LYS cc_start: 0.8832 (tttt) cc_final: 0.8477 (tttm) REVERT: C 56 GLU cc_start: 0.7639 (tt0) cc_final: 0.6986 (tt0) REVERT: C 64 GLU cc_start: 0.8490 (tt0) cc_final: 0.8023 (pt0) REVERT: C 72 ASP cc_start: 0.8013 (m-30) cc_final: 0.7697 (m-30) REVERT: C 75 LYS cc_start: 0.9243 (mptt) cc_final: 0.8519 (mmtt) REVERT: C 91 GLU cc_start: 0.7596 (pt0) cc_final: 0.7338 (pt0) REVERT: D 44 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8543 (tm-30) REVERT: E 60 LEU cc_start: 0.8382 (tp) cc_final: 0.7834 (tt) REVERT: E 93 GLN cc_start: 0.8685 (tt0) cc_final: 0.7988 (tp40) REVERT: F 25 ASN cc_start: 0.5923 (OUTLIER) cc_final: 0.5625 (m-40) REVERT: F 74 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7749 (tm-30) REVERT: F 88 TYR cc_start: 0.8527 (m-10) cc_final: 0.8200 (m-80) REVERT: G 36 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8638 (mmtp) REVERT: G 38 ASN cc_start: 0.8796 (p0) cc_final: 0.8537 (p0) REVERT: G 95 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8410 (mtpp) REVERT: H 59 MET cc_start: 0.8849 (tpp) cc_final: 0.8648 (tpp) REVERT: H 80 TYR cc_start: 0.7968 (m-10) cc_final: 0.7580 (m-10) REVERT: H 102 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7407 (tm-30) REVERT: O 775 LEU cc_start: 0.9071 (tt) cc_final: 0.8864 (pp) REVERT: O 790 LEU cc_start: 0.8775 (tp) cc_final: 0.8451 (tt) REVERT: O 1053 MET cc_start: 0.8547 (ppp) cc_final: 0.8032 (ppp) REVERT: O 1055 LEU cc_start: 0.8199 (mt) cc_final: 0.7833 (mt) REVERT: O 1096 LEU cc_start: 0.8683 (mt) cc_final: 0.8435 (mt) REVERT: O 1112 MET cc_start: 0.7390 (mmt) cc_final: 0.7083 (mmm) REVERT: O 1300 MET cc_start: 0.6230 (ttp) cc_final: 0.5863 (ptm) outliers start: 42 outliers final: 27 residues processed: 249 average time/residue: 0.1275 time to fit residues: 47.5503 Evaluate side-chains 239 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068112 restraints weight = 60148.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.069826 restraints weight = 30004.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070884 restraints weight = 20422.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071456 restraints weight = 16784.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.071697 restraints weight = 15299.625| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17686 Z= 0.144 Angle : 0.660 9.475 25128 Z= 0.358 Chirality : 0.043 0.374 2863 Planarity : 0.004 0.055 2167 Dihedral : 29.861 179.356 4686 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.32 % Favored : 94.53 % Rotamer: Outliers : 4.61 % Allowed : 18.28 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1316 helix: 0.93 (0.19), residues: 762 sheet: -1.69 (0.61), residues: 72 loop : -1.28 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O1299 TYR 0.018 0.002 TYR C 57 PHE 0.022 0.002 PHE O1063 TRP 0.017 0.002 TRP O 777 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (17686) covalent geometry : angle 0.66005 / 0.36 (25128) hydrogen bonds : bond 0.04089 / 2.76 ( 854) hydrogen bonds : angle 4.02060 / 2.93 ( 2241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: B 53 GLU cc_start: 0.7753 (tp30) cc_final: 0.7528 (tp30) REVERT: B 74 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 84 MET cc_start: 0.8486 (mmm) cc_final: 0.7904 (tpt) REVERT: C 56 GLU cc_start: 0.7739 (tt0) cc_final: 0.7139 (tt0) REVERT: C 64 GLU cc_start: 0.8481 (tt0) cc_final: 0.8128 (pt0) REVERT: C 72 ASP cc_start: 0.8037 (m-30) cc_final: 0.7741 (m-30) REVERT: C 91 GLU cc_start: 0.7607 (pt0) cc_final: 0.7343 (pt0) REVERT: D 44 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8589 (tm-30) REVERT: D 105 LYS cc_start: 0.8373 (ptmm) cc_final: 0.8077 (pttm) REVERT: E 93 GLN cc_start: 0.8677 (tt0) cc_final: 0.7993 (tp40) REVERT: F 25 ASN cc_start: 0.5910 (OUTLIER) cc_final: 0.5614 (m-40) REVERT: F 84 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8337 (mmm) REVERT: F 88 TYR cc_start: 0.8538 (m-10) cc_final: 0.8288 (m-80) REVERT: G 24 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8175 (mp10) REVERT: G 36 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8627 (mmtp) REVERT: G 38 ASN cc_start: 0.8756 (p0) cc_final: 0.8439 (p0) REVERT: G 95 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8372 (mtpp) REVERT: H 80 TYR cc_start: 0.8003 (m-10) cc_final: 0.7645 (m-10) REVERT: H 102 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7378 (tm-30) REVERT: H 103 LEU cc_start: 0.9182 (tp) cc_final: 0.8890 (mt) REVERT: O 760 SER cc_start: 0.8936 (m) cc_final: 0.8701 (p) REVERT: O 790 LEU cc_start: 0.8799 (tp) cc_final: 0.8451 (tt) REVERT: O 1053 MET cc_start: 0.8581 (ppp) cc_final: 0.8155 (ppp) REVERT: O 1096 LEU cc_start: 0.8736 (mt) cc_final: 0.8469 (mt) REVERT: O 1112 MET cc_start: 0.7410 (mmt) cc_final: 0.7105 (mmm) REVERT: O 1300 MET cc_start: 0.6182 (ttp) cc_final: 0.5856 (ptm) outliers start: 53 outliers final: 43 residues processed: 247 average time/residue: 0.1266 time to fit residues: 47.4810 Evaluate side-chains 254 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 766 THR Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 897 HIS Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 954 GLU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1018 LEU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1290 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 23 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 785 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 = 0.3847 r_free = 0.3847 target = 0.097066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.068912 restraints weight = 61072.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070662 restraints weight = 30207.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071763 restraints weight = 20391.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072353 restraints weight = 16683.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.072632 restraints weight = 15159.424| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17686 Z= 0.137 Angle : 0.667 17.713 25128 Z= 0.358 Chirality : 0.043 0.371 2863 Planarity : 0.004 0.055 2167 Dihedral : 29.832 179.821 4686 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.17 % Favored : 94.60 % Rotamer: Outliers : 3.48 % Allowed : 19.32 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1316 helix: 1.01 (0.19), residues: 760 sheet: -1.64 (0.61), residues: 72 loop : -1.27 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O1299 TYR 0.031 0.002 TYR C 57 PHE 0.022 0.002 PHE O1063 TRP 0.018 0.002 TRP O 777 HIS 0.007 0.001 HIS O 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (17686) covalent geometry : angle 0.66726 / 0.36 (25128) hydrogen bonds : bond 0.03977 / 2.69 ( 854) hydrogen bonds : angle 3.97046 / 2.89 ( 2241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: B 53 GLU cc_start: 0.7864 (tp30) cc_final: 0.7650 (tp30) REVERT: B 74 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 84 MET cc_start: 0.8510 (mmm) cc_final: 0.8117 (mmm) REVERT: C 56 GLU cc_start: 0.7720 (tt0) cc_final: 0.7088 (tt0) REVERT: C 64 GLU cc_start: 0.8463 (tt0) cc_final: 0.8123 (pt0) REVERT: C 72 ASP cc_start: 0.8109 (m-30) cc_final: 0.7838 (m-30) REVERT: C 91 GLU cc_start: 0.7578 (pt0) cc_final: 0.7364 (pt0) REVERT: D 44 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8583 (tm-30) REVERT: D 105 LYS cc_start: 0.8252 (ptmm) cc_final: 0.7996 (pttm) REVERT: E 93 GLN cc_start: 0.8653 (tt0) cc_final: 0.8013 (tp40) REVERT: F 25 ASN cc_start: 0.6172 (OUTLIER) cc_final: 0.5816 (m-40) REVERT: F 88 TYR cc_start: 0.8508 (m-10) cc_final: 0.8280 (m-80) REVERT: F 91 LYS cc_start: 0.9075 (tppt) cc_final: 0.8862 (ttpt) REVERT: G 24 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8159 (mp10) REVERT: G 36 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8647 (mmtp) REVERT: G 38 ASN cc_start: 0.8707 (p0) cc_final: 0.8411 (p0) REVERT: G 95 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8366 (mtpp) REVERT: H 80 TYR cc_start: 0.7996 (m-10) cc_final: 0.7735 (m-10) REVERT: H 102 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7303 (tm-30) REVERT: H 103 LEU cc_start: 0.9136 (tp) cc_final: 0.8860 (mt) REVERT: O 760 SER cc_start: 0.8930 (m) cc_final: 0.8670 (p) REVERT: O 790 LEU cc_start: 0.8790 (tp) cc_final: 0.8435 (tt) REVERT: O 1015 MET cc_start: 0.7948 (mmt) cc_final: 0.7294 (mmt) REVERT: O 1053 MET cc_start: 0.8574 (ppp) cc_final: 0.8148 (ppp) REVERT: O 1096 LEU cc_start: 0.8729 (mt) cc_final: 0.8449 (mt) REVERT: O 1112 MET cc_start: 0.7413 (mmt) cc_final: 0.7130 (mmm) REVERT: O 1116 MET cc_start: 0.7412 (tmm) cc_final: 0.7202 (tmm) REVERT: O 1291 ASP cc_start: 0.7906 (p0) cc_final: 0.7430 (p0) REVERT: O 1300 MET cc_start: 0.6196 (ttp) cc_final: 0.5929 (ptm) outliers start: 40 outliers final: 33 residues processed: 241 average time/residue: 0.1260 time to fit residues: 45.9676 Evaluate side-chains 242 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Chi-restraints excluded: chain O residue 1290 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 121 optimal weight: 0.0470 chunk 73 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.097253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.068964 restraints weight = 61452.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.070666 restraints weight = 30926.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.071754 restraints weight = 21067.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072338 restraints weight = 17313.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072523 restraints weight = 15764.135| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17686 Z= 0.137 Angle : 0.662 12.083 25128 Z= 0.358 Chirality : 0.042 0.367 2863 Planarity : 0.004 0.055 2167 Dihedral : 29.822 179.483 4686 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.40 % Favored : 94.38 % Rotamer: Outliers : 3.39 % Allowed : 20.10 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1316 helix: 1.10 (0.19), residues: 759 sheet: -1.62 (0.62), residues: 72 loop : -1.27 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O1299 TYR 0.031 0.002 TYR C 57 PHE 0.022 0.002 PHE O1063 TRP 0.020 0.002 TRP O 777 HIS 0.007 0.001 HIS O 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (17686) covalent geometry : angle 0.66179 / 0.36 (25128) hydrogen bonds : bond 0.03944 / 2.66 ( 854) hydrogen bonds : angle 3.94200 / 2.87 ( 2241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (tt0) REVERT: B 53 GLU cc_start: 0.7973 (tp30) cc_final: 0.7636 (tp30) REVERT: B 80 THR cc_start: 0.9460 (m) cc_final: 0.9250 (p) REVERT: B 84 MET cc_start: 0.8522 (mmm) cc_final: 0.8103 (mmm) REVERT: B 91 LYS cc_start: 0.8625 (tttt) cc_final: 0.8269 (tttm) REVERT: C 56 GLU cc_start: 0.7764 (tt0) cc_final: 0.7132 (tt0) REVERT: C 64 GLU cc_start: 0.8471 (tt0) cc_final: 0.8114 (pt0) REVERT: C 72 ASP cc_start: 0.8133 (m-30) cc_final: 0.7834 (m-30) REVERT: D 44 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8648 (tm-30) REVERT: D 76 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7802 (ptm-80) REVERT: D 105 LYS cc_start: 0.8239 (ptmm) cc_final: 0.8014 (pttm) REVERT: E 93 GLN cc_start: 0.8653 (tt0) cc_final: 0.8024 (tp40) REVERT: F 25 ASN cc_start: 0.6009 (OUTLIER) cc_final: 0.5741 (m-40) REVERT: F 74 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7804 (tm-30) REVERT: F 88 TYR cc_start: 0.8499 (m-10) cc_final: 0.8277 (m-80) REVERT: F 91 LYS cc_start: 0.9094 (tppt) cc_final: 0.8885 (ttpt) REVERT: F 93 GLN cc_start: 0.8917 (tp40) cc_final: 0.8561 (tt0) REVERT: G 24 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8177 (mp10) REVERT: G 36 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8660 (mmtp) REVERT: G 38 ASN cc_start: 0.8707 (p0) cc_final: 0.8420 (p0) REVERT: G 95 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8278 (mtpp) REVERT: H 80 TYR cc_start: 0.8031 (m-10) cc_final: 0.7772 (m-10) REVERT: H 102 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7290 (tm-30) REVERT: H 103 LEU cc_start: 0.9163 (tp) cc_final: 0.8922 (mt) REVERT: O 760 SER cc_start: 0.8947 (m) cc_final: 0.8688 (p) REVERT: O 790 LEU cc_start: 0.8789 (tp) cc_final: 0.8442 (tt) REVERT: O 1015 MET cc_start: 0.7955 (mmt) cc_final: 0.7292 (mmt) REVERT: O 1053 MET cc_start: 0.8556 (ppp) cc_final: 0.8137 (ppp) REVERT: O 1096 LEU cc_start: 0.8753 (mt) cc_final: 0.8446 (mt) REVERT: O 1112 MET cc_start: 0.7427 (mmt) cc_final: 0.7131 (mmm) REVERT: O 1291 ASP cc_start: 0.7923 (p0) cc_final: 0.7469 (p0) outliers start: 39 outliers final: 34 residues processed: 239 average time/residue: 0.1225 time to fit residues: 44.5266 Evaluate side-chains 249 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 19 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.095269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066922 restraints weight = 60408.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.068607 restraints weight = 30226.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.069643 restraints weight = 20614.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070128 restraints weight = 16974.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070510 restraints weight = 15535.065| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17686 Z= 0.173 Angle : 0.690 9.901 25128 Z= 0.370 Chirality : 0.043 0.370 2863 Planarity : 0.004 0.056 2167 Dihedral : 29.923 179.968 4686 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.09 % Favored : 94.68 % Rotamer: Outliers : 3.74 % Allowed : 20.02 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1316 helix: 1.09 (0.19), residues: 760 sheet: -1.67 (0.62), residues: 72 loop : -1.24 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O1299 TYR 0.030 0.002 TYR C 57 PHE 0.022 0.002 PHE O1063 TRP 0.020 0.002 TRP O 777 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (17686) covalent geometry : angle 0.69034 / 0.37 (25128) hydrogen bonds : bond 0.04316 / 2.91 ( 854) hydrogen bonds : angle 3.99346 / 2.91 ( 2241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8158 (pm20) cc_final: 0.7534 (pm20) REVERT: B 74 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 84 MET cc_start: 0.8571 (mmm) cc_final: 0.8179 (mmm) REVERT: B 91 LYS cc_start: 0.8858 (tttt) cc_final: 0.8404 (tttm) REVERT: C 64 GLU cc_start: 0.8487 (tt0) cc_final: 0.8018 (pt0) REVERT: C 72 ASP cc_start: 0.8170 (m-30) cc_final: 0.7881 (m-30) REVERT: D 44 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8636 (tm-30) REVERT: D 68 GLU cc_start: 0.8394 (tp30) cc_final: 0.8184 (tp30) REVERT: D 76 ARG cc_start: 0.8232 (ptm160) cc_final: 0.7967 (ptm-80) REVERT: D 105 LYS cc_start: 0.8276 (ptmm) cc_final: 0.8038 (pttm) REVERT: F 25 ASN cc_start: 0.6034 (OUTLIER) cc_final: 0.5751 (m-40) REVERT: F 88 TYR cc_start: 0.8618 (m-10) cc_final: 0.8358 (m-80) REVERT: G 24 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8198 (mp10) REVERT: G 36 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8642 (mmtp) REVERT: G 38 ASN cc_start: 0.8777 (p0) cc_final: 0.8535 (p0) REVERT: G 95 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8407 (mtpp) REVERT: H 80 TYR cc_start: 0.8053 (m-10) cc_final: 0.7721 (m-10) REVERT: H 102 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7193 (tm-30) REVERT: H 103 LEU cc_start: 0.9207 (tp) cc_final: 0.8963 (mt) REVERT: O 760 SER cc_start: 0.8952 (m) cc_final: 0.8698 (p) REVERT: O 790 LEU cc_start: 0.8855 (tp) cc_final: 0.8503 (tt) REVERT: O 1015 MET cc_start: 0.7880 (mmt) cc_final: 0.7296 (mmt) REVERT: O 1096 LEU cc_start: 0.8630 (mt) cc_final: 0.8348 (mt) REVERT: O 1112 MET cc_start: 0.7488 (mmt) cc_final: 0.7181 (mmm) REVERT: O 1291 ASP cc_start: 0.7869 (p0) cc_final: 0.7430 (p0) outliers start: 43 outliers final: 40 residues processed: 232 average time/residue: 0.1372 time to fit residues: 47.9369 Evaluate side-chains 246 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain O residue 823 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 927 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 942 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1018 LEU Chi-restraints excluded: chain O residue 1023 TYR Chi-restraints excluded: chain O residue 1072 ILE Chi-restraints excluded: chain O residue 1158 CYS Chi-restraints excluded: chain O residue 1220 VAL Chi-restraints excluded: chain O residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 141 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 81 ASN E 93 GLN ** O 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.094305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065798 restraints weight = 60038.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067439 restraints weight = 30528.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.068456 restraints weight = 21044.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.068995 restraints weight = 17424.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069172 restraints weight = 15945.538| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17686 Z= 0.177 Angle : 0.700 11.112 25128 Z= 0.376 Chirality : 0.044 0.387 2863 Planarity : 0.005 0.055 2167 Dihedral : 29.982 179.686 4686 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.40 % Favored : 94.38 % Rotamer: Outliers : 3.66 % Allowed : 20.28 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1316 helix: 1.07 (0.19), residues: 760 sheet: -1.73 (0.61), residues: 72 loop : -1.23 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O1299 TYR 0.028 0.002 TYR C 57 PHE 0.023 0.002 PHE O1063 TRP 0.021 0.002 TRP O 777 HIS 0.007 0.001 HIS O 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (17686) covalent geometry : angle 0.70019 / 0.38 (25128) hydrogen bonds : bond 0.04340 / 2.94 ( 854) hydrogen bonds : angle 4.04828 / 2.95 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.45 seconds wall clock time: 55 minutes 38.02 seconds (3338.02 seconds total)