Starting phenix.real_space_refine on Thu Aug 6 12:28:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux9_64577/08_2026/9ux9_64577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux9_64577/08_2026/9ux9_64577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ux9_64577/08_2026/9ux9_64577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux9_64577/08_2026/9ux9_64577.map" model { file = "/net/cci-nas-00/data/ceres_data/9ux9_64577/08_2026/9ux9_64577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux9_64577/08_2026/9ux9_64577.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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: 8 Type Number sf(0) Gaussians P 238 5.49 5 Mg 1 5.21 5 S 37 5.16 5 Be 1 3.05 5 C 8721 2.51 5 N 2763 2.21 5 O 3224 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14988 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 745 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} 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: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 746 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 695 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 738 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} 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: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 746 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2425 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "J" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2412 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "K" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4499 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 20, 'TRANS': 526} Chain breaks: 6 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.41, per 1000 atoms: 0.23 Number of scatterers: 14988 At special positions: 0 Unit cell: (102.2, 116.8, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 37 16.00 P 238 15.00 Mg 1 11.99 F 3 9.00 O 3224 8.00 N 2763 7.00 C 8721 6.00 Be 1 4.00 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: 1.28 Conformation dependent library (CDL) restraints added in 588.2 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 63.0% alpha, 3.7% beta 87 base pairs and 175 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.679A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.205A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.883A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.576A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.652A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.447A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.716A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.612A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.656A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.546A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 39 Processing helix chain 'F' and resid 49 through 74 removed outlier: 3.609A 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 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.249A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.527A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 120 Processing helix chain 'K' and resid 548 through 556 removed outlier: 3.762A pdb=" N LEU K 554 " --> pdb=" O ARG K 550 " (cutoff:3.500A) Processing helix chain 'K' and resid 756 through 770 removed outlier: 4.097A pdb=" N ILE K 760 " --> pdb=" O LYS K 756 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS K 761 " --> pdb=" O GLN K 757 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR K 770 " --> pdb=" O LEU K 766 " (cutoff:3.500A) Processing helix chain 'K' and resid 786 through 798 Processing helix chain 'K' and resid 812 through 814 No H-bonds generated for 'chain 'K' and resid 812 through 814' Processing helix chain 'K' and resid 815 through 827 Processing helix chain 'K' and resid 838 through 843 removed outlier: 3.651A pdb=" N ARG K 843 " --> pdb=" O PRO K 839 " (cutoff:3.500A) Processing helix chain 'K' and resid 845 through 851 Processing helix chain 'K' and resid 861 through 866 removed outlier: 3.873A pdb=" N ILE K 865 " --> pdb=" O TYR K 861 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS K 866 " --> pdb=" O GLU K 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 861 through 866' Processing helix chain 'K' and resid 867 through 872 removed outlier: 3.519A pdb=" N LEU K 871 " --> pdb=" O ASP K 867 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA K 872 " --> pdb=" O LYS K 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 867 through 872' Processing helix chain 'K' and resid 883 through 888 removed outlier: 4.105A pdb=" N ARG K 886 " --> pdb=" O GLU K 883 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET K 887 " --> pdb=" O GLY K 884 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 888 " --> pdb=" O HIS K 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 883 through 888' Processing helix chain 'K' and resid 892 through 899 removed outlier: 3.528A pdb=" N ASN K 899 " --> pdb=" O THR K 895 " (cutoff:3.500A) Processing helix chain 'K' and resid 920 through 930 removed outlier: 4.079A pdb=" N ALA K 924 " --> pdb=" O PRO K 920 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU K 925 " --> pdb=" O GLU K 921 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE K 928 " --> pdb=" O ALA K 924 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU K 929 " --> pdb=" O LEU K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 971 removed outlier: 3.736A pdb=" N LYS K 971 " --> pdb=" O ARG K 968 " (cutoff:3.500A) Processing helix chain 'K' and resid 973 through 977 removed outlier: 3.558A pdb=" N LEU K 977 " --> pdb=" O ARG K 974 " (cutoff:3.500A) Processing helix chain 'K' and resid 1002 through 1014 removed outlier: 4.174A pdb=" N ALA K1014 " --> pdb=" O ARG K1010 " (cutoff:3.500A) Processing helix chain 'K' and resid 1038 through 1048 removed outlier: 3.743A pdb=" N ARG K1044 " --> pdb=" O ILE K1040 " (cutoff:3.500A) Processing helix chain 'K' and resid 1049 through 1052 Processing helix chain 'K' and resid 1053 through 1061 Processing helix chain 'K' and resid 1074 through 1079 removed outlier: 3.533A pdb=" N ALA K1079 " --> pdb=" O ASP K1075 " (cutoff:3.500A) Processing helix chain 'K' and resid 1080 through 1087 removed outlier: 4.073A pdb=" N LEU K1085 " --> pdb=" O GLY K1081 " (cutoff:3.500A) Processing helix chain 'K' and resid 1089 through 1096 Processing helix chain 'K' and resid 1107 through 1120 removed outlier: 4.003A pdb=" N THR K1111 " --> pdb=" O THR K1107 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE K1112 " --> pdb=" O SER K1108 " (cutoff:3.500A) Processing helix chain 'K' and resid 1138 through 1144 Processing helix chain 'K' and resid 1156 through 1161 Processing helix chain 'K' and resid 1181 through 1189 removed outlier: 3.641A pdb=" N ASP K1189 " --> pdb=" O LEU K1185 " (cutoff:3.500A) Processing helix chain 'K' and resid 1210 through 1230 removed outlier: 4.437A pdb=" N LYS K1214 " --> pdb=" O SER K1210 " (cutoff:3.500A) Processing helix chain 'K' and resid 1243 through 1253 removed outlier: 3.706A pdb=" N PHE K1247 " --> pdb=" O GLU K1243 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA K1250 " --> pdb=" O ALA K1246 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE K1251 " --> pdb=" O PHE K1247 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU K1252 " --> pdb=" O LEU K1248 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU K1253 " --> pdb=" O GLN K1249 " (cutoff:3.500A) Processing helix chain 'K' and resid 1302 through 1306 Processing helix chain 'K' and resid 1310 through 1316 removed outlier: 3.983A pdb=" N PHE K1314 " --> pdb=" O HIS K1310 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU K1316 " --> pdb=" O GLU K1312 " (cutoff:3.500A) Processing helix chain 'K' and resid 1319 through 1324 removed outlier: 3.833A pdb=" N ARG K1324 " --> pdb=" O MET K1320 " (cutoff:3.500A) Processing helix chain 'K' and resid 1325 through 1330 removed outlier: 4.664A pdb=" N GLU K1328 " --> pdb=" O ARG K1325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.539A 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 'B' and resid 96 through 97 removed outlier: 6.335A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.394A 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 'C' and resid 100 through 102 removed outlier: 6.377A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.856A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 776 through 779 removed outlier: 3.903A pdb=" N GLY K 776 " --> pdb=" O ARG K 907 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU K 909 " --> pdb=" O GLY K 776 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET K 879 " --> pdb=" O LEU K 908 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU K 910 " --> pdb=" O MET K 879 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL K 881 " --> pdb=" O LEU K 910 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE K 809 " --> pdb=" O THR K 859 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL K 833 " --> pdb=" O LEU K 858 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 1124 through 1126 removed outlier: 6.238A pdb=" N LEU K1125 " --> pdb=" O LEU K1154 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL K1100 " --> pdb=" O PHE K1153 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU K1101 " --> pdb=" O ILE K1173 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 228 hydrogen bonds 452 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 175 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3943 1.34 - 1.46: 3860 1.46 - 1.58: 7393 1.58 - 1.70: 473 1.70 - 1.82: 66 Bond restraints: 15735 Sorted by residual: bond pdb=" C3' DG I 126 " pdb=" C2' DG I 126 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT I 35 " pdb=" C2' DT I 35 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DT I 105 " pdb=" C2' DT I 105 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.38e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.33e+00 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.80e+00 ... (remaining 15730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 21998 2.35 - 4.69: 227 4.69 - 7.04: 21 7.04 - 9.39: 2 9.39 - 11.74: 1 Bond angle restraints: 22249 Sorted by residual: angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 102.38 3.62 6.00e-01 2.78e+00 3.65e+01 angle pdb=" O4' DA J 71 " pdb=" C4' DA J 71 " pdb=" C3' DA J 71 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT J 79 " pdb=" C4 DT J 79 " pdb=" O4 DT J 79 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 22244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.86: 7482 31.86 - 63.72: 1364 63.72 - 95.58: 31 95.58 - 127.45: 0 127.45 - 159.31: 2 Dihedral angle restraints: 8879 sinusoidal: 5203 harmonic: 3676 Sorted by residual: dihedral pdb=" C4' DA I 120 " pdb=" C3' DA I 120 " pdb=" O3' DA I 120 " pdb=" P DG I 121 " ideal model delta sinusoidal sigma weight residual -140.00 19.31 -159.31 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual -140.00 -11.89 -128.11 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " pdb=" CZ ARG B 92 " ideal model delta sinusoidal sigma weight residual 90.00 41.20 48.80 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2424 0.089 - 0.177: 99 0.177 - 0.266: 1 0.266 - 0.355: 0 0.355 - 0.443: 1 Chirality restraints: 2525 Sorted by residual: chirality pdb=" P DA I 120 " pdb=" OP1 DA I 120 " pdb=" OP2 DA I 120 " pdb=" O5' DA I 120 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" C3' DA I 120 " pdb=" C4' DA I 120 " pdb=" O3' DA I 120 " pdb=" C2' DA I 120 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL K 993 " pdb=" N VAL K 993 " pdb=" C VAL K 993 " pdb=" CB VAL K 993 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 2522 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K1372 " 0.197 9.50e-02 1.11e+02 8.84e-02 4.80e+00 pdb=" NE ARG K1372 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG K1372 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG K1372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K1372 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR K 913 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO K 914 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO K 914 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 914 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 765 " 0.009 2.00e-02 2.50e+03 1.05e-02 2.76e+00 pdb=" CG TRP K 765 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP K 765 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP K 765 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 765 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 765 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 765 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 765 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 765 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP K 765 " -0.001 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 241 2.65 - 3.21: 12507 3.21 - 3.78: 25541 3.78 - 4.34: 32350 4.34 - 4.90: 49211 Nonbonded interactions: 119850 Sorted by model distance: nonbonded pdb="MG MG K1702 " pdb=" O2B ADP K1703 " model vdw 2.089 2.170 nonbonded pdb=" OH TYR K 861 " pdb=" O ASP K 882 " model vdw 2.221 3.040 nonbonded pdb=" N GLN K 988 " pdb=" OE1 GLN K 988 " model vdw 2.266 3.120 nonbonded pdb=" F2 BEF K1701 " pdb=" O2B ADP K1703 " model vdw 2.269 2.990 nonbonded pdb=" O GLU K1301 " pdb=" N VAL K1303 " model vdw 2.272 3.120 ... (remaining 119845 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 44 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 15 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 111)) selection = (chain 'G' and (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 111)) } ncs_group { reference = chain 'D' selection = (chain 'H' and ((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 (name N or name CA or name \ C or name O or name CB )) or resid 56 through 120)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 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 : 0.004 0.045 15735 Z= 0.396 Angle : 0.623 11.736 22249 Z= 0.514 Chirality : 0.041 0.443 2525 Planarity : 0.004 0.088 1993 Dihedral : 24.689 159.307 6495 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.39 % Favored : 95.29 % Rotamer: Outliers : 0.28 % Allowed : 22.38 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1231 helix: 1.95 (0.20), residues: 732 sheet: -0.18 (0.79), residues: 54 loop : -1.57 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.017 0.001 TYR K 821 PHE 0.010 0.001 PHE K1153 TRP 0.027 0.001 TRP K 765 HIS 0.001 0.000 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.40 (15735) covalent geometry : angle 0.62272 / 0.51 (22249) hydrogen bonds : bond 0.16564 / 11.29 ( 732) hydrogen bonds : angle 4.44095 / 3.18 ( 1934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 825 LYS cc_start: 0.7070 (ptmt) cc_final: 0.6824 (tttt) REVERT: K 1047 CYS cc_start: 0.7927 (m) cc_final: 0.7649 (m) REVERT: K 1057 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7075 (tp30) REVERT: K 1186 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6514 (mt0) REVERT: K 1200 VAL cc_start: 0.6309 (t) cc_final: 0.5467 (p) REVERT: K 1212 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6806 (mt-10) REVERT: K 1339 MET cc_start: 0.5983 (mmm) cc_final: 0.5772 (tpt) outliers start: 3 outliers final: 1 residues processed: 230 average time/residue: 0.1465 time to fit residues: 47.8232 Evaluate side-chains 191 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1318 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 84 GLN D 46 HIS D 106 HIS G 73 ASN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1042 GLN ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.164381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139613 restraints weight = 26306.192| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.89 r_work: 0.3727 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 15735 Z= 0.340 Angle : 0.873 11.036 22249 Z= 0.470 Chirality : 0.053 0.251 2525 Planarity : 0.008 0.090 1993 Dihedral : 27.584 165.677 3967 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.85 % Favored : 93.83 % Rotamer: Outliers : 4.83 % Allowed : 19.41 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.23), residues: 1231 helix: 0.70 (0.18), residues: 748 sheet: -1.14 (0.64), residues: 63 loop : -1.65 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K1120 TYR 0.034 0.004 TYR K1116 PHE 0.047 0.005 PHE K1317 TRP 0.024 0.004 TRP K 765 HIS 0.011 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.34 (15735) covalent geometry : angle 0.87260 / 0.47 (22249) hydrogen bonds : bond 0.06748 / 4.58 ( 732) hydrogen bonds : angle 3.90563 / 2.81 ( 1934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.459 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: E 59 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: E 109 LEU cc_start: 0.8486 (mt) cc_final: 0.8196 (mt) REVERT: E 120 MET cc_start: 0.7808 (mmm) cc_final: 0.7514 (mtt) REVERT: F 85 ASP cc_start: 0.7728 (m-30) cc_final: 0.7499 (m-30) REVERT: F 88 TYR cc_start: 0.8132 (m-10) cc_final: 0.7796 (m-80) REVERT: G 73 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8418 (t0) REVERT: H 56 MET cc_start: 0.8728 (mmm) cc_final: 0.8403 (tpp) REVERT: H 98 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8365 (mt) REVERT: K 798 MET cc_start: 0.6644 (ppp) cc_final: 0.6320 (ppp) REVERT: K 822 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7253 (mm-30) REVERT: K 823 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: K 873 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8092 (mttm) REVERT: K 981 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6175 (tt) REVERT: K 1038 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7282 (t0) REVERT: K 1047 CYS cc_start: 0.8141 (m) cc_final: 0.7723 (m) REVERT: K 1117 PHE cc_start: 0.7762 (m-10) cc_final: 0.7537 (m-10) REVERT: K 1182 HIS cc_start: 0.6213 (t-90) cc_final: 0.5991 (t-90) REVERT: K 1189 ASP cc_start: 0.5972 (m-30) cc_final: 0.5662 (m-30) REVERT: K 1192 HIS cc_start: 0.8462 (t-170) cc_final: 0.8228 (t-170) REVERT: K 1212 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7248 (mt-10) REVERT: K 1339 MET cc_start: 0.6962 (mmm) cc_final: 0.6424 (tpt) outliers start: 52 outliers final: 18 residues processed: 237 average time/residue: 0.1604 time to fit residues: 52.4193 Evaluate side-chains 217 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 823 PHE Chi-restraints excluded: chain K residue 885 HIS Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 991 GLU Chi-restraints excluded: chain K residue 1038 ASN Chi-restraints excluded: chain K residue 1056 ILE Chi-restraints excluded: chain K residue 1092 LYS Chi-restraints excluded: chain K residue 1127 LEU Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN K 789 GLN K 855 ASN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1049 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 = 0.4187 r_free = 0.4187 target = 0.162999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.138103 restraints weight = 26350.233| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.94 r_work: 0.3705 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15735 Z= 0.156 Angle : 0.597 10.430 22249 Z= 0.325 Chirality : 0.042 0.296 2525 Planarity : 0.004 0.046 1993 Dihedral : 27.346 161.472 3964 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 3.34 % Allowed : 20.06 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.24), residues: 1231 helix: 1.44 (0.19), residues: 756 sheet: -1.34 (0.68), residues: 60 loop : -1.75 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 906 TYR 0.020 0.002 TYR D 118 PHE 0.036 0.002 PHE K1122 TRP 0.015 0.002 TRP K 765 HIS 0.007 0.001 HIS K1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (15735) covalent geometry : angle 0.59713 / 0.32 (22249) hydrogen bonds : bond 0.04778 / 3.22 ( 732) hydrogen bonds : angle 3.31923 / 2.35 ( 1934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8709 (tp) REVERT: C 77 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8302 (mtm-85) REVERT: E 59 GLU cc_start: 0.8399 (pm20) cc_final: 0.8118 (pm20) REVERT: F 79 LYS cc_start: 0.8244 (mptt) cc_final: 0.8024 (mtmm) REVERT: F 88 TYR cc_start: 0.8081 (m-10) cc_final: 0.7796 (m-80) REVERT: H 98 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8318 (mt) REVERT: K 798 MET cc_start: 0.6562 (ppp) cc_final: 0.6237 (ppp) REVERT: K 823 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: K 865 ILE cc_start: 0.8657 (tt) cc_final: 0.8448 (mt) REVERT: K 981 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6212 (tt) REVERT: K 982 LYS cc_start: 0.5891 (mttt) cc_final: 0.5616 (mttt) REVERT: K 1047 CYS cc_start: 0.8327 (m) cc_final: 0.7854 (m) REVERT: K 1182 HIS cc_start: 0.6116 (OUTLIER) cc_final: 0.5896 (t-90) REVERT: K 1212 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7302 (mt-10) REVERT: K 1326 ARG cc_start: 0.7007 (tmt170) cc_final: 0.5915 (tmm160) REVERT: K 1339 MET cc_start: 0.6979 (mmm) cc_final: 0.6411 (tpt) outliers start: 36 outliers final: 18 residues processed: 221 average time/residue: 0.1623 time to fit residues: 49.3645 Evaluate side-chains 211 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 823 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 885 HIS Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 991 GLU Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1127 LEU Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1182 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 38 ASN E 55 GLN G 73 ASN K 789 GLN K 869 HIS ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130519 restraints weight = 25706.555| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.95 r_work: 0.3626 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15735 Z= 0.161 Angle : 0.597 9.091 22249 Z= 0.324 Chirality : 0.041 0.242 2525 Planarity : 0.005 0.072 1993 Dihedral : 27.333 165.440 3964 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.12 % Favored : 94.64 % Rotamer: Outliers : 2.88 % Allowed : 22.10 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1231 helix: 1.62 (0.19), residues: 753 sheet: -1.16 (0.70), residues: 60 loop : -1.73 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K1324 TYR 0.017 0.002 TYR K1150 PHE 0.011 0.001 PHE K1317 TRP 0.017 0.002 TRP K 819 HIS 0.011 0.001 HIS K 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (15735) covalent geometry : angle 0.59749 / 0.32 (22249) hydrogen bonds : bond 0.04629 / 3.13 ( 732) hydrogen bonds : angle 3.18824 / 2.27 ( 1934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8254 (mtm-85) REVERT: E 59 GLU cc_start: 0.8525 (pm20) cc_final: 0.8180 (pm20) REVERT: F 88 TYR cc_start: 0.8075 (m-10) cc_final: 0.7741 (m-80) REVERT: H 98 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (mt) REVERT: K 782 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.5923 (mtm) REVERT: K 873 LYS cc_start: 0.8344 (mttm) cc_final: 0.7947 (ttmt) REVERT: K 998 LYS cc_start: 0.8050 (mttm) cc_final: 0.7547 (mtpt) REVERT: K 1047 CYS cc_start: 0.8355 (m) cc_final: 0.7972 (m) REVERT: K 1182 HIS cc_start: 0.6132 (OUTLIER) cc_final: 0.5859 (t-90) REVERT: K 1212 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7363 (mt-10) REVERT: K 1213 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6910 (mt-10) REVERT: K 1317 PHE cc_start: 0.4176 (m-80) cc_final: 0.3729 (m-80) REVERT: K 1320 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6636 (pmm) REVERT: K 1339 MET cc_start: 0.7129 (mmm) cc_final: 0.6539 (tpt) outliers start: 31 outliers final: 20 residues processed: 216 average time/residue: 0.1527 time to fit residues: 45.8700 Evaluate side-chains 208 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 782 MET Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 823 PHE Chi-restraints excluded: chain K residue 885 HIS Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 991 GLU Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1127 LEU Chi-restraints excluded: chain K residue 1138 MET Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1177 SER Chi-restraints excluded: chain K residue 1182 HIS Chi-restraints excluded: chain K residue 1320 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 101 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1049 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 = 0.4084 r_free = 0.4084 target = 0.153880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128416 restraints weight = 25744.707| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.96 r_work: 0.3589 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15735 Z= 0.152 Angle : 0.576 10.673 22249 Z= 0.312 Chirality : 0.041 0.308 2525 Planarity : 0.004 0.040 1993 Dihedral : 27.290 164.247 3964 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.04 % Favored : 94.64 % Rotamer: Outliers : 3.25 % Allowed : 20.33 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.25), residues: 1231 helix: 1.74 (0.19), residues: 752 sheet: -1.01 (0.72), residues: 60 loop : -1.74 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.009 0.001 TYR H 39 PHE 0.014 0.001 PHE K1317 TRP 0.021 0.002 TRP K 819 HIS 0.007 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (15735) covalent geometry : angle 0.57632 / 0.31 (22249) hydrogen bonds : bond 0.04358 / 2.95 ( 732) hydrogen bonds : angle 3.14457 / 2.24 ( 1934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8262 (mt0) cc_final: 0.8046 (mm-40) REVERT: C 77 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8349 (mtm-85) REVERT: E 59 GLU cc_start: 0.8781 (pm20) cc_final: 0.8413 (pm20) REVERT: F 88 TYR cc_start: 0.8179 (m-10) cc_final: 0.7815 (m-80) REVERT: G 73 ASN cc_start: 0.8665 (t0) cc_final: 0.7810 (t0) REVERT: H 59 MET cc_start: 0.8805 (mmm) cc_final: 0.8499 (mmt) REVERT: H 98 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8391 (mt) REVERT: K 782 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.5859 (mtm) REVERT: K 793 LEU cc_start: 0.7970 (tt) cc_final: 0.7720 (tp) REVERT: K 823 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: K 873 LYS cc_start: 0.8445 (mttm) cc_final: 0.8004 (ttmt) REVERT: K 1047 CYS cc_start: 0.8579 (m) cc_final: 0.8249 (m) REVERT: K 1119 TYR cc_start: 0.7798 (t80) cc_final: 0.7560 (t80) REVERT: K 1182 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6192 (t-90) REVERT: K 1326 ARG cc_start: 0.7029 (tmt170) cc_final: 0.6666 (tmm160) REVERT: K 1339 MET cc_start: 0.7274 (mmm) cc_final: 0.6692 (tpt) outliers start: 35 outliers final: 21 residues processed: 216 average time/residue: 0.1497 time to fit residues: 45.4140 Evaluate side-chains 214 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 782 MET Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 807 PHE Chi-restraints excluded: chain K residue 823 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 885 HIS Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1127 LEU Chi-restraints excluded: chain K residue 1138 MET Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1177 SER Chi-restraints excluded: chain K residue 1182 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 789 GLN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123284 restraints weight = 25444.456| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.94 r_work: 0.3527 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15735 Z= 0.172 Angle : 0.612 10.142 22249 Z= 0.329 Chirality : 0.041 0.252 2525 Planarity : 0.005 0.077 1993 Dihedral : 27.377 164.637 3964 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.44 % Favored : 94.23 % Rotamer: Outliers : 3.53 % Allowed : 21.17 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.25), residues: 1231 helix: 1.80 (0.19), residues: 749 sheet: -1.34 (0.66), residues: 65 loop : -1.74 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K1337 TYR 0.019 0.002 TYR K1150 PHE 0.010 0.001 PHE E 67 TRP 0.024 0.002 TRP K 819 HIS 0.007 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15735) covalent geometry : angle 0.61186 / 0.33 (22249) hydrogen bonds : bond 0.04742 / 3.23 ( 732) hydrogen bonds : angle 3.17523 / 2.27 ( 1934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8725 (m) cc_final: 0.8523 (t) REVERT: C 77 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8392 (mtm-85) REVERT: E 59 GLU cc_start: 0.8778 (pm20) cc_final: 0.8405 (pm20) REVERT: F 88 TYR cc_start: 0.8203 (m-10) cc_final: 0.7782 (m-80) REVERT: H 98 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8439 (mt) REVERT: K 752 ASN cc_start: 0.8306 (t0) cc_final: 0.8034 (t0) REVERT: K 763 LEU cc_start: 0.7973 (tp) cc_final: 0.7754 (tt) REVERT: K 796 TYR cc_start: 0.8074 (t80) cc_final: 0.7817 (t80) REVERT: K 873 LYS cc_start: 0.8494 (mttm) cc_final: 0.8065 (ttmt) REVERT: K 918 LYS cc_start: 0.6571 (tppt) cc_final: 0.6356 (tppt) REVERT: K 998 LYS cc_start: 0.8352 (mttm) cc_final: 0.7934 (mtpt) REVERT: K 1182 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.6101 (t-90) REVERT: K 1213 GLU cc_start: 0.7148 (mp0) cc_final: 0.6787 (mp0) REVERT: K 1320 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6554 (pmm) REVERT: K 1326 ARG cc_start: 0.7046 (tmt170) cc_final: 0.5872 (tmm160) REVERT: K 1339 MET cc_start: 0.7242 (mmm) cc_final: 0.6387 (tpt) outliers start: 38 outliers final: 26 residues processed: 219 average time/residue: 0.1491 time to fit residues: 45.6750 Evaluate side-chains 219 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 807 PHE Chi-restraints excluded: chain K residue 823 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 864 ILE Chi-restraints excluded: chain K residue 885 HIS Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 991 GLU Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1127 LEU Chi-restraints excluded: chain K residue 1138 MET Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1177 SER Chi-restraints excluded: chain K residue 1182 HIS Chi-restraints excluded: chain K residue 1320 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 0.0070 chunk 39 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 chunk 128 optimal weight: 0.0010 chunk 52 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN K 789 GLN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127050 restraints weight = 25525.348| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.90 r_work: 0.3541 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15735 Z= 0.126 Angle : 0.570 11.108 22249 Z= 0.310 Chirality : 0.039 0.250 2525 Planarity : 0.004 0.041 1993 Dihedral : 27.299 165.977 3964 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.87 % Favored : 94.88 % Rotamer: Outliers : 2.51 % Allowed : 22.19 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1231 helix: 1.93 (0.19), residues: 749 sheet: -0.99 (0.71), residues: 59 loop : -1.74 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.018 0.001 TYR K1119 PHE 0.009 0.001 PHE K 823 TRP 0.025 0.002 TRP K 819 HIS 0.007 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (15735) covalent geometry : angle 0.57008 / 0.31 (22249) hydrogen bonds : bond 0.04046 / 2.71 ( 732) hydrogen bonds : angle 3.08764 / 2.20 ( 1934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8366 (mtm-85) REVERT: C 95 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8468 (ttmm) REVERT: E 59 GLU cc_start: 0.8789 (pm20) cc_final: 0.8411 (pm20) REVERT: F 88 TYR cc_start: 0.8127 (m-10) cc_final: 0.7764 (m-80) REVERT: K 752 ASN cc_start: 0.8334 (t0) cc_final: 0.8019 (t0) REVERT: K 763 LEU cc_start: 0.7958 (tp) cc_final: 0.7752 (tt) REVERT: K 873 LYS cc_start: 0.8474 (mttm) cc_final: 0.8058 (ttmt) REVERT: K 918 LYS cc_start: 0.6604 (tppt) cc_final: 0.6390 (tppt) REVERT: K 998 LYS cc_start: 0.8266 (mttm) cc_final: 0.7908 (mtpt) REVERT: K 1135 ASP cc_start: 0.7813 (m-30) cc_final: 0.7500 (m-30) REVERT: K 1182 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.6036 (t-90) REVERT: K 1189 ASP cc_start: 0.6800 (OUTLIER) cc_final: 0.6513 (t0) REVERT: K 1213 GLU cc_start: 0.6929 (mp0) cc_final: 0.6687 (mp0) REVERT: K 1234 MET cc_start: 0.3286 (tpt) cc_final: 0.1423 (tpt) REVERT: K 1326 ARG cc_start: 0.6977 (tmt170) cc_final: 0.6623 (tmm160) REVERT: K 1339 MET cc_start: 0.7273 (mmm) cc_final: 0.6380 (tpt) outliers start: 27 outliers final: 15 residues processed: 206 average time/residue: 0.1555 time to fit residues: 44.7962 Evaluate side-chains 199 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 807 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 1138 MET Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1182 HIS Chi-restraints excluded: chain K residue 1189 ASP Chi-restraints excluded: chain K residue 1215 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 52 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN K 757 GLN K 789 GLN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122407 restraints weight = 25583.110| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.95 r_work: 0.3515 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15735 Z= 0.141 Angle : 0.594 11.800 22249 Z= 0.319 Chirality : 0.040 0.291 2525 Planarity : 0.004 0.041 1993 Dihedral : 27.325 167.335 3964 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.36 % Favored : 94.31 % Rotamer: Outliers : 2.14 % Allowed : 23.49 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.25), residues: 1231 helix: 1.91 (0.19), residues: 747 sheet: -1.00 (0.71), residues: 59 loop : -1.74 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 129 TYR 0.033 0.002 TYR K 796 PHE 0.008 0.001 PHE A 67 TRP 0.031 0.002 TRP K 819 HIS 0.005 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (15735) covalent geometry : angle 0.59351 / 0.32 (22249) hydrogen bonds : bond 0.04222 / 2.84 ( 732) hydrogen bonds : angle 3.10021 / 2.22 ( 1934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.8422 (pm20) REVERT: E 72 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8276 (mtt-85) REVERT: F 88 TYR cc_start: 0.8196 (m-10) cc_final: 0.7773 (m-80) REVERT: K 752 ASN cc_start: 0.8381 (t0) cc_final: 0.8098 (t0) REVERT: K 763 LEU cc_start: 0.8057 (tp) cc_final: 0.7836 (tt) REVERT: K 873 LYS cc_start: 0.8512 (mttm) cc_final: 0.8102 (ttmt) REVERT: K 918 LYS cc_start: 0.6772 (tppt) cc_final: 0.6521 (tppt) REVERT: K 998 LYS cc_start: 0.8352 (mttm) cc_final: 0.7989 (mtpt) REVERT: K 1110 MET cc_start: 0.7802 (mmt) cc_final: 0.6123 (mmt) REVERT: K 1135 ASP cc_start: 0.7764 (m-30) cc_final: 0.7477 (m-30) REVERT: K 1182 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.6017 (t-90) REVERT: K 1189 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6612 (t0) REVERT: K 1234 MET cc_start: 0.3156 (tpt) cc_final: 0.1363 (tpt) REVERT: K 1320 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6387 (pmm) REVERT: K 1326 ARG cc_start: 0.6973 (tmt170) cc_final: 0.5779 (tmm160) REVERT: K 1339 MET cc_start: 0.7249 (mmm) cc_final: 0.6446 (tpt) outliers start: 23 outliers final: 18 residues processed: 206 average time/residue: 0.1628 time to fit residues: 46.2181 Evaluate side-chains 208 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 807 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 856 VAL Chi-restraints excluded: chain K residue 864 ILE Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 991 GLU Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1177 SER Chi-restraints excluded: chain K residue 1182 HIS Chi-restraints excluded: chain K residue 1189 ASP Chi-restraints excluded: chain K residue 1320 MET Chi-restraints excluded: chain K residue 1322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 37 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS K 789 GLN K 818 ASN ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.139729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114478 restraints weight = 25328.996| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.92 r_work: 0.3389 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15735 Z= 0.216 Angle : 0.678 12.732 22249 Z= 0.360 Chirality : 0.046 0.315 2525 Planarity : 0.005 0.063 1993 Dihedral : 27.615 162.933 3964 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 2.79 % Allowed : 22.93 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1231 helix: 1.48 (0.19), residues: 758 sheet: -1.02 (0.75), residues: 54 loop : -1.97 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 52 TYR 0.024 0.002 TYR K1119 PHE 0.026 0.002 PHE K1122 TRP 0.033 0.002 TRP K 819 HIS 0.012 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (15735) covalent geometry : angle 0.67755 / 0.36 (22249) hydrogen bonds : bond 0.05592 / 3.86 ( 732) hydrogen bonds : angle 3.34197 / 2.41 ( 1934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 SER cc_start: 0.8874 (t) cc_final: 0.8305 (m) REVERT: F 88 TYR cc_start: 0.8332 (m-10) cc_final: 0.7906 (m-80) REVERT: K 752 ASN cc_start: 0.8504 (t0) cc_final: 0.8289 (t0) REVERT: K 873 LYS cc_start: 0.8566 (mttm) cc_final: 0.8179 (ttmt) REVERT: K 918 LYS cc_start: 0.7285 (tppt) cc_final: 0.6964 (tppt) REVERT: K 993 VAL cc_start: 0.5792 (OUTLIER) cc_final: 0.5508 (t) REVERT: K 998 LYS cc_start: 0.8683 (mttm) cc_final: 0.8326 (mtpt) REVERT: K 1051 TYR cc_start: 0.7540 (m-80) cc_final: 0.7300 (m-80) REVERT: K 1092 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6498 (ttmm) REVERT: K 1135 ASP cc_start: 0.7618 (m-30) cc_final: 0.7302 (m-30) REVERT: K 1182 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5976 (t-170) REVERT: K 1189 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6907 (t0) REVERT: K 1234 MET cc_start: 0.3546 (tpt) cc_final: 0.1492 (tpt) REVERT: K 1320 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6653 (pmm) REVERT: K 1326 ARG cc_start: 0.7056 (tmt170) cc_final: 0.6673 (tmm160) REVERT: K 1339 MET cc_start: 0.7413 (mmm) cc_final: 0.6632 (tpt) outliers start: 30 outliers final: 18 residues processed: 218 average time/residue: 0.1627 time to fit residues: 48.9283 Evaluate side-chains 215 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 807 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 856 VAL Chi-restraints excluded: chain K residue 864 ILE Chi-restraints excluded: chain K residue 885 HIS Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 993 VAL Chi-restraints excluded: chain K residue 1092 LYS Chi-restraints excluded: chain K residue 1138 MET Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1182 HIS Chi-restraints excluded: chain K residue 1189 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 789 GLN ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114358 restraints weight = 25404.096| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.95 r_work: 0.3409 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15735 Z= 0.150 Angle : 0.634 13.291 22249 Z= 0.338 Chirality : 0.043 0.413 2525 Planarity : 0.004 0.050 1993 Dihedral : 27.539 164.975 3964 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.31 % Rotamer: Outliers : 2.04 % Allowed : 23.77 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.24), residues: 1231 helix: 1.62 (0.19), residues: 758 sheet: -0.73 (0.77), residues: 54 loop : -1.89 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K1120 TYR 0.019 0.002 TYR K 796 PHE 0.009 0.001 PHE K1103 TRP 0.034 0.003 TRP K 819 HIS 0.010 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (15735) covalent geometry : angle 0.63395 / 0.34 (22249) hydrogen bonds : bond 0.04487 / 3.02 ( 732) hydrogen bonds : angle 3.21253 / 2.31 ( 1934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 SER cc_start: 0.8867 (t) cc_final: 0.8299 (m) REVERT: F 88 TYR cc_start: 0.8330 (m-10) cc_final: 0.7886 (m-80) REVERT: K 752 ASN cc_start: 0.8500 (t0) cc_final: 0.8079 (t0) REVERT: K 819 TRP cc_start: 0.8718 (m100) cc_final: 0.8460 (m100) REVERT: K 825 LYS cc_start: 0.7926 (tppt) cc_final: 0.7630 (tptm) REVERT: K 873 LYS cc_start: 0.8571 (mttm) cc_final: 0.8202 (tttt) REVERT: K 918 LYS cc_start: 0.7244 (tppt) cc_final: 0.6937 (tppt) REVERT: K 998 LYS cc_start: 0.8626 (mttm) cc_final: 0.8279 (mtpt) REVERT: K 1135 ASP cc_start: 0.7732 (m-30) cc_final: 0.7434 (m-30) REVERT: K 1189 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6821 (t0) REVERT: K 1234 MET cc_start: 0.3379 (tpt) cc_final: 0.1302 (tpt) REVERT: K 1320 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6171 (pmm) REVERT: K 1326 ARG cc_start: 0.7027 (tmt170) cc_final: 0.6651 (tmm160) REVERT: K 1339 MET cc_start: 0.7393 (mmm) cc_final: 0.6604 (tpt) outliers start: 22 outliers final: 15 residues processed: 205 average time/residue: 0.1615 time to fit residues: 45.5924 Evaluate side-chains 201 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain K residue 551 LEU Chi-restraints excluded: chain K residue 797 LEU Chi-restraints excluded: chain K residue 807 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 856 VAL Chi-restraints excluded: chain K residue 864 ILE Chi-restraints excluded: chain K residue 909 LEU Chi-restraints excluded: chain K residue 911 THR Chi-restraints excluded: chain K residue 922 LEU Chi-restraints excluded: chain K residue 964 LEU Chi-restraints excluded: chain K residue 968 ARG Chi-restraints excluded: chain K residue 970 HIS Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1189 ASP Chi-restraints excluded: chain K residue 1320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 789 GLN ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.139736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114838 restraints weight = 25386.172| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.94 r_work: 0.3427 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15735 Z= 0.136 Angle : 0.627 23.155 22249 Z= 0.331 Chirality : 0.042 0.290 2525 Planarity : 0.004 0.052 1993 Dihedral : 27.500 168.568 3964 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 1.95 % Allowed : 23.58 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1231 helix: 1.70 (0.19), residues: 757 sheet: -0.22 (0.83), residues: 48 loop : -1.85 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 843 TYR 0.017 0.001 TYR K 796 PHE 0.008 0.001 PHE A 67 TRP 0.029 0.002 TRP K 819 HIS 0.010 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (15735) covalent geometry : angle 0.62665 / 0.33 (22249) hydrogen bonds : bond 0.04163 / 2.78 ( 732) hydrogen bonds : angle 3.17318 / 2.28 ( 1934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4097.23 seconds wall clock time: 70 minutes 58.28 seconds (4258.28 seconds total)