Starting phenix.real_space_refine on Fri Jul 3 17:17:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux9_64577/07_2026/9ux9_64577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux9_64577/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ux9_64577/07_2026/9ux9_64577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux9_64577/07_2026/9ux9_64577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ux9_64577/07_2026/9ux9_64577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux9_64577/07_2026/9ux9_64577.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.82, per 1000 atoms: 0.19 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: 1.08 Conformation dependent library (CDL) restraints added in 581.5 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: 2.16 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: 3.02 Time building geometry restraints manager: 1.45 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.120 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- 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 : 0.619 11.736 22249 Z= 0.510 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 0.61897 / 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 : 0.468 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: 0.6823 (tttt) REVERT: K 1047 CYS cc_start: 0.7927 (m) cc_final: 0.7648 (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: 0.6513 (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: 0.6807 (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: 0.1406 time to fit residues: 45.8450 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 : 0.412 ------------------------------------------------------------------------------- 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: 4.9990 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 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 = 0.4225 r_free = 0.4225 target = 0.166208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140725 restraints weight = 26109.819| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.03 r_work: 0.3733 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 15735 Z= 0.300 Angle : 0.839 11.261 22249 Z= 0.444 Chirality : 0.053 0.237 2525 Planarity : 0.007 0.082 1993 Dihedral : 27.575 165.971 3967 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.77 % Favored : 93.91 % Rotamer: Outliers : 4.64 % Allowed : 19.13 % Favored : 76.23 % 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: -0.26 (0.23), residues: 1231 helix: 0.77 (0.18), residues: 749 sheet: -1.24 (0.63), residues: 63 loop : -1.68 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K1120 TYR 0.031 0.003 TYR K1116 PHE 0.028 0.003 PHE C 25 TRP 0.029 0.003 TRP K 765 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.30 (15735) covalent geometry : angle 0.83872 / 0.44 (22249) hydrogen bonds : bond 0.06693 / 4.54 ( 732) hydrogen bonds : angle 3.84666 / 2.75 ( 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: 50 poor density : 209 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: E 109 LEU cc_start: 0.8432 (mt) cc_final: 0.8168 (mt) REVERT: E 120 MET cc_start: 0.7801 (mmm) cc_final: 0.7357 (mtt) REVERT: F 85 ASP cc_start: 0.7713 (m-30) cc_final: 0.7430 (m-30) REVERT: F 88 TYR cc_start: 0.8111 (m-10) cc_final: 0.7786 (m-80) REVERT: G 73 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8369 (t0) REVERT: H 56 MET cc_start: 0.8691 (mmm) cc_final: 0.8394 (tpp) REVERT: H 98 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8304 (mt) REVERT: K 822 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7292 (mm-30) REVERT: K 823 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: K 873 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8069 (mttm) REVERT: K 981 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6163 (tt) REVERT: K 1038 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7291 (t0) REVERT: K 1047 CYS cc_start: 0.8217 (m) cc_final: 0.7789 (m) REVERT: K 1182 HIS cc_start: 0.6274 (t-90) cc_final: 0.6029 (t-90) REVERT: K 1189 ASP cc_start: 0.5987 (m-30) cc_final: 0.5698 (m-30) REVERT: K 1212 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7180 (mt-10) REVERT: K 1339 MET cc_start: 0.6991 (mmm) cc_final: 0.6403 (tpt) outliers start: 50 outliers final: 17 residues processed: 234 average time/residue: 0.1650 time to fit residues: 53.0137 Evaluate side-chains 219 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 84 SER 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 823 PHE Chi-restraints excluded: chain K residue 885 HIS 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 1127 LEU Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1177 SER Chi-restraints excluded: chain K residue 1309 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 32 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN K 855 ASN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.166020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140732 restraints weight = 26625.353| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.02 r_work: 0.3733 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4026 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= 0.138 Angle : 0.567 8.550 22249 Z= 0.312 Chirality : 0.040 0.235 2525 Planarity : 0.004 0.055 1993 Dihedral : 27.321 160.915 3964 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.04 % Favored : 94.72 % Rotamer: Outliers : 3.34 % Allowed : 20.71 % Favored : 75.95 % 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: 0.42 (0.24), residues: 1231 helix: 1.49 (0.19), residues: 747 sheet: -1.45 (0.66), residues: 60 loop : -1.70 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K1324 TYR 0.021 0.002 TYR D 118 PHE 0.033 0.002 PHE K1122 TRP 0.015 0.002 TRP K 765 HIS 0.006 0.001 HIS K1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (15735) covalent geometry : angle 0.56729 / 0.31 (22249) hydrogen bonds : bond 0.04603 / 3.10 ( 732) hydrogen bonds : angle 3.29414 / 2.33 ( 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 226 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (mttt) REVERT: C 77 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8271 (mtm-85) REVERT: E 59 GLU cc_start: 0.8349 (pm20) cc_final: 0.8057 (pm20) REVERT: F 79 LYS cc_start: 0.8236 (mptt) cc_final: 0.8004 (mtmm) REVERT: F 88 TYR cc_start: 0.8064 (m-10) cc_final: 0.7765 (m-80) REVERT: H 98 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8240 (mt) REVERT: K 822 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7296 (mm-30) REVERT: K 873 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8080 (mttm) REVERT: K 1047 CYS cc_start: 0.8302 (m) cc_final: 0.7899 (m) REVERT: K 1182 HIS cc_start: 0.6124 (t-90) cc_final: 0.5891 (t-90) REVERT: K 1192 HIS cc_start: 0.8472 (t-170) cc_final: 0.8202 (t-170) REVERT: K 1212 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7281 (mt-10) REVERT: K 1339 MET cc_start: 0.7024 (mmm) cc_final: 0.6379 (tpt) outliers start: 36 outliers final: 18 residues processed: 213 average time/residue: 0.1553 time to fit residues: 45.8641 Evaluate side-chains 202 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 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 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 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 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: 9.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 38 ASN D 79 HIS E 55 GLN G 73 ASN H 81 ASN K 789 GLN K 869 HIS ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 HIS ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.157917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132699 restraints weight = 25787.983| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.94 r_work: 0.3659 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4678 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= 0.160 Angle : 0.569 10.030 22249 Z= 0.313 Chirality : 0.040 0.221 2525 Planarity : 0.004 0.049 1993 Dihedral : 27.325 163.772 3964 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 3.06 % Allowed : 20.24 % Favored : 76.69 % 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: 0.63 (0.24), residues: 1231 helix: 1.69 (0.19), residues: 753 sheet: -1.41 (0.68), residues: 58 loop : -1.74 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K1324 TYR 0.015 0.002 TYR K1150 PHE 0.011 0.002 PHE K1317 TRP 0.010 0.001 TRP K 765 HIS 0.012 0.001 HIS K 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (15735) covalent geometry : angle 0.56949 / 0.31 (22249) hydrogen bonds : bond 0.04512 / 3.03 ( 732) hydrogen bonds : angle 3.14549 / 2.24 ( 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 234 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8642 (mttt) REVERT: C 77 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8237 (mtm-85) REVERT: E 59 GLU cc_start: 0.8491 (pm20) cc_final: 0.8144 (pm20) REVERT: F 79 LYS cc_start: 0.8229 (mptt) cc_final: 0.7978 (mtmm) REVERT: F 88 TYR cc_start: 0.8041 (m-10) cc_final: 0.7698 (m-80) REVERT: H 98 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8241 (mt) REVERT: K 782 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5946 (mtm) REVERT: K 873 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8191 (mttm) REVERT: K 1047 CYS cc_start: 0.8325 (m) cc_final: 0.7876 (m) REVERT: K 1182 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5899 (t-90) REVERT: K 1212 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7341 (mt-10) REVERT: K 1326 ARG cc_start: 0.6959 (tmt170) cc_final: 0.5840 (tmm160) REVERT: K 1339 MET cc_start: 0.7056 (mmm) cc_final: 0.6455 (tpt) outliers start: 33 outliers final: 21 residues processed: 220 average time/residue: 0.1552 time to fit residues: 47.5523 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 : 0.451 ------------------------------------------------------------------------------- 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 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 557 GLN Chi-restraints excluded: chain K residue 782 MET Chi-restraints excluded: chain K residue 789 GLN 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 1182 HIS Chi-restraints excluded: chain K residue 1205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS E 55 GLN ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 HIS ** 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 = 0.4045 r_free = 0.4045 target = 0.150835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125445 restraints weight = 25677.963| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.94 r_work: 0.3555 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 15735 Z= 0.211 Angle : 0.628 8.871 22249 Z= 0.340 Chirality : 0.042 0.268 2525 Planarity : 0.005 0.045 1993 Dihedral : 27.415 160.502 3964 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.77 % Favored : 94.07 % Rotamer: Outliers : 3.90 % Allowed : 20.15 % Favored : 75.95 % 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: 0.53 (0.24), residues: 1231 helix: 1.63 (0.19), residues: 748 sheet: -1.45 (0.70), residues: 58 loop : -1.77 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K1324 TYR 0.061 0.002 TYR K 796 PHE 0.013 0.002 PHE E 67 TRP 0.021 0.002 TRP K 765 HIS 0.015 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (15735) covalent geometry : angle 0.62792 / 0.34 (22249) hydrogen bonds : bond 0.05101 / 3.50 ( 732) hydrogen bonds : angle 3.24818 / 2.33 ( 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 238 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.9019 (mttt) cc_final: 0.8806 (mttt) REVERT: C 75 LYS cc_start: 0.8396 (mttt) cc_final: 0.7890 (tptt) REVERT: C 77 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8364 (mtm-85) REVERT: C 95 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8486 (ttmm) REVERT: E 59 GLU cc_start: 0.8766 (pm20) cc_final: 0.8375 (pm20) REVERT: F 25 ASN cc_start: 0.8367 (m-40) cc_final: 0.8103 (m110) REVERT: F 88 TYR cc_start: 0.8228 (m-10) cc_final: 0.7845 (m-80) REVERT: G 73 ASN cc_start: 0.8736 (t0) cc_final: 0.7818 (t0) REVERT: H 98 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8419 (mt) REVERT: K 763 LEU cc_start: 0.8057 (tp) cc_final: 0.7816 (tt) REVERT: K 865 ILE cc_start: 0.8865 (tt) cc_final: 0.8652 (mt) REVERT: K 873 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8282 (mttm) REVERT: K 1047 CYS cc_start: 0.8628 (m) cc_final: 0.8246 (m) REVERT: K 1119 TYR cc_start: 0.7804 (t80) cc_final: 0.7529 (t80) REVERT: K 1182 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.6129 (t-90) REVERT: K 1212 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7628 (mt-10) REVERT: K 1326 ARG cc_start: 0.7017 (tmt170) cc_final: 0.6579 (tmm160) REVERT: K 1339 MET cc_start: 0.7361 (mmm) cc_final: 0.6794 (tpt) outliers start: 42 outliers final: 27 residues processed: 224 average time/residue: 0.1519 time to fit residues: 47.5381 Evaluate side-chains 218 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain K residue 735 VAL Chi-restraints excluded: chain K residue 789 GLN 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 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 1138 MET Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1143 PHE 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 1215 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 HIS ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.127926 restraints weight = 25647.478| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.95 r_work: 0.3550 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15735 Z= 0.144 Angle : 0.580 9.744 22249 Z= 0.315 Chirality : 0.040 0.231 2525 Planarity : 0.004 0.059 1993 Dihedral : 27.373 161.731 3964 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 2.69 % Allowed : 20.89 % 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: 0.64 (0.25), residues: 1231 helix: 1.73 (0.19), residues: 748 sheet: -1.30 (0.72), residues: 58 loop : -1.78 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 129 TYR 0.044 0.002 TYR K 796 PHE 0.011 0.001 PHE K 976 TRP 0.023 0.002 TRP K 765 HIS 0.007 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15735) covalent geometry : angle 0.57984 / 0.32 (22249) hydrogen bonds : bond 0.04327 / 2.92 ( 732) hydrogen bonds : angle 3.16718 / 2.25 ( 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 223 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8695 (mtpp) REVERT: C 74 LYS cc_start: 0.8981 (mttt) cc_final: 0.8774 (mttt) REVERT: C 75 LYS cc_start: 0.8371 (mttt) cc_final: 0.7875 (tptt) REVERT: C 77 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8358 (mtm-85) REVERT: C 95 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8474 (ttmm) REVERT: E 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8383 (pm20) REVERT: F 25 ASN cc_start: 0.8380 (m-40) cc_final: 0.8055 (m110) REVERT: F 88 TYR cc_start: 0.8201 (m-10) cc_final: 0.7816 (m-80) REVERT: H 98 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8454 (mt) REVERT: K 763 LEU cc_start: 0.8185 (tp) cc_final: 0.7935 (tt) REVERT: K 873 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8294 (mttm) REVERT: K 1047 CYS cc_start: 0.8683 (m) cc_final: 0.8307 (m) REVERT: K 1168 SER cc_start: 0.8421 (p) cc_final: 0.8213 (t) REVERT: K 1182 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.6048 (t-90) REVERT: K 1326 ARG cc_start: 0.6957 (tmt170) cc_final: 0.6558 (tmm160) REVERT: K 1339 MET cc_start: 0.7238 (mmm) cc_final: 0.6469 (tpt) outliers start: 29 outliers final: 18 residues processed: 216 average time/residue: 0.1462 time to fit residues: 44.3481 Evaluate side-chains 213 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 797 LEU Chi-restraints excluded: chain K residue 807 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 981 LEU Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 1138 MET Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1182 HIS 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: 0.3980 chunk 35 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 128 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS G 73 ASN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 HIS ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.153236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128627 restraints weight = 25620.157| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.87 r_work: 0.3570 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5786 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 : 0.574 10.801 22249 Z= 0.311 Chirality : 0.039 0.229 2525 Planarity : 0.004 0.040 1993 Dihedral : 27.315 163.898 3964 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.20 % Favored : 94.56 % Rotamer: Outliers : 2.41 % Allowed : 21.08 % Favored : 76.51 % 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: 0.79 (0.25), residues: 1231 helix: 1.88 (0.19), residues: 748 sheet: -1.26 (0.74), residues: 54 loop : -1.78 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 129 TYR 0.021 0.001 TYR K 995 PHE 0.008 0.001 PHE A 67 TRP 0.025 0.001 TRP K 765 HIS 0.008 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (15735) covalent geometry : angle 0.57437 / 0.31 (22249) hydrogen bonds : bond 0.04027 / 2.69 ( 732) hydrogen bonds : angle 3.08358 / 2.19 ( 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 226 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8678 (mtmm) REVERT: C 74 LYS cc_start: 0.9010 (mttt) cc_final: 0.8803 (mttt) REVERT: C 75 LYS cc_start: 0.8366 (mttt) cc_final: 0.7844 (tptt) REVERT: C 77 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8351 (mtm-85) REVERT: C 95 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8459 (ttmm) REVERT: E 59 GLU cc_start: 0.8784 (pm20) cc_final: 0.8431 (pm20) REVERT: F 25 ASN cc_start: 0.8390 (m-40) cc_final: 0.8055 (m110) REVERT: F 88 TYR cc_start: 0.8144 (m-10) cc_final: 0.7794 (m-80) REVERT: K 873 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8290 (mttm) REVERT: K 1047 CYS cc_start: 0.8572 (m) cc_final: 0.8028 (m) REVERT: K 1135 ASP cc_start: 0.7811 (m-30) cc_final: 0.7545 (m-30) REVERT: K 1168 SER cc_start: 0.8387 (p) cc_final: 0.8171 (t) REVERT: K 1182 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.6096 (t-90) REVERT: K 1234 MET cc_start: 0.2992 (tpt) cc_final: 0.1909 (tpt) REVERT: K 1326 ARG cc_start: 0.6934 (tmt170) cc_final: 0.6445 (tmm160) REVERT: K 1339 MET cc_start: 0.7249 (mmm) cc_final: 0.6386 (tpt) outliers start: 26 outliers final: 14 residues processed: 221 average time/residue: 0.1548 time to fit residues: 47.8165 Evaluate side-chains 203 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 807 PHE Chi-restraints excluded: chain K residue 851 SER Chi-restraints excluded: chain K residue 864 ILE 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 981 LEU Chi-restraints excluded: chain K residue 1171 THR Chi-restraints excluded: chain K residue 1182 HIS Chi-restraints excluded: chain K residue 1205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 104 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 HIS ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122059 restraints weight = 25815.615| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.95 r_work: 0.3526 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15735 Z= 0.147 Angle : 0.597 11.933 22249 Z= 0.321 Chirality : 0.041 0.407 2525 Planarity : 0.004 0.042 1993 Dihedral : 27.358 164.920 3964 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.52 % Favored : 94.23 % Rotamer: Outliers : 2.04 % Allowed : 21.82 % Favored : 76.14 % 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: 0.74 (0.25), residues: 1231 helix: 1.86 (0.19), residues: 746 sheet: -1.72 (0.65), residues: 65 loop : -1.73 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 129 TYR 0.020 0.002 TYR K 995 PHE 0.010 0.001 PHE K 976 TRP 0.021 0.002 TRP K 765 HIS 0.011 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (15735) covalent geometry : angle 0.59670 / 0.32 (22249) hydrogen bonds : bond 0.04291 / 2.87 ( 732) hydrogen bonds : angle 3.11786 / 2.23 ( 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 213 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.9057 (mttt) cc_final: 0.8849 (mttt) REVERT: C 77 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8362 (mtm-85) REVERT: E 59 GLU cc_start: 0.8781 (pm20) cc_final: 0.8442 (pm20) REVERT: F 25 ASN cc_start: 0.8431 (m-40) cc_final: 0.8146 (m110) REVERT: F 88 TYR cc_start: 0.8223 (m-10) cc_final: 0.7834 (m-80) REVERT: K 873 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8311 (mttm) REVERT: K 998 LYS cc_start: 0.8365 (mttm) cc_final: 0.7995 (mtpt) REVERT: K 1047 CYS cc_start: 0.8436 (m) cc_final: 0.8172 (m) REVERT: K 1106 MET cc_start: 0.8470 (mpp) cc_final: 0.8092 (mpp) REVERT: K 1135 ASP cc_start: 0.7814 (m-30) cc_final: 0.7513 (m-30) REVERT: K 1168 SER cc_start: 0.8446 (p) cc_final: 0.8236 (t) REVERT: K 1182 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.5970 (t-90) REVERT: K 1213 GLU cc_start: 0.6845 (mp0) cc_final: 0.6580 (mp0) REVERT: K 1234 MET cc_start: 0.2979 (tpt) cc_final: 0.1708 (tpt) REVERT: K 1245 ARG cc_start: 0.7018 (mmm-85) cc_final: 0.6728 (mmm-85) REVERT: K 1326 ARG cc_start: 0.6951 (tmt170) cc_final: 0.6672 (tmm160) REVERT: K 1339 MET cc_start: 0.7210 (mmm) cc_final: 0.6427 (tpt) outliers start: 22 outliers final: 19 residues processed: 209 average time/residue: 0.1437 time to fit residues: 42.6180 Evaluate side-chains 207 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 981 LEU Chi-restraints excluded: chain K residue 985 VAL Chi-restraints excluded: chain K residue 991 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** K 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 818 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117887 restraints weight = 25689.969| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.94 r_work: 0.3459 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15735 Z= 0.166 Angle : 0.625 12.016 22249 Z= 0.337 Chirality : 0.041 0.241 2525 Planarity : 0.004 0.041 1993 Dihedral : 27.459 164.186 3964 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.36 % Favored : 94.39 % Rotamer: Outliers : 2.14 % Allowed : 22.01 % Favored : 75.86 % 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: 0.66 (0.25), residues: 1231 helix: 1.74 (0.19), residues: 751 sheet: -1.54 (0.69), residues: 59 loop : -1.73 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 129 TYR 0.016 0.002 TYR K 796 PHE 0.010 0.001 PHE E 67 TRP 0.051 0.003 TRP K 819 HIS 0.011 0.001 HIS K1242 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (15735) covalent geometry : angle 0.62508 / 0.34 (22249) hydrogen bonds : bond 0.04594 / 3.13 ( 732) hydrogen bonds : angle 3.15404 / 2.25 ( 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 216 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.9049 (mttt) cc_final: 0.8844 (mttt) REVERT: E 59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8431 (pm20) REVERT: F 88 TYR cc_start: 0.8269 (m-10) cc_final: 0.7833 (m-80) REVERT: K 752 ASN cc_start: 0.8470 (t0) cc_final: 0.8257 (t0) REVERT: K 769 LEU cc_start: 0.7462 (mm) cc_final: 0.6950 (mm) REVERT: K 819 TRP cc_start: 0.8685 (m100) cc_final: 0.8448 (m100) REVERT: K 873 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8381 (mttm) REVERT: K 998 LYS cc_start: 0.8485 (mttm) cc_final: 0.8132 (mtpt) REVERT: K 1047 CYS cc_start: 0.8587 (m) cc_final: 0.8341 (m) REVERT: K 1135 ASP cc_start: 0.7706 (m-30) cc_final: 0.7416 (m-30) REVERT: K 1213 GLU cc_start: 0.7042 (mp0) cc_final: 0.6740 (mp0) REVERT: K 1234 MET cc_start: 0.3147 (tpt) cc_final: 0.1671 (tpt) REVERT: K 1320 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6372 (pmm) REVERT: K 1326 ARG cc_start: 0.7040 (tmt170) cc_final: 0.5807 (tmm160) REVERT: K 1339 MET cc_start: 0.7290 (mmm) cc_final: 0.6473 (tpt) outliers start: 23 outliers final: 20 residues processed: 209 average time/residue: 0.1585 time to fit residues: 45.7919 Evaluate side-chains 206 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 K residue 551 LEU Chi-restraints excluded: chain K residue 787 THR 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 970 HIS Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain K residue 991 GLU 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 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: 5.9990 chunk 121 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 0.0670 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** K 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 927 ASN ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118301 restraints weight = 25655.388| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.94 r_work: 0.3473 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15735 Z= 0.138 Angle : 0.603 11.795 22249 Z= 0.325 Chirality : 0.040 0.240 2525 Planarity : 0.004 0.044 1993 Dihedral : 27.430 165.583 3964 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.04 % Favored : 94.72 % Rotamer: Outliers : 1.76 % Allowed : 22.56 % Favored : 75.67 % 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: 0.74 (0.25), residues: 1231 helix: 1.81 (0.19), residues: 750 sheet: -1.43 (0.70), residues: 59 loop : -1.72 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 129 TYR 0.018 0.001 TYR K1150 PHE 0.008 0.001 PHE K1103 TRP 0.026 0.003 TRP K 765 HIS 0.008 0.001 HIS K 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (15735) covalent geometry : angle 0.60262 / 0.32 (22249) hydrogen bonds : bond 0.04165 / 2.80 ( 732) hydrogen bonds : angle 3.10830 / 2.21 ( 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 201 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.9030 (mttt) cc_final: 0.8821 (mttt) REVERT: E 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8446 (pm20) REVERT: F 88 TYR cc_start: 0.8254 (m-10) cc_final: 0.7835 (m-80) REVERT: H 59 MET cc_start: 0.8630 (mmm) cc_final: 0.8400 (mmm) REVERT: K 752 ASN cc_start: 0.8471 (t0) cc_final: 0.8240 (t0) REVERT: K 769 LEU cc_start: 0.7414 (mm) cc_final: 0.6904 (mm) REVERT: K 819 TRP cc_start: 0.8725 (m100) cc_final: 0.8500 (m100) REVERT: K 864 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8178 (mt) REVERT: K 873 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8377 (mttm) REVERT: K 998 LYS cc_start: 0.8502 (mttm) cc_final: 0.8139 (mtpt) REVERT: K 1047 CYS cc_start: 0.8576 (m) cc_final: 0.8337 (m) REVERT: K 1135 ASP cc_start: 0.7754 (m-30) cc_final: 0.7459 (m-30) REVERT: K 1213 GLU cc_start: 0.6980 (mp0) cc_final: 0.6637 (mp0) REVERT: K 1234 MET cc_start: 0.3332 (tpt) cc_final: 0.1801 (tpt) REVERT: K 1326 ARG cc_start: 0.7101 (tmt170) cc_final: 0.6760 (tmm160) REVERT: K 1339 MET cc_start: 0.7278 (mmm) cc_final: 0.6480 (tpt) outliers start: 19 outliers final: 15 residues processed: 200 average time/residue: 0.1561 time to fit residues: 43.2581 Evaluate side-chains 195 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 927 ASN Chi-restraints excluded: chain K residue 964 LEU 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 1171 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 0.0980 chunk 93 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** K 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 927 ASN ** K1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117908 restraints weight = 25519.782| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.94 r_work: 0.3466 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15735 Z= 0.139 Angle : 0.611 17.410 22249 Z= 0.325 Chirality : 0.040 0.245 2525 Planarity : 0.004 0.048 1993 Dihedral : 27.430 166.664 3964 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 1.76 % Allowed : 22.66 % Favored : 75.58 % 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: 0.76 (0.25), residues: 1231 helix: 1.83 (0.19), residues: 752 sheet: -1.46 (0.70), residues: 59 loop : -1.72 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 843 TYR 0.018 0.001 TYR K1119 PHE 0.014 0.001 PHE K 928 TRP 0.025 0.002 TRP K 765 HIS 0.009 0.001 HIS K1182 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (15735) covalent geometry : angle 0.61097 / 0.33 (22249) hydrogen bonds : bond 0.04136 / 2.78 ( 732) hydrogen bonds : angle 3.09314 / 2.20 ( 1934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.18 seconds wall clock time: 71 minutes 52.93 seconds (4312.93 seconds total)