Starting phenix.real_space_refine on Sat Sep 12 14:49:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x0y_6700/09_2026/5x0y_6700.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0y_6700/09_2026/5x0y_6700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5x0y_6700/09_2026/5x0y_6700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0y_6700/09_2026/5x0y_6700.map" model { file = "/net/cci-nas-00/data/ceres_data/5x0y_6700/09_2026/5x0y_6700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0y_6700/09_2026/5x0y_6700.cif" } resolution = 4.69 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 29 5.16 5 C 9677 2.51 5 N 3098 2.21 5 O 3702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16798 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4789 Classifications: {'peptide': 583} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 566} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.02, per 1000 atoms: 0.18 Number of scatterers: 16798 At special positions: 0 Unit cell: (143.88, 126.72, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 292 15.00 O 3702 8.00 N 3098 7.00 C 9677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 610.7 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 67.5% alpha, 3.3% beta 145 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.563A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.923A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.999A 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 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.255A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.563A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (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 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.668A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.602A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.254A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'O' and resid 671 through 689 Processing helix chain 'O' and resid 744 through 749 Processing helix chain 'O' and resid 769 through 784 Processing helix chain 'O' and resid 797 through 812 Processing helix chain 'O' and resid 824 through 838 removed outlier: 4.593A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 863 removed outlier: 4.108A pdb=" N GLU O 853 " --> pdb=" O GLY O 849 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 854 " --> pdb=" O SER O 850 " (cutoff:3.500A) Processing helix chain 'O' and resid 872 through 886 removed outlier: 5.199A pdb=" N ALA O 881 " --> pdb=" O ILE O 877 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU O 882 " --> pdb=" O LYS O 878 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL O 886 " --> pdb=" O LEU O 882 " (cutoff:3.500A) Processing helix chain 'O' and resid 895 through 901 removed outlier: 3.971A pdb=" N ASN O 901 " --> pdb=" O ARG O 898 " (cutoff:3.500A) Processing helix chain 'O' and resid 905 through 914 Processing helix chain 'O' and resid 932 through 942 removed outlier: 3.969A pdb=" N LEU O 937 " --> pdb=" O GLU O 933 " (cutoff:3.500A) Processing helix chain 'O' and resid 942 through 958 Processing helix chain 'O' and resid 973 through 979 removed outlier: 4.293A pdb=" N LEU O 978 " --> pdb=" O GLU O 974 " (cutoff:3.500A) Processing helix chain 'O' and resid 980 through 988 Processing helix chain 'O' and resid 995 through 1000 Processing helix chain 'O' and resid 1020 through 1032 Processing helix chain 'O' and resid 1049 through 1061 removed outlier: 3.963A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) Processing helix chain 'O' and resid 1066 through 1073 Processing helix chain 'O' and resid 1081 through 1086 removed outlier: 4.465A pdb=" N ALA O1086 " --> pdb=" O ILE O1082 " (cutoff:3.500A) Processing helix chain 'O' and resid 1086 through 1103 removed outlier: 3.774A pdb=" N GLU O1090 " --> pdb=" O ALA O1086 " (cutoff:3.500A) Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1113 through 1127 removed outlier: 3.864A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP O1121 " --> pdb=" O ASP O1117 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE O1126 " --> pdb=" O PHE O1122 " (cutoff:3.500A) Processing helix chain 'O' and resid 1138 through 1150 Processing helix chain 'O' and resid 1163 through 1168 Processing helix chain 'O' and resid 1187 through 1196 Processing helix chain 'O' and resid 1216 through 1243 removed outlier: 3.671A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY O1233 " --> pdb=" O LEU O1229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS O1234 " --> pdb=" O ASP O1230 " (cutoff:3.500A) Processing helix chain 'O' and resid 1246 through 1267 removed outlier: 4.110A pdb=" N GLN O1250 " --> pdb=" O THR O1246 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG O1255 " --> pdb=" O GLU O1251 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1287 removed outlier: 4.138A pdb=" N ILE O1283 " --> pdb=" O LYS O1279 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1307 removed outlier: 3.706A pdb=" N MET O1294 " --> pdb=" O ASN O1290 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1348 removed outlier: 3.986A pdb=" N GLU O1341 " --> pdb=" O ARG O1337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.876A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.133A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.156A 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 removed outlier: 3.766A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.200A 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 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'O' and resid 868 through 871 removed outlier: 6.195A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL O 889 " --> pdb=" O TYR O 918 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LEU O 920 " --> pdb=" O VAL O 889 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET O 891 " --> pdb=" O LEU O 920 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N LEU O 922 " --> pdb=" O MET O 891 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE O 893 " --> pdb=" O LEU O 922 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY O 788 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE O 789 " --> pdb=" O LEU O 992 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 1007 through 1008 removed outlier: 7.087A pdb=" N VAL O1007 " --> pdb=" O ILE O1208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 1130 through 1132 removed outlier: 6.196A pdb=" N VAL O1106 " --> pdb=" O PHE O1159 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2846 1.32 - 1.44: 5676 1.44 - 1.56: 8524 1.56 - 1.68: 582 1.68 - 1.80: 53 Bond restraints: 17681 Sorted by residual: bond pdb=" C3' DG J 68 " pdb=" O3' DG J 68 " ideal model delta sigma weight residual 1.435 1.359 0.076 1.30e-02 5.92e+03 3.45e+01 bond pdb=" N9 DA I 52 " pdb=" C4 DA I 52 " ideal model delta sigma weight residual 1.374 1.345 0.029 6.00e-03 2.78e+04 2.41e+01 bond pdb=" N9 DA I 41 " pdb=" C4 DA I 41 " ideal model delta sigma weight residual 1.374 1.345 0.029 6.00e-03 2.78e+04 2.36e+01 bond pdb=" N9 DG I 14 " pdb=" C4 DG I 14 " ideal model delta sigma weight residual 1.375 1.336 0.039 8.00e-03 1.56e+04 2.32e+01 bond pdb=" C3' DA J 60 " pdb=" O3' DA J 60 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.22e+01 ... (remaining 17676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 24363 2.85 - 5.70: 645 5.70 - 8.55: 68 8.55 - 11.40: 31 11.40 - 14.25: 5 Bond angle restraints: 25112 Sorted by residual: angle pdb=" O4' DG J 120 " pdb=" C4' DG J 120 " pdb=" C3' DG J 120 " ideal model delta sigma weight residual 106.00 101.29 4.71 6.00e-01 2.78e+00 6.17e+01 angle pdb=" O4' DT I 15 " pdb=" C4' DT I 15 " pdb=" C3' DT I 15 " ideal model delta sigma weight residual 106.00 101.55 4.45 6.00e-01 2.78e+00 5.49e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 101.61 4.39 6.00e-01 2.78e+00 5.34e+01 angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.25 110.38 -7.13 1.05e+00 9.07e-01 4.61e+01 angle pdb=" O4' DG I 44 " pdb=" C4' DG I 44 " pdb=" C3' DG I 44 " ideal model delta sigma weight residual 106.00 102.06 3.94 6.00e-01 2.78e+00 4.31e+01 ... (remaining 25107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 8380 35.11 - 70.23: 1512 70.23 - 105.34: 48 105.34 - 140.45: 5 140.45 - 175.56: 3 Dihedral angle restraints: 9948 sinusoidal: 6014 harmonic: 3934 Sorted by residual: dihedral pdb=" CA LEU O 931 " pdb=" C LEU O 931 " pdb=" N PRO O 932 " pdb=" CA PRO O 932 " ideal model delta harmonic sigma weight residual 180.00 133.10 46.90 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA LYS O 768 " pdb=" C LYS O 768 " pdb=" N ASP O 769 " pdb=" CA ASP O 769 " ideal model delta harmonic sigma weight residual -180.00 -142.86 -37.14 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA THR E 58 " pdb=" C THR E 58 " pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta harmonic sigma weight residual -180.00 -146.24 -33.76 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1789 0.050 - 0.099: 787 0.099 - 0.148: 236 0.148 - 0.198: 44 0.198 - 0.247: 3 Chirality restraints: 2859 Sorted by residual: chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C3' DC J 114 " pdb=" C4' DC J 114 " pdb=" O3' DC J 114 " pdb=" C2' DC J 114 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DG J 124 " pdb=" C4' DG J 124 " pdb=" O3' DG J 124 " pdb=" C2' DG J 124 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2856 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 16 " 0.005 2.00e-02 2.50e+03 2.79e-02 1.75e+01 pdb=" N1 DC J 16 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 16 " 0.067 2.00e-02 2.50e+03 pdb=" O2 DC J 16 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DC J 16 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC J 16 " 0.018 2.00e-02 2.50e+03 pdb=" N4 DC J 16 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC J 16 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC J 16 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 24 " 0.002 2.00e-02 2.50e+03 2.48e-02 1.38e+01 pdb=" N1 DC I 24 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 24 " 0.062 2.00e-02 2.50e+03 pdb=" O2 DC I 24 " -0.039 2.00e-02 2.50e+03 pdb=" N3 DC I 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 24 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 24 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 24 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC I 24 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 131 " -0.049 2.00e-02 2.50e+03 2.12e-02 1.23e+01 pdb=" N9 DA I 131 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DA I 131 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA I 131 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 131 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA I 131 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 131 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 131 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 131 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 131 " 0.004 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 260 2.53 - 3.12: 16288 3.12 - 3.71: 33264 3.71 - 4.31: 43391 4.31 - 4.90: 60499 Nonbonded interactions: 153702 Sorted by model distance: nonbonded pdb=" O2 DC I 111 " pdb=" N2 DG J 37 " model vdw 1.932 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 1.964 3.040 nonbonded pdb=" N6 DA I 60 " pdb=" O4 DT J 87 " model vdw 1.987 3.120 nonbonded pdb=" NE2 GLN O1173 " pdb=" O ARG O1199 " model vdw 2.063 3.120 nonbonded pdb=" NH2 ARG O1105 " pdb=" O PHE O1149 " model vdw 2.090 3.120 ... (remaining 153697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.012 0.076 17681 Z= 0.954 Angle : 1.198 14.254 25112 Z= 0.858 Chirality : 0.059 0.247 2859 Planarity : 0.006 0.048 2171 Dihedral : 26.087 175.563 7394 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 49.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.84 % Favored : 88.70 % Rotamer: Outliers : 0.26 % Allowed : 0.70 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.46 % 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: -5.59 (0.16), residues: 1319 helix: -4.42 (0.09), residues: 799 sheet: -2.49 (0.70), residues: 38 loop : -2.04 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG O1264 TYR 0.045 0.004 TYR F 98 PHE 0.044 0.004 PHE O 946 TRP 0.056 0.006 TRP O 955 HIS 0.017 0.004 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.01178 / 0.95 (17681) covalent geometry : angle 1.19784 / 0.86 (25112) hydrogen bonds : bond 0.16843 / 11.37 ( 1001) hydrogen bonds : angle 10.44548 / 7.48 ( 2590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 371 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9079 (mt) cc_final: 0.8449 (mp) REVERT: A 106 ASP cc_start: 0.9237 (m-30) cc_final: 0.8980 (m-30) REVERT: B 63 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8824 (tp30) REVERT: C 56 GLU cc_start: 0.8912 (tt0) cc_final: 0.7826 (tm-30) REVERT: C 59 THR cc_start: 0.9464 (m) cc_final: 0.9176 (p) REVERT: C 64 GLU cc_start: 0.9115 (tt0) cc_final: 0.8704 (tm-30) REVERT: C 68 ASN cc_start: 0.8602 (m-40) cc_final: 0.6961 (m-40) REVERT: C 79 ILE cc_start: 0.9297 (pt) cc_final: 0.8896 (mt) REVERT: D 42 LEU cc_start: 0.9254 (tp) cc_final: 0.8898 (tt) REVERT: D 49 THR cc_start: 0.8106 (m) cc_final: 0.7883 (m) REVERT: D 69 ARG cc_start: 0.9110 (mtt180) cc_final: 0.8811 (mtm-85) REVERT: D 86 ILE cc_start: 0.8672 (mt) cc_final: 0.8392 (tt) REVERT: E 52 ARG cc_start: 0.9159 (mtt90) cc_final: 0.8852 (ttm110) REVERT: E 74 ILE cc_start: 0.9319 (mt) cc_final: 0.8862 (mm) REVERT: E 76 GLN cc_start: 0.8882 (mt0) cc_final: 0.8659 (mm-40) REVERT: E 82 LEU cc_start: 0.8333 (mt) cc_final: 0.7776 (mt) REVERT: E 106 ASP cc_start: 0.9342 (m-30) cc_final: 0.8894 (t70) REVERT: E 112 ILE cc_start: 0.9373 (mt) cc_final: 0.9145 (mt) REVERT: E 113 HIS cc_start: 0.8423 (t70) cc_final: 0.8142 (t70) REVERT: E 133 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6457 (mt-10) REVERT: F 44 LYS cc_start: 0.8293 (tttt) cc_final: 0.8029 (ttmt) REVERT: F 67 ARG cc_start: 0.8965 (ptp-170) cc_final: 0.8540 (tpt170) REVERT: F 88 TYR cc_start: 0.8618 (m-80) cc_final: 0.7928 (m-10) REVERT: H 117 LYS cc_start: 0.9312 (tttp) cc_final: 0.8966 (ttpp) REVERT: O 892 ILE cc_start: 0.9097 (mp) cc_final: 0.8897 (mt) REVERT: O 1159 PHE cc_start: 0.6706 (t80) cc_final: 0.6474 (t80) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.1612 time to fit residues: 83.5354 Evaluate side-chains 208 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN C 38 ASN C 73 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 749 HIS ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1054 GLN O1073 ASN O1111 GLN ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.053242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.038852 restraints weight = 130937.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039939 restraints weight = 76316.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.040707 restraints weight = 53603.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041217 restraints weight = 42234.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041507 restraints weight = 36156.063| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17681 Z= 0.228 Angle : 0.926 10.903 25112 Z= 0.517 Chirality : 0.056 0.332 2859 Planarity : 0.008 0.127 2171 Dihedral : 31.949 179.255 4676 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 25.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 0.44 % Allowed : 2.61 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.20), residues: 1319 helix: -1.75 (0.15), residues: 851 sheet: -2.03 (0.62), residues: 62 loop : -1.71 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 898 TYR 0.043 0.003 TYR F 88 PHE 0.049 0.003 PHE O 946 TRP 0.025 0.003 TRP O 955 HIS 0.010 0.003 HIS O1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.23 (17681) covalent geometry : angle 0.92620 / 0.52 (25112) hydrogen bonds : bond 0.09185 / 5.99 ( 1001) hydrogen bonds : angle 6.68548 / 4.77 ( 2590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 321 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9004 (tt0) cc_final: 0.8781 (tm-30) REVERT: A 90 MET cc_start: 0.9154 (tmm) cc_final: 0.8854 (tmm) REVERT: A 94 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 99 TYR cc_start: 0.8656 (t80) cc_final: 0.8056 (t80) REVERT: A 106 ASP cc_start: 0.9130 (m-30) cc_final: 0.8553 (m-30) REVERT: B 84 MET cc_start: 0.8604 (mmp) cc_final: 0.8382 (mmm) REVERT: B 85 ASP cc_start: 0.8416 (m-30) cc_final: 0.7493 (m-30) REVERT: C 41 GLU cc_start: 0.8558 (pm20) cc_final: 0.8097 (pp20) REVERT: C 56 GLU cc_start: 0.8970 (tt0) cc_final: 0.7981 (tm-30) REVERT: C 61 GLU cc_start: 0.9273 (tp30) cc_final: 0.8893 (tp30) REVERT: C 64 GLU cc_start: 0.9450 (tt0) cc_final: 0.8607 (tm-30) REVERT: C 68 ASN cc_start: 0.8818 (m-40) cc_final: 0.7570 (m-40) REVERT: C 73 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8791 (t0) REVERT: C 92 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 94 ASN cc_start: 0.8844 (t0) cc_final: 0.8399 (t0) REVERT: D 56 MET cc_start: 0.8735 (mtm) cc_final: 0.8522 (mtm) REVERT: D 65 ASP cc_start: 0.9028 (t0) cc_final: 0.8776 (t0) REVERT: D 69 ARG cc_start: 0.9467 (mtt180) cc_final: 0.9155 (mtm-85) REVERT: D 76 ARG cc_start: 0.8613 (mtp85) cc_final: 0.7665 (mtp-110) REVERT: D 80 TYR cc_start: 0.6898 (m-80) cc_final: 0.6528 (m-80) REVERT: D 86 ILE cc_start: 0.8265 (mt) cc_final: 0.7979 (tt) REVERT: E 56 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8235 (mtmm) REVERT: E 60 LEU cc_start: 0.8823 (mt) cc_final: 0.8469 (mt) REVERT: E 61 LEU cc_start: 0.9387 (mt) cc_final: 0.9180 (mt) REVERT: E 62 ILE cc_start: 0.9249 (mm) cc_final: 0.8594 (mm) REVERT: E 106 ASP cc_start: 0.9151 (m-30) cc_final: 0.8848 (t0) REVERT: E 123 ASP cc_start: 0.8796 (m-30) cc_final: 0.8419 (m-30) REVERT: F 67 ARG cc_start: 0.8795 (ptp-170) cc_final: 0.8517 (tpt-90) REVERT: F 98 TYR cc_start: 0.8449 (m-80) cc_final: 0.8180 (m-80) REVERT: G 90 ASP cc_start: 0.8130 (t0) cc_final: 0.7916 (t0) REVERT: G 94 ASN cc_start: 0.8931 (t0) cc_final: 0.8128 (t0) REVERT: H 64 ASN cc_start: 0.9711 (m-40) cc_final: 0.9492 (m-40) REVERT: H 69 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8177 (ttm170) REVERT: H 80 TYR cc_start: 0.7824 (m-80) cc_final: 0.7143 (m-80) REVERT: H 83 ARG cc_start: 0.9181 (mmt-90) cc_final: 0.8818 (mmt-90) REVERT: H 92 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7778 (tm-30) REVERT: H 103 LEU cc_start: 0.9428 (mt) cc_final: 0.9176 (mm) REVERT: H 117 LYS cc_start: 0.9398 (tttp) cc_final: 0.9118 (ttpp) REVERT: O 681 HIS cc_start: 0.8478 (m-70) cc_final: 0.7972 (m-70) REVERT: O 778 MET cc_start: 0.9437 (mmm) cc_final: 0.9107 (mmm) REVERT: O 866 PHE cc_start: 0.8365 (p90) cc_final: 0.8083 (p90) REVERT: O 1015 MET cc_start: 0.8079 (mtp) cc_final: 0.7274 (mtp) REVERT: O 1022 MET cc_start: 0.8755 (tpp) cc_final: 0.8516 (tpt) REVERT: O 1159 PHE cc_start: 0.8726 (t80) cc_final: 0.8402 (t80) REVERT: O 1255 ARG cc_start: 0.9266 (mtt180) cc_final: 0.8843 (ttm-80) outliers start: 5 outliers final: 1 residues processed: 323 average time/residue: 0.1560 time to fit residues: 71.7233 Evaluate side-chains 220 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 53 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1198 HIS ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.039633 restraints weight = 132448.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.040774 restraints weight = 77132.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041561 restraints weight = 53761.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042105 restraints weight = 42402.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042410 restraints weight = 36207.693| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 17681 Z= 0.192 Angle : 0.825 12.155 25112 Z= 0.466 Chirality : 0.052 0.344 2859 Planarity : 0.007 0.107 2171 Dihedral : 31.627 177.549 4676 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.84 % Favored : 94.01 % Rotamer: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1319 helix: -0.28 (0.17), residues: 847 sheet: -1.43 (0.63), residues: 65 loop : -1.38 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 816 TYR 0.031 0.003 TYR F 88 PHE 0.043 0.003 PHE O 946 TRP 0.022 0.002 TRP O 955 HIS 0.012 0.002 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.19 (17681) covalent geometry : angle 0.82547 / 0.47 (25112) hydrogen bonds : bond 0.07847 / 5.08 ( 1001) hydrogen bonds : angle 5.94525 / 4.24 ( 2590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8984 (tttt) cc_final: 0.8682 (tppt) REVERT: A 90 MET cc_start: 0.9066 (tmm) cc_final: 0.8693 (tmm) REVERT: A 94 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 59 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9110 (tptp) REVERT: B 73 THR cc_start: 0.9084 (m) cc_final: 0.8662 (m) REVERT: B 84 MET cc_start: 0.8635 (mmp) cc_final: 0.8424 (mmp) REVERT: B 85 ASP cc_start: 0.8624 (m-30) cc_final: 0.7612 (m-30) REVERT: C 24 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8469 (mm-40) REVERT: C 56 GLU cc_start: 0.8931 (tt0) cc_final: 0.8163 (tm-30) REVERT: C 61 GLU cc_start: 0.9194 (tp30) cc_final: 0.8876 (tm-30) REVERT: C 64 GLU cc_start: 0.9481 (tt0) cc_final: 0.8805 (tm-30) REVERT: C 68 ASN cc_start: 0.8851 (m-40) cc_final: 0.7424 (m110) REVERT: C 94 ASN cc_start: 0.8716 (t0) cc_final: 0.8312 (m-40) REVERT: D 56 MET cc_start: 0.8736 (mtm) cc_final: 0.8525 (mtm) REVERT: D 69 ARG cc_start: 0.9520 (mtt180) cc_final: 0.9091 (ttm-80) REVERT: D 76 ARG cc_start: 0.8415 (mtp85) cc_final: 0.7400 (mtp-110) REVERT: D 80 TYR cc_start: 0.6993 (m-10) cc_final: 0.6670 (m-80) REVERT: D 86 ILE cc_start: 0.8261 (mt) cc_final: 0.8025 (tt) REVERT: E 68 GLN cc_start: 0.8976 (pp30) cc_final: 0.8769 (pp30) REVERT: E 84 PHE cc_start: 0.8513 (m-80) cc_final: 0.8297 (m-80) REVERT: E 106 ASP cc_start: 0.9060 (m-30) cc_final: 0.8783 (t70) REVERT: E 120 MET cc_start: 0.7373 (mtm) cc_final: 0.7074 (mtp) REVERT: E 123 ASP cc_start: 0.9022 (m-30) cc_final: 0.8785 (m-30) REVERT: E 130 ILE cc_start: 0.9457 (mm) cc_final: 0.9210 (mm) REVERT: F 63 GLU cc_start: 0.9042 (tp30) cc_final: 0.8755 (tp30) REVERT: F 67 ARG cc_start: 0.8770 (ptp-170) cc_final: 0.8328 (tpt-90) REVERT: F 68 ASP cc_start: 0.9486 (m-30) cc_final: 0.8995 (m-30) REVERT: F 97 LEU cc_start: 0.8806 (tp) cc_final: 0.8523 (tp) REVERT: G 90 ASP cc_start: 0.8017 (t0) cc_final: 0.7659 (t0) REVERT: G 92 GLU cc_start: 0.8771 (tp30) cc_final: 0.8365 (tt0) REVERT: G 94 ASN cc_start: 0.8909 (t0) cc_final: 0.8180 (t0) REVERT: H 32 GLU cc_start: 0.7032 (mp0) cc_final: 0.6817 (mp0) REVERT: H 83 ARG cc_start: 0.9130 (mmt-90) cc_final: 0.8858 (mmt-90) REVERT: H 90 GLU cc_start: 0.9361 (mp0) cc_final: 0.9123 (mp0) REVERT: H 92 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7707 (tm-30) REVERT: H 97 LEU cc_start: 0.9192 (mt) cc_final: 0.8912 (tp) REVERT: O 681 HIS cc_start: 0.8530 (m-70) cc_final: 0.8044 (m-70) REVERT: O 778 MET cc_start: 0.9452 (mmm) cc_final: 0.8999 (mmm) REVERT: O 838 TRP cc_start: 0.6772 (m100) cc_final: 0.6519 (m100) REVERT: O 848 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8729 (pttp) REVERT: O 866 PHE cc_start: 0.8309 (p90) cc_final: 0.8048 (p90) REVERT: O 879 GLU cc_start: 0.8413 (mp0) cc_final: 0.8062 (mp0) REVERT: O 920 LEU cc_start: 0.9158 (tp) cc_final: 0.8772 (tt) REVERT: O 1022 MET cc_start: 0.8639 (tpp) cc_final: 0.8410 (tpt) REVERT: O 1052 ILE cc_start: 0.8764 (tt) cc_final: 0.8274 (tt) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.1594 time to fit residues: 71.6823 Evaluate side-chains 224 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 143 optimal weight: 0.0970 chunk 74 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** 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 = 0.3281 r_free = 0.3281 target = 0.055345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040431 restraints weight = 128523.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041614 restraints weight = 74785.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042433 restraints weight = 52002.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.042999 restraints weight = 40817.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043306 restraints weight = 34749.592| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17681 Z= 0.173 Angle : 0.785 11.362 25112 Z= 0.442 Chirality : 0.051 0.359 2859 Planarity : 0.006 0.063 2171 Dihedral : 31.336 179.502 4676 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.08 % 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: -0.54 (0.23), residues: 1319 helix: 0.20 (0.18), residues: 850 sheet: -1.19 (0.64), residues: 63 loop : -1.21 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1031 TYR 0.024 0.002 TYR O1226 PHE 0.039 0.002 PHE O 946 TRP 0.021 0.002 TRP O 935 HIS 0.011 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (17681) covalent geometry : angle 0.78492 / 0.44 (25112) hydrogen bonds : bond 0.07215 / 4.66 ( 1001) hydrogen bonds : angle 5.57462 / 3.98 ( 2590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8974 (tmm) cc_final: 0.8758 (tmm) REVERT: B 20 LYS cc_start: 0.7951 (tttt) cc_final: 0.7659 (ttpt) REVERT: B 59 LYS cc_start: 0.9273 (tmtt) cc_final: 0.9015 (tptp) REVERT: B 70 VAL cc_start: 0.9659 (p) cc_final: 0.9350 (p) REVERT: B 73 THR cc_start: 0.8865 (m) cc_final: 0.8565 (m) REVERT: B 81 VAL cc_start: 0.8871 (t) cc_final: 0.8600 (t) REVERT: B 85 ASP cc_start: 0.8837 (m-30) cc_final: 0.8054 (m-30) REVERT: C 56 GLU cc_start: 0.8897 (tt0) cc_final: 0.8026 (tm-30) REVERT: C 61 GLU cc_start: 0.9252 (tp30) cc_final: 0.8990 (tm-30) REVERT: C 64 GLU cc_start: 0.9486 (tt0) cc_final: 0.8915 (tm-30) REVERT: C 68 ASN cc_start: 0.8848 (m-40) cc_final: 0.7423 (m110) REVERT: C 85 LEU cc_start: 0.9596 (mt) cc_final: 0.9022 (tt) REVERT: C 90 ASP cc_start: 0.9298 (t0) cc_final: 0.8775 (t0) REVERT: C 94 ASN cc_start: 0.8833 (t0) cc_final: 0.8448 (m-40) REVERT: C 95 LYS cc_start: 0.8870 (pptt) cc_final: 0.8446 (pptt) REVERT: C 99 ARG cc_start: 0.7568 (mmm160) cc_final: 0.7337 (mmm160) REVERT: D 34 TYR cc_start: 0.9463 (m-80) cc_final: 0.9236 (m-80) REVERT: D 69 ARG cc_start: 0.9517 (mtt180) cc_final: 0.9284 (ttm-80) REVERT: D 76 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7263 (mtp-110) REVERT: D 86 ILE cc_start: 0.8324 (mt) cc_final: 0.8048 (tt) REVERT: E 97 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8551 (mm-30) REVERT: E 120 MET cc_start: 0.7337 (mtm) cc_final: 0.6801 (mtp) REVERT: E 123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8531 (m-30) REVERT: F 31 LYS cc_start: 0.8834 (mppt) cc_final: 0.8421 (mmtm) REVERT: F 63 GLU cc_start: 0.8976 (tp30) cc_final: 0.8664 (tp30) REVERT: F 68 ASP cc_start: 0.9428 (m-30) cc_final: 0.9046 (m-30) REVERT: G 90 ASP cc_start: 0.7862 (t0) cc_final: 0.7592 (t0) REVERT: G 94 ASN cc_start: 0.8918 (t0) cc_final: 0.8281 (t0) REVERT: H 32 GLU cc_start: 0.7088 (mp0) cc_final: 0.6780 (mp0) REVERT: H 83 ARG cc_start: 0.9118 (mmt-90) cc_final: 0.8763 (mmt-90) REVERT: H 90 GLU cc_start: 0.9395 (mp0) cc_final: 0.9158 (mp0) REVERT: H 92 GLN cc_start: 0.8507 (tm-30) cc_final: 0.7723 (tm-30) REVERT: H 97 LEU cc_start: 0.9021 (mt) cc_final: 0.8675 (tp) REVERT: O 778 MET cc_start: 0.9377 (mmm) cc_final: 0.9042 (mmm) REVERT: O 866 PHE cc_start: 0.8234 (p90) cc_final: 0.7935 (p90) REVERT: O 920 LEU cc_start: 0.9211 (tp) cc_final: 0.8979 (tp) REVERT: O 1015 MET cc_start: 0.7679 (mtp) cc_final: 0.7166 (mtp) REVERT: O 1136 HIS cc_start: 0.8592 (t-90) cc_final: 0.8200 (t70) REVERT: O 1159 PHE cc_start: 0.8495 (t80) cc_final: 0.8247 (t80) REVERT: O 1300 MET cc_start: 0.9048 (tpp) cc_final: 0.8737 (tmm) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.1375 time to fit residues: 61.7812 Evaluate side-chains 231 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 156 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 24 GLN C 31 HIS D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 681 HIS ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 911 ASN ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1049 ASN ** O1237 GLN ** 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 = 0.3280 r_free = 0.3280 target = 0.055559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.040560 restraints weight = 128445.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.041759 restraints weight = 75640.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.042598 restraints weight = 52457.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.043162 restraints weight = 41068.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.043485 restraints weight = 34909.287| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17681 Z= 0.173 Angle : 0.764 9.771 25112 Z= 0.431 Chirality : 0.049 0.354 2859 Planarity : 0.006 0.121 2171 Dihedral : 31.121 179.936 4676 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.43 (0.23), residues: 1319 helix: 0.28 (0.18), residues: 844 sheet: -1.14 (0.64), residues: 63 loop : -1.15 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 35 TYR 0.043 0.002 TYR G 39 PHE 0.041 0.002 PHE O 946 TRP 0.014 0.002 TRP O 955 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (17681) covalent geometry : angle 0.76449 / 0.43 (25112) hydrogen bonds : bond 0.06987 / 4.51 ( 1001) hydrogen bonds : angle 5.43883 / 3.89 ( 2590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8580 (pm20) cc_final: 0.8330 (pm20) REVERT: A 94 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 20 LYS cc_start: 0.7974 (tttt) cc_final: 0.7652 (ttpt) REVERT: B 54 THR cc_start: 0.9547 (m) cc_final: 0.9210 (p) REVERT: B 59 LYS cc_start: 0.9288 (tmtt) cc_final: 0.8969 (tptt) REVERT: B 73 THR cc_start: 0.8907 (m) cc_final: 0.8561 (m) REVERT: B 74 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8535 (tm-30) REVERT: B 85 ASP cc_start: 0.8821 (m-30) cc_final: 0.8263 (m-30) REVERT: C 56 GLU cc_start: 0.8835 (tt0) cc_final: 0.8179 (tm-30) REVERT: C 61 GLU cc_start: 0.9160 (tp30) cc_final: 0.8942 (tm-30) REVERT: C 85 LEU cc_start: 0.9603 (mt) cc_final: 0.9147 (tt) REVERT: C 94 ASN cc_start: 0.8911 (t0) cc_final: 0.8437 (m-40) REVERT: C 95 LYS cc_start: 0.8767 (pptt) cc_final: 0.8482 (pptt) REVERT: D 69 ARG cc_start: 0.9500 (mtt180) cc_final: 0.9275 (ttm-80) REVERT: D 76 ARG cc_start: 0.8525 (mtp85) cc_final: 0.7872 (mtp-110) REVERT: D 86 ILE cc_start: 0.8359 (mt) cc_final: 0.8111 (tt) REVERT: D 96 ARG cc_start: 0.9014 (ttm110) cc_final: 0.8447 (ttp80) REVERT: E 67 PHE cc_start: 0.9404 (t80) cc_final: 0.9202 (t80) REVERT: E 84 PHE cc_start: 0.8158 (m-80) cc_final: 0.7895 (m-10) REVERT: E 97 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8607 (mm-30) REVERT: E 123 ASP cc_start: 0.9066 (m-30) cc_final: 0.8755 (m-30) REVERT: F 63 GLU cc_start: 0.8955 (tp30) cc_final: 0.8687 (tm-30) REVERT: G 94 ASN cc_start: 0.8957 (t0) cc_final: 0.8299 (t0) REVERT: H 32 GLU cc_start: 0.7051 (mp0) cc_final: 0.6791 (mp0) REVERT: H 83 ARG cc_start: 0.9117 (mmt-90) cc_final: 0.8744 (mmt-90) REVERT: H 92 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7947 (tm-30) REVERT: O 778 MET cc_start: 0.9377 (mmm) cc_final: 0.8926 (mmm) REVERT: O 838 TRP cc_start: 0.7087 (m100) cc_final: 0.6823 (m100) REVERT: O 866 PHE cc_start: 0.8401 (p90) cc_final: 0.7953 (p90) REVERT: O 879 GLU cc_start: 0.8480 (mp0) cc_final: 0.8238 (mp0) REVERT: O 920 LEU cc_start: 0.9213 (tp) cc_final: 0.9002 (tp) REVERT: O 1015 MET cc_start: 0.7732 (mtp) cc_final: 0.6828 (mtm) REVERT: O 1022 MET cc_start: 0.8532 (tpt) cc_final: 0.8226 (tpt) REVERT: O 1052 ILE cc_start: 0.8345 (tt) cc_final: 0.8126 (tt) REVERT: O 1136 HIS cc_start: 0.8439 (t-90) cc_final: 0.8199 (t70) REVERT: O 1192 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8405 (mm-40) REVERT: O 1300 MET cc_start: 0.9034 (tpp) cc_final: 0.8722 (tmm) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1407 time to fit residues: 59.6342 Evaluate side-chains 216 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 81 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 31 HIS D 106 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.055218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.040307 restraints weight = 128425.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.041487 restraints weight = 76182.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.042329 restraints weight = 52934.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.042905 restraints weight = 41383.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043246 restraints weight = 35046.144| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17681 Z= 0.179 Angle : 0.743 10.549 25112 Z= 0.421 Chirality : 0.047 0.350 2859 Planarity : 0.006 0.059 2171 Dihedral : 30.930 178.873 4676 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.69 % Rotamer: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.32 (0.23), residues: 1319 helix: 0.36 (0.18), residues: 857 sheet: -0.89 (0.66), residues: 63 loop : -1.16 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 880 TYR 0.032 0.002 TYR H 80 PHE 0.043 0.002 PHE A 104 TRP 0.014 0.002 TRP O 955 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 (17681) covalent geometry : angle 0.74258 / 0.42 (25112) hydrogen bonds : bond 0.06825 / 4.41 ( 1001) hydrogen bonds : angle 5.35357 / 3.82 ( 2590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9098 (tptm) cc_final: 0.8855 (mmmm) REVERT: A 59 GLU cc_start: 0.8538 (pm20) cc_final: 0.8322 (pm20) REVERT: A 90 MET cc_start: 0.9006 (tmm) cc_final: 0.8652 (tmm) REVERT: A 94 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 97 GLU cc_start: 0.7527 (pp20) cc_final: 0.7122 (pp20) REVERT: A 106 ASP cc_start: 0.8708 (t70) cc_final: 0.8461 (t70) REVERT: B 54 THR cc_start: 0.9472 (m) cc_final: 0.9250 (p) REVERT: B 59 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9099 (tptt) REVERT: B 73 THR cc_start: 0.8923 (m) cc_final: 0.8617 (m) REVERT: B 85 ASP cc_start: 0.8917 (m-30) cc_final: 0.8413 (m-30) REVERT: C 56 GLU cc_start: 0.8860 (tt0) cc_final: 0.8165 (tm-30) REVERT: C 61 GLU cc_start: 0.9164 (tp30) cc_final: 0.8915 (tm-30) REVERT: C 93 LEU cc_start: 0.9083 (tp) cc_final: 0.8680 (tp) REVERT: C 94 ASN cc_start: 0.8895 (t0) cc_final: 0.8412 (m-40) REVERT: C 95 LYS cc_start: 0.8969 (pptt) cc_final: 0.8738 (pptt) REVERT: D 69 ARG cc_start: 0.9530 (mtt180) cc_final: 0.9283 (ttm-80) REVERT: D 76 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7660 (mtp-110) REVERT: D 80 TYR cc_start: 0.6818 (m-80) cc_final: 0.6469 (m-80) REVERT: D 86 ILE cc_start: 0.8365 (mt) cc_final: 0.8055 (tt) REVERT: E 84 PHE cc_start: 0.8126 (m-80) cc_final: 0.7890 (m-10) REVERT: E 97 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8427 (mm-30) REVERT: E 123 ASP cc_start: 0.9074 (m-30) cc_final: 0.8790 (m-30) REVERT: F 63 GLU cc_start: 0.9023 (tp30) cc_final: 0.8463 (tm-30) REVERT: G 90 ASP cc_start: 0.7829 (t0) cc_final: 0.7588 (t0) REVERT: G 94 ASN cc_start: 0.8866 (t0) cc_final: 0.8221 (t0) REVERT: H 32 GLU cc_start: 0.7013 (mp0) cc_final: 0.6714 (mp0) REVERT: H 83 ARG cc_start: 0.9123 (mmt-90) cc_final: 0.8790 (mmt-90) REVERT: H 90 GLU cc_start: 0.9560 (mp0) cc_final: 0.9180 (mp0) REVERT: H 92 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8202 (tm-30) REVERT: O 778 MET cc_start: 0.9423 (mmm) cc_final: 0.9135 (mmm) REVERT: O 1015 MET cc_start: 0.7768 (mtp) cc_final: 0.6960 (mtm) REVERT: O 1022 MET cc_start: 0.8597 (tpt) cc_final: 0.8376 (tpt) REVERT: O 1112 MET cc_start: 0.7341 (tpt) cc_final: 0.7110 (mmm) REVERT: O 1136 HIS cc_start: 0.8687 (t-90) cc_final: 0.8462 (t70) REVERT: O 1163 THR cc_start: 0.7404 (p) cc_final: 0.6665 (p) REVERT: O 1192 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8422 (mm-40) REVERT: O 1300 MET cc_start: 0.9052 (tpp) cc_final: 0.8756 (tmm) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.1374 time to fit residues: 58.4019 Evaluate side-chains 217 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 93 GLN C 68 ASN E 93 GLN G 68 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN ** O1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** 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 = 0.3280 r_free = 0.3280 target = 0.055579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040743 restraints weight = 127034.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.041917 restraints weight = 74996.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042765 restraints weight = 52187.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.043331 restraints weight = 40703.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.043610 restraints weight = 34511.627| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17681 Z= 0.170 Angle : 0.735 10.057 25112 Z= 0.416 Chirality : 0.047 0.352 2859 Planarity : 0.005 0.060 2171 Dihedral : 30.772 178.280 4676 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.30 (0.23), residues: 1319 helix: 0.37 (0.18), residues: 863 sheet: -0.90 (0.65), residues: 63 loop : -1.17 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 95 TYR 0.025 0.002 TYR D 80 PHE 0.025 0.002 PHE O 835 TRP 0.014 0.002 TRP O 955 HIS 0.012 0.002 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (17681) covalent geometry : angle 0.73490 / 0.42 (25112) hydrogen bonds : bond 0.06700 / 4.34 ( 1001) hydrogen bonds : angle 5.25560 / 3.75 ( 2590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9125 (tptm) cc_final: 0.8882 (mmmm) REVERT: A 90 MET cc_start: 0.8991 (tmm) cc_final: 0.8694 (tmm) REVERT: A 94 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 97 GLU cc_start: 0.7587 (pp20) cc_final: 0.7254 (pp20) REVERT: B 54 THR cc_start: 0.9530 (m) cc_final: 0.9206 (p) REVERT: B 59 LYS cc_start: 0.9360 (tmmt) cc_final: 0.9077 (tptt) REVERT: B 73 THR cc_start: 0.9065 (m) cc_final: 0.8769 (m) REVERT: B 85 ASP cc_start: 0.8783 (m-30) cc_final: 0.8132 (m-30) REVERT: C 56 GLU cc_start: 0.8908 (tt0) cc_final: 0.8130 (tm-30) REVERT: C 61 GLU cc_start: 0.9132 (tp30) cc_final: 0.8886 (tm-30) REVERT: C 85 LEU cc_start: 0.9438 (mm) cc_final: 0.8800 (tt) REVERT: C 93 LEU cc_start: 0.9099 (tp) cc_final: 0.8735 (tp) REVERT: C 94 ASN cc_start: 0.8870 (t0) cc_final: 0.8354 (m-40) REVERT: C 101 THR cc_start: 0.9369 (t) cc_final: 0.9089 (t) REVERT: D 34 TYR cc_start: 0.9471 (m-80) cc_final: 0.9226 (m-80) REVERT: D 69 ARG cc_start: 0.9522 (mtt180) cc_final: 0.9284 (ttm-80) REVERT: D 76 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7688 (mtp-110) REVERT: D 80 TYR cc_start: 0.6759 (m-80) cc_final: 0.6494 (m-80) REVERT: D 86 ILE cc_start: 0.8353 (mt) cc_final: 0.7982 (tt) REVERT: D 96 ARG cc_start: 0.9018 (ttm110) cc_final: 0.8527 (ttt-90) REVERT: E 84 PHE cc_start: 0.8349 (m-80) cc_final: 0.8112 (m-10) REVERT: E 87 SER cc_start: 0.9174 (p) cc_final: 0.8910 (p) REVERT: E 94 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8827 (mm-30) REVERT: E 97 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8864 (mm-30) REVERT: E 123 ASP cc_start: 0.9063 (m-30) cc_final: 0.8702 (m-30) REVERT: F 88 TYR cc_start: 0.8138 (m-10) cc_final: 0.7896 (m-10) REVERT: G 90 ASP cc_start: 0.7835 (t0) cc_final: 0.7512 (t0) REVERT: G 94 ASN cc_start: 0.8923 (t0) cc_final: 0.8238 (t0) REVERT: H 32 GLU cc_start: 0.7060 (mp0) cc_final: 0.6778 (mp0) REVERT: H 83 ARG cc_start: 0.9132 (mmt-90) cc_final: 0.8823 (mmt90) REVERT: H 90 GLU cc_start: 0.9474 (mp0) cc_final: 0.9172 (mp0) REVERT: H 92 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8306 (tm-30) REVERT: H 97 LEU cc_start: 0.8912 (tp) cc_final: 0.8630 (tp) REVERT: H 102 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8882 (mm-30) REVERT: O 778 MET cc_start: 0.9397 (mmm) cc_final: 0.9168 (mmm) REVERT: O 920 LEU cc_start: 0.9151 (tp) cc_final: 0.8880 (tp) REVERT: O 1015 MET cc_start: 0.7465 (mtp) cc_final: 0.6862 (mtm) REVERT: O 1022 MET cc_start: 0.8568 (tpt) cc_final: 0.8057 (tpt) REVERT: O 1112 MET cc_start: 0.7482 (tpt) cc_final: 0.7165 (mmt) REVERT: O 1136 HIS cc_start: 0.8740 (t-90) cc_final: 0.8358 (t70) REVERT: O 1159 PHE cc_start: 0.8593 (t80) cc_final: 0.8319 (t80) REVERT: O 1192 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8355 (mm-40) REVERT: O 1300 MET cc_start: 0.9160 (tpp) cc_final: 0.8876 (tmm) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1376 time to fit residues: 57.1951 Evaluate side-chains 216 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN ** O1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.056413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041371 restraints weight = 125698.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.042607 restraints weight = 73554.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043474 restraints weight = 50818.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044059 restraints weight = 39602.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044379 restraints weight = 33525.862| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17681 Z= 0.159 Angle : 0.735 10.092 25112 Z= 0.413 Chirality : 0.047 0.357 2859 Planarity : 0.005 0.059 2171 Dihedral : 30.603 177.978 4676 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1319 helix: 0.48 (0.18), residues: 856 sheet: -0.74 (0.66), residues: 63 loop : -1.02 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1031 TYR 0.022 0.002 TYR D 80 PHE 0.041 0.003 PHE A 104 TRP 0.018 0.002 TRP O 838 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (17681) covalent geometry : angle 0.73486 / 0.41 (25112) hydrogen bonds : bond 0.06546 / 4.23 ( 1001) hydrogen bonds : angle 5.18170 / 3.71 ( 2590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9099 (tptm) cc_final: 0.8816 (mmmm) REVERT: A 61 LEU cc_start: 0.8926 (mt) cc_final: 0.8660 (mt) REVERT: A 94 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 97 GLU cc_start: 0.7586 (pp20) cc_final: 0.7108 (pp20) REVERT: B 59 LYS cc_start: 0.9306 (tmmt) cc_final: 0.9054 (tptt) REVERT: B 73 THR cc_start: 0.9037 (m) cc_final: 0.8755 (m) REVERT: B 74 GLU cc_start: 0.8592 (pm20) cc_final: 0.8060 (pm20) REVERT: B 75 HIS cc_start: 0.7826 (t-90) cc_final: 0.7048 (t-90) REVERT: B 85 ASP cc_start: 0.8929 (m-30) cc_final: 0.8233 (m-30) REVERT: C 56 GLU cc_start: 0.8804 (tt0) cc_final: 0.8069 (tm-30) REVERT: C 61 GLU cc_start: 0.9142 (tp30) cc_final: 0.8914 (tm-30) REVERT: C 64 GLU cc_start: 0.9487 (tt0) cc_final: 0.8939 (tm-30) REVERT: C 68 ASN cc_start: 0.8778 (m-40) cc_final: 0.7205 (m-40) REVERT: C 85 LEU cc_start: 0.9433 (mm) cc_final: 0.8792 (tt) REVERT: C 93 LEU cc_start: 0.9010 (tp) cc_final: 0.8661 (tp) REVERT: C 94 ASN cc_start: 0.8814 (t0) cc_final: 0.8336 (m-40) REVERT: D 56 MET cc_start: 0.8373 (mpp) cc_final: 0.8123 (mpp) REVERT: D 69 ARG cc_start: 0.9551 (mtt180) cc_final: 0.9283 (ttm-80) REVERT: D 76 ARG cc_start: 0.8379 (mtp85) cc_final: 0.7557 (mtp-110) REVERT: D 80 TYR cc_start: 0.6594 (m-80) cc_final: 0.6208 (m-80) REVERT: D 86 ILE cc_start: 0.8387 (mt) cc_final: 0.8109 (tt) REVERT: D 96 ARG cc_start: 0.9052 (ttm110) cc_final: 0.8561 (ttt180) REVERT: E 56 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8176 (mttp) REVERT: E 84 PHE cc_start: 0.8345 (m-80) cc_final: 0.8097 (m-10) REVERT: E 87 SER cc_start: 0.9147 (p) cc_final: 0.8858 (p) REVERT: E 120 MET cc_start: 0.7800 (mtm) cc_final: 0.7496 (mpp) REVERT: E 123 ASP cc_start: 0.8975 (m-30) cc_final: 0.8416 (m-30) REVERT: F 45 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8152 (mtp-110) REVERT: F 88 TYR cc_start: 0.8030 (m-10) cc_final: 0.7806 (m-10) REVERT: G 90 ASP cc_start: 0.7834 (t0) cc_final: 0.7462 (t0) REVERT: G 94 ASN cc_start: 0.8870 (t0) cc_final: 0.8199 (t0) REVERT: H 32 GLU cc_start: 0.6977 (mp0) cc_final: 0.6464 (mp0) REVERT: H 83 ARG cc_start: 0.9142 (mmt-90) cc_final: 0.8778 (mmt90) REVERT: H 90 GLU cc_start: 0.9412 (mp0) cc_final: 0.9107 (mp0) REVERT: H 92 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8189 (tm-30) REVERT: H 96 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8516 (mtt180) REVERT: H 97 LEU cc_start: 0.9024 (tp) cc_final: 0.8757 (tp) REVERT: H 102 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8845 (mm-30) REVERT: O 757 LYS cc_start: 0.7831 (mttt) cc_final: 0.7284 (ttpt) REVERT: O 778 MET cc_start: 0.9414 (mmm) cc_final: 0.9077 (mmm) REVERT: O 920 LEU cc_start: 0.9125 (tp) cc_final: 0.8842 (tp) REVERT: O 1015 MET cc_start: 0.7487 (mtp) cc_final: 0.6841 (mtm) REVERT: O 1022 MET cc_start: 0.8490 (tpt) cc_final: 0.7973 (tpt) REVERT: O 1112 MET cc_start: 0.7248 (tpt) cc_final: 0.6888 (mmt) REVERT: O 1136 HIS cc_start: 0.8664 (t-90) cc_final: 0.8426 (t70) REVERT: O 1159 PHE cc_start: 0.8481 (t80) cc_final: 0.8228 (t80) REVERT: O 1192 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8381 (mt0) REVERT: O 1300 MET cc_start: 0.9170 (tpp) cc_final: 0.8891 (tmm) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1506 time to fit residues: 63.3558 Evaluate side-chains 232 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 0.0050 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN O1079 ASN ** O1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.056626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041415 restraints weight = 124625.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042626 restraints weight = 73499.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043394 restraints weight = 51046.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044028 restraints weight = 40315.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044425 restraints weight = 34110.203| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17681 Z= 0.154 Angle : 0.725 10.089 25112 Z= 0.408 Chirality : 0.046 0.354 2859 Planarity : 0.005 0.059 2171 Dihedral : 30.429 177.806 4676 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.09 % Allowed : 0.78 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1319 helix: 0.55 (0.18), residues: 853 sheet: -0.61 (0.67), residues: 63 loop : -0.97 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 71 TYR 0.021 0.002 TYR D 80 PHE 0.030 0.002 PHE O1110 TRP 0.014 0.002 TRP O 955 HIS 0.010 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (17681) covalent geometry : angle 0.72475 / 0.41 (25112) hydrogen bonds : bond 0.06455 / 4.16 ( 1001) hydrogen bonds : angle 5.13064 / 3.67 ( 2590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9115 (tptm) cc_final: 0.8856 (mmmm) REVERT: A 94 GLU cc_start: 0.8714 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 97 GLU cc_start: 0.7526 (pp20) cc_final: 0.7134 (pp20) REVERT: B 59 LYS cc_start: 0.9244 (tmmt) cc_final: 0.9027 (tptt) REVERT: B 74 GLU cc_start: 0.8438 (pm20) cc_final: 0.7790 (pm20) REVERT: B 75 HIS cc_start: 0.7690 (t-90) cc_final: 0.7127 (t-90) REVERT: B 85 ASP cc_start: 0.8941 (m-30) cc_final: 0.7894 (t0) REVERT: C 56 GLU cc_start: 0.8841 (tt0) cc_final: 0.8070 (tm-30) REVERT: C 61 GLU cc_start: 0.9149 (tp30) cc_final: 0.8908 (tm-30) REVERT: C 64 GLU cc_start: 0.9491 (tt0) cc_final: 0.8929 (tp30) REVERT: C 68 ASN cc_start: 0.8976 (m-40) cc_final: 0.8025 (m-40) REVERT: C 93 LEU cc_start: 0.9052 (tp) cc_final: 0.8664 (tp) REVERT: C 94 ASN cc_start: 0.8829 (t0) cc_final: 0.8363 (m-40) REVERT: D 56 MET cc_start: 0.8370 (mpp) cc_final: 0.8075 (mpp) REVERT: D 69 ARG cc_start: 0.9530 (mtt180) cc_final: 0.9234 (ttm-80) REVERT: D 76 ARG cc_start: 0.8381 (mtp85) cc_final: 0.7604 (mtp-110) REVERT: D 80 TYR cc_start: 0.6869 (m-80) cc_final: 0.6557 (m-80) REVERT: D 86 ILE cc_start: 0.8418 (mt) cc_final: 0.8119 (tt) REVERT: D 96 ARG cc_start: 0.8946 (ttm110) cc_final: 0.8440 (ttt180) REVERT: E 49 ARG cc_start: 0.9356 (ttp-110) cc_final: 0.8884 (mtt90) REVERT: E 56 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8233 (pttm) REVERT: E 84 PHE cc_start: 0.8311 (m-80) cc_final: 0.8069 (m-10) REVERT: E 87 SER cc_start: 0.9174 (p) cc_final: 0.8866 (p) REVERT: E 123 ASP cc_start: 0.8758 (m-30) cc_final: 0.8456 (m-30) REVERT: F 49 LEU cc_start: 0.9586 (mp) cc_final: 0.9034 (mp) REVERT: F 79 LYS cc_start: 0.8393 (mttp) cc_final: 0.8186 (mttp) REVERT: G 90 ASP cc_start: 0.7907 (t0) cc_final: 0.7451 (t0) REVERT: G 94 ASN cc_start: 0.8910 (t0) cc_final: 0.8072 (m-40) REVERT: H 80 TYR cc_start: 0.7167 (m-10) cc_final: 0.6139 (m-80) REVERT: H 83 ARG cc_start: 0.9122 (mmt-90) cc_final: 0.8720 (mmt-90) REVERT: H 90 GLU cc_start: 0.9427 (mp0) cc_final: 0.9099 (mp0) REVERT: H 92 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8245 (tm-30) REVERT: H 96 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8511 (mtt180) REVERT: H 97 LEU cc_start: 0.9026 (tp) cc_final: 0.8810 (tp) REVERT: O 757 LYS cc_start: 0.7898 (mttt) cc_final: 0.7421 (tttm) REVERT: O 778 MET cc_start: 0.9363 (mmm) cc_final: 0.9101 (mmm) REVERT: O 920 LEU cc_start: 0.9057 (tp) cc_final: 0.8747 (tp) REVERT: O 1015 MET cc_start: 0.7244 (mtp) cc_final: 0.6282 (mpp) REVERT: O 1022 MET cc_start: 0.8498 (tpt) cc_final: 0.8101 (tpt) REVERT: O 1112 MET cc_start: 0.7272 (tpt) cc_final: 0.6806 (mmt) REVERT: O 1192 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8355 (mt0) REVERT: O 1300 MET cc_start: 0.9178 (tpp) cc_final: 0.8897 (tmm) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.1532 time to fit residues: 65.0355 Evaluate side-chains 220 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 133 optimal weight: 0.0070 chunk 149 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN ** O1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** 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 = 0.3296 r_free = 0.3296 target = 0.056492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.041382 restraints weight = 124581.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042579 restraints weight = 73011.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043416 restraints weight = 50806.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043941 restraints weight = 39821.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044348 restraints weight = 34027.816| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17681 Z= 0.175 Angle : 0.737 10.144 25112 Z= 0.414 Chirality : 0.046 0.348 2859 Planarity : 0.006 0.069 2171 Dihedral : 30.372 177.857 4676 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -0.13 (0.23), residues: 1319 helix: 0.47 (0.18), residues: 859 sheet: -0.66 (0.66), residues: 63 loop : -1.03 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG O 816 TYR 0.020 0.002 TYR G 39 PHE 0.043 0.003 PHE A 104 TRP 0.014 0.002 TRP O 955 HIS 0.016 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (17681) covalent geometry : angle 0.73695 / 0.41 (25112) hydrogen bonds : bond 0.06548 / 4.26 ( 1001) hydrogen bonds : angle 5.17468 / 3.70 ( 2590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9114 (tptm) cc_final: 0.8846 (mmmm) REVERT: A 57 SER cc_start: 0.9580 (m) cc_final: 0.9358 (m) REVERT: A 60 LEU cc_start: 0.7949 (tp) cc_final: 0.7582 (tp) REVERT: A 94 GLU cc_start: 0.8687 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 97 GLU cc_start: 0.7631 (pp20) cc_final: 0.7155 (pp20) REVERT: B 59 LYS cc_start: 0.9279 (tmmt) cc_final: 0.9045 (tptp) REVERT: B 64 ASN cc_start: 0.8740 (m-40) cc_final: 0.8097 (m-40) REVERT: B 73 THR cc_start: 0.9071 (m) cc_final: 0.8817 (m) REVERT: B 74 GLU cc_start: 0.8542 (pm20) cc_final: 0.8209 (pm20) REVERT: B 75 HIS cc_start: 0.7853 (t-90) cc_final: 0.7233 (t-90) REVERT: B 81 VAL cc_start: 0.8842 (t) cc_final: 0.8488 (t) REVERT: B 85 ASP cc_start: 0.8884 (m-30) cc_final: 0.8242 (m-30) REVERT: C 56 GLU cc_start: 0.8879 (tt0) cc_final: 0.8106 (tm-30) REVERT: C 61 GLU cc_start: 0.9176 (tp30) cc_final: 0.8916 (tm-30) REVERT: C 64 GLU cc_start: 0.9507 (tt0) cc_final: 0.8918 (tp30) REVERT: C 68 ASN cc_start: 0.8993 (m-40) cc_final: 0.8095 (m-40) REVERT: C 90 ASP cc_start: 0.9070 (t0) cc_final: 0.8805 (t0) REVERT: C 93 LEU cc_start: 0.9109 (tp) cc_final: 0.8673 (tp) REVERT: C 94 ASN cc_start: 0.8832 (t0) cc_final: 0.8339 (m-40) REVERT: D 56 MET cc_start: 0.8418 (mpp) cc_final: 0.8197 (mpp) REVERT: D 69 ARG cc_start: 0.9543 (mtt180) cc_final: 0.9290 (ttm-80) REVERT: D 76 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7514 (mtp-110) REVERT: D 80 TYR cc_start: 0.6713 (m-80) cc_final: 0.6405 (m-80) REVERT: D 86 ILE cc_start: 0.8423 (mt) cc_final: 0.8086 (tt) REVERT: D 96 ARG cc_start: 0.8976 (ttm110) cc_final: 0.8559 (ttt-90) REVERT: E 56 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8272 (mttp) REVERT: E 87 SER cc_start: 0.9071 (p) cc_final: 0.8870 (p) REVERT: E 97 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8874 (mm-30) REVERT: E 123 ASP cc_start: 0.9018 (m-30) cc_final: 0.8662 (m-30) REVERT: F 49 LEU cc_start: 0.9480 (mp) cc_final: 0.9128 (mp) REVERT: F 79 LYS cc_start: 0.8369 (mttp) cc_final: 0.8144 (mttp) REVERT: G 90 ASP cc_start: 0.8005 (t0) cc_final: 0.7646 (t0) REVERT: G 94 ASN cc_start: 0.8917 (t0) cc_final: 0.8112 (m-40) REVERT: H 83 ARG cc_start: 0.9135 (mmt-90) cc_final: 0.8740 (mmt-90) REVERT: H 90 GLU cc_start: 0.9446 (mp0) cc_final: 0.9085 (mp0) REVERT: H 92 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8077 (tm-30) REVERT: O 757 LYS cc_start: 0.7904 (mttt) cc_final: 0.7431 (tttm) REVERT: O 778 MET cc_start: 0.9375 (mmm) cc_final: 0.9106 (mmm) REVERT: O 920 LEU cc_start: 0.9096 (tp) cc_final: 0.8793 (tp) REVERT: O 1015 MET cc_start: 0.7313 (mtp) cc_final: 0.6284 (mpp) REVERT: O 1022 MET cc_start: 0.8478 (tpt) cc_final: 0.8080 (tpt) REVERT: O 1112 MET cc_start: 0.7046 (tpt) cc_final: 0.6812 (mmm) REVERT: O 1192 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8452 (mt0) REVERT: O 1300 MET cc_start: 0.9177 (tpp) cc_final: 0.8872 (tmm) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1513 time to fit residues: 60.9112 Evaluate side-chains 225 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 0.0670 chunk 138 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 92 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN ** O1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.041056 restraints weight = 124546.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042260 restraints weight = 73860.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043092 restraints weight = 51200.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043583 restraints weight = 40213.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044012 restraints weight = 34390.507| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17681 Z= 0.185 Angle : 0.738 10.214 25112 Z= 0.416 Chirality : 0.046 0.346 2859 Planarity : 0.006 0.059 2171 Dihedral : 30.320 177.730 4676 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.76 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: 1319 helix: 0.36 (0.18), residues: 877 sheet: -0.71 (0.65), residues: 63 loop : -1.12 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O1076 TYR 0.050 0.003 TYR H 80 PHE 0.023 0.002 PHE A 104 TRP 0.013 0.002 TRP O 955 HIS 0.012 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.19 (17681) covalent geometry : angle 0.73847 / 0.42 (25112) hydrogen bonds : bond 0.06626 / 4.32 ( 1001) hydrogen bonds : angle 5.18749 / 3.71 ( 2590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2793.95 seconds wall clock time: 49 minutes 11.91 seconds (2951.91 seconds total)