Starting phenix.real_space_refine on Sat Sep 12 14:38:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x0x_6699/09_2026/5x0x_6699.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0x_6699/09_2026/5x0x_6699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5x0x_6699/09_2026/5x0x_6699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0x_6699/09_2026/5x0x_6699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x0x_6699/09_2026/5x0x_6699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0x_6699/09_2026/5x0x_6699.map" } resolution = 3.97 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= 0.004 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 9647 2.51 5 N 3083 2.21 5 O 3697 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: 16748 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: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 18 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: 3.65, per 1000 atoms: 0.22 Number of scatterers: 16748 At special positions: 0 Unit cell: (139.92, 149.16, 112.2, 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 3697 8.00 N 3083 7.00 C 9647 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: 1.44 Conformation dependent library (CDL) restraints added in 537.4 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 68.1% alpha, 4.1% beta 133 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.665A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.235A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.224A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.723A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.525A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.802A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.493A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.808A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.744A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.665A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.234A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.224A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 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: 3.723A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.526A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.802A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.493A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.809A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.744A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 689 removed outlier: 3.937A pdb=" N LEU O 683 " --> pdb=" O ILE O 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 744 through 749 Processing helix chain 'O' and resid 768 through 784 removed outlier: 3.580A pdb=" N PHE O 782 " --> pdb=" O MET O 778 " (cutoff:3.500A) Processing helix chain 'O' and resid 797 through 811 Processing helix chain 'O' and resid 824 through 838 removed outlier: 4.004A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 863 removed outlier: 3.726A pdb=" N GLU O 853 " --> pdb=" O GLY O 849 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG O 854 " --> pdb=" O SER O 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 856 " --> pdb=" O ASN O 852 " (cutoff:3.500A) Processing helix chain 'O' and resid 873 through 879 removed outlier: 3.645A pdb=" N ILE O 877 " --> pdb=" O PHE O 873 " (cutoff:3.500A) Processing helix chain 'O' and resid 879 through 886 Processing helix chain 'O' and resid 895 through 901 removed outlier: 4.377A pdb=" N ASN O 901 " --> pdb=" O ARG O 898 " (cutoff:3.500A) Processing helix chain 'O' and resid 904 through 913 removed outlier: 3.724A pdb=" N LEU O 908 " --> pdb=" O SER O 904 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN O 911 " --> pdb=" O SER O 907 " (cutoff:3.500A) Processing helix chain 'O' and resid 932 through 942 removed outlier: 3.525A pdb=" N LEU O 942 " --> pdb=" O LEU O 938 " (cutoff:3.500A) Processing helix chain 'O' and resid 942 through 948 Processing helix chain 'O' and resid 948 through 958 removed outlier: 4.842A pdb=" N TRP O 955 " --> pdb=" O SER O 951 " (cutoff:3.500A) Processing helix chain 'O' and resid 968 through 973 Processing helix chain 'O' and resid 975 through 988 removed outlier: 5.346A pdb=" N ARG O 981 " --> pdb=" O LEU O 977 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS O 984 " --> pdb=" O ILE O 980 " (cutoff:3.500A) Processing helix chain 'O' and resid 1016 through 1022 removed outlier: 4.613A pdb=" N MET O1022 " --> pdb=" O LEU O1018 " (cutoff:3.500A) Processing helix chain 'O' and resid 1025 through 1030 removed outlier: 3.596A pdb=" N TYR O1029 " --> pdb=" O GLN O1025 " (cutoff:3.500A) Processing helix chain 'O' and resid 1053 through 1058 removed outlier: 4.161A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE O1058 " --> pdb=" O GLN O1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1053 through 1058' Processing helix chain 'O' and resid 1066 through 1073 Processing helix chain 'O' and resid 1086 through 1103 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1114 through 1127 removed outlier: 4.332A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) Processing helix chain 'O' and resid 1138 through 1151 Processing helix chain 'O' and resid 1162 through 1167 Processing helix chain 'O' and resid 1187 through 1199 removed outlier: 4.065A pdb=" N ALA O1197 " --> pdb=" O ALA O1193 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG O1199 " --> pdb=" O ASP O1195 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1245 removed outlier: 3.947A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) Processing helix chain 'O' and resid 1247 through 1269 removed outlier: 3.898A pdb=" N GLU O1262 " --> pdb=" O LEU O1258 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU O1269 " --> pdb=" O ARG O1265 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1287 Processing helix chain 'O' and resid 1292 through 1307 removed outlier: 3.595A pdb=" N THR O1298 " --> pdb=" O MET O1294 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1349 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.619A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.846A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (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: 6.678A 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 789 through 790 removed outlier: 6.961A pdb=" N ILE O 789 " --> pdb=" O LEU O 992 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 844 through 845 removed outlier: 5.561A pdb=" N ILE O 845 " --> pdb=" O LEU O 870 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR O 872 " --> pdb=" O ILE O 845 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL O 889 " --> pdb=" O ALA O 916 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 1009 through 1011 removed outlier: 3.510A pdb=" N LYS O1009 " --> pdb=" O ILE O1208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG O1210 " --> pdb=" O LYS O1009 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU O1131 " --> pdb=" O ILE O1160 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 331 hydrogen bonds 618 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 1.97 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: 2532 1.32 - 1.44: 5857 1.44 - 1.57: 8606 1.57 - 1.69: 582 1.69 - 1.81: 53 Bond restraints: 17630 Sorted by residual: bond pdb=" N7 DA I 39 " pdb=" C5 DA I 39 " ideal model delta sigma weight residual 1.388 1.361 0.027 6.00e-03 2.78e+04 1.96e+01 bond pdb=" C3' DA J 14 " pdb=" O3' DA J 14 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" C3' DC I 42 " pdb=" O3' DC I 42 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.68e+01 bond pdb=" C3' DT I 38 " pdb=" O3' DT I 38 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.62e+01 ... (remaining 17625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 24538 2.85 - 5.70: 450 5.70 - 8.55: 49 8.55 - 11.41: 9 11.41 - 14.26: 1 Bond angle restraints: 25047 Sorted by residual: angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.51 110.40 -6.89 9.60e-01 1.09e+00 5.15e+01 angle pdb=" O4' DG I 132 " pdb=" C4' DG I 132 " pdb=" C3' DG I 132 " ideal model delta sigma weight residual 106.00 102.09 3.91 6.00e-01 2.78e+00 4.24e+01 angle pdb=" O4' DA I 131 " pdb=" C4' DA I 131 " pdb=" C3' DA I 131 " ideal model delta sigma weight residual 106.00 102.44 3.56 6.00e-01 2.78e+00 3.51e+01 angle pdb=" O4' DA J 36 " pdb=" C4' DA J 36 " pdb=" C3' DA J 36 " ideal model delta sigma weight residual 106.00 102.47 3.53 6.00e-01 2.78e+00 3.46e+01 angle pdb=" O4' DC I 95 " pdb=" C4' DC I 95 " pdb=" C3' DC I 95 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 ... (remaining 25042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.91: 8224 29.91 - 59.81: 1612 59.81 - 89.72: 74 89.72 - 119.63: 2 119.63 - 149.54: 2 Dihedral angle restraints: 9914 sinusoidal: 5995 harmonic: 3919 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 180.00 136.27 43.73 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CA PRO O 926 " pdb=" C PRO O 926 " pdb=" N LEU O 927 " pdb=" CA LEU O 927 " ideal model delta harmonic sigma weight residual -180.00 -148.63 -31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA HIS O 915 " pdb=" C HIS O 915 " pdb=" N ALA O 916 " pdb=" CA ALA O 916 " ideal model delta harmonic sigma weight residual 180.00 149.64 30.36 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1787 0.048 - 0.096: 781 0.096 - 0.144: 257 0.144 - 0.191: 27 0.191 - 0.239: 2 Chirality restraints: 2854 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 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1' DG I 85 " pdb=" O4' DG I 85 " pdb=" C2' DG I 85 " pdb=" N9 DG I 85 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 2851 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 946 " 0.025 2.00e-02 2.50e+03 2.21e-02 8.54e+00 pdb=" CG PHE O 946 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE O 946 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE O 946 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE O 946 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE O 946 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE O 946 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL O 823 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO O 824 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO O 824 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO O 824 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.030 2.00e-02 2.50e+03 1.46e-02 5.84e+00 pdb=" N9 DA I 39 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.023 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 246 2.57 - 3.15: 15870 3.15 - 3.73: 31100 3.73 - 4.32: 40947 4.32 - 4.90: 59006 Nonbonded interactions: 147169 Sorted by model distance: nonbonded pdb=" O ARG O 880 " pdb=" OG SER O 884 " model vdw 1.986 3.040 nonbonded pdb=" O GLU O1338 " pdb=" OG SER O1342 " model vdw 2.015 3.040 nonbonded pdb=" O2 DC I 11 " pdb=" N2 DG J 137 " model vdw 2.047 2.496 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.058 2.496 nonbonded pdb=" O2 DC I 110 " pdb=" N2 DG J 38 " model vdw 2.061 2.496 ... (remaining 147164 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 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.970 Find NCS groups from input model: 0.170 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.011 0.060 17630 Z= 0.841 Angle : 1.042 14.257 25047 Z= 0.774 Chirality : 0.056 0.239 2854 Planarity : 0.005 0.067 2163 Dihedral : 24.667 149.536 7370 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 28.05 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.06 % Favored : 90.49 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.16 % 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: -5.29 (0.16), residues: 1314 helix: -3.93 (0.10), residues: 826 sheet: -3.72 (0.39), residues: 70 loop : -1.89 (0.24), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG O 982 TYR 0.033 0.004 TYR B 98 PHE 0.049 0.004 PHE O 946 TRP 0.012 0.003 TRP O 831 HIS 0.014 0.003 HIS O 897 Details of bonding type rmsd/Z covalent geometry : bond 0.01106 / 0.84 (17630) covalent geometry : angle 1.04163 / 0.77 (25047) hydrogen bonds : bond 0.14482 / 9.18 ( 952) hydrogen bonds : angle 9.94739 / 7.06 ( 2442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.523 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: A 41 TYR cc_start: 0.7708 (m-80) cc_final: 0.7352 (m-80) REVERT: A 58 THR cc_start: 0.9183 (p) cc_final: 0.8935 (t) REVERT: A 87 SER cc_start: 0.9040 (p) cc_final: 0.8827 (t) REVERT: A 125 GLN cc_start: 0.9053 (mt0) cc_final: 0.8802 (mm-40) REVERT: B 53 GLU cc_start: 0.9020 (tp30) cc_final: 0.8734 (mm-30) REVERT: B 59 LYS cc_start: 0.8811 (tttt) cc_final: 0.8181 (tttm) REVERT: B 63 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8350 (mt-10) REVERT: C 38 ASN cc_start: 0.8458 (m-40) cc_final: 0.8134 (m-40) REVERT: D 37 TYR cc_start: 0.8769 (m-80) cc_final: 0.8547 (m-80) REVERT: D 56 MET cc_start: 0.8984 (tpp) cc_final: 0.8743 (tpp) REVERT: D 82 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8689 (mmtm) REVERT: D 102 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8442 (mm-30) REVERT: D 117 LYS cc_start: 0.8880 (tttp) cc_final: 0.8299 (ttmt) REVERT: E 56 LYS cc_start: 0.9284 (tttp) cc_final: 0.8976 (tppt) REVERT: E 73 GLU cc_start: 0.8587 (tt0) cc_final: 0.8002 (tt0) REVERT: E 93 GLN cc_start: 0.8592 (tt0) cc_final: 0.8192 (tt0) REVERT: E 120 MET cc_start: 0.9182 (mtp) cc_final: 0.8959 (mtp) REVERT: E 125 GLN cc_start: 0.8790 (mt0) cc_final: 0.8530 (mp10) REVERT: F 25 ASN cc_start: 0.8504 (m-40) cc_final: 0.7299 (m110) REVERT: F 52 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8727 (mm-30) REVERT: F 53 GLU cc_start: 0.8579 (tp30) cc_final: 0.7752 (tp30) REVERT: F 55 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8023 (mtm-85) REVERT: F 96 THR cc_start: 0.9362 (m) cc_final: 0.9106 (p) REVERT: H 37 TYR cc_start: 0.9246 (m-80) cc_final: 0.8883 (m-80) REVERT: H 59 MET cc_start: 0.8821 (mmm) cc_final: 0.8508 (mmm) REVERT: H 83 ARG cc_start: 0.8773 (mmt-90) cc_final: 0.7482 (mmt90) REVERT: H 85 THR cc_start: 0.8960 (m) cc_final: 0.8744 (t) REVERT: O 888 TRP cc_start: 0.6233 (m100) cc_final: 0.5843 (m100) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.1960 time to fit residues: 113.5803 Evaluate side-chains 252 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 92 GLN F 25 ASN F 64 ASN G 94 ASN H 81 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 928 GLN ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 947 ASN O1025 GLN ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1188 HIS O1198 HIS O1204 ASN O1347 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.081653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059057 restraints weight = 61517.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060672 restraints weight = 32380.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061701 restraints weight = 21742.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062295 restraints weight = 17234.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062651 restraints weight = 15174.155| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17630 Z= 0.221 Angle : 0.833 13.370 25047 Z= 0.465 Chirality : 0.050 0.255 2854 Planarity : 0.007 0.092 2163 Dihedral : 29.985 151.122 4669 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 3.32 % Allowed : 11.79 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.16 % 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: -2.23 (0.20), residues: 1314 helix: -1.19 (0.16), residues: 829 sheet: -3.05 (0.46), residues: 69 loop : -1.39 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 982 TYR 0.025 0.003 TYR B 98 PHE 0.047 0.003 PHE O 946 TRP 0.023 0.003 TRP O 955 HIS 0.009 0.002 HIS O1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (17630) covalent geometry : angle 0.83275 / 0.46 (25047) hydrogen bonds : bond 0.08887 / 5.84 ( 952) hydrogen bonds : angle 6.13447 / 4.39 ( 2442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 0.491 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: A 87 SER cc_start: 0.8987 (p) cc_final: 0.8709 (t) REVERT: B 59 LYS cc_start: 0.8673 (tttt) cc_final: 0.8148 (tttm) REVERT: B 63 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 92 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8275 (tpt90) REVERT: D 90 GLU cc_start: 0.8305 (mp0) cc_final: 0.8092 (mp0) REVERT: D 117 LYS cc_start: 0.8702 (tttp) cc_final: 0.8072 (ttmt) REVERT: E 56 LYS cc_start: 0.8752 (tttp) cc_final: 0.8450 (tppt) REVERT: E 79 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8532 (ttmt) REVERT: E 90 MET cc_start: 0.8225 (mmm) cc_final: 0.7491 (mmm) REVERT: E 94 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7686 (mm-30) REVERT: F 29 ILE cc_start: 0.9099 (mm) cc_final: 0.8864 (mm) REVERT: F 53 GLU cc_start: 0.8009 (tp30) cc_final: 0.6638 (tp30) REVERT: F 55 ARG cc_start: 0.8555 (mtt90) cc_final: 0.8135 (mtm-85) REVERT: G 91 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8093 (tm-30) REVERT: G 101 THR cc_start: 0.9224 (m) cc_final: 0.8945 (p) REVERT: H 82 LYS cc_start: 0.9074 (mptt) cc_final: 0.8832 (mmtt) REVERT: H 90 GLU cc_start: 0.8269 (mp0) cc_final: 0.8012 (mp0) REVERT: O 843 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8324 (ttm110) REVERT: O 891 MET cc_start: 0.8741 (ttm) cc_final: 0.8001 (mtp) REVERT: O 1116 MET cc_start: 0.7866 (mtm) cc_final: 0.7439 (mtt) REVERT: O 1119 MET cc_start: 0.8349 (ttp) cc_final: 0.8097 (ttp) REVERT: O 1158 CYS cc_start: 0.7609 (m) cc_final: 0.7109 (t) REVERT: O 1294 MET cc_start: 0.8050 (mmm) cc_final: 0.7630 (mmm) outliers start: 38 outliers final: 21 residues processed: 327 average time/residue: 0.1507 time to fit residues: 71.8190 Evaluate side-chains 271 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 820 LEU Chi-restraints excluded: chain O residue 981 ARG Chi-restraints excluded: chain O residue 1001 LYS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1229 LEU Chi-restraints excluded: chain O residue 1248 GLU Chi-restraints excluded: chain O residue 1263 GLU Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 85 GLN A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN ** O 783 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 ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1204 ASN O1347 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.081826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059187 restraints weight = 61624.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060800 restraints weight = 32295.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061812 restraints weight = 21737.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062406 restraints weight = 17276.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062755 restraints weight = 15215.208| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17630 Z= 0.200 Angle : 0.762 12.155 25047 Z= 0.429 Chirality : 0.048 0.259 2854 Planarity : 0.006 0.066 2163 Dihedral : 29.740 150.866 4669 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 3.14 % Allowed : 15.20 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.16 % 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: -0.95 (0.22), residues: 1314 helix: -0.08 (0.18), residues: 828 sheet: -2.66 (0.47), residues: 71 loop : -1.13 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 81 TYR 0.034 0.003 TYR F 51 PHE 0.044 0.003 PHE O 946 TRP 0.016 0.002 TRP O 777 HIS 0.004 0.001 HIS O 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (17630) covalent geometry : angle 0.76209 / 0.43 (25047) hydrogen bonds : bond 0.08073 / 5.27 ( 952) hydrogen bonds : angle 5.46278 / 3.89 ( 2442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 0.520 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 73 GLU cc_start: 0.7976 (tt0) cc_final: 0.7424 (tt0) REVERT: A 87 SER cc_start: 0.9006 (p) cc_final: 0.8743 (t) REVERT: B 53 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7896 (tp30) REVERT: B 59 LYS cc_start: 0.8675 (tttt) cc_final: 0.8225 (tttt) REVERT: B 63 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 100 PHE cc_start: 0.8694 (m-80) cc_final: 0.8472 (m-10) REVERT: C 94 ASN cc_start: 0.9024 (t0) cc_final: 0.8797 (t0) REVERT: D 117 LYS cc_start: 0.8680 (tttp) cc_final: 0.8075 (ttpp) REVERT: E 56 LYS cc_start: 0.8803 (tttp) cc_final: 0.8452 (tppt) REVERT: E 90 MET cc_start: 0.8105 (mmm) cc_final: 0.7632 (mmm) REVERT: F 25 ASN cc_start: 0.8402 (m-40) cc_final: 0.7256 (m-40) REVERT: F 52 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8108 (mm-30) REVERT: F 92 ARG cc_start: 0.8275 (tpt90) cc_final: 0.8034 (tpt90) REVERT: F 93 GLN cc_start: 0.8803 (mt0) cc_final: 0.8571 (mt0) REVERT: G 61 GLU cc_start: 0.7966 (tp30) cc_final: 0.7573 (tp30) REVERT: G 84 GLN cc_start: 0.9047 (tp40) cc_final: 0.8525 (tm-30) REVERT: G 91 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7128 (tm-30) REVERT: G 92 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: G 101 THR cc_start: 0.9140 (m) cc_final: 0.8872 (p) REVERT: O 935 TRP cc_start: 0.8016 (m-10) cc_final: 0.7294 (m100) REVERT: O 1112 MET cc_start: 0.8255 (mtp) cc_final: 0.8028 (mtp) REVERT: O 1116 MET cc_start: 0.7892 (mtm) cc_final: 0.7443 (mtm) REVERT: O 1158 CYS cc_start: 0.7739 (m) cc_final: 0.7055 (t) REVERT: O 1248 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: O 1294 MET cc_start: 0.8106 (mmm) cc_final: 0.7717 (mmm) outliers start: 36 outliers final: 23 residues processed: 298 average time/residue: 0.1450 time to fit residues: 63.5543 Evaluate side-chains 265 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1229 LEU Chi-restraints excluded: chain O residue 1248 GLU Chi-restraints excluded: chain O residue 1263 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1050 ASN ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.081199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058746 restraints weight = 61590.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.060205 restraints weight = 34224.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.061121 restraints weight = 23821.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061689 restraints weight = 19316.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061910 restraints weight = 17113.368| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17630 Z= 0.224 Angle : 0.762 12.465 25047 Z= 0.425 Chirality : 0.046 0.238 2854 Planarity : 0.005 0.070 2163 Dihedral : 29.611 150.106 4669 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 4.89 % Allowed : 15.63 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1314 helix: 0.05 (0.18), residues: 840 sheet: -2.44 (0.49), residues: 71 loop : -1.13 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 843 TYR 0.034 0.002 TYR F 88 PHE 0.045 0.003 PHE O 946 TRP 0.016 0.003 TRP O 777 HIS 0.005 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (17630) covalent geometry : angle 0.76248 / 0.42 (25047) hydrogen bonds : bond 0.07937 / 5.18 ( 952) hydrogen bonds : angle 5.28686 / 3.74 ( 2442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 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: A 73 GLU cc_start: 0.7942 (tt0) cc_final: 0.7275 (tt0) REVERT: A 87 SER cc_start: 0.9030 (p) cc_final: 0.8814 (t) REVERT: A 105 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 53 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7911 (tp30) REVERT: B 59 LYS cc_start: 0.8711 (tttt) cc_final: 0.8209 (tttt) REVERT: B 63 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 68 ASP cc_start: 0.8531 (m-30) cc_final: 0.8307 (m-30) REVERT: B 80 THR cc_start: 0.8809 (p) cc_final: 0.8486 (p) REVERT: C 84 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.8753 (tp40) REVERT: D 117 LYS cc_start: 0.8720 (tttp) cc_final: 0.7979 (ttmt) REVERT: E 56 LYS cc_start: 0.8861 (tttp) cc_final: 0.8485 (tppt) REVERT: E 108 ASN cc_start: 0.9303 (t0) cc_final: 0.8906 (t0) REVERT: F 25 ASN cc_start: 0.8260 (m-40) cc_final: 0.7307 (m-40) REVERT: F 92 ARG cc_start: 0.8305 (tpt90) cc_final: 0.8076 (tpt90) REVERT: F 93 GLN cc_start: 0.8755 (mt0) cc_final: 0.8530 (mt0) REVERT: G 25 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.9017 (m-80) REVERT: G 61 GLU cc_start: 0.8041 (tp30) cc_final: 0.7610 (tp30) REVERT: G 84 GLN cc_start: 0.8944 (tp40) cc_final: 0.8416 (tp40) REVERT: G 89 ASN cc_start: 0.8746 (m-40) cc_final: 0.8436 (m110) REVERT: G 91 GLU cc_start: 0.8010 (tm-30) cc_final: 0.6958 (tm-30) REVERT: G 92 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: O 1026 MET cc_start: 0.7128 (mmm) cc_final: 0.6836 (tpp) REVERT: O 1053 MET cc_start: 0.9072 (mtt) cc_final: 0.8825 (mtt) REVERT: O 1112 MET cc_start: 0.8239 (mtp) cc_final: 0.7924 (mtp) REVERT: O 1158 CYS cc_start: 0.7755 (m) cc_final: 0.7041 (t) REVERT: O 1248 GLU cc_start: 0.8939 (tp30) cc_final: 0.8075 (pm20) REVERT: O 1294 MET cc_start: 0.8077 (mmm) cc_final: 0.7670 (mmm) REVERT: O 1337 ARG cc_start: 0.7615 (mmp80) cc_final: 0.7297 (mmp80) outliers start: 56 outliers final: 40 residues processed: 282 average time/residue: 0.1381 time to fit residues: 57.6900 Evaluate side-chains 277 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain O residue 828 LEU Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1200 ILE Chi-restraints excluded: chain O residue 1229 LEU Chi-restraints excluded: chain O residue 1263 GLU Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.060159 restraints weight = 60887.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061798 restraints weight = 31857.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062818 restraints weight = 21346.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063412 restraints weight = 16947.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063750 restraints weight = 14917.127| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17630 Z= 0.160 Angle : 0.708 14.898 25047 Z= 0.399 Chirality : 0.045 0.239 2854 Planarity : 0.005 0.070 2163 Dihedral : 29.424 150.328 4669 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.84 % Allowed : 16.07 % Favored : 80.09 % 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: -0.36 (0.23), residues: 1314 helix: 0.42 (0.18), residues: 842 sheet: -1.88 (0.53), residues: 72 loop : -1.13 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 919 TYR 0.026 0.002 TYR H 37 PHE 0.039 0.002 PHE O 946 TRP 0.018 0.003 TRP O 777 HIS 0.004 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (17630) covalent geometry : angle 0.70795 / 0.40 (25047) hydrogen bonds : bond 0.07605 / 4.94 ( 952) hydrogen bonds : angle 4.99332 / 3.55 ( 2442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.498 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: A 125 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8040 (mm-40) REVERT: B 59 LYS cc_start: 0.8728 (tttt) cc_final: 0.8126 (tttt) REVERT: B 63 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 80 THR cc_start: 0.8735 (p) cc_final: 0.8443 (p) REVERT: D 102 GLU cc_start: 0.7898 (pm20) cc_final: 0.7516 (pp20) REVERT: D 117 LYS cc_start: 0.8707 (tttp) cc_final: 0.7955 (ttmt) REVERT: E 56 LYS cc_start: 0.8679 (tttp) cc_final: 0.8332 (tppt) REVERT: E 73 GLU cc_start: 0.7636 (tt0) cc_final: 0.7187 (mt-10) REVERT: E 105 GLU cc_start: 0.7516 (tp30) cc_final: 0.7284 (tp30) REVERT: E 108 ASN cc_start: 0.9351 (t0) cc_final: 0.9054 (t0) REVERT: E 125 GLN cc_start: 0.8197 (mp10) cc_final: 0.7920 (mp10) REVERT: F 25 ASN cc_start: 0.7909 (m-40) cc_final: 0.6721 (m-40) REVERT: F 92 ARG cc_start: 0.8280 (tpt90) cc_final: 0.7949 (tpt90) REVERT: G 84 GLN cc_start: 0.8971 (tp40) cc_final: 0.8633 (tm-30) REVERT: G 89 ASN cc_start: 0.8708 (m-40) cc_final: 0.8181 (m110) REVERT: G 91 GLU cc_start: 0.7995 (tm-30) cc_final: 0.6936 (tm-30) REVERT: G 92 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: H 32 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7749 (tm-30) REVERT: O 1026 MET cc_start: 0.6858 (mmm) cc_final: 0.6579 (tpp) REVERT: O 1053 MET cc_start: 0.9092 (mtt) cc_final: 0.8837 (mtt) REVERT: O 1112 MET cc_start: 0.8125 (mtp) cc_final: 0.7837 (mtp) REVERT: O 1158 CYS cc_start: 0.7724 (m) cc_final: 0.7012 (t) REVERT: O 1248 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: O 1294 MET cc_start: 0.7991 (mmm) cc_final: 0.7606 (mmm) outliers start: 44 outliers final: 28 residues processed: 298 average time/residue: 0.1339 time to fit residues: 59.4756 Evaluate side-chains 271 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1229 LEU Chi-restraints excluded: chain O residue 1248 GLU Chi-restraints excluded: chain O residue 1263 GLU Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 137 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 939 ASN ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.081956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.059269 restraints weight = 60893.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060902 restraints weight = 31907.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061925 restraints weight = 21392.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062463 restraints weight = 16937.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062864 restraints weight = 15002.955| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17630 Z= 0.198 Angle : 0.728 12.315 25047 Z= 0.408 Chirality : 0.045 0.238 2854 Planarity : 0.005 0.071 2163 Dihedral : 29.383 149.266 4669 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.49 % Allowed : 18.60 % Favored : 77.90 % 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: -0.37 (0.23), residues: 1314 helix: 0.42 (0.18), residues: 846 sheet: -1.63 (0.55), residues: 72 loop : -1.24 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 89 TYR 0.042 0.002 TYR F 88 PHE 0.039 0.002 PHE O 946 TRP 0.054 0.003 TRP O 935 HIS 0.004 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (17630) covalent geometry : angle 0.72789 / 0.41 (25047) hydrogen bonds : bond 0.07580 / 4.92 ( 952) hydrogen bonds : angle 4.99973 / 3.54 ( 2442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8051 (tt0) cc_final: 0.7360 (tt0) REVERT: A 105 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 125 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8074 (mm-40) REVERT: B 35 ARG cc_start: 0.8382 (mmm160) cc_final: 0.8148 (mmm160) REVERT: B 59 LYS cc_start: 0.8717 (tttt) cc_final: 0.8159 (tttt) REVERT: B 63 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 80 THR cc_start: 0.8778 (p) cc_final: 0.8461 (p) REVERT: C 84 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8826 (tp40) REVERT: D 82 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8380 (mmmt) REVERT: D 117 LYS cc_start: 0.8730 (tttp) cc_final: 0.7974 (ttmt) REVERT: E 56 LYS cc_start: 0.8823 (tttp) cc_final: 0.8479 (tppt) REVERT: E 73 GLU cc_start: 0.7524 (tt0) cc_final: 0.7068 (mt-10) REVERT: E 105 GLU cc_start: 0.7641 (tp30) cc_final: 0.7401 (tp30) REVERT: E 108 ASN cc_start: 0.9465 (t0) cc_final: 0.9107 (t0) REVERT: F 25 ASN cc_start: 0.7933 (m-40) cc_final: 0.6857 (m-40) REVERT: F 53 GLU cc_start: 0.7420 (tp30) cc_final: 0.7186 (tp30) REVERT: F 92 ARG cc_start: 0.8318 (tpt90) cc_final: 0.8035 (tpt90) REVERT: G 84 GLN cc_start: 0.8918 (tp40) cc_final: 0.8600 (tm-30) REVERT: G 89 ASN cc_start: 0.8709 (m-40) cc_final: 0.8243 (m110) REVERT: G 91 GLU cc_start: 0.7977 (tm-30) cc_final: 0.6957 (tm-30) REVERT: G 92 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: H 32 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7839 (tm-30) REVERT: O 935 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.6462 (m100) REVERT: O 1015 MET cc_start: 0.6220 (ttt) cc_final: 0.5961 (ttm) REVERT: O 1026 MET cc_start: 0.6895 (mmm) cc_final: 0.6614 (tpp) REVERT: O 1053 MET cc_start: 0.9098 (mtt) cc_final: 0.8777 (mtt) REVERT: O 1158 CYS cc_start: 0.7766 (m) cc_final: 0.7032 (t) REVERT: O 1248 GLU cc_start: 0.8817 (tp30) cc_final: 0.8171 (pm20) REVERT: O 1294 MET cc_start: 0.7858 (mmm) cc_final: 0.7477 (mmm) outliers start: 40 outliers final: 29 residues processed: 276 average time/residue: 0.1474 time to fit residues: 59.8906 Evaluate side-chains 271 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1061 HIS ** O1198 HIS ** 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 = 0.3534 r_free = 0.3534 target = 0.083017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.060202 restraints weight = 60242.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061836 restraints weight = 31519.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062857 restraints weight = 21182.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063438 restraints weight = 16803.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063812 restraints weight = 14815.794| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17630 Z= 0.159 Angle : 0.688 12.567 25047 Z= 0.391 Chirality : 0.044 0.241 2854 Planarity : 0.005 0.069 2163 Dihedral : 29.246 149.276 4669 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 3.23 % Allowed : 19.13 % Favored : 77.64 % 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: -0.13 (0.23), residues: 1314 helix: 0.62 (0.18), residues: 844 sheet: -1.44 (0.57), residues: 78 loop : -1.18 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.027 0.002 TYR H 37 PHE 0.036 0.002 PHE O 946 TRP 0.046 0.004 TRP O 935 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (17630) covalent geometry : angle 0.68836 / 0.39 (25047) hydrogen bonds : bond 0.07391 / 4.79 ( 952) hydrogen bonds : angle 4.75165 / 3.38 ( 2442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7970 (tt0) cc_final: 0.7479 (tt0) REVERT: A 105 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 125 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8040 (mm-40) REVERT: B 35 ARG cc_start: 0.8362 (mmm160) cc_final: 0.8145 (mmm160) REVERT: B 47 SER cc_start: 0.8917 (t) cc_final: 0.8554 (m) REVERT: B 63 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 80 THR cc_start: 0.8800 (p) cc_final: 0.8488 (p) REVERT: C 84 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8806 (tp40) REVERT: D 82 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8331 (mmmt) REVERT: D 90 GLU cc_start: 0.8281 (mp0) cc_final: 0.8056 (mp0) REVERT: D 117 LYS cc_start: 0.8686 (tttp) cc_final: 0.7933 (ttmt) REVERT: E 56 LYS cc_start: 0.8731 (tttp) cc_final: 0.8365 (tppt) REVERT: E 73 GLU cc_start: 0.7506 (tt0) cc_final: 0.6844 (mt-10) REVERT: E 105 GLU cc_start: 0.7563 (tp30) cc_final: 0.7348 (tp30) REVERT: E 108 ASN cc_start: 0.9377 (t0) cc_final: 0.9061 (t0) REVERT: F 25 ASN cc_start: 0.7856 (m-40) cc_final: 0.6397 (m-40) REVERT: F 92 ARG cc_start: 0.8337 (tpt90) cc_final: 0.8092 (tpt90) REVERT: G 84 GLN cc_start: 0.8930 (tp40) cc_final: 0.8636 (tm-30) REVERT: G 89 ASN cc_start: 0.8727 (m-40) cc_final: 0.8210 (m110) REVERT: G 91 GLU cc_start: 0.7999 (tm-30) cc_final: 0.6989 (tm-30) REVERT: G 92 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: O 935 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.6195 (m100) REVERT: O 946 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7797 (p90) REVERT: O 1026 MET cc_start: 0.6684 (mmm) cc_final: 0.6417 (tpp) REVERT: O 1053 MET cc_start: 0.9111 (mtt) cc_final: 0.8790 (mtt) REVERT: O 1158 CYS cc_start: 0.7702 (m) cc_final: 0.7001 (t) REVERT: O 1248 GLU cc_start: 0.8718 (tp30) cc_final: 0.8086 (pm20) REVERT: O 1249 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8008 (mt-10) REVERT: O 1294 MET cc_start: 0.7711 (mmm) cc_final: 0.7351 (mmm) outliers start: 37 outliers final: 29 residues processed: 292 average time/residue: 0.1409 time to fit residues: 61.0443 Evaluate side-chains 283 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 946 PHE Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 145 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 154 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 93 GLN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060672 restraints weight = 60367.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.062331 restraints weight = 31387.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063371 restraints weight = 20979.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064000 restraints weight = 16634.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064354 restraints weight = 14614.206| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17630 Z= 0.161 Angle : 0.703 13.300 25047 Z= 0.395 Chirality : 0.044 0.241 2854 Planarity : 0.005 0.069 2163 Dihedral : 29.197 148.859 4669 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.06 % Allowed : 20.26 % Favored : 76.68 % 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: -0.01 (0.23), residues: 1314 helix: 0.73 (0.18), residues: 844 sheet: -1.40 (0.57), residues: 78 loop : -1.19 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.024 0.002 TYR H 37 PHE 0.036 0.002 PHE O 946 TRP 0.046 0.004 TRP O 777 HIS 0.007 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (17630) covalent geometry : angle 0.70280 / 0.40 (25047) hydrogen bonds : bond 0.07349 / 4.76 ( 952) hydrogen bonds : angle 4.70420 / 3.34 ( 2442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.521 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: A 73 GLU cc_start: 0.8002 (tt0) cc_final: 0.7487 (tt0) REVERT: A 105 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 47 SER cc_start: 0.8806 (t) cc_final: 0.8430 (m) REVERT: B 63 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7873 (mt-10) REVERT: B 80 THR cc_start: 0.8605 (p) cc_final: 0.8289 (p) REVERT: C 84 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8757 (tp40) REVERT: C 100 VAL cc_start: 0.9608 (t) cc_final: 0.9346 (p) REVERT: D 82 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8337 (mmmt) REVERT: D 117 LYS cc_start: 0.8676 (tttp) cc_final: 0.7914 (ttmt) REVERT: E 56 LYS cc_start: 0.8700 (tttp) cc_final: 0.8362 (tppt) REVERT: E 73 GLU cc_start: 0.7502 (tt0) cc_final: 0.6786 (mt-10) REVERT: E 93 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7309 (tm-30) REVERT: E 108 ASN cc_start: 0.9391 (t0) cc_final: 0.9071 (t0) REVERT: F 25 ASN cc_start: 0.7867 (m-40) cc_final: 0.6329 (m-40) REVERT: F 53 GLU cc_start: 0.7685 (tp30) cc_final: 0.6946 (tp30) REVERT: F 92 ARG cc_start: 0.8358 (tpt90) cc_final: 0.8129 (tpt90) REVERT: G 84 GLN cc_start: 0.8915 (tp40) cc_final: 0.8664 (tm-30) REVERT: G 89 ASN cc_start: 0.8705 (m-40) cc_final: 0.8202 (m110) REVERT: G 91 GLU cc_start: 0.7971 (tm-30) cc_final: 0.6935 (tm-30) REVERT: G 92 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: H 59 MET cc_start: 0.8893 (mmm) cc_final: 0.8592 (mmm) REVERT: O 790 LEU cc_start: 0.7469 (tp) cc_final: 0.7090 (tt) REVERT: O 935 TRP cc_start: 0.7752 (OUTLIER) cc_final: 0.6477 (m100) REVERT: O 946 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7562 (p90) REVERT: O 987 LEU cc_start: 0.8428 (mt) cc_final: 0.8220 (tp) REVERT: O 1026 MET cc_start: 0.6857 (mmm) cc_final: 0.6606 (tpp) REVERT: O 1053 MET cc_start: 0.9136 (mtt) cc_final: 0.8792 (mtt) REVERT: O 1116 MET cc_start: 0.7577 (mpp) cc_final: 0.6755 (mtt) REVERT: O 1158 CYS cc_start: 0.7597 (m) cc_final: 0.6851 (t) REVERT: O 1248 GLU cc_start: 0.8622 (tp30) cc_final: 0.7886 (pm20) REVERT: O 1249 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8356 (mt-10) REVERT: O 1294 MET cc_start: 0.7711 (mmm) cc_final: 0.7355 (mmm) outliers start: 35 outliers final: 26 residues processed: 282 average time/residue: 0.1401 time to fit residues: 59.2387 Evaluate side-chains 277 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 946 PHE Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1073 ASN ** O1198 HIS ** 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 = 0.3536 r_free = 0.3536 target = 0.083145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.060226 restraints weight = 60313.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061850 restraints weight = 31490.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062878 restraints weight = 21150.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063424 restraints weight = 16807.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063817 restraints weight = 14879.264| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17630 Z= 0.169 Angle : 0.722 16.180 25047 Z= 0.400 Chirality : 0.044 0.244 2854 Planarity : 0.005 0.061 2163 Dihedral : 29.144 148.214 4669 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 3.06 % Allowed : 20.61 % Favored : 76.33 % 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: 0.06 (0.23), residues: 1314 helix: 0.75 (0.18), residues: 852 sheet: -1.26 (0.59), residues: 78 loop : -1.13 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 89 TYR 0.024 0.002 TYR H 37 PHE 0.036 0.002 PHE O 946 TRP 0.059 0.005 TRP O 777 HIS 0.004 0.001 HIS O1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (17630) covalent geometry : angle 0.72215 / 0.40 (25047) hydrogen bonds : bond 0.07329 / 4.75 ( 952) hydrogen bonds : angle 4.70885 / 3.34 ( 2442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.535 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: A 105 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 120 MET cc_start: 0.8521 (mmm) cc_final: 0.8269 (mmm) REVERT: B 47 SER cc_start: 0.8761 (t) cc_final: 0.8406 (m) REVERT: B 63 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 80 THR cc_start: 0.8600 (p) cc_final: 0.8306 (p) REVERT: C 84 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8747 (tp40) REVERT: D 82 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8365 (mmmt) REVERT: D 117 LYS cc_start: 0.8750 (tttp) cc_final: 0.8007 (ttmt) REVERT: E 56 LYS cc_start: 0.8703 (tttp) cc_final: 0.8419 (tppt) REVERT: E 73 GLU cc_start: 0.7538 (tt0) cc_final: 0.7187 (mt-10) REVERT: E 108 ASN cc_start: 0.9412 (t0) cc_final: 0.9088 (t0) REVERT: F 53 GLU cc_start: 0.7543 (tp30) cc_final: 0.7163 (tp30) REVERT: F 92 ARG cc_start: 0.8387 (tpt90) cc_final: 0.8182 (tpt90) REVERT: G 84 GLN cc_start: 0.8879 (tp40) cc_final: 0.8183 (tp-100) REVERT: G 89 ASN cc_start: 0.8725 (m-40) cc_final: 0.8260 (m110) REVERT: G 90 ASP cc_start: 0.8607 (t70) cc_final: 0.8182 (t0) REVERT: G 91 GLU cc_start: 0.7943 (tm-30) cc_final: 0.6945 (tm-30) REVERT: G 92 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: O 790 LEU cc_start: 0.7465 (tp) cc_final: 0.7022 (tt) REVERT: O 888 TRP cc_start: 0.7090 (m100) cc_final: 0.6486 (m100) REVERT: O 935 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.6551 (m100) REVERT: O 946 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7577 (p90) REVERT: O 1053 MET cc_start: 0.9149 (mtt) cc_final: 0.8808 (mtt) REVERT: O 1112 MET cc_start: 0.7735 (ttt) cc_final: 0.7499 (ttm) REVERT: O 1116 MET cc_start: 0.7854 (mpp) cc_final: 0.7274 (mtm) REVERT: O 1122 PHE cc_start: 0.7818 (t80) cc_final: 0.6844 (t80) REVERT: O 1158 CYS cc_start: 0.7632 (m) cc_final: 0.6848 (t) REVERT: O 1248 GLU cc_start: 0.8643 (tp30) cc_final: 0.7913 (pm20) REVERT: O 1249 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8254 (mt-10) REVERT: O 1294 MET cc_start: 0.7762 (mmm) cc_final: 0.7403 (mmm) outliers start: 35 outliers final: 28 residues processed: 273 average time/residue: 0.1372 time to fit residues: 56.3567 Evaluate side-chains 275 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 946 PHE Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1184 ASP Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1111 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.083211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060300 restraints weight = 60396.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061909 restraints weight = 31823.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062923 restraints weight = 21461.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063526 restraints weight = 17041.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063768 restraints weight = 14991.429| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17630 Z= 0.178 Angle : 0.730 12.084 25047 Z= 0.404 Chirality : 0.044 0.244 2854 Planarity : 0.005 0.066 2163 Dihedral : 29.110 147.830 4669 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.06 % Allowed : 21.14 % Favored : 75.81 % 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: 0.12 (0.23), residues: 1314 helix: 0.80 (0.18), residues: 850 sheet: -1.20 (0.59), residues: 78 loop : -1.11 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.026 0.002 TYR H 37 PHE 0.036 0.002 PHE O 946 TRP 0.094 0.006 TRP O 777 HIS 0.004 0.001 HIS O1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (17630) covalent geometry : angle 0.73034 / 0.40 (25047) hydrogen bonds : bond 0.07327 / 4.74 ( 952) hydrogen bonds : angle 4.70955 / 3.34 ( 2442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 120 MET cc_start: 0.8505 (mmm) cc_final: 0.8272 (mmm) REVERT: B 35 ARG cc_start: 0.8387 (mmm160) cc_final: 0.8126 (mmm160) REVERT: B 47 SER cc_start: 0.8830 (t) cc_final: 0.8419 (m) REVERT: B 63 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 80 THR cc_start: 0.8643 (p) cc_final: 0.8357 (p) REVERT: C 84 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.8760 (tp40) REVERT: D 82 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8357 (mmmt) REVERT: D 117 LYS cc_start: 0.8750 (tttp) cc_final: 0.8009 (ttmt) REVERT: E 56 LYS cc_start: 0.8697 (tttp) cc_final: 0.8410 (tppt) REVERT: E 73 GLU cc_start: 0.7590 (tt0) cc_final: 0.7218 (mt-10) REVERT: E 97 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6764 (mt-10) REVERT: E 108 ASN cc_start: 0.9474 (t0) cc_final: 0.9132 (t0) REVERT: F 92 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8196 (tpt90) REVERT: G 84 GLN cc_start: 0.8864 (tp40) cc_final: 0.8179 (tp-100) REVERT: G 89 ASN cc_start: 0.8709 (m-40) cc_final: 0.8274 (m110) REVERT: G 90 ASP cc_start: 0.8614 (t70) cc_final: 0.8237 (t0) REVERT: G 91 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7051 (tm-30) REVERT: G 92 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: O 790 LEU cc_start: 0.7584 (tp) cc_final: 0.7357 (tt) REVERT: O 888 TRP cc_start: 0.7108 (m100) cc_final: 0.6461 (m100) REVERT: O 935 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.6600 (m100) REVERT: O 946 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7627 (p90) REVERT: O 955 TRP cc_start: 0.5175 (m100) cc_final: 0.4759 (m100) REVERT: O 1053 MET cc_start: 0.9042 (mtt) cc_final: 0.8841 (mtt) REVERT: O 1112 MET cc_start: 0.7630 (ttt) cc_final: 0.7374 (ttm) REVERT: O 1116 MET cc_start: 0.7653 (mpp) cc_final: 0.7324 (mtm) REVERT: O 1158 CYS cc_start: 0.7648 (m) cc_final: 0.6851 (t) REVERT: O 1248 GLU cc_start: 0.8711 (tp30) cc_final: 0.8076 (pm20) REVERT: O 1249 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8367 (mt-10) REVERT: O 1294 MET cc_start: 0.7740 (mmm) cc_final: 0.7391 (mmm) outliers start: 35 outliers final: 30 residues processed: 269 average time/residue: 0.1321 time to fit residues: 53.1353 Evaluate side-chains 277 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 946 PHE Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1184 ASP Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060381 restraints weight = 60568.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061995 restraints weight = 31918.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.063009 restraints weight = 21425.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063599 restraints weight = 17023.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063920 restraints weight = 14996.960| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17630 Z= 0.184 Angle : 0.738 12.276 25047 Z= 0.407 Chirality : 0.044 0.246 2854 Planarity : 0.005 0.064 2163 Dihedral : 29.086 147.668 4669 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.06 % Allowed : 21.66 % Favored : 75.28 % 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: 0.11 (0.23), residues: 1314 helix: 0.78 (0.18), residues: 853 sheet: -0.94 (0.63), residues: 62 loop : -1.18 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 35 TYR 0.027 0.002 TYR H 37 PHE 0.037 0.002 PHE O 946 TRP 0.119 0.007 TRP O 777 HIS 0.005 0.001 HIS O1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (17630) covalent geometry : angle 0.73767 / 0.41 (25047) hydrogen bonds : bond 0.07333 / 4.75 ( 952) hydrogen bonds : angle 4.71789 / 3.35 ( 2442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.06 seconds wall clock time: 53 minutes 8.34 seconds (3188.34 seconds total)