Starting phenix.real_space_refine on Tue Nov 18 18:50:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x0x_6699/11_2025/5x0x_6699.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0x_6699/11_2025/5x0x_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_6699/11_2025/5x0x_6699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0x_6699/11_2025/5x0x_6699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x0x_6699/11_2025/5x0x_6699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0x_6699/11_2025/5x0x_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-2.0-5881/lib/python3.9/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: 3.63, 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: 1.47 Conformation dependent library (CDL) restraints added in 546.0 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: 2.57 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: 4.30 Time building geometry restraints manager: 2.02 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=" C ARG C 99 " pdb=" N VAL C 100 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" C ARG G 99 " pdb=" N VAL G 100 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" CB LYS O 944 " pdb=" CG LYS O 944 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CB ILE O 945 " pdb=" CG2 ILE O 945 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 bond pdb=" CB TYR H 39 " pdb=" CG TYR H 39 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.20e-02 2.07e+03 3.28e+00 ... (remaining 17625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 24653 2.85 - 5.70: 335 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=" N CYS O1059 " pdb=" CA CYS O1059 " pdb=" C CYS O1059 " ideal model delta sigma weight residual 113.51 106.22 7.29 1.52e+00 4.33e-01 2.30e+01 angle pdb=" CA THR O 958 " pdb=" C THR O 958 " pdb=" N PRO O 959 " ideal model delta sigma weight residual 120.58 117.09 3.49 7.40e-01 1.83e+00 2.22e+01 angle pdb=" CA LEU O1253 " pdb=" CB LEU O1253 " pdb=" CG LEU O1253 " ideal model delta sigma weight residual 116.30 102.04 14.26 3.50e+00 8.16e-02 1.66e+01 angle pdb=" C LEU O 775 " pdb=" N GLN O 776 " pdb=" CA GLN O 776 " ideal model delta sigma weight residual 120.38 125.91 -5.53 1.37e+00 5.33e-01 1.63e+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: 1927 0.048 - 0.096: 757 0.096 - 0.144: 158 0.144 - 0.191: 11 0.191 - 0.239: 1 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=" 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 2.42 2.24 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.66e-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: 1.150 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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= 0.492 Angle : 0.955 14.257 25047 Z= 0.537 Chirality : 0.049 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 covalent geometry : bond 0.01079 (17630) covalent geometry : angle 0.95528 (25047) hydrogen bonds : bond 0.14482 ( 952) hydrogen bonds : angle 9.94739 ( 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 : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7708 (m-80) cc_final: 0.7350 (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: 0.8826 (t) REVERT: A 125 GLN cc_start: 0.9053 (mt0) cc_final: 0.8801 (mm-40) REVERT: B 53 GLU cc_start: 0.9020 (tp30) cc_final: 0.8735 (mm-30) REVERT: B 59 LYS cc_start: 0.8811 (tttt) cc_final: 0.8180 (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: 0.8133 (m-40) REVERT: D 37 TYR cc_start: 0.8769 (m-80) cc_final: 0.8548 (m-80) REVERT: D 56 MET cc_start: 0.8984 (tpp) cc_final: 0.8741 (tpp) REVERT: D 82 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8720 (mmtm) REVERT: D 102 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8444 (mm-30) REVERT: D 117 LYS cc_start: 0.8880 (tttp) cc_final: 0.8295 (ttmt) REVERT: E 56 LYS cc_start: 0.9284 (tttp) cc_final: 0.8978 (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: 0.8213 (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: 0.8531 (mp10) REVERT: F 25 ASN cc_start: 0.8504 (m-40) cc_final: 0.7302 (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: 0.7750 (tp30) REVERT: F 55 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8022 (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: 0.8884 (m-80) REVERT: H 59 MET cc_start: 0.8821 (mmm) cc_final: 0.8507 (mmm) REVERT: H 85 THR cc_start: 0.8960 (m) cc_final: 0.8759 (t) REVERT: O 888 TRP cc_start: 0.6233 (m100) cc_final: 0.5844 (m100) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.2042 time to fit residues: 116.0505 Evaluate side-chains 249 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 38 ASN G 94 ASN H 81 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 928 GLN ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1173 GLN O1198 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.083229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060712 restraints weight = 60590.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062354 restraints weight = 31451.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063380 restraints weight = 21011.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063990 restraints weight = 16655.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064287 restraints weight = 14649.421| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3111 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= 0.187 Angle : 0.697 14.359 25047 Z= 0.393 Chirality : 0.040 0.166 2854 Planarity : 0.005 0.062 2163 Dihedral : 29.475 149.699 4669 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 2.45 % Allowed : 12.84 % Favored : 84.72 % 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: -1.58 (0.21), residues: 1314 helix: -0.67 (0.17), residues: 836 sheet: -2.67 (0.44), residues: 71 loop : -1.17 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 988 TYR 0.025 0.002 TYR B 98 PHE 0.047 0.003 PHE O 946 TRP 0.023 0.003 TRP O 955 HIS 0.011 0.002 HIS O1198 Details of bonding type rmsd covalent geometry : bond 0.00401 (17630) covalent geometry : angle 0.69667 (25047) hydrogen bonds : bond 0.07466 ( 952) hydrogen bonds : angle 5.39843 ( 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 380 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 352 time to evaluate : 0.407 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 93 GLN cc_start: 0.8535 (tt0) cc_final: 0.7821 (tt0) REVERT: A 105 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 30 THR cc_start: 0.9223 (p) cc_final: 0.9019 (t) REVERT: B 59 LYS cc_start: 0.8650 (tttt) cc_final: 0.8140 (tttt) REVERT: B 63 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 56 MET cc_start: 0.8543 (tpp) cc_final: 0.8331 (tpp) REVERT: E 56 LYS cc_start: 0.8766 (tttp) cc_final: 0.8287 (tppt) REVERT: E 64 LYS cc_start: 0.8269 (mmtp) cc_final: 0.8000 (mmtp) REVERT: E 96 SER cc_start: 0.9300 (p) cc_final: 0.8911 (p) REVERT: E 105 GLU cc_start: 0.7354 (tp30) cc_final: 0.7117 (tp30) REVERT: E 108 ASN cc_start: 0.9177 (t0) cc_final: 0.8797 (t0) REVERT: F 29 ILE cc_start: 0.9055 (mm) cc_final: 0.8690 (tp) REVERT: F 53 GLU cc_start: 0.7731 (tp30) cc_final: 0.7445 (tp30) REVERT: F 55 ARG cc_start: 0.8496 (mtt90) cc_final: 0.8207 (mtm-85) REVERT: F 88 TYR cc_start: 0.8117 (m-10) cc_final: 0.7883 (m-10) REVERT: F 92 ARG cc_start: 0.8444 (tpt90) cc_final: 0.8155 (tpt90) REVERT: G 84 GLN cc_start: 0.9005 (tp40) cc_final: 0.8298 (tm-30) REVERT: G 89 ASN cc_start: 0.8683 (t0) cc_final: 0.8440 (m110) REVERT: G 101 THR cc_start: 0.9120 (m) cc_final: 0.8783 (p) REVERT: H 59 MET cc_start: 0.8870 (mmm) cc_final: 0.8643 (mmm) REVERT: H 118 TYR cc_start: 0.9272 (t80) cc_final: 0.8957 (t80) REVERT: O 935 TRP cc_start: 0.8071 (m-10) cc_final: 0.7103 (m100) REVERT: O 1116 MET cc_start: 0.7401 (mtm) cc_final: 0.6974 (mtt) REVERT: O 1158 CYS cc_start: 0.7474 (m) cc_final: 0.6973 (t) REVERT: O 1232 ASP cc_start: 0.7783 (p0) cc_final: 0.7543 (p0) REVERT: O 1248 GLU cc_start: 0.8745 (tp30) cc_final: 0.7912 (pm20) REVERT: O 1249 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8558 (mt-10) REVERT: O 1262 GLU cc_start: 0.8908 (tp30) cc_final: 0.8604 (tp30) REVERT: O 1263 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: O 1278 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7556 (pt) REVERT: O 1294 MET cc_start: 0.7911 (mmm) cc_final: 0.7445 (mmp) outliers start: 28 outliers final: 11 residues processed: 360 average time/residue: 0.1390 time to fit residues: 72.5683 Evaluate side-chains 264 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 108 VAL 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 H residue 108 VAL Chi-restraints excluded: chain O residue 1139 SER 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: 0.3980 chunk 2 optimal weight: 0.0370 chunk 124 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 947 ASN O1050 ASN ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.083624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060988 restraints weight = 61372.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062658 restraints weight = 31808.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063702 restraints weight = 21219.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064273 restraints weight = 16796.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064649 restraints weight = 14833.236| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17630 Z= 0.169 Angle : 0.651 13.061 25047 Z= 0.366 Chirality : 0.039 0.205 2854 Planarity : 0.005 0.054 2163 Dihedral : 29.006 147.666 4669 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 3.58 % Allowed : 15.55 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1314 helix: 0.46 (0.18), residues: 845 sheet: -1.84 (0.49), residues: 72 loop : -0.91 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1268 TYR 0.023 0.002 TYR H 37 PHE 0.044 0.003 PHE O 946 TRP 0.011 0.002 TRP O 955 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00368 (17630) covalent geometry : angle 0.65059 (25047) hydrogen bonds : bond 0.06984 ( 952) hydrogen bonds : angle 4.82625 ( 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 334 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.352 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 76 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: A 93 GLN cc_start: 0.8122 (tt0) cc_final: 0.7894 (tt0) REVERT: A 105 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 59 LYS cc_start: 0.8674 (tttt) cc_final: 0.8151 (tttt) REVERT: B 63 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 80 THR cc_start: 0.8820 (p) cc_final: 0.8530 (p) REVERT: D 56 MET cc_start: 0.8693 (tpp) cc_final: 0.8429 (tpp) REVERT: D 102 GLU cc_start: 0.7887 (pm20) cc_final: 0.7514 (pp20) REVERT: D 117 LYS cc_start: 0.8629 (tttp) cc_final: 0.7903 (ttmt) REVERT: E 54 TYR cc_start: 0.9082 (m-80) cc_final: 0.8881 (m-10) REVERT: E 56 LYS cc_start: 0.8688 (tttp) cc_final: 0.8006 (tppt) REVERT: E 64 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8241 (mmtp) REVERT: E 79 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8268 (ttmm) REVERT: E 108 ASN cc_start: 0.9253 (t0) cc_final: 0.9053 (t0) REVERT: E 120 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: F 25 ASN cc_start: 0.8137 (m-40) cc_final: 0.6215 (m-40) REVERT: F 29 ILE cc_start: 0.9120 (mm) cc_final: 0.8856 (tp) REVERT: F 53 GLU cc_start: 0.7471 (tp30) cc_final: 0.6705 (tp30) REVERT: F 92 ARG cc_start: 0.8358 (tpt90) cc_final: 0.8077 (tpt90) REVERT: G 84 GLN cc_start: 0.8967 (tp40) cc_final: 0.8489 (tm-30) REVERT: G 90 ASP cc_start: 0.8663 (t70) cc_final: 0.8453 (t70) REVERT: H 32 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8102 (tm-30) REVERT: H 56 MET cc_start: 0.8961 (tpp) cc_final: 0.8757 (tpp) REVERT: H 80 TYR cc_start: 0.7954 (m-10) cc_final: 0.7216 (m-10) REVERT: H 118 TYR cc_start: 0.9278 (t80) cc_final: 0.9032 (t80) REVERT: O 935 TRP cc_start: 0.7874 (m-10) cc_final: 0.6916 (m100) REVERT: O 1119 MET cc_start: 0.8198 (ttp) cc_final: 0.7798 (ptm) REVERT: O 1158 CYS cc_start: 0.7609 (m) cc_final: 0.6919 (t) REVERT: O 1248 GLU cc_start: 0.8678 (tp30) cc_final: 0.7923 (pm20) REVERT: O 1249 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8424 (mt-10) REVERT: O 1262 GLU cc_start: 0.8901 (tp30) cc_final: 0.8675 (tp30) REVERT: O 1278 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7572 (pt) REVERT: O 1294 MET cc_start: 0.7805 (mmm) cc_final: 0.7439 (mmm) outliers start: 41 outliers final: 23 residues processed: 313 average time/residue: 0.1451 time to fit residues: 66.2732 Evaluate side-chains 278 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU 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 D residue 70 ILE 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 120 MET Chi-restraints excluded: chain F residue 60 VAL 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 H residue 63 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain O residue 674 THR Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 868 VAL Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1263 GLU Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 53 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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 93 GLN G 89 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** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1073 ASN O1173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059432 restraints weight = 61097.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.061003 restraints weight = 32304.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061992 restraints weight = 21861.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062567 restraints weight = 17440.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062812 restraints weight = 15396.496| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17630 Z= 0.220 Angle : 0.664 8.993 25047 Z= 0.373 Chirality : 0.039 0.163 2854 Planarity : 0.005 0.051 2163 Dihedral : 28.896 146.589 4669 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 4.28 % Allowed : 17.12 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1314 helix: 0.59 (0.18), residues: 844 sheet: -1.58 (0.52), residues: 78 loop : -0.81 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O1268 TYR 0.022 0.002 TYR H 37 PHE 0.041 0.002 PHE O 946 TRP 0.015 0.002 TRP O1083 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00492 (17630) covalent geometry : angle 0.66398 (25047) hydrogen bonds : bond 0.07082 ( 952) hydrogen bonds : angle 4.76179 ( 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 309 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7508 (mp10) cc_final: 0.6808 (mp10) REVERT: A 93 GLN cc_start: 0.8298 (tt0) cc_final: 0.8075 (tt0) REVERT: A 105 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 30 THR cc_start: 0.9246 (p) cc_final: 0.8827 (t) REVERT: B 59 LYS cc_start: 0.8755 (tttt) cc_final: 0.8098 (tttt) REVERT: B 63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 80 THR cc_start: 0.8694 (p) cc_final: 0.8385 (p) REVERT: D 56 MET cc_start: 0.8757 (tpp) cc_final: 0.8461 (tpp) REVERT: D 102 GLU cc_start: 0.7993 (pm20) cc_final: 0.7604 (pp20) REVERT: D 117 LYS cc_start: 0.8753 (tttp) cc_final: 0.7999 (ttmt) REVERT: E 56 LYS cc_start: 0.8615 (tttp) cc_final: 0.8137 (tppt) REVERT: E 64 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8406 (mmmm) REVERT: E 108 ASN cc_start: 0.9381 (t0) cc_final: 0.9149 (t0) REVERT: F 25 ASN cc_start: 0.8047 (m-40) cc_final: 0.7700 (m-40) REVERT: G 84 GLN cc_start: 0.9078 (tp40) cc_final: 0.8304 (tm-30) REVERT: G 90 ASP cc_start: 0.8658 (t70) cc_final: 0.8439 (t0) REVERT: H 32 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8103 (tm-30) REVERT: H 80 TYR cc_start: 0.7921 (m-10) cc_final: 0.7453 (m-10) REVERT: O 888 TRP cc_start: 0.7188 (m100) cc_final: 0.6306 (m100) REVERT: O 1015 MET cc_start: 0.5850 (ttt) cc_final: 0.5630 (ttt) REVERT: O 1026 MET cc_start: 0.6117 (tpp) cc_final: 0.5877 (mmm) REVERT: O 1112 MET cc_start: 0.7937 (ttm) cc_final: 0.7608 (ttm) REVERT: O 1158 CYS cc_start: 0.7725 (m) cc_final: 0.6948 (t) REVERT: O 1248 GLU cc_start: 0.8628 (tp30) cc_final: 0.8024 (pm20) REVERT: O 1249 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8378 (mt-10) REVERT: O 1278 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7646 (pp) REVERT: O 1294 MET cc_start: 0.7741 (mmm) cc_final: 0.7347 (mmm) REVERT: O 1337 ARG cc_start: 0.7547 (mmp80) cc_final: 0.7269 (mmp80) outliers start: 49 outliers final: 36 residues processed: 282 average time/residue: 0.1408 time to fit residues: 58.9438 Evaluate side-chains 269 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN 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 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 51 ILE 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 81 ASP 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 91 GLU 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 O residue 829 SER Chi-restraints excluded: chain O residue 931 LEU 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 1077 GLU Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS 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: 7.9990 chunk 8 optimal weight: 0.0770 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN E 76 GLN E 108 ASN ** F 75 HIS ** 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** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.084466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061750 restraints weight = 60583.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063424 restraints weight = 31530.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064492 restraints weight = 21070.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065045 restraints weight = 16636.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065427 restraints weight = 14708.806| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17630 Z= 0.155 Angle : 0.614 9.397 25047 Z= 0.348 Chirality : 0.037 0.148 2854 Planarity : 0.005 0.069 2163 Dihedral : 28.655 146.550 4669 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 3.76 % Allowed : 17.21 % Favored : 79.04 % 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: 0.47 (0.23), residues: 1314 helix: 1.01 (0.18), residues: 842 sheet: -1.21 (0.56), residues: 73 loop : -0.76 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.030 0.002 TYR F 51 PHE 0.037 0.002 PHE O 946 TRP 0.023 0.002 TRP O 777 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (17630) covalent geometry : angle 0.61360 (25047) hydrogen bonds : bond 0.06826 ( 952) hydrogen bonds : angle 4.38972 ( 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 320 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.494 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 68 GLN cc_start: 0.8746 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 30 THR cc_start: 0.9224 (p) cc_final: 0.8876 (t) REVERT: B 47 SER cc_start: 0.8799 (t) cc_final: 0.8465 (m) REVERT: B 59 LYS cc_start: 0.8670 (tttt) cc_final: 0.8213 (tttt) REVERT: B 63 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 80 THR cc_start: 0.8609 (p) cc_final: 0.8287 (p) REVERT: C 84 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.8727 (tp40) REVERT: D 56 MET cc_start: 0.8711 (tpp) cc_final: 0.8453 (tpp) REVERT: D 82 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8314 (mmmt) REVERT: D 102 GLU cc_start: 0.7921 (pm20) cc_final: 0.7513 (pp20) REVERT: D 117 LYS cc_start: 0.8795 (tttp) cc_final: 0.8044 (ttmt) REVERT: E 56 LYS cc_start: 0.8452 (tttp) cc_final: 0.7863 (tppt) REVERT: E 64 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8373 (mmtp) REVERT: G 84 GLN cc_start: 0.8985 (tp40) cc_final: 0.8587 (tm-30) REVERT: G 90 ASP cc_start: 0.8474 (t70) cc_final: 0.8116 (t0) REVERT: H 32 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7909 (tm-30) REVERT: H 49 THR cc_start: 0.9251 (m) cc_final: 0.8956 (t) REVERT: O 888 TRP cc_start: 0.6991 (m100) cc_final: 0.6673 (m100) REVERT: O 987 LEU cc_start: 0.8280 (mt) cc_final: 0.8055 (tp) REVERT: O 1112 MET cc_start: 0.7736 (ttm) cc_final: 0.7431 (ttm) REVERT: O 1158 CYS cc_start: 0.7781 (m) cc_final: 0.6965 (t) REVERT: O 1248 GLU cc_start: 0.8645 (tp30) cc_final: 0.8082 (pm20) REVERT: O 1249 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8405 (mt-10) REVERT: O 1294 MET cc_start: 0.7745 (mmm) cc_final: 0.7434 (mmm) outliers start: 43 outliers final: 26 residues processed: 299 average time/residue: 0.1289 time to fit residues: 57.5202 Evaluate side-chains 276 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 112 ILE 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 C residue 84 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 65 VAL 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 O residue 763 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 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 137 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 18 optimal weight: 0.0370 chunk 129 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN G 112 GLN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.084236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.061482 restraints weight = 60532.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063101 restraints weight = 32132.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064117 restraints weight = 21658.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064727 restraints weight = 17219.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064966 restraints weight = 15134.771| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17630 Z= 0.166 Angle : 0.626 14.613 25047 Z= 0.349 Chirality : 0.037 0.154 2854 Planarity : 0.004 0.066 2163 Dihedral : 28.544 145.041 4669 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 3.58 % Allowed : 18.34 % Favored : 78.08 % 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: 0.60 (0.23), residues: 1314 helix: 1.15 (0.18), residues: 847 sheet: -1.12 (0.56), residues: 74 loop : -0.83 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.041 0.002 TYR F 51 PHE 0.038 0.002 PHE O1122 TRP 0.036 0.003 TRP O 777 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (17630) covalent geometry : angle 0.62576 (25047) hydrogen bonds : bond 0.06739 ( 952) hydrogen bonds : angle 4.34856 ( 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 304 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9279 (p) cc_final: 0.8952 (t) REVERT: B 47 SER cc_start: 0.8838 (t) cc_final: 0.8406 (m) REVERT: B 59 LYS cc_start: 0.8741 (tttt) cc_final: 0.8208 (tttt) REVERT: B 63 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 80 THR cc_start: 0.8661 (p) cc_final: 0.8376 (p) REVERT: C 73 ASN cc_start: 0.8906 (t0) cc_final: 0.8667 (t0) REVERT: C 84 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.8755 (tp40) REVERT: D 56 MET cc_start: 0.8738 (tpp) cc_final: 0.8521 (tpp) REVERT: D 82 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8322 (mmmt) REVERT: D 85 THR cc_start: 0.9546 (m) cc_final: 0.9327 (p) REVERT: D 90 GLU cc_start: 0.8370 (mp0) cc_final: 0.8084 (mp0) REVERT: D 102 GLU cc_start: 0.7893 (pm20) cc_final: 0.7625 (pp20) REVERT: D 117 LYS cc_start: 0.8869 (tttp) cc_final: 0.8113 (ttmt) REVERT: E 56 LYS cc_start: 0.8350 (tttp) cc_final: 0.7825 (tppt) REVERT: E 64 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8370 (mmtp) REVERT: E 106 ASP cc_start: 0.8634 (m-30) cc_final: 0.8304 (m-30) REVERT: E 108 ASN cc_start: 0.9351 (t0) cc_final: 0.9118 (t0) REVERT: F 92 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8368 (ttp80) REVERT: G 84 GLN cc_start: 0.9060 (tp40) cc_final: 0.8658 (tm-30) REVERT: G 90 ASP cc_start: 0.8498 (t70) cc_final: 0.8099 (t0) REVERT: G 91 GLU cc_start: 0.8249 (pp20) cc_final: 0.7389 (pp20) REVERT: H 32 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8063 (tm-30) REVERT: H 56 MET cc_start: 0.9128 (tpp) cc_final: 0.8601 (tpp) REVERT: O 888 TRP cc_start: 0.7052 (m100) cc_final: 0.6625 (m100) REVERT: O 892 ILE cc_start: 0.9008 (mp) cc_final: 0.8666 (mm) REVERT: O 946 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7423 (p90) REVERT: O 1026 MET cc_start: 0.6805 (mmm) cc_final: 0.6490 (mmm) REVERT: O 1112 MET cc_start: 0.7910 (ttm) cc_final: 0.7536 (ttm) REVERT: O 1158 CYS cc_start: 0.7695 (m) cc_final: 0.6962 (t) REVERT: O 1248 GLU cc_start: 0.8595 (tp30) cc_final: 0.8081 (pm20) REVERT: O 1249 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8379 (mt-10) REVERT: O 1294 MET cc_start: 0.7714 (mmm) cc_final: 0.7418 (mmm) outliers start: 41 outliers final: 29 residues processed: 284 average time/residue: 0.1285 time to fit residues: 54.9684 Evaluate side-chains 267 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE 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 E residue 96 SER 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 79 ILE Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 908 LEU 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 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1241 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 133 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 139 optimal weight: 0.3980 chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN G 89 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062664 restraints weight = 59965.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064268 restraints weight = 31626.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.065294 restraints weight = 21361.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065867 restraints weight = 16982.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066242 restraints weight = 14996.718| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17630 Z= 0.153 Angle : 0.620 11.342 25047 Z= 0.348 Chirality : 0.036 0.151 2854 Planarity : 0.004 0.063 2163 Dihedral : 28.384 144.809 4669 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 3.58 % Allowed : 19.21 % Favored : 77.21 % 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: 0.73 (0.23), residues: 1314 helix: 1.21 (0.18), residues: 849 sheet: -0.70 (0.60), residues: 68 loop : -0.77 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.032 0.002 TYR F 88 PHE 0.035 0.002 PHE O 946 TRP 0.051 0.003 TRP O 777 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (17630) covalent geometry : angle 0.62000 (25047) hydrogen bonds : bond 0.06688 ( 952) hydrogen bonds : angle 4.25603 ( 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 310 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 0.503 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 54 TYR cc_start: 0.8972 (m-10) cc_final: 0.8491 (m-10) REVERT: A 68 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: B 30 THR cc_start: 0.9302 (p) cc_final: 0.8891 (t) REVERT: B 47 SER cc_start: 0.8802 (t) cc_final: 0.8388 (m) REVERT: B 80 THR cc_start: 0.8636 (p) cc_final: 0.8392 (p) REVERT: C 73 ASN cc_start: 0.8942 (t0) cc_final: 0.8725 (t0) REVERT: C 84 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.8820 (tp40) REVERT: D 56 MET cc_start: 0.8698 (tpp) cc_final: 0.8489 (tpp) REVERT: D 82 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8332 (mmmt) REVERT: D 90 GLU cc_start: 0.8326 (mp0) cc_final: 0.8076 (mp0) REVERT: D 102 GLU cc_start: 0.7925 (pm20) cc_final: 0.7547 (pp20) REVERT: D 117 LYS cc_start: 0.8839 (tttp) cc_final: 0.8091 (ttmt) REVERT: E 56 LYS cc_start: 0.8386 (tttp) cc_final: 0.7849 (tppt) REVERT: E 64 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8306 (mmtp) REVERT: E 90 MET cc_start: 0.8022 (mmm) cc_final: 0.7761 (mmm) REVERT: E 108 ASN cc_start: 0.9344 (t0) cc_final: 0.9133 (t0) REVERT: F 84 MET cc_start: 0.7647 (tpp) cc_final: 0.7198 (tpp) REVERT: F 88 TYR cc_start: 0.7967 (m-10) cc_final: 0.5965 (m-10) REVERT: F 92 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8300 (ttp80) REVERT: F 98 TYR cc_start: 0.9190 (m-10) cc_final: 0.8775 (m-80) REVERT: G 84 GLN cc_start: 0.9020 (tp40) cc_final: 0.8652 (tm-30) REVERT: G 90 ASP cc_start: 0.8376 (t70) cc_final: 0.7897 (t0) REVERT: H 39 TYR cc_start: 0.6553 (t80) cc_final: 0.5881 (t80) REVERT: H 49 THR cc_start: 0.9221 (m) cc_final: 0.8888 (t) REVERT: H 51 ILE cc_start: 0.9007 (tt) cc_final: 0.8806 (pt) REVERT: O 946 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7221 (p90) REVERT: O 1022 MET cc_start: 0.4844 (mmm) cc_final: 0.4599 (mmt) REVERT: O 1053 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8230 (ptp) REVERT: O 1064 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.8005 (t) REVERT: O 1158 CYS cc_start: 0.7691 (m) cc_final: 0.7237 (t) REVERT: O 1248 GLU cc_start: 0.8450 (tp30) cc_final: 0.8018 (pm20) REVERT: O 1249 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8352 (mt-10) REVERT: O 1294 MET cc_start: 0.7581 (mmm) cc_final: 0.7376 (mmm) outliers start: 41 outliers final: 28 residues processed: 292 average time/residue: 0.1335 time to fit residues: 58.6169 Evaluate side-chains 277 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 112 ILE 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 C residue 84 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 98 LEU 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 E residue 96 SER Chi-restraints excluded: chain E residue 100 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 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 946 PHE Chi-restraints excluded: chain O residue 1053 MET Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1064 VAL Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1241 PHE 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: 0.1980 chunk 157 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 939 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.084950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.062079 restraints weight = 60354.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063695 restraints weight = 31949.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064715 restraints weight = 21606.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065327 restraints weight = 17212.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.065627 restraints weight = 15156.505| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17630 Z= 0.165 Angle : 0.633 11.957 25047 Z= 0.354 Chirality : 0.037 0.194 2854 Planarity : 0.005 0.060 2163 Dihedral : 28.349 143.764 4669 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 3.84 % Allowed : 20.52 % Favored : 75.63 % 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: 0.71 (0.23), residues: 1314 helix: 1.18 (0.18), residues: 851 sheet: -0.66 (0.59), residues: 68 loop : -0.76 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.038 0.002 TYR F 88 PHE 0.035 0.002 PHE O 946 TRP 0.038 0.003 TRP O 777 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00362 (17630) covalent geometry : angle 0.63296 (25047) hydrogen bonds : bond 0.06716 ( 952) hydrogen bonds : angle 4.26239 ( 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 290 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: A 120 MET cc_start: 0.8481 (mmm) cc_final: 0.8121 (mmm) REVERT: B 30 THR cc_start: 0.9361 (p) cc_final: 0.9015 (t) REVERT: B 47 SER cc_start: 0.8772 (t) cc_final: 0.8553 (m) REVERT: B 80 THR cc_start: 0.8712 (p) cc_final: 0.8478 (p) REVERT: C 84 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.8763 (tp40) REVERT: D 56 MET cc_start: 0.8695 (tpp) cc_final: 0.8495 (tpp) REVERT: D 76 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7721 (ttm-80) REVERT: D 82 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8315 (mmmt) REVERT: D 83 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7714 (mpt180) REVERT: D 102 GLU cc_start: 0.7902 (pm20) cc_final: 0.7531 (pp20) REVERT: D 117 LYS cc_start: 0.8859 (tttp) cc_final: 0.8114 (ttmt) REVERT: E 56 LYS cc_start: 0.8404 (tttp) cc_final: 0.7830 (tppt) REVERT: E 64 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8335 (mmtp) REVERT: E 108 ASN cc_start: 0.9215 (t0) cc_final: 0.8660 (t0) REVERT: F 35 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8570 (tpp80) REVERT: F 84 MET cc_start: 0.7731 (tpp) cc_final: 0.7271 (tpp) REVERT: F 92 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8392 (ttp80) REVERT: G 84 GLN cc_start: 0.9047 (tp40) cc_final: 0.8675 (tm-30) REVERT: G 90 ASP cc_start: 0.8459 (t70) cc_final: 0.8048 (t0) REVERT: H 32 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8234 (tm-30) REVERT: H 49 THR cc_start: 0.9226 (m) cc_final: 0.8912 (t) REVERT: H 56 MET cc_start: 0.9085 (tpp) cc_final: 0.8291 (tpp) REVERT: O 888 TRP cc_start: 0.7057 (m100) cc_final: 0.6615 (m100) REVERT: O 922 LEU cc_start: 0.8584 (tt) cc_final: 0.8339 (tp) REVERT: O 1064 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7962 (t) REVERT: O 1112 MET cc_start: 0.7708 (ttm) cc_final: 0.7379 (tpp) REVERT: O 1158 CYS cc_start: 0.7580 (m) cc_final: 0.7068 (t) REVERT: O 1248 GLU cc_start: 0.8488 (tp30) cc_final: 0.8049 (pm20) REVERT: O 1249 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8209 (mt-10) outliers start: 44 outliers final: 31 residues processed: 271 average time/residue: 0.1417 time to fit residues: 56.8440 Evaluate side-chains 267 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 112 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 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 48 LEU 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 E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 29 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 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 1001 LYS Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1064 VAL 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: 3.9990 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 89 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061562 restraints weight = 60373.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063172 restraints weight = 31869.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064195 restraints weight = 21533.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064751 restraints weight = 17111.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065132 restraints weight = 15161.276| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17630 Z= 0.181 Angle : 0.656 10.991 25047 Z= 0.365 Chirality : 0.038 0.177 2854 Planarity : 0.005 0.059 2163 Dihedral : 28.360 143.708 4669 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 3.58 % Allowed : 21.05 % Favored : 75.37 % 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: 0.54 (0.23), residues: 1314 helix: 1.06 (0.18), residues: 854 sheet: -0.82 (0.56), residues: 73 loop : -0.85 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.053 0.002 TYR F 88 PHE 0.034 0.002 PHE O 946 TRP 0.047 0.003 TRP O 777 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (17630) covalent geometry : angle 0.65551 (25047) hydrogen bonds : bond 0.06833 ( 952) hydrogen bonds : angle 4.35386 ( 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: 41 poor density : 249 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: A 120 MET cc_start: 0.8472 (mmm) cc_final: 0.8092 (mmm) REVERT: B 30 THR cc_start: 0.9338 (p) cc_final: 0.8994 (t) REVERT: B 47 SER cc_start: 0.9013 (t) cc_final: 0.8701 (m) REVERT: B 80 THR cc_start: 0.8734 (p) cc_final: 0.8495 (p) REVERT: C 84 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.8750 (tp40) REVERT: D 56 MET cc_start: 0.8751 (tpp) cc_final: 0.8546 (tpp) REVERT: D 76 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: D 82 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8271 (mmmt) REVERT: D 83 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7836 (mpt180) REVERT: D 102 GLU cc_start: 0.7954 (pm20) cc_final: 0.7564 (pp20) REVERT: D 110 GLU cc_start: 0.8056 (tp30) cc_final: 0.7706 (tm-30) REVERT: D 117 LYS cc_start: 0.8866 (tttp) cc_final: 0.8137 (ttmt) REVERT: E 56 LYS cc_start: 0.8385 (tttp) cc_final: 0.7800 (tppt) REVERT: E 64 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8403 (mmtp) REVERT: E 108 ASN cc_start: 0.9274 (t0) cc_final: 0.8707 (t0) REVERT: F 35 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8546 (tpp80) REVERT: F 92 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8400 (ttp80) REVERT: F 98 TYR cc_start: 0.9188 (m-10) cc_final: 0.8781 (m-80) REVERT: G 84 GLN cc_start: 0.9037 (tp40) cc_final: 0.8602 (tm-30) REVERT: G 90 ASP cc_start: 0.8356 (t70) cc_final: 0.7981 (t0) REVERT: G 91 GLU cc_start: 0.8053 (pp20) cc_final: 0.7124 (pp20) REVERT: H 32 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8135 (tm-30) REVERT: H 56 MET cc_start: 0.9111 (tpp) cc_final: 0.8565 (tpp) REVERT: H 82 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8791 (mmmt) REVERT: O 888 TRP cc_start: 0.7112 (m100) cc_final: 0.6672 (m100) REVERT: O 1064 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8038 (t) REVERT: O 1112 MET cc_start: 0.7813 (ttm) cc_final: 0.7440 (ttm) REVERT: O 1158 CYS cc_start: 0.7607 (m) cc_final: 0.7059 (t) REVERT: O 1248 GLU cc_start: 0.8404 (tp30) cc_final: 0.7925 (pm20) REVERT: O 1249 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8258 (mt-10) REVERT: O 1292 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7847 (pt0) REVERT: O 1294 MET cc_start: 0.7438 (mmm) cc_final: 0.7137 (mmm) outliers start: 41 outliers final: 33 residues processed: 272 average time/residue: 0.1295 time to fit residues: 53.3299 Evaluate side-chains 263 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 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 51 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 48 LEU 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 E residue 112 ILE 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 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 937 LEU Chi-restraints excluded: chain O residue 1001 LYS Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1064 VAL Chi-restraints excluded: chain O residue 1065 PHE 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: 0.9990 chunk 61 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 119 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.086476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064574 restraints weight = 61290.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065901 restraints weight = 36185.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066770 restraints weight = 26225.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067204 restraints weight = 21601.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067553 restraints weight = 19553.186| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17630 Z= 0.169 Angle : 0.663 11.561 25047 Z= 0.369 Chirality : 0.038 0.244 2854 Planarity : 0.005 0.056 2163 Dihedral : 28.327 143.778 4669 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.76 % Allowed : 22.10 % Favored : 74.15 % 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: 0.54 (0.23), residues: 1314 helix: 1.07 (0.18), residues: 852 sheet: -0.68 (0.56), residues: 73 loop : -0.91 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.074 0.002 TYR F 88 PHE 0.034 0.002 PHE O 946 TRP 0.083 0.004 TRP O 777 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (17630) covalent geometry : angle 0.66267 (25047) hydrogen bonds : bond 0.06816 ( 952) hydrogen bonds : angle 4.33902 ( 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 282 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: A 120 MET cc_start: 0.8385 (mmm) cc_final: 0.8118 (mmm) REVERT: B 30 THR cc_start: 0.9283 (p) cc_final: 0.9026 (t) REVERT: B 47 SER cc_start: 0.8969 (t) cc_final: 0.8673 (m) REVERT: B 80 THR cc_start: 0.8589 (p) cc_final: 0.8348 (p) REVERT: C 84 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8733 (tp40) REVERT: D 56 MET cc_start: 0.8560 (tpp) cc_final: 0.8319 (tpp) REVERT: D 76 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7624 (ttm-80) REVERT: D 83 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7766 (mpt180) REVERT: D 102 GLU cc_start: 0.7830 (pm20) cc_final: 0.7457 (pp20) REVERT: D 117 LYS cc_start: 0.8813 (tttp) cc_final: 0.8084 (ttmt) REVERT: E 56 LYS cc_start: 0.8285 (tttp) cc_final: 0.7817 (tppt) REVERT: E 64 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8416 (mmmm) REVERT: E 108 ASN cc_start: 0.9193 (t0) cc_final: 0.8622 (t0) REVERT: F 35 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8349 (tpp80) REVERT: F 84 MET cc_start: 0.7784 (tpp) cc_final: 0.7204 (tpp) REVERT: F 92 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8085 (tmt-80) REVERT: F 98 TYR cc_start: 0.9151 (m-10) cc_final: 0.8758 (m-80) REVERT: G 84 GLN cc_start: 0.9037 (tp40) cc_final: 0.8637 (tm-30) REVERT: G 90 ASP cc_start: 0.8290 (t70) cc_final: 0.7870 (t0) REVERT: H 32 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8079 (tm-30) REVERT: O 888 TRP cc_start: 0.7003 (m100) cc_final: 0.6556 (m100) REVERT: O 1064 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7995 (t) REVERT: O 1112 MET cc_start: 0.7606 (ttm) cc_final: 0.7386 (ttm) REVERT: O 1119 MET cc_start: 0.8123 (ttp) cc_final: 0.7520 (ppp) REVERT: O 1158 CYS cc_start: 0.7485 (m) cc_final: 0.6991 (t) REVERT: O 1248 GLU cc_start: 0.8407 (tp30) cc_final: 0.7955 (pm20) REVERT: O 1249 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7981 (mt-10) outliers start: 43 outliers final: 36 residues processed: 262 average time/residue: 0.1297 time to fit residues: 51.6697 Evaluate side-chains 265 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE 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 51 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 48 LEU 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 E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 31 LYS 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 38 ASN Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 937 LEU Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1064 VAL Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.0010 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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** F 27 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063981 restraints weight = 61501.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065342 restraints weight = 35929.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.066228 restraints weight = 25822.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066673 restraints weight = 21190.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.067045 restraints weight = 19114.503| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5878 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= 0.187 Angle : 0.681 13.369 25047 Z= 0.376 Chirality : 0.038 0.236 2854 Planarity : 0.005 0.054 2163 Dihedral : 28.357 143.501 4669 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.58 % Allowed : 22.45 % Favored : 73.97 % 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: 0.55 (0.23), residues: 1314 helix: 1.04 (0.18), residues: 854 sheet: -0.51 (0.57), residues: 73 loop : -0.85 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.071 0.002 TYR F 88 PHE 0.034 0.002 PHE O 946 TRP 0.105 0.005 TRP O 777 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (17630) covalent geometry : angle 0.68096 (25047) hydrogen bonds : bond 0.06873 ( 952) hydrogen bonds : angle 4.38420 ( 2442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.46 seconds wall clock time: 53 minutes 17.13 seconds (3197.13 seconds total)