Starting phenix.real_space_refine on Sat Dec 20 16:38:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x0y_6700/12_2025/5x0y_6700.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0y_6700/12_2025/5x0y_6700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5x0y_6700/12_2025/5x0y_6700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0y_6700/12_2025/5x0y_6700.map" model { file = "/net/cci-nas-00/data/ceres_data/5x0y_6700/12_2025/5x0y_6700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0y_6700/12_2025/5x0y_6700.cif" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 29 5.16 5 C 9677 2.51 5 N 3098 2.21 5 O 3702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16798 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4789 Classifications: {'peptide': 583} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 566} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.61, per 1000 atoms: 0.21 Number of scatterers: 16798 At special positions: 0 Unit cell: (143.88, 126.72, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 292 15.00 O 3702 8.00 N 3098 7.00 C 9677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 565.1 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 67.5% alpha, 3.3% beta 145 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.563A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.923A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.999A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.255A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.563A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.668A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.602A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.254A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'O' and resid 671 through 689 Processing helix chain 'O' and resid 744 through 749 Processing helix chain 'O' and resid 769 through 784 Processing helix chain 'O' and resid 797 through 812 Processing helix chain 'O' and resid 824 through 838 removed outlier: 4.593A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 863 removed outlier: 4.108A pdb=" N GLU O 853 " --> pdb=" O GLY O 849 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 854 " --> pdb=" O SER O 850 " (cutoff:3.500A) Processing helix chain 'O' and resid 872 through 886 removed outlier: 5.199A pdb=" N ALA O 881 " --> pdb=" O ILE O 877 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU O 882 " --> pdb=" O LYS O 878 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL O 886 " --> pdb=" O LEU O 882 " (cutoff:3.500A) Processing helix chain 'O' and resid 895 through 901 removed outlier: 3.971A pdb=" N ASN O 901 " --> pdb=" O ARG O 898 " (cutoff:3.500A) Processing helix chain 'O' and resid 905 through 914 Processing helix chain 'O' and resid 932 through 942 removed outlier: 3.969A pdb=" N LEU O 937 " --> pdb=" O GLU O 933 " (cutoff:3.500A) Processing helix chain 'O' and resid 942 through 958 Processing helix chain 'O' and resid 973 through 979 removed outlier: 4.293A pdb=" N LEU O 978 " --> pdb=" O GLU O 974 " (cutoff:3.500A) Processing helix chain 'O' and resid 980 through 988 Processing helix chain 'O' and resid 995 through 1000 Processing helix chain 'O' and resid 1020 through 1032 Processing helix chain 'O' and resid 1049 through 1061 removed outlier: 3.963A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) Processing helix chain 'O' and resid 1066 through 1073 Processing helix chain 'O' and resid 1081 through 1086 removed outlier: 4.465A pdb=" N ALA O1086 " --> pdb=" O ILE O1082 " (cutoff:3.500A) Processing helix chain 'O' and resid 1086 through 1103 removed outlier: 3.774A pdb=" N GLU O1090 " --> pdb=" O ALA O1086 " (cutoff:3.500A) Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1113 through 1127 removed outlier: 3.864A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP O1121 " --> pdb=" O ASP O1117 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE O1126 " --> pdb=" O PHE O1122 " (cutoff:3.500A) Processing helix chain 'O' and resid 1138 through 1150 Processing helix chain 'O' and resid 1163 through 1168 Processing helix chain 'O' and resid 1187 through 1196 Processing helix chain 'O' and resid 1216 through 1243 removed outlier: 3.671A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY O1233 " --> pdb=" O LEU O1229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS O1234 " --> pdb=" O ASP O1230 " (cutoff:3.500A) Processing helix chain 'O' and resid 1246 through 1267 removed outlier: 4.110A pdb=" N GLN O1250 " --> pdb=" O THR O1246 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG O1255 " --> pdb=" O GLU O1251 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1287 removed outlier: 4.138A pdb=" N ILE O1283 " --> pdb=" O LYS O1279 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1307 removed outlier: 3.706A pdb=" N MET O1294 " --> pdb=" O ASN O1290 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1348 removed outlier: 3.986A pdb=" N GLU O1341 " --> pdb=" O ARG O1337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.876A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.133A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.156A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.766A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.200A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'O' and resid 868 through 871 removed outlier: 6.195A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL O 889 " --> pdb=" O TYR O 918 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LEU O 920 " --> pdb=" O VAL O 889 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET O 891 " --> pdb=" O LEU O 920 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N LEU O 922 " --> pdb=" O MET O 891 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE O 893 " --> pdb=" O LEU O 922 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY O 788 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE O 789 " --> pdb=" O LEU O 992 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 1007 through 1008 removed outlier: 7.087A pdb=" N VAL O1007 " --> pdb=" O ILE O1208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 1130 through 1132 removed outlier: 6.196A pdb=" N VAL O1106 " --> pdb=" O PHE O1159 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2846 1.32 - 1.44: 5676 1.44 - 1.56: 8524 1.56 - 1.68: 582 1.68 - 1.80: 53 Bond restraints: 17681 Sorted by residual: bond pdb=" C LYS O 757 " pdb=" N GLN O 758 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.07e-02 2.33e+03 1.35e+01 bond pdb=" C1' DC J 108 " pdb=" N1 DC J 108 " ideal model delta sigma weight residual 1.490 1.413 0.077 3.00e-02 1.11e+03 6.62e+00 bond pdb=" C1' DT J 51 " pdb=" N1 DT J 51 " ideal model delta sigma weight residual 1.490 1.414 0.076 3.00e-02 1.11e+03 6.38e+00 bond pdb=" C1' DT J 109 " pdb=" N1 DT J 109 " ideal model delta sigma weight residual 1.490 1.420 0.070 3.00e-02 1.11e+03 5.45e+00 bond pdb=" CG GLN O1173 " pdb=" CD GLN O1173 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.11e+00 ... (remaining 17676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 24479 2.85 - 5.70: 530 5.70 - 8.55: 67 8.55 - 11.40: 31 11.40 - 14.25: 5 Bond angle restraints: 25112 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 103.25 110.38 -7.13 1.05e+00 9.07e-01 4.61e+01 angle pdb=" N PRO O 932 " pdb=" CA PRO O 932 " pdb=" C PRO O 932 " ideal model delta sigma weight residual 113.86 105.96 7.90 1.25e+00 6.40e-01 4.00e+01 angle pdb=" C TRP O1185 " pdb=" N ASN O1186 " pdb=" CA ASN O1186 " ideal model delta sigma weight residual 121.80 134.36 -12.56 2.44e+00 1.68e-01 2.65e+01 angle pdb=" CA ARG O1299 " pdb=" CB ARG O1299 " pdb=" CG ARG O1299 " ideal model delta sigma weight residual 114.10 104.38 9.72 2.00e+00 2.50e-01 2.36e+01 angle pdb=" CA ARG O1031 " pdb=" CB ARG O1031 " pdb=" CG ARG O1031 " ideal model delta sigma weight residual 114.10 104.44 9.66 2.00e+00 2.50e-01 2.33e+01 ... (remaining 25107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 8380 35.11 - 70.23: 1512 70.23 - 105.34: 48 105.34 - 140.45: 5 140.45 - 175.56: 3 Dihedral angle restraints: 9948 sinusoidal: 6014 harmonic: 3934 Sorted by residual: dihedral pdb=" CA LEU O 931 " pdb=" C LEU O 931 " pdb=" N PRO O 932 " pdb=" CA PRO O 932 " ideal model delta harmonic sigma weight residual 180.00 133.10 46.90 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA LYS O 768 " pdb=" C LYS O 768 " pdb=" N ASP O 769 " pdb=" CA ASP O 769 " ideal model delta harmonic sigma weight residual -180.00 -142.86 -37.14 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA THR E 58 " pdb=" C THR E 58 " pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta harmonic sigma weight residual -180.00 -146.24 -33.76 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1895 0.049 - 0.099: 772 0.099 - 0.148: 167 0.148 - 0.198: 23 0.198 - 0.247: 2 Chirality restraints: 2859 Sorted by residual: chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1' DC I 42 " pdb=" O4' DC I 42 " pdb=" C2' DC I 42 " pdb=" N1 DC I 42 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG O1299 " pdb=" N ARG O1299 " pdb=" C ARG O1299 " pdb=" CB ARG O1299 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 2856 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 16 " 0.005 2.00e-02 2.50e+03 2.79e-02 1.75e+01 pdb=" N1 DC J 16 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 16 " 0.067 2.00e-02 2.50e+03 pdb=" O2 DC J 16 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DC J 16 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC J 16 " 0.018 2.00e-02 2.50e+03 pdb=" N4 DC J 16 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC J 16 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC J 16 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 24 " 0.002 2.00e-02 2.50e+03 2.48e-02 1.38e+01 pdb=" N1 DC I 24 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 24 " 0.062 2.00e-02 2.50e+03 pdb=" O2 DC I 24 " -0.039 2.00e-02 2.50e+03 pdb=" N3 DC I 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 24 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 24 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 24 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC I 24 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 131 " -0.049 2.00e-02 2.50e+03 2.12e-02 1.23e+01 pdb=" N9 DA I 131 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DA I 131 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA I 131 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 131 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA I 131 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 131 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 131 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 131 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 131 " 0.004 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 260 2.53 - 3.12: 16288 3.12 - 3.71: 33264 3.71 - 4.31: 43391 4.31 - 4.90: 60499 Nonbonded interactions: 153702 Sorted by model distance: nonbonded pdb=" O2 DC I 111 " pdb=" N2 DG J 37 " model vdw 1.932 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 1.964 3.040 nonbonded pdb=" N6 DA I 60 " pdb=" O4 DT J 87 " model vdw 1.987 3.120 nonbonded pdb=" NE2 GLN O1173 " pdb=" O ARG O1199 " model vdw 2.063 3.120 nonbonded pdb=" NH2 ARG O1105 " pdb=" O PHE O1149 " model vdw 2.090 3.120 ... (remaining 153697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.210 Find NCS groups from input model: 0.160 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.077 17681 Z= 0.550 Angle : 1.121 14.254 25112 Z= 0.612 Chirality : 0.054 0.247 2859 Planarity : 0.006 0.048 2171 Dihedral : 26.087 175.563 7394 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 49.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.84 % Favored : 88.70 % Rotamer: Outliers : 0.26 % Allowed : 0.70 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.59 (0.16), residues: 1319 helix: -4.42 (0.09), residues: 799 sheet: -2.49 (0.70), residues: 38 loop : -2.04 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG O1264 TYR 0.045 0.004 TYR F 98 PHE 0.044 0.004 PHE O 946 TRP 0.056 0.006 TRP O 955 HIS 0.017 0.004 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.01177 (17681) covalent geometry : angle 1.12089 (25112) hydrogen bonds : bond 0.16843 ( 1001) hydrogen bonds : angle 10.44548 ( 2590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 371 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9079 (mt) cc_final: 0.8447 (mp) REVERT: A 93 GLN cc_start: 0.9295 (tt0) cc_final: 0.9093 (tt0) REVERT: A 106 ASP cc_start: 0.9237 (m-30) cc_final: 0.8973 (m-30) REVERT: B 63 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8829 (tp30) REVERT: C 56 GLU cc_start: 0.8912 (tt0) cc_final: 0.7834 (tm-30) REVERT: C 59 THR cc_start: 0.9464 (m) cc_final: 0.9178 (p) REVERT: C 64 GLU cc_start: 0.9115 (tt0) cc_final: 0.8699 (tm-30) REVERT: C 68 ASN cc_start: 0.8602 (m-40) cc_final: 0.6961 (m-40) REVERT: C 79 ILE cc_start: 0.9297 (pt) cc_final: 0.8918 (mt) REVERT: D 42 LEU cc_start: 0.9254 (tp) cc_final: 0.8897 (tt) REVERT: D 69 ARG cc_start: 0.9110 (mtt180) cc_final: 0.8810 (mtm-85) REVERT: D 86 ILE cc_start: 0.8672 (mt) cc_final: 0.8372 (tt) REVERT: D 108 VAL cc_start: 0.9330 (t) cc_final: 0.9127 (t) REVERT: E 52 ARG cc_start: 0.9159 (mtt90) cc_final: 0.8854 (ttm110) REVERT: E 74 ILE cc_start: 0.9319 (mt) cc_final: 0.8858 (mm) REVERT: E 76 GLN cc_start: 0.8882 (mt0) cc_final: 0.8658 (mm-40) REVERT: E 82 LEU cc_start: 0.8333 (mt) cc_final: 0.7777 (mt) REVERT: E 106 ASP cc_start: 0.9342 (m-30) cc_final: 0.8898 (t70) REVERT: E 112 ILE cc_start: 0.9373 (mt) cc_final: 0.9150 (mt) REVERT: E 113 HIS cc_start: 0.8423 (t70) cc_final: 0.8145 (t70) REVERT: E 133 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6452 (mt-10) REVERT: F 44 LYS cc_start: 0.8293 (tttt) cc_final: 0.8059 (ttmt) REVERT: F 67 ARG cc_start: 0.8965 (ptp-170) cc_final: 0.8540 (tpt170) REVERT: F 88 TYR cc_start: 0.8618 (m-80) cc_final: 0.7927 (m-10) REVERT: H 117 LYS cc_start: 0.9312 (tttp) cc_final: 0.8972 (ttpp) REVERT: O 892 ILE cc_start: 0.9097 (mp) cc_final: 0.8894 (mt) REVERT: O 1159 PHE cc_start: 0.6706 (t80) cc_final: 0.6480 (t80) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.1749 time to fit residues: 89.7271 Evaluate side-chains 208 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 73 ASN E 68 GLN E 93 GLN O 749 HIS ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1054 GLN O1111 GLN ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1198 HIS ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.054617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.039966 restraints weight = 128178.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.041091 restraints weight = 74629.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.041874 restraints weight = 52109.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042441 restraints weight = 40829.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.042730 restraints weight = 34727.349| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17681 Z= 0.202 Angle : 0.756 10.561 25112 Z= 0.429 Chirality : 0.042 0.179 2859 Planarity : 0.006 0.074 2171 Dihedral : 31.377 176.994 4676 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.26 % Allowed : 1.83 % Favored : 97.91 % 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: -2.04 (0.21), residues: 1319 helix: -1.11 (0.16), residues: 856 sheet: -1.64 (0.61), residues: 58 loop : -1.44 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 880 TYR 0.038 0.003 TYR O1226 PHE 0.043 0.003 PHE O 946 TRP 0.025 0.002 TRP O 955 HIS 0.009 0.002 HIS O 913 Details of bonding type rmsd covalent geometry : bond 0.00425 (17681) covalent geometry : angle 0.75559 (25112) hydrogen bonds : bond 0.07214 ( 1001) hydrogen bonds : angle 5.93709 ( 2590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8781 (tttt) cc_final: 0.8490 (mmmm) REVERT: A 94 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 99 TYR cc_start: 0.8734 (t80) cc_final: 0.8303 (t80) REVERT: A 105 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 106 ASP cc_start: 0.9042 (m-30) cc_final: 0.8569 (m-30) REVERT: B 31 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7086 (tmtt) REVERT: B 63 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8633 (tp30) REVERT: B 73 THR cc_start: 0.9099 (m) cc_final: 0.8648 (m) REVERT: B 85 ASP cc_start: 0.8822 (m-30) cc_final: 0.7882 (m-30) REVERT: C 41 GLU cc_start: 0.8414 (pm20) cc_final: 0.8127 (pp20) REVERT: C 42 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7750 (ttp-110) REVERT: C 56 GLU cc_start: 0.9094 (tt0) cc_final: 0.8187 (tm-30) REVERT: C 61 GLU cc_start: 0.9177 (tp30) cc_final: 0.8932 (tm-30) REVERT: C 62 ILE cc_start: 0.9463 (tp) cc_final: 0.9133 (tp) REVERT: C 64 GLU cc_start: 0.9489 (tt0) cc_final: 0.8817 (tm-30) REVERT: C 68 ASN cc_start: 0.8886 (m-40) cc_final: 0.7443 (m-40) REVERT: C 92 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 93 LEU cc_start: 0.9290 (mt) cc_final: 0.8605 (tp) REVERT: C 94 ASN cc_start: 0.8965 (t0) cc_final: 0.8339 (m-40) REVERT: D 56 MET cc_start: 0.8762 (mtm) cc_final: 0.8542 (mtm) REVERT: D 76 ARG cc_start: 0.8509 (mtp85) cc_final: 0.7575 (mtp-110) REVERT: D 80 TYR cc_start: 0.7192 (m-80) cc_final: 0.6954 (m-10) REVERT: E 62 ILE cc_start: 0.9084 (mm) cc_final: 0.8498 (mm) REVERT: E 74 ILE cc_start: 0.9398 (mt) cc_final: 0.9152 (mm) REVERT: E 82 LEU cc_start: 0.8787 (mt) cc_final: 0.8380 (mt) REVERT: E 84 PHE cc_start: 0.7966 (m-10) cc_final: 0.7426 (m-10) REVERT: E 123 ASP cc_start: 0.8818 (m-30) cc_final: 0.8500 (m-30) REVERT: F 49 LEU cc_start: 0.9462 (mp) cc_final: 0.8929 (mp) REVERT: F 54 THR cc_start: 0.9452 (m) cc_final: 0.9180 (p) REVERT: F 67 ARG cc_start: 0.8783 (ptp-170) cc_final: 0.8455 (tpt-90) REVERT: F 68 ASP cc_start: 0.9506 (m-30) cc_final: 0.9110 (m-30) REVERT: G 90 ASP cc_start: 0.7939 (t0) cc_final: 0.7575 (t0) REVERT: G 94 ASN cc_start: 0.9090 (t0) cc_final: 0.8409 (t0) REVERT: H 44 GLN cc_start: 0.9204 (mt0) cc_final: 0.8923 (mm-40) REVERT: H 65 ASP cc_start: 0.9110 (t70) cc_final: 0.8832 (t0) REVERT: H 69 ARG cc_start: 0.8710 (mtt180) cc_final: 0.7891 (ttm170) REVERT: H 77 LEU cc_start: 0.9563 (mm) cc_final: 0.9323 (mm) REVERT: H 80 TYR cc_start: 0.7840 (m-80) cc_final: 0.7478 (m-80) REVERT: H 83 ARG cc_start: 0.9182 (mmt-90) cc_final: 0.8872 (mmt-90) REVERT: H 90 GLU cc_start: 0.9310 (mp0) cc_final: 0.9099 (mp0) REVERT: H 92 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7730 (tm-30) REVERT: H 96 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8570 (mtp85) REVERT: H 97 LEU cc_start: 0.8893 (mt) cc_final: 0.8648 (tp) REVERT: O 681 HIS cc_start: 0.8533 (m-70) cc_final: 0.8032 (m-70) REVERT: O 778 MET cc_start: 0.9486 (mmm) cc_final: 0.9105 (mmm) REVERT: O 838 TRP cc_start: 0.7212 (m100) cc_final: 0.6911 (m100) REVERT: O 866 PHE cc_start: 0.8449 (p90) cc_final: 0.7997 (p90) REVERT: O 891 MET cc_start: 0.8525 (mpp) cc_final: 0.8290 (mmm) REVERT: O 920 LEU cc_start: 0.9201 (tp) cc_final: 0.8774 (tt) REVERT: O 1015 MET cc_start: 0.7899 (mtp) cc_final: 0.7584 (mtp) REVERT: O 1119 MET cc_start: 0.8896 (tmm) cc_final: 0.8650 (tmm) REVERT: O 1159 PHE cc_start: 0.8724 (t80) cc_final: 0.8480 (t80) REVERT: O 1300 MET cc_start: 0.9161 (tpp) cc_final: 0.8845 (tmm) outliers start: 3 outliers final: 1 residues processed: 343 average time/residue: 0.1642 time to fit residues: 78.3865 Evaluate side-chains 242 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 80 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 44 GLN D 106 HIS G 68 ASN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1049 ASN O1073 ASN ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1237 GLN O1347 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.040906 restraints weight = 127455.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042078 restraints weight = 75158.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042883 restraints weight = 52476.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043362 restraints weight = 41347.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043781 restraints weight = 35690.727| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17681 Z= 0.175 Angle : 0.681 12.331 25112 Z= 0.388 Chirality : 0.039 0.189 2859 Planarity : 0.005 0.071 2171 Dihedral : 30.706 178.357 4676 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.31 % Favored : 94.54 % Rotamer: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % 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: -0.27 (0.23), residues: 1319 helix: 0.40 (0.18), residues: 853 sheet: -0.58 (0.65), residues: 61 loop : -1.19 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O1164 TYR 0.023 0.002 TYR H 80 PHE 0.044 0.002 PHE O 946 TRP 0.019 0.001 TRP O 955 HIS 0.011 0.002 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00366 (17681) covalent geometry : angle 0.68146 (25112) hydrogen bonds : bond 0.06242 ( 1001) hydrogen bonds : angle 5.18007 ( 2590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 105 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 106 ASP cc_start: 0.8933 (m-30) cc_final: 0.8562 (t70) REVERT: A 112 ILE cc_start: 0.9536 (mm) cc_final: 0.9305 (mm) REVERT: B 63 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8341 (tp30) REVERT: B 67 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8395 (ttp-110) REVERT: B 73 THR cc_start: 0.9068 (m) cc_final: 0.8758 (m) REVERT: B 85 ASP cc_start: 0.8852 (m-30) cc_final: 0.8370 (m-30) REVERT: C 38 ASN cc_start: 0.8523 (m-40) cc_final: 0.8286 (m-40) REVERT: C 42 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7565 (ttp-110) REVERT: C 56 GLU cc_start: 0.8904 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 64 GLU cc_start: 0.9471 (tt0) cc_final: 0.8982 (tm-30) REVERT: C 68 ASN cc_start: 0.8950 (m-40) cc_final: 0.7323 (m110) REVERT: C 85 LEU cc_start: 0.9606 (mt) cc_final: 0.9156 (tt) REVERT: C 94 ASN cc_start: 0.9020 (t0) cc_final: 0.8670 (t0) REVERT: C 99 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7234 (mmm160) REVERT: D 49 THR cc_start: 0.8417 (m) cc_final: 0.8132 (p) REVERT: D 56 MET cc_start: 0.8738 (mtm) cc_final: 0.8496 (mtm) REVERT: D 69 ARG cc_start: 0.9477 (mtm-85) cc_final: 0.9088 (ttm-80) REVERT: D 73 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 76 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7366 (mtp-110) REVERT: D 89 ARG cc_start: 0.8999 (ptm-80) cc_final: 0.8614 (ttt-90) REVERT: D 96 ARG cc_start: 0.8947 (ttm110) cc_final: 0.8241 (ttt180) REVERT: E 62 ILE cc_start: 0.9049 (mm) cc_final: 0.8275 (pt) REVERT: E 94 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8383 (mm-30) REVERT: E 123 ASP cc_start: 0.9127 (m-30) cc_final: 0.8700 (m-30) REVERT: F 35 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8209 (ttp80) REVERT: F 45 ARG cc_start: 0.8303 (ttt180) cc_final: 0.7808 (ttm170) REVERT: F 54 THR cc_start: 0.9304 (m) cc_final: 0.9016 (p) REVERT: F 63 GLU cc_start: 0.9059 (tp30) cc_final: 0.8690 (tp30) REVERT: F 67 ARG cc_start: 0.8789 (ptp-170) cc_final: 0.8293 (tpt-90) REVERT: F 68 ASP cc_start: 0.9434 (m-30) cc_final: 0.9126 (m-30) REVERT: F 88 TYR cc_start: 0.8370 (m-10) cc_final: 0.8107 (m-10) REVERT: G 90 ASP cc_start: 0.7621 (t0) cc_final: 0.7380 (t0) REVERT: G 94 ASN cc_start: 0.9009 (t0) cc_final: 0.8258 (t0) REVERT: H 44 GLN cc_start: 0.9216 (mt0) cc_final: 0.8896 (mm-40) REVERT: H 65 ASP cc_start: 0.9157 (t70) cc_final: 0.8924 (t0) REVERT: H 68 GLU cc_start: 0.8566 (tt0) cc_final: 0.8327 (tt0) REVERT: H 69 ARG cc_start: 0.8567 (mtt180) cc_final: 0.7923 (ttm170) REVERT: H 80 TYR cc_start: 0.8097 (m-10) cc_final: 0.7528 (m-80) REVERT: H 83 ARG cc_start: 0.9059 (mmt-90) cc_final: 0.8687 (mmt-90) REVERT: H 92 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7771 (tm-30) REVERT: O 757 LYS cc_start: 0.7798 (mttt) cc_final: 0.7257 (ttpt) REVERT: O 778 MET cc_start: 0.9441 (mmm) cc_final: 0.9169 (mmm) REVERT: O 920 LEU cc_start: 0.9118 (tp) cc_final: 0.8888 (tp) REVERT: O 1015 MET cc_start: 0.7570 (mtp) cc_final: 0.6978 (mtm) REVERT: O 1052 ILE cc_start: 0.8282 (tt) cc_final: 0.8071 (tt) REVERT: O 1159 PHE cc_start: 0.8846 (t80) cc_final: 0.8500 (t80) REVERT: O 1192 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8507 (mm-40) REVERT: O 1300 MET cc_start: 0.9242 (tpp) cc_final: 0.8942 (tmm) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.1534 time to fit residues: 71.6639 Evaluate side-chains 240 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 112 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.041548 restraints weight = 127878.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.042744 restraints weight = 75686.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043580 restraints weight = 52890.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044116 restraints weight = 41465.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044519 restraints weight = 35613.949| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17681 Z= 0.171 Angle : 0.660 11.349 25112 Z= 0.375 Chirality : 0.038 0.201 2859 Planarity : 0.005 0.073 2171 Dihedral : 30.337 177.455 4676 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.82 % 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: 0.14 (0.23), residues: 1319 helix: 0.67 (0.18), residues: 872 sheet: -0.19 (0.68), residues: 61 loop : -1.02 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 816 TYR 0.025 0.002 TYR D 80 PHE 0.041 0.002 PHE O 946 TRP 0.015 0.002 TRP O 935 HIS 0.007 0.001 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00362 (17681) covalent geometry : angle 0.65984 (25112) hydrogen bonds : bond 0.06059 ( 1001) hydrogen bonds : angle 4.93654 ( 2590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8235 (tm-30) REVERT: A 106 ASP cc_start: 0.8934 (m-30) cc_final: 0.8505 (t70) REVERT: B 63 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8921 (tp30) REVERT: B 73 THR cc_start: 0.8978 (m) cc_final: 0.8728 (m) REVERT: B 74 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8380 (tm-30) REVERT: B 81 VAL cc_start: 0.8680 (t) cc_final: 0.8414 (t) REVERT: B 85 ASP cc_start: 0.8947 (m-30) cc_final: 0.8449 (m-30) REVERT: B 93 GLN cc_start: 0.8671 (tt0) cc_final: 0.8403 (tm-30) REVERT: C 41 GLU cc_start: 0.7168 (pp20) cc_final: 0.6957 (pp20) REVERT: C 42 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7845 (ttp-110) REVERT: C 56 GLU cc_start: 0.9061 (tt0) cc_final: 0.8222 (tm-30) REVERT: C 64 GLU cc_start: 0.9479 (tt0) cc_final: 0.8929 (tm-30) REVERT: C 68 ASN cc_start: 0.8971 (m-40) cc_final: 0.7464 (m-40) REVERT: C 92 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 94 ASN cc_start: 0.9008 (t0) cc_final: 0.8614 (t0) REVERT: D 51 ILE cc_start: 0.8805 (pt) cc_final: 0.8465 (mm) REVERT: D 73 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 76 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8032 (mtp-110) REVERT: D 96 ARG cc_start: 0.9035 (ttm110) cc_final: 0.8290 (ttp80) REVERT: E 84 PHE cc_start: 0.8429 (m-80) cc_final: 0.8156 (m-10) REVERT: E 94 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8292 (mm-30) REVERT: E 123 ASP cc_start: 0.9049 (m-30) cc_final: 0.8571 (m-30) REVERT: F 35 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8220 (ttp80) REVERT: F 45 ARG cc_start: 0.8467 (ttt180) cc_final: 0.7821 (ttm170) REVERT: G 90 ASP cc_start: 0.7926 (t0) cc_final: 0.7542 (t0) REVERT: G 94 ASN cc_start: 0.8920 (t0) cc_final: 0.8200 (t0) REVERT: H 68 GLU cc_start: 0.8650 (tt0) cc_final: 0.8386 (tt0) REVERT: H 80 TYR cc_start: 0.7906 (m-10) cc_final: 0.6841 (m-80) REVERT: H 83 ARG cc_start: 0.9115 (mmt-90) cc_final: 0.8681 (mmt-90) REVERT: H 92 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7700 (tm-30) REVERT: H 96 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8528 (mtp85) REVERT: O 757 LYS cc_start: 0.7834 (mttt) cc_final: 0.7422 (tttm) REVERT: O 778 MET cc_start: 0.9409 (mmm) cc_final: 0.9199 (mmm) REVERT: O 838 TRP cc_start: 0.7165 (m100) cc_final: 0.6774 (m100) REVERT: O 920 LEU cc_start: 0.9137 (tp) cc_final: 0.8920 (tp) REVERT: O 1022 MET cc_start: 0.8457 (tpt) cc_final: 0.8082 (tpt) REVERT: O 1052 ILE cc_start: 0.7972 (tt) cc_final: 0.7767 (tt) REVERT: O 1159 PHE cc_start: 0.8736 (t80) cc_final: 0.8457 (t80) REVERT: O 1300 MET cc_start: 0.9219 (tpp) cc_final: 0.9004 (tmm) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.1622 time to fit residues: 68.8808 Evaluate side-chains 224 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 156 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041762 restraints weight = 126019.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042939 restraints weight = 74730.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043685 restraints weight = 52153.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044310 restraints weight = 41477.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044686 restraints weight = 35280.319| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17681 Z= 0.179 Angle : 0.661 11.030 25112 Z= 0.375 Chirality : 0.038 0.198 2859 Planarity : 0.005 0.060 2171 Dihedral : 30.114 176.935 4676 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.47 % Rotamer: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1319 helix: 0.82 (0.18), residues: 873 sheet: -0.09 (0.69), residues: 61 loop : -1.02 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.027 0.002 TYR D 80 PHE 0.018 0.002 PHE O1181 TRP 0.065 0.003 TRP O 935 HIS 0.013 0.002 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00382 (17681) covalent geometry : angle 0.66095 (25112) hydrogen bonds : bond 0.06082 ( 1001) hydrogen bonds : angle 4.82558 ( 2590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8702 (pm20) cc_final: 0.8469 (pm20) REVERT: A 105 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 106 ASP cc_start: 0.8911 (m-30) cc_final: 0.8513 (t70) REVERT: B 59 LYS cc_start: 0.8938 (tmtt) cc_final: 0.8084 (tmtt) REVERT: B 63 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8487 (mt-10) REVERT: B 73 THR cc_start: 0.8980 (m) cc_final: 0.8713 (m) REVERT: B 85 ASP cc_start: 0.8860 (m-30) cc_final: 0.8280 (m-30) REVERT: C 38 ASN cc_start: 0.8582 (m110) cc_final: 0.7477 (m-40) REVERT: C 41 GLU cc_start: 0.7220 (pp20) cc_final: 0.6883 (pp20) REVERT: C 42 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7795 (ttp-110) REVERT: C 56 GLU cc_start: 0.8941 (tt0) cc_final: 0.8191 (tm-30) REVERT: C 68 ASN cc_start: 0.8933 (m-40) cc_final: 0.8651 (t0) REVERT: C 85 LEU cc_start: 0.9339 (mm) cc_final: 0.8831 (tt) REVERT: C 94 ASN cc_start: 0.8984 (t0) cc_final: 0.8624 (m-40) REVERT: D 51 ILE cc_start: 0.8786 (pt) cc_final: 0.8577 (pt) REVERT: D 76 ARG cc_start: 0.8722 (mtp85) cc_final: 0.7368 (mtp-110) REVERT: D 96 ARG cc_start: 0.9138 (ttm110) cc_final: 0.8410 (ttp80) REVERT: E 84 PHE cc_start: 0.8504 (m-80) cc_final: 0.8197 (m-10) REVERT: E 87 SER cc_start: 0.9212 (p) cc_final: 0.8949 (p) REVERT: E 94 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8228 (mm-30) REVERT: E 123 ASP cc_start: 0.9092 (m-30) cc_final: 0.8729 (m-30) REVERT: F 63 GLU cc_start: 0.9097 (tp30) cc_final: 0.8846 (tp30) REVERT: F 67 ARG cc_start: 0.8710 (ptp-170) cc_final: 0.8458 (tpt170) REVERT: G 38 ASN cc_start: 0.8529 (m-40) cc_final: 0.7874 (t0) REVERT: G 90 ASP cc_start: 0.7815 (t0) cc_final: 0.7399 (t0) REVERT: G 94 ASN cc_start: 0.8968 (t0) cc_final: 0.8272 (t0) REVERT: H 30 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7684 (ttm170) REVERT: H 80 TYR cc_start: 0.8025 (m-10) cc_final: 0.5502 (m-80) REVERT: O 757 LYS cc_start: 0.7793 (mttt) cc_final: 0.7316 (tttm) REVERT: O 778 MET cc_start: 0.9441 (mmm) cc_final: 0.9173 (mmm) REVERT: O 838 TRP cc_start: 0.7237 (m100) cc_final: 0.6808 (m100) REVERT: O 920 LEU cc_start: 0.9091 (tp) cc_final: 0.8867 (tp) REVERT: O 935 TRP cc_start: 0.7583 (m-90) cc_final: 0.6963 (m-90) REVERT: O 1015 MET cc_start: 0.6954 (mtp) cc_final: 0.6321 (mpp) REVERT: O 1022 MET cc_start: 0.8488 (tpt) cc_final: 0.8003 (tpp) REVERT: O 1026 MET cc_start: 0.9405 (mmp) cc_final: 0.8478 (mmm) REVERT: O 1052 ILE cc_start: 0.7864 (tt) cc_final: 0.7576 (tt) REVERT: O 1159 PHE cc_start: 0.8707 (t80) cc_final: 0.8322 (t80) REVERT: O 1300 MET cc_start: 0.9208 (tpp) cc_final: 0.8959 (tmm) outliers start: 1 outliers final: 0 residues processed: 298 average time/residue: 0.1529 time to fit residues: 64.9216 Evaluate side-chains 223 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043028 restraints weight = 125555.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044239 restraints weight = 74635.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045102 restraints weight = 52177.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045583 restraints weight = 40735.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046060 restraints weight = 35071.969| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17681 Z= 0.160 Angle : 0.637 10.614 25112 Z= 0.362 Chirality : 0.037 0.197 2859 Planarity : 0.005 0.057 2171 Dihedral : 29.802 176.961 4676 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1319 helix: 0.96 (0.18), residues: 867 sheet: 0.40 (0.71), residues: 59 loop : -1.02 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.023 0.002 TYR B 88 PHE 0.020 0.002 PHE O1089 TRP 0.048 0.002 TRP O 935 HIS 0.005 0.001 HIS O 913 Details of bonding type rmsd covalent geometry : bond 0.00336 (17681) covalent geometry : angle 0.63714 (25112) hydrogen bonds : bond 0.05772 ( 1001) hydrogen bonds : angle 4.57989 ( 2590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.439 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 59 GLU cc_start: 0.8525 (pm20) cc_final: 0.8287 (pm20) REVERT: A 94 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 97 GLU cc_start: 0.7398 (pp20) cc_final: 0.6999 (pp20) REVERT: A 106 ASP cc_start: 0.8972 (m-30) cc_final: 0.8532 (t70) REVERT: B 63 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8789 (tp30) REVERT: B 73 THR cc_start: 0.8950 (m) cc_final: 0.8683 (m) REVERT: B 85 ASP cc_start: 0.8848 (m-30) cc_final: 0.8270 (m-30) REVERT: B 93 GLN cc_start: 0.8649 (tt0) cc_final: 0.8372 (tm-30) REVERT: C 38 ASN cc_start: 0.8368 (m110) cc_final: 0.7452 (m110) REVERT: C 41 GLU cc_start: 0.7156 (pp20) cc_final: 0.6723 (pp20) REVERT: C 42 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7556 (ttp-110) REVERT: C 56 GLU cc_start: 0.8957 (tt0) cc_final: 0.8184 (tm-30) REVERT: C 64 GLU cc_start: 0.8763 (tp30) cc_final: 0.8481 (tp30) REVERT: C 85 LEU cc_start: 0.9398 (mm) cc_final: 0.8938 (tt) REVERT: C 92 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7941 (mt-10) REVERT: C 94 ASN cc_start: 0.8976 (t0) cc_final: 0.8666 (t0) REVERT: D 49 THR cc_start: 0.8576 (m) cc_final: 0.8125 (p) REVERT: D 51 ILE cc_start: 0.8939 (pt) cc_final: 0.8585 (mm) REVERT: D 73 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8560 (mm-30) REVERT: D 96 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8447 (ttp80) REVERT: E 56 LYS cc_start: 0.8437 (mttp) cc_final: 0.8222 (mttp) REVERT: E 84 PHE cc_start: 0.8413 (m-80) cc_final: 0.8114 (m-10) REVERT: E 87 SER cc_start: 0.9144 (p) cc_final: 0.8834 (p) REVERT: E 94 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8482 (mm-30) REVERT: E 123 ASP cc_start: 0.9084 (m-30) cc_final: 0.8636 (m-30) REVERT: F 45 ARG cc_start: 0.8320 (ttt180) cc_final: 0.7715 (ttm170) REVERT: F 49 LEU cc_start: 0.9558 (mp) cc_final: 0.9336 (mp) REVERT: F 67 ARG cc_start: 0.8753 (ptp-170) cc_final: 0.8483 (tpt170) REVERT: G 38 ASN cc_start: 0.8491 (m-40) cc_final: 0.8084 (t0) REVERT: G 68 ASN cc_start: 0.8495 (m-40) cc_final: 0.8102 (m-40) REVERT: G 90 ASP cc_start: 0.7935 (t0) cc_final: 0.7691 (t0) REVERT: G 94 ASN cc_start: 0.8914 (t0) cc_final: 0.8161 (m-40) REVERT: H 30 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7840 (ttm170) REVERT: H 81 ASN cc_start: 0.9051 (m-40) cc_final: 0.7983 (p0) REVERT: H 83 ARG cc_start: 0.9192 (mmt-90) cc_final: 0.8503 (mmt180) REVERT: H 103 LEU cc_start: 0.9459 (mm) cc_final: 0.9142 (mm) REVERT: H 118 TYR cc_start: 0.8501 (t80) cc_final: 0.8101 (t80) REVERT: O 757 LYS cc_start: 0.7669 (mttt) cc_final: 0.7313 (tttm) REVERT: O 778 MET cc_start: 0.9373 (mmm) cc_final: 0.8835 (mmm) REVERT: O 812 MET cc_start: 0.8962 (mmp) cc_final: 0.8524 (mmm) REVERT: O 838 TRP cc_start: 0.7492 (m100) cc_final: 0.6910 (m100) REVERT: O 894 ASP cc_start: 0.8626 (m-30) cc_final: 0.8164 (m-30) REVERT: O 920 LEU cc_start: 0.9095 (tp) cc_final: 0.8861 (tp) REVERT: O 1022 MET cc_start: 0.8533 (tpt) cc_final: 0.8053 (tpp) REVERT: O 1026 MET cc_start: 0.9438 (mmp) cc_final: 0.8609 (mmm) REVERT: O 1119 MET cc_start: 0.9042 (tmm) cc_final: 0.8692 (tmm) REVERT: O 1120 GLU cc_start: 0.8822 (mt-10) cc_final: 0.7928 (mm-30) REVERT: O 1159 PHE cc_start: 0.8661 (t80) cc_final: 0.8279 (t80) REVERT: O 1300 MET cc_start: 0.9253 (tpp) cc_final: 0.9039 (tmm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1657 time to fit residues: 70.7691 Evaluate side-chains 226 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 68 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042708 restraints weight = 124177.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043913 restraints weight = 73959.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044733 restraints weight = 51830.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045346 restraints weight = 40649.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045561 restraints weight = 34440.232| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17681 Z= 0.163 Angle : 0.643 10.660 25112 Z= 0.365 Chirality : 0.037 0.186 2859 Planarity : 0.005 0.058 2171 Dihedral : 29.655 176.244 4676 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1319 helix: 0.96 (0.18), residues: 874 sheet: 0.62 (0.72), residues: 61 loop : -1.02 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 816 TYR 0.020 0.002 TYR B 88 PHE 0.022 0.002 PHE O 946 TRP 0.074 0.003 TRP O 935 HIS 0.007 0.001 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00350 (17681) covalent geometry : angle 0.64316 (25112) hydrogen bonds : bond 0.05823 ( 1001) hydrogen bonds : angle 4.58657 ( 2590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8525 (pm20) cc_final: 0.8288 (pm20) REVERT: A 94 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 20 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7563 (mtmt) REVERT: B 54 THR cc_start: 0.9665 (m) cc_final: 0.9406 (p) REVERT: B 63 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8676 (tp30) REVERT: B 64 ASN cc_start: 0.8813 (m-40) cc_final: 0.7999 (m110) REVERT: B 75 HIS cc_start: 0.7805 (t-90) cc_final: 0.7193 (t-90) REVERT: B 85 ASP cc_start: 0.8797 (m-30) cc_final: 0.8150 (t0) REVERT: B 93 GLN cc_start: 0.8582 (tt0) cc_final: 0.8279 (tm-30) REVERT: C 38 ASN cc_start: 0.8388 (m110) cc_final: 0.7233 (m110) REVERT: C 56 GLU cc_start: 0.8926 (tt0) cc_final: 0.8097 (tm-30) REVERT: C 64 GLU cc_start: 0.8942 (tp30) cc_final: 0.8432 (tp30) REVERT: C 68 ASN cc_start: 0.8400 (m-40) cc_final: 0.8091 (m110) REVERT: C 94 ASN cc_start: 0.8999 (t0) cc_final: 0.8712 (t0) REVERT: D 51 ILE cc_start: 0.8864 (pt) cc_final: 0.8518 (mm) REVERT: D 96 ARG cc_start: 0.8997 (ttm110) cc_final: 0.8603 (ttt180) REVERT: D 103 LEU cc_start: 0.9532 (mt) cc_final: 0.8817 (mt) REVERT: E 49 ARG cc_start: 0.9067 (ttp-110) cc_final: 0.8782 (mtt180) REVERT: E 84 PHE cc_start: 0.8380 (m-80) cc_final: 0.8091 (m-10) REVERT: E 94 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8569 (mm-30) REVERT: E 123 ASP cc_start: 0.9168 (m-30) cc_final: 0.8881 (m-30) REVERT: F 45 ARG cc_start: 0.8307 (ttt180) cc_final: 0.7711 (ttm170) REVERT: F 63 GLU cc_start: 0.9075 (tp30) cc_final: 0.8838 (tp30) REVERT: F 67 ARG cc_start: 0.8709 (ptp-170) cc_final: 0.8456 (tpt170) REVERT: G 38 ASN cc_start: 0.8519 (m-40) cc_final: 0.8270 (t0) REVERT: G 68 ASN cc_start: 0.8401 (m-40) cc_final: 0.8024 (m-40) REVERT: G 90 ASP cc_start: 0.7959 (t0) cc_final: 0.7623 (t0) REVERT: G 94 ASN cc_start: 0.8877 (t0) cc_final: 0.8192 (t0) REVERT: H 30 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7719 (ttm170) REVERT: H 76 ARG cc_start: 0.8981 (ttm-80) cc_final: 0.8704 (ttm-80) REVERT: H 81 ASN cc_start: 0.9047 (m-40) cc_final: 0.8088 (p0) REVERT: H 118 TYR cc_start: 0.8501 (t80) cc_final: 0.8106 (t80) REVERT: O 757 LYS cc_start: 0.7847 (mttt) cc_final: 0.7447 (tttm) REVERT: O 769 ASP cc_start: 0.8646 (m-30) cc_final: 0.7886 (p0) REVERT: O 778 MET cc_start: 0.9352 (mmm) cc_final: 0.8931 (mmm) REVERT: O 812 MET cc_start: 0.9022 (mmp) cc_final: 0.8481 (mmm) REVERT: O 838 TRP cc_start: 0.7459 (m100) cc_final: 0.6854 (m100) REVERT: O 920 LEU cc_start: 0.9006 (tp) cc_final: 0.8623 (tt) REVERT: O 1015 MET cc_start: 0.6561 (ptp) cc_final: 0.6129 (ptp) REVERT: O 1159 PHE cc_start: 0.8640 (t80) cc_final: 0.8057 (t80) REVERT: O 1215 ASN cc_start: 0.8842 (m-40) cc_final: 0.8562 (p0) REVERT: O 1234 LYS cc_start: 0.8867 (tttt) cc_final: 0.8607 (mtpt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1430 time to fit residues: 61.4195 Evaluate side-chains 227 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 156 optimal weight: 0.0010 chunk 118 optimal weight: 0.4980 chunk 119 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 75 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 685 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043771 restraints weight = 123446.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044995 restraints weight = 73153.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045847 restraints weight = 50978.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046362 restraints weight = 39925.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046837 restraints weight = 34187.097| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17681 Z= 0.153 Angle : 0.636 10.608 25112 Z= 0.359 Chirality : 0.036 0.187 2859 Planarity : 0.005 0.058 2171 Dihedral : 29.471 176.357 4676 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1319 helix: 1.01 (0.18), residues: 877 sheet: 0.88 (0.73), residues: 61 loop : -0.92 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 67 TYR 0.021 0.002 TYR B 88 PHE 0.023 0.002 PHE O 946 TRP 0.071 0.003 TRP O 935 HIS 0.014 0.001 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00327 (17681) covalent geometry : angle 0.63648 (25112) hydrogen bonds : bond 0.05710 ( 1001) hydrogen bonds : angle 4.48070 ( 2590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8466 (pm20) cc_final: 0.8262 (pm20) REVERT: A 99 TYR cc_start: 0.8895 (t80) cc_final: 0.8075 (t80) REVERT: A 119 ILE cc_start: 0.8536 (pt) cc_final: 0.8301 (pt) REVERT: B 20 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7509 (mtmt) REVERT: B 54 THR cc_start: 0.9671 (m) cc_final: 0.9439 (p) REVERT: B 63 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8672 (tp30) REVERT: B 64 ASN cc_start: 0.8762 (m-40) cc_final: 0.7991 (m110) REVERT: B 75 HIS cc_start: 0.7995 (t-90) cc_final: 0.7210 (t-90) REVERT: B 85 ASP cc_start: 0.8884 (m-30) cc_final: 0.8261 (t0) REVERT: B 93 GLN cc_start: 0.8569 (tt0) cc_final: 0.8311 (tm-30) REVERT: B 98 TYR cc_start: 0.8011 (m-80) cc_final: 0.7786 (m-80) REVERT: C 38 ASN cc_start: 0.8357 (m110) cc_final: 0.7573 (m110) REVERT: C 56 GLU cc_start: 0.8943 (tt0) cc_final: 0.8006 (tm-30) REVERT: C 64 GLU cc_start: 0.9006 (tp30) cc_final: 0.8533 (tp30) REVERT: C 68 ASN cc_start: 0.8520 (m-40) cc_final: 0.8297 (m110) REVERT: C 94 ASN cc_start: 0.8987 (t0) cc_final: 0.8544 (m-40) REVERT: D 51 ILE cc_start: 0.8885 (pt) cc_final: 0.8595 (mm) REVERT: D 96 ARG cc_start: 0.8949 (ttm110) cc_final: 0.8555 (ttt180) REVERT: E 84 PHE cc_start: 0.8417 (m-80) cc_final: 0.8133 (m-10) REVERT: E 87 SER cc_start: 0.9071 (p) cc_final: 0.8865 (p) REVERT: E 94 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8484 (mm-30) REVERT: E 97 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8710 (mm-30) REVERT: E 123 ASP cc_start: 0.9109 (m-30) cc_final: 0.8810 (m-30) REVERT: F 45 ARG cc_start: 0.8308 (ttt180) cc_final: 0.7682 (ttm170) REVERT: F 49 LEU cc_start: 0.9556 (mp) cc_final: 0.9099 (mp) REVERT: F 67 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8448 (tpt170) REVERT: G 68 ASN cc_start: 0.8389 (m-40) cc_final: 0.7951 (m-40) REVERT: G 94 ASN cc_start: 0.8932 (t0) cc_final: 0.8301 (t0) REVERT: H 30 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7917 (ttm170) REVERT: H 59 MET cc_start: 0.8687 (tpp) cc_final: 0.7974 (mmm) REVERT: H 77 LEU cc_start: 0.8974 (tp) cc_final: 0.8766 (tt) REVERT: H 81 ASN cc_start: 0.8866 (m-40) cc_final: 0.8129 (p0) REVERT: H 97 LEU cc_start: 0.9032 (tp) cc_final: 0.8608 (tp) REVERT: H 118 TYR cc_start: 0.8515 (t80) cc_final: 0.8106 (t80) REVERT: O 744 TYR cc_start: 0.7573 (m-80) cc_final: 0.6893 (m-80) REVERT: O 769 ASP cc_start: 0.8488 (m-30) cc_final: 0.7976 (p0) REVERT: O 778 MET cc_start: 0.9313 (mmm) cc_final: 0.8990 (mmm) REVERT: O 812 MET cc_start: 0.9035 (mmp) cc_final: 0.8621 (mmm) REVERT: O 838 TRP cc_start: 0.7565 (m100) cc_final: 0.7013 (m100) REVERT: O 879 GLU cc_start: 0.8610 (mp0) cc_final: 0.8388 (pm20) REVERT: O 920 LEU cc_start: 0.8946 (tp) cc_final: 0.8582 (tt) REVERT: O 1022 MET cc_start: 0.8365 (tpt) cc_final: 0.8155 (tpp) REVERT: O 1119 MET cc_start: 0.9024 (tmm) cc_final: 0.8571 (tmm) REVERT: O 1120 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7946 (mm-30) REVERT: O 1159 PHE cc_start: 0.8659 (t80) cc_final: 0.8060 (t80) REVERT: O 1215 ASN cc_start: 0.8923 (m-40) cc_final: 0.8663 (p0) REVERT: O 1234 LYS cc_start: 0.8765 (tttt) cc_final: 0.8541 (mtpt) REVERT: O 1337 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7309 (tpm170) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1500 time to fit residues: 64.1825 Evaluate side-chains 233 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.057981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042453 restraints weight = 124691.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043681 restraints weight = 74841.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044493 restraints weight = 52437.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045098 restraints weight = 41228.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045425 restraints weight = 34951.844| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17681 Z= 0.174 Angle : 0.644 10.761 25112 Z= 0.366 Chirality : 0.037 0.172 2859 Planarity : 0.005 0.057 2171 Dihedral : 29.427 176.177 4676 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1319 helix: 1.00 (0.18), residues: 875 sheet: 0.76 (0.70), residues: 61 loop : -0.94 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 76 TYR 0.028 0.002 TYR O1226 PHE 0.037 0.002 PHE O1089 TRP 0.055 0.003 TRP O 935 HIS 0.013 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00375 (17681) covalent geometry : angle 0.64413 (25112) hydrogen bonds : bond 0.05888 ( 1001) hydrogen bonds : angle 4.48989 ( 2590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8611 (pm20) cc_final: 0.8344 (pm20) REVERT: A 60 LEU cc_start: 0.8530 (mt) cc_final: 0.8314 (mt) REVERT: A 94 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 16 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8913 (mtmt) REVERT: B 54 THR cc_start: 0.9695 (m) cc_final: 0.9428 (p) REVERT: B 63 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8579 (tp30) REVERT: B 64 ASN cc_start: 0.8790 (m-40) cc_final: 0.8142 (m110) REVERT: B 85 ASP cc_start: 0.8865 (m-30) cc_final: 0.8297 (t0) REVERT: B 93 GLN cc_start: 0.8611 (tt0) cc_final: 0.8409 (tm-30) REVERT: B 98 TYR cc_start: 0.8229 (m-80) cc_final: 0.7999 (m-80) REVERT: C 38 ASN cc_start: 0.8038 (m110) cc_final: 0.7400 (m110) REVERT: C 56 GLU cc_start: 0.8985 (tt0) cc_final: 0.8118 (tm-30) REVERT: C 64 GLU cc_start: 0.8980 (tp30) cc_final: 0.8475 (tp30) REVERT: C 94 ASN cc_start: 0.9023 (t0) cc_final: 0.8497 (t0) REVERT: D 51 ILE cc_start: 0.8748 (pt) cc_final: 0.8548 (mm) REVERT: D 73 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8308 (mm-30) REVERT: D 96 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8580 (ttt180) REVERT: E 84 PHE cc_start: 0.8445 (m-80) cc_final: 0.8095 (m-10) REVERT: E 87 SER cc_start: 0.9130 (p) cc_final: 0.8886 (p) REVERT: E 94 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8632 (mm-30) REVERT: E 96 SER cc_start: 0.9268 (m) cc_final: 0.8883 (p) REVERT: E 123 ASP cc_start: 0.9113 (m-30) cc_final: 0.8817 (m-30) REVERT: F 45 ARG cc_start: 0.8423 (ttt180) cc_final: 0.7745 (ttm170) REVERT: F 49 LEU cc_start: 0.9375 (mp) cc_final: 0.9070 (mp) REVERT: F 67 ARG cc_start: 0.8712 (ptp-170) cc_final: 0.8503 (tpt170) REVERT: G 68 ASN cc_start: 0.8346 (m-40) cc_final: 0.7947 (m-40) REVERT: G 94 ASN cc_start: 0.8969 (t0) cc_final: 0.8361 (t0) REVERT: H 30 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7704 (ttm170) REVERT: H 97 LEU cc_start: 0.8815 (tp) cc_final: 0.8494 (tp) REVERT: H 118 TYR cc_start: 0.8564 (t80) cc_final: 0.8135 (t80) REVERT: O 769 ASP cc_start: 0.8717 (m-30) cc_final: 0.8231 (p0) REVERT: O 778 MET cc_start: 0.9380 (mmm) cc_final: 0.9047 (mmm) REVERT: O 812 MET cc_start: 0.9086 (mmp) cc_final: 0.8706 (mmm) REVERT: O 838 TRP cc_start: 0.7521 (m100) cc_final: 0.6869 (m100) REVERT: O 879 GLU cc_start: 0.8616 (mp0) cc_final: 0.8395 (pm20) REVERT: O 920 LEU cc_start: 0.8928 (tp) cc_final: 0.8569 (tt) REVERT: O 1013 CYS cc_start: 0.8669 (m) cc_final: 0.7414 (t) REVERT: O 1159 PHE cc_start: 0.8712 (t80) cc_final: 0.8101 (t80) REVERT: O 1215 ASN cc_start: 0.8939 (m-40) cc_final: 0.8733 (p0) REVERT: O 1234 LYS cc_start: 0.9109 (tttt) cc_final: 0.8607 (mtpt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1510 time to fit residues: 60.8546 Evaluate side-chains 222 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 68 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.058146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042739 restraints weight = 123213.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043943 restraints weight = 73335.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044781 restraints weight = 51237.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045371 restraints weight = 40193.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045700 restraints weight = 34109.881| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17681 Z= 0.167 Angle : 0.650 10.673 25112 Z= 0.366 Chirality : 0.037 0.159 2859 Planarity : 0.005 0.059 2171 Dihedral : 29.343 176.712 4676 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1319 helix: 0.91 (0.18), residues: 879 sheet: 0.77 (0.69), residues: 61 loop : -1.02 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.025 0.002 TYR O1226 PHE 0.029 0.002 PHE O1089 TRP 0.043 0.002 TRP O 935 HIS 0.011 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00360 (17681) covalent geometry : angle 0.64979 (25112) hydrogen bonds : bond 0.05822 ( 1001) hydrogen bonds : angle 4.47354 ( 2590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.519 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 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8330 (pm20) REVERT: A 99 TYR cc_start: 0.8924 (t80) cc_final: 0.8106 (t80) REVERT: B 20 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7398 (mttt) REVERT: B 54 THR cc_start: 0.9701 (m) cc_final: 0.9446 (p) REVERT: B 63 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8553 (tp30) REVERT: B 64 ASN cc_start: 0.8868 (m-40) cc_final: 0.8182 (m110) REVERT: B 85 ASP cc_start: 0.8880 (m-30) cc_final: 0.8308 (t0) REVERT: B 93 GLN cc_start: 0.8629 (tt0) cc_final: 0.8348 (tm-30) REVERT: B 98 TYR cc_start: 0.8231 (m-80) cc_final: 0.7953 (m-80) REVERT: C 38 ASN cc_start: 0.8052 (m110) cc_final: 0.7375 (m110) REVERT: C 56 GLU cc_start: 0.8989 (tt0) cc_final: 0.8009 (tm-30) REVERT: C 72 ASP cc_start: 0.8725 (m-30) cc_final: 0.8488 (m-30) REVERT: C 92 GLU cc_start: 0.7279 (tt0) cc_final: 0.6854 (tt0) REVERT: C 94 ASN cc_start: 0.8924 (t0) cc_final: 0.8721 (t0) REVERT: D 73 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 96 ARG cc_start: 0.8995 (ttm110) cc_final: 0.8576 (ttt180) REVERT: E 84 PHE cc_start: 0.8438 (m-80) cc_final: 0.8104 (m-10) REVERT: E 87 SER cc_start: 0.9102 (p) cc_final: 0.8875 (p) REVERT: E 94 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8591 (mm-30) REVERT: E 123 ASP cc_start: 0.9050 (m-30) cc_final: 0.8807 (m-30) REVERT: F 45 ARG cc_start: 0.8414 (ttt180) cc_final: 0.7860 (ttm170) REVERT: F 67 ARG cc_start: 0.8730 (ptp-170) cc_final: 0.8487 (tpt170) REVERT: G 36 LYS cc_start: 0.9266 (mmtm) cc_final: 0.8844 (mmtm) REVERT: G 61 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7826 (tm-30) REVERT: G 68 ASN cc_start: 0.8500 (m-40) cc_final: 0.8125 (m-40) REVERT: G 90 ASP cc_start: 0.7815 (t0) cc_final: 0.7511 (t0) REVERT: G 94 ASN cc_start: 0.8878 (t0) cc_final: 0.8158 (m-40) REVERT: G 99 ARG cc_start: 0.8269 (mmt180) cc_final: 0.8066 (tpm170) REVERT: G 110 ASN cc_start: 0.9147 (m110) cc_final: 0.8687 (t0) REVERT: H 30 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.7888 (ttm170) REVERT: H 77 LEU cc_start: 0.9200 (tt) cc_final: 0.8976 (tt) REVERT: H 80 TYR cc_start: 0.8020 (m-10) cc_final: 0.5937 (m-80) REVERT: H 81 ASN cc_start: 0.9005 (m-40) cc_final: 0.8101 (p0) REVERT: H 118 TYR cc_start: 0.8565 (t80) cc_final: 0.8143 (t80) REVERT: O 744 TYR cc_start: 0.7891 (m-80) cc_final: 0.7174 (m-80) REVERT: O 778 MET cc_start: 0.9376 (mmm) cc_final: 0.9043 (mmm) REVERT: O 812 MET cc_start: 0.9117 (mmp) cc_final: 0.8750 (mmm) REVERT: O 838 TRP cc_start: 0.7342 (m100) cc_final: 0.6697 (m100) REVERT: O 920 LEU cc_start: 0.8912 (tp) cc_final: 0.8533 (tt) REVERT: O 1013 CYS cc_start: 0.8678 (m) cc_final: 0.7467 (t) REVERT: O 1022 MET cc_start: 0.8367 (tpt) cc_final: 0.8114 (tpp) REVERT: O 1119 MET cc_start: 0.9064 (tmm) cc_final: 0.8644 (tmm) REVERT: O 1120 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7833 (mm-30) REVERT: O 1159 PHE cc_start: 0.8786 (t80) cc_final: 0.7975 (t80) REVERT: O 1215 ASN cc_start: 0.8950 (m-40) cc_final: 0.8732 (p0) REVERT: O 1234 LYS cc_start: 0.9105 (tttt) cc_final: 0.8674 (mtpt) REVERT: O 1300 MET cc_start: 0.8816 (tmm) cc_final: 0.8596 (tmm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1521 time to fit residues: 61.0320 Evaluate side-chains 216 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 108 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 157 optimal weight: 0.0070 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044541 restraints weight = 122017.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.045823 restraints weight = 72599.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046663 restraints weight = 50367.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047333 restraints weight = 39315.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047771 restraints weight = 33108.106| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17681 Z= 0.150 Angle : 0.641 10.471 25112 Z= 0.359 Chirality : 0.037 0.169 2859 Planarity : 0.005 0.060 2171 Dihedral : 29.145 176.871 4676 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.70 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1319 helix: 0.93 (0.18), residues: 883 sheet: 0.94 (0.70), residues: 61 loop : -0.99 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.023 0.002 TYR O1226 PHE 0.024 0.002 PHE O1089 TRP 0.049 0.002 TRP O 935 HIS 0.012 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00319 (17681) covalent geometry : angle 0.64128 (25112) hydrogen bonds : bond 0.05733 ( 1001) hydrogen bonds : angle 4.33613 ( 2590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.25 seconds wall clock time: 49 minutes 0.39 seconds (2940.39 seconds total)