Starting phenix.real_space_refine on Sun Sep 13 03:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rja_4901/09_2026/6rja_4901.cif" } resolution = 3.0 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= 0.011 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 194 5.49 5 S 50 5.16 5 C 12214 2.51 5 N 3522 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20372 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6638 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 795} Chain breaks: 7 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNAv2': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Restraints were copied for chains: B, F, G, H Time building chain proxies: 8.19, per 1000 atoms: 0.40 Number of scatterers: 20372 At special positions: 0 Unit cell: (120.015, 207.137, 107.569, 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 50 16.00 P 194 15.00 O 4392 8.00 N 3522 7.00 C 12214 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: 1.58 Conformation dependent library (CDL) restraints added in 672.8 milliseconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 20 sheets defined 45.6% alpha, 13.8% beta 64 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.774A pdb=" N LYS A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 51 " --> pdb=" O ILE A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.541A pdb=" N VAL A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.782A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.544A pdb=" N TYR A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.775A pdb=" N LYS B 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 51 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.540A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.781A pdb=" N ALA B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.545A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.543A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.634A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 147 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.813A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.007A pdb=" N ILE C 254 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.623A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 315 through 327 removed outlier: 3.940A pdb=" N LEU C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 384 through 395 Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.812A pdb=" N VAL C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 470 through 476 Processing helix chain 'C' and resid 479 through 500 Processing helix chain 'C' and resid 692 through 705 Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 854 through 868 removed outlier: 3.798A pdb=" N TYR C 858 " --> pdb=" O THR C 854 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 859 " --> pdb=" O GLN C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.772A pdb=" N ARG C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 891 Proline residue: C 888 - end of helix removed outlier: 3.717A pdb=" N GLU C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 removed outlier: 3.502A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.544A pdb=" N LEU F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.634A pdb=" N HIS F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 185 through 204 removed outlier: 3.814A pdb=" N TYR F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 250 through 254 removed outlier: 4.006A pdb=" N ILE F 254 " --> pdb=" O ILE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 removed outlier: 3.624A pdb=" N GLN F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 315 through 327 removed outlier: 3.940A pdb=" N LEU F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 356 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 395 Processing helix chain 'F' and resid 402 through 416 removed outlier: 3.812A pdb=" N VAL F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 436 Processing helix chain 'F' and resid 445 through 454 Processing helix chain 'F' and resid 470 through 476 Processing helix chain 'F' and resid 479 through 500 Processing helix chain 'F' and resid 692 through 705 Processing helix chain 'F' and resid 737 through 748 Processing helix chain 'F' and resid 854 through 868 removed outlier: 3.798A pdb=" N TYR F 858 " --> pdb=" O THR F 854 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP F 859 " --> pdb=" O GLN F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 869 through 871 No H-bonds generated for 'chain 'F' and resid 869 through 871' Processing helix chain 'F' and resid 872 through 878 removed outlier: 3.771A pdb=" N ARG F 876 " --> pdb=" O PHE F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 891 Proline residue: F 888 - end of helix removed outlier: 3.717A pdb=" N GLU F 891 " --> pdb=" O GLU F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 910 through 918 Processing helix chain 'F' and resid 986 through 988 No H-bonds generated for 'chain 'F' and resid 986 through 988' Processing helix chain 'F' and resid 1000 through 1011 removed outlier: 3.503A pdb=" N TYR F1004 " --> pdb=" O SER F1000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.634A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.648A pdb=" N SER A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 6.634A pdb=" N ILE B 115 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 136 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 117 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 134 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY B 119 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET B 121 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 130 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.648A pdb=" N SER B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 710 through 712 removed outlier: 3.764A pdb=" N ILE C 10 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.746A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 935 through 941 removed outlier: 3.509A pdb=" N LEU C 935 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 958 " --> pdb=" O TYR C 828 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 967 " --> pdb=" O THR C1022 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C1022 " --> pdb=" O ALA C 967 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 969 " --> pdb=" O LYS C1020 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB3, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.273A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C1098 " --> pdb=" O ILE C1110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 710 through 712 removed outlier: 3.765A pdb=" N ILE F 10 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 168 through 172 Processing sheet with id=AB6, first strand: chain 'F' and resid 268 through 269 removed outlier: 3.746A pdb=" N ALA F 268 " --> pdb=" O HIS F 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 935 through 941 removed outlier: 3.509A pdb=" N LEU F 935 " --> pdb=" O ILE F 849 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL F 845 " --> pdb=" O ASP F 939 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS F 941 " --> pdb=" O THR F 843 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 843 " --> pdb=" O LYS F 941 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA F 829 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 958 " --> pdb=" O TYR F 828 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS F 977 " --> pdb=" O ASN F 972 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 972 " --> pdb=" O LYS F 977 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU F 983 " --> pdb=" O TRP F 965 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS F 977 " --> pdb=" O ASN F 972 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 972 " --> pdb=" O LYS F 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 967 " --> pdb=" O THR F1022 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR F1022 " --> pdb=" O ALA F 967 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL F 969 " --> pdb=" O LYS F1020 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 989 through 990 Processing sheet with id=AC2, first strand: chain 'F' and resid 1085 through 1088 removed outlier: 4.273A pdb=" N CYS F1085 " --> pdb=" O LEU F1058 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU F1057 " --> pdb=" O LEU F1045 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F1028 " --> pdb=" O VAL F1099 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F1098 " --> pdb=" O ILE F1110 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4442 1.33 - 1.45: 5508 1.45 - 1.57: 10714 1.57 - 1.69: 380 1.69 - 1.81: 92 Bond restraints: 21136 Sorted by residual: bond pdb=" C1' DC H 5 " pdb=" N1 DC H 5 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" C1' DC E 5 " pdb=" N1 DC E 5 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" C1' DC E 12 " pdb=" N1 DC E 12 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" C1' DC H 12 " pdb=" N1 DC H 12 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C1' DC E 17 " pdb=" N1 DC E 17 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.11e+01 ... (remaining 21131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 27549 1.90 - 3.80: 1522 3.80 - 5.70: 204 5.70 - 7.60: 19 7.60 - 9.50: 8 Bond angle restraints: 29302 Sorted by residual: angle pdb=" O4' DT H 6 " pdb=" C4' DT H 6 " pdb=" C3' DT H 6 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+01 angle pdb=" O4' DT E 6 " pdb=" C4' DT E 6 " pdb=" C3' DT E 6 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.54e+01 angle pdb=" C ASN C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C ASN F 21 " pdb=" N LYS F 22 " pdb=" CA LYS F 22 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" O4' DT E 9 " pdb=" C4' DT E 9 " pdb=" C3' DT E 9 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.44e+01 ... (remaining 29297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10564 17.76 - 35.51: 1311 35.51 - 53.27: 387 53.27 - 71.03: 118 71.03 - 88.78: 24 Dihedral angle restraints: 12404 sinusoidal: 6578 harmonic: 5826 Sorted by residual: dihedral pdb=" C4' U D 8 " pdb=" C3' U D 8 " pdb=" C2' U D 8 " pdb=" C1' U D 8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.57 73.92 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' U G 8 " pdb=" C3' U G 8 " pdb=" C2' U G 8 " pdb=" C1' U G 8 " ideal model delta sinusoidal sigma weight residual 36.35 -37.51 73.85 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' U D 74 " pdb=" C3' U D 74 " pdb=" C2' U D 74 " pdb=" C1' U D 74 " ideal model delta sinusoidal sigma weight residual 36.34 -36.51 72.85 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 12401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2677 0.074 - 0.149: 416 0.149 - 0.223: 112 0.223 - 0.297: 109 0.297 - 0.371: 4 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C2' U G 8 " pdb=" C3' U G 8 " pdb=" O2' U G 8 " pdb=" C1' U G 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.42 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C2' U D 8 " pdb=" C3' U D 8 " pdb=" O2' U D 8 " pdb=" C1' U D 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.42 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C2' U D 73 " pdb=" C3' U D 73 " pdb=" O2' U D 73 " pdb=" C1' U D 73 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3315 not shown) Planarity restraints: 3048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U G 7 " 0.033 2.00e-02 2.50e+03 1.84e-02 7.62e+00 pdb=" N1 U G 7 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U G 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U G 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U G 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U G 7 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U G 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U G 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U G 7 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " -0.032 2.00e-02 2.50e+03 1.83e-02 7.54e+00 pdb=" N1 U D 7 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U D 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U D 7 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U D 7 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 150 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO C 151 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.034 5.00e-02 4.00e+02 ... (remaining 3045 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6071 2.83 - 3.35: 15898 3.35 - 3.87: 33821 3.87 - 4.38: 40115 4.38 - 4.90: 64548 Nonbonded interactions: 160453 Sorted by model distance: nonbonded pdb=" O SER F 101 " pdb=" OG SER F 101 " model vdw 2.314 3.040 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 101 " model vdw 2.314 3.040 nonbonded pdb=" OH TYR F 225 " pdb=" OG1 THR F 383 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR C 225 " pdb=" OG1 THR C 383 " model vdw 2.320 3.040 nonbonded pdb=" O ALA F 376 " pdb=" OG1 THR F 380 " model vdw 2.351 3.040 ... (remaining 160448 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.006 0.054 21136 Z= 0.315 Angle : 0.947 9.496 29302 Z= 0.526 Chirality : 0.076 0.371 3318 Planarity : 0.006 0.061 3048 Dihedral : 16.836 88.785 8668 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.23 % Allowed : 8.09 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.15), residues: 1960 helix: -1.92 (0.14), residues: 814 sheet: -0.73 (0.33), residues: 234 loop : -3.18 (0.15), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 223 TYR 0.029 0.002 TYR A 26 PHE 0.020 0.003 PHE F1042 TRP 0.010 0.002 TRP F 424 HIS 0.014 0.002 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.31 (21136) covalent geometry : angle 0.94737 / 0.53 (29302) hydrogen bonds : bond 0.13800 / 9.01 ( 872) hydrogen bonds : angle 6.37483 / 4.49 ( 2410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 289 time to evaluate : 0.680 Fit side-chains REVERT: A 105 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8123 (ttpp) REVERT: B 40 LYS cc_start: 0.8055 (mttt) cc_final: 0.7850 (mttm) REVERT: B 105 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7975 (tttp) REVERT: C 314 MET cc_start: 0.5047 (tpt) cc_final: 0.4280 (mtp) REVERT: C 355 LYS cc_start: 0.7583 (tptt) cc_final: 0.7027 (tptp) REVERT: C 412 PHE cc_start: 0.7510 (t80) cc_final: 0.7294 (t80) REVERT: C 844 TYR cc_start: 0.7876 (m-80) cc_final: 0.7545 (m-80) REVERT: C 1010 LYS cc_start: 0.8312 (tptt) cc_final: 0.7939 (ttmt) REVERT: C 1038 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6361 (mt-10) REVERT: F 314 MET cc_start: 0.4953 (tpt) cc_final: 0.4296 (mtp) REVERT: F 355 LYS cc_start: 0.7728 (tptt) cc_final: 0.7176 (tptp) REVERT: F 844 TYR cc_start: 0.7915 (m-80) cc_final: 0.7657 (m-80) REVERT: F 1010 LYS cc_start: 0.8220 (tptt) cc_final: 0.7811 (ttmt) REVERT: F 1038 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6344 (mt-10) REVERT: F 1111 LYS cc_start: 0.7624 (tppt) cc_final: 0.6928 (tttt) outliers start: 4 outliers final: 1 residues processed: 291 average time/residue: 0.6386 time to fit residues: 210.1974 Evaluate side-chains 197 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 282 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 78 ASN A 101 GLN A 127 ASN A 151 GLN A 177 ASN B 37 ASN B 78 ASN B 101 GLN B 127 ASN B 151 GLN B 177 ASN C 31 ASN C 231 ASN C 279 ASN C 282 ASN C 285 ASN C 300 GLN C 303 GLN C 405 GLN C 416 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN C1039 GLN C1081 ASN C1112 ASN F 31 ASN F 279 ASN F 282 ASN F 285 ASN F 300 GLN F 302 ASN F 303 GLN F 348 HIS F 405 GLN F 416 ASN ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1039 GLN F1081 ASN F1112 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.196927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.164501 restraints weight = 24008.827| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.32 r_work: 0.3291 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21136 Z= 0.166 Angle : 0.943 19.180 29302 Z= 0.416 Chirality : 0.084 1.108 3318 Planarity : 0.004 0.037 3048 Dihedral : 14.366 121.776 4488 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.60 % Allowed : 14.31 % Favored : 83.09 % 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: -1.96 (0.17), residues: 1960 helix: -0.07 (0.18), residues: 822 sheet: -0.52 (0.33), residues: 234 loop : -2.78 (0.15), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 385 TYR 0.022 0.001 TYR F 307 PHE 0.015 0.001 PHE F1042 TRP 0.007 0.001 TRP B 38 HIS 0.005 0.001 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (21136) covalent geometry : angle 0.94345 / 0.42 (29302) hydrogen bonds : bond 0.05250 / 3.34 ( 872) hydrogen bonds : angle 4.81473 / 3.40 ( 2410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.718 Fit side-chains REVERT: A 43 ASN cc_start: 0.7910 (m-40) cc_final: 0.7700 (m-40) REVERT: A 105 LYS cc_start: 0.8454 (ttmm) cc_final: 0.7902 (tttt) REVERT: B 40 LYS cc_start: 0.8212 (mttt) cc_final: 0.7915 (mttm) REVERT: B 105 LYS cc_start: 0.8468 (ttmm) cc_final: 0.7937 (tttt) REVERT: B 145 SER cc_start: 0.8284 (t) cc_final: 0.8069 (m) REVERT: C 355 LYS cc_start: 0.6969 (tptt) cc_final: 0.6014 (tptp) REVERT: C 385 ARG cc_start: 0.7910 (tmm-80) cc_final: 0.7671 (tmm-80) REVERT: C 390 GLU cc_start: 0.7813 (tp30) cc_final: 0.7417 (tm-30) REVERT: C 412 PHE cc_start: 0.6850 (t80) cc_final: 0.6525 (t80) REVERT: C 844 TYR cc_start: 0.8316 (m-80) cc_final: 0.7887 (m-80) REVERT: C 878 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.5916 (t70) REVERT: C 911 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8105 (tp) REVERT: C 1010 LYS cc_start: 0.8204 (tptt) cc_final: 0.7729 (ttmt) REVERT: C 1038 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6095 (mt-10) REVERT: F 314 MET cc_start: 0.5156 (tpt) cc_final: 0.3644 (mtm) REVERT: F 321 LYS cc_start: 0.5453 (OUTLIER) cc_final: 0.5125 (mttp) REVERT: F 355 LYS cc_start: 0.7041 (tptt) cc_final: 0.6084 (tptp) REVERT: F 411 GLN cc_start: 0.5686 (mm110) cc_final: 0.5301 (mm110) REVERT: F 432 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5380 (ttp) REVERT: F 844 TYR cc_start: 0.8378 (m-80) cc_final: 0.8034 (m-80) REVERT: F 878 ASP cc_start: 0.6551 (OUTLIER) cc_final: 0.5644 (t70) REVERT: F 1010 LYS cc_start: 0.8092 (tptt) cc_final: 0.7520 (ttmt) REVERT: F 1038 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6154 (mt-10) REVERT: F 1111 LYS cc_start: 0.7891 (tppt) cc_final: 0.7001 (tttt) outliers start: 46 outliers final: 13 residues processed: 230 average time/residue: 0.6106 time to fit residues: 159.7862 Evaluate side-chains 201 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1066 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 202 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 ASN C 494 ASN C 813 GLN C1112 ASN F 302 ASN ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN F 813 GLN F 944 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.196544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156111 restraints weight = 23982.843| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.88 r_work: 0.3267 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21136 Z= 0.168 Angle : 0.759 14.019 29302 Z= 0.355 Chirality : 0.061 0.755 3318 Planarity : 0.004 0.036 3048 Dihedral : 13.993 142.493 4486 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.22 % Allowed : 15.89 % Favored : 80.88 % 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: -1.39 (0.18), residues: 1960 helix: 0.55 (0.18), residues: 826 sheet: -0.78 (0.31), residues: 258 loop : -2.50 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 921 TYR 0.018 0.001 TYR A 26 PHE 0.017 0.002 PHE F1042 TRP 0.006 0.001 TRP B 38 HIS 0.004 0.001 HIS C 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (21136) covalent geometry : angle 0.75947 / 0.35 (29302) hydrogen bonds : bond 0.05056 / 3.24 ( 872) hydrogen bonds : angle 4.45587 / 3.14 ( 2410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.627 Fit side-chains REVERT: A 105 LYS cc_start: 0.8464 (ttmm) cc_final: 0.7913 (tttt) REVERT: A 162 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7462 (pp20) REVERT: B 40 LYS cc_start: 0.8250 (mttt) cc_final: 0.7926 (mttm) REVERT: B 105 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8004 (tttt) REVERT: B 145 SER cc_start: 0.8313 (t) cc_final: 0.8078 (m) REVERT: B 162 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: C 314 MET cc_start: 0.5326 (tpt) cc_final: 0.5032 (tpt) REVERT: C 355 LYS cc_start: 0.6881 (tptt) cc_final: 0.5919 (tptp) REVERT: C 385 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7656 (tmm-80) REVERT: C 390 GLU cc_start: 0.7974 (tp30) cc_final: 0.7450 (tm-30) REVERT: C 432 MET cc_start: 0.6402 (tpp) cc_final: 0.5470 (ttp) REVERT: C 844 TYR cc_start: 0.8240 (m-80) cc_final: 0.7985 (m-80) REVERT: C 878 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.5981 (t70) REVERT: C 952 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8028 (p0) REVERT: C 1010 LYS cc_start: 0.8311 (tptt) cc_final: 0.7836 (ttmt) REVERT: C 1038 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6055 (mt-10) REVERT: F 321 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.5134 (mttp) REVERT: F 355 LYS cc_start: 0.7021 (tptt) cc_final: 0.6161 (tptp) REVERT: F 385 ARG cc_start: 0.7825 (tmm-80) cc_final: 0.7598 (tmm-80) REVERT: F 390 GLU cc_start: 0.7747 (tp30) cc_final: 0.7389 (tm-30) REVERT: F 432 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5368 (ttm) REVERT: F 844 TYR cc_start: 0.8357 (m-80) cc_final: 0.8132 (m-80) REVERT: F 878 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.5689 (t70) REVERT: F 1010 LYS cc_start: 0.8292 (tptt) cc_final: 0.7767 (ttmt) REVERT: F 1038 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6100 (mt-10) REVERT: F 1111 LYS cc_start: 0.7917 (tppt) cc_final: 0.7023 (tttt) outliers start: 57 outliers final: 15 residues processed: 232 average time/residue: 0.6210 time to fit residues: 163.7550 Evaluate side-chains 206 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 952 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1066 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN C 61 HIS C 231 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN F 61 HIS F 302 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F 944 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.200152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162063 restraints weight = 24019.760| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.64 r_work: 0.3311 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21136 Z= 0.117 Angle : 0.651 13.039 29302 Z= 0.308 Chirality : 0.053 0.445 3318 Planarity : 0.003 0.036 3048 Dihedral : 13.814 137.238 4486 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.60 % Allowed : 16.57 % Favored : 80.83 % 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: -0.91 (0.18), residues: 1960 helix: 1.06 (0.18), residues: 828 sheet: -0.61 (0.31), residues: 258 loop : -2.33 (0.17), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 921 TYR 0.019 0.001 TYR F 307 PHE 0.014 0.001 PHE C1042 TRP 0.006 0.001 TRP B 38 HIS 0.004 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (21136) covalent geometry : angle 0.65072 / 0.31 (29302) hydrogen bonds : bond 0.04013 / 2.58 ( 872) hydrogen bonds : angle 4.22021 / 2.98 ( 2410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.630 Fit side-chains REVERT: A 105 LYS cc_start: 0.8459 (ttmm) cc_final: 0.7900 (tttm) REVERT: A 145 SER cc_start: 0.8209 (t) cc_final: 0.8002 (m) REVERT: A 162 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7433 (pp20) REVERT: B 89 MET cc_start: 0.8376 (ptp) cc_final: 0.8139 (ptm) REVERT: B 105 LYS cc_start: 0.8468 (ttmm) cc_final: 0.7940 (tttm) REVERT: B 145 SER cc_start: 0.8298 (t) cc_final: 0.8072 (m) REVERT: B 162 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7495 (pp20) REVERT: C 314 MET cc_start: 0.5420 (tpt) cc_final: 0.5075 (tpt) REVERT: C 355 LYS cc_start: 0.6822 (tptt) cc_final: 0.5856 (tptp) REVERT: C 385 ARG cc_start: 0.8006 (tmm-80) cc_final: 0.7725 (tmm-80) REVERT: C 390 GLU cc_start: 0.8112 (tp30) cc_final: 0.7500 (tm-30) REVERT: C 408 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: C 412 PHE cc_start: 0.6900 (t80) cc_final: 0.6596 (t80) REVERT: C 432 MET cc_start: 0.6662 (tpp) cc_final: 0.5562 (ttp) REVERT: C 810 PHE cc_start: 0.6816 (m-80) cc_final: 0.6560 (m-10) REVERT: C 844 TYR cc_start: 0.8211 (m-80) cc_final: 0.7995 (m-80) REVERT: C 878 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.5893 (t70) REVERT: C 1010 LYS cc_start: 0.8246 (tptt) cc_final: 0.7787 (ttmt) REVERT: C 1038 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6052 (mt-10) REVERT: F 314 MET cc_start: 0.4813 (mmm) cc_final: 0.3603 (mtm) REVERT: F 355 LYS cc_start: 0.7075 (tptt) cc_final: 0.6324 (tptp) REVERT: F 370 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: F 385 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.7672 (tmm-80) REVERT: F 390 GLU cc_start: 0.7858 (tp30) cc_final: 0.7400 (tm-30) REVERT: F 432 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5523 (ttp) REVERT: F 844 TYR cc_start: 0.8365 (m-80) cc_final: 0.8087 (m-80) REVERT: F 878 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.5787 (t70) REVERT: F 1010 LYS cc_start: 0.8250 (tptt) cc_final: 0.7666 (ttmt) REVERT: F 1038 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6063 (mt-10) REVERT: F 1111 LYS cc_start: 0.7896 (tppt) cc_final: 0.7019 (tttt) outliers start: 46 outliers final: 17 residues processed: 233 average time/residue: 0.6155 time to fit residues: 163.1665 Evaluate side-chains 216 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 370 GLU Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1066 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 163 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN F 178 HIS F 302 ASN ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F 944 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.198040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.165334 restraints weight = 23923.882| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.29 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21136 Z= 0.220 Angle : 0.748 13.702 29302 Z= 0.356 Chirality : 0.058 0.618 3318 Planarity : 0.004 0.042 3048 Dihedral : 13.723 139.403 4486 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.56 % Allowed : 16.74 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 1960 helix: 0.95 (0.18), residues: 830 sheet: -0.71 (0.32), residues: 254 loop : -2.27 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 57 TYR 0.020 0.002 TYR B 26 PHE 0.020 0.002 PHE C1042 TRP 0.006 0.002 TRP B 106 HIS 0.005 0.001 HIS F 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (21136) covalent geometry : angle 0.74807 / 0.36 (29302) hydrogen bonds : bond 0.05631 / 3.63 ( 872) hydrogen bonds : angle 4.24304 / 2.98 ( 2410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 0.732 Fit side-chains REVERT: A 105 LYS cc_start: 0.8306 (ttmm) cc_final: 0.8033 (tttt) REVERT: A 112 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7065 (p0) REVERT: A 145 SER cc_start: 0.8425 (t) cc_final: 0.8190 (m) REVERT: A 162 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: B 105 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8051 (tttt) REVERT: B 113 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7508 (t0) REVERT: B 162 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7428 (pp20) REVERT: C 314 MET cc_start: 0.5376 (tpt) cc_final: 0.5076 (tpt) REVERT: C 355 LYS cc_start: 0.7693 (tptt) cc_final: 0.7440 (tptp) REVERT: C 408 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: C 432 MET cc_start: 0.5946 (tpp) cc_final: 0.5635 (ttp) REVERT: C 878 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6135 (t70) REVERT: C 952 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7939 (p0) REVERT: C 1010 LYS cc_start: 0.8285 (tptt) cc_final: 0.7931 (ttmt) REVERT: F 321 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5912 (mttp) REVERT: F 408 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7018 (pp20) REVERT: F 878 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.5889 (t70) REVERT: F 1010 LYS cc_start: 0.8223 (tptt) cc_final: 0.7885 (ttmt) outliers start: 63 outliers final: 30 residues processed: 230 average time/residue: 0.5882 time to fit residues: 154.9258 Evaluate side-chains 225 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 952 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1066 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1112 ASN F 348 HIS ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 944 ASN F1112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.202729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170690 restraints weight = 23892.669| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.27 r_work: 0.3370 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21136 Z= 0.120 Angle : 0.647 13.518 29302 Z= 0.310 Chirality : 0.051 0.423 3318 Planarity : 0.003 0.033 3048 Dihedral : 13.660 137.542 4486 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.34 % Allowed : 18.38 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 1960 helix: 1.29 (0.18), residues: 832 sheet: -0.48 (0.32), residues: 250 loop : -2.20 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 921 TYR 0.017 0.001 TYR F 162 PHE 0.016 0.001 PHE C1042 TRP 0.007 0.001 TRP A 38 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (21136) covalent geometry : angle 0.64718 / 0.31 (29302) hydrogen bonds : bond 0.04195 / 2.70 ( 872) hydrogen bonds : angle 4.14014 / 2.91 ( 2410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.700 Fit side-chains REVERT: A 105 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8021 (tttm) REVERT: A 145 SER cc_start: 0.8313 (t) cc_final: 0.8071 (m) REVERT: A 162 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7686 (pp20) REVERT: B 43 ASN cc_start: 0.7746 (m110) cc_final: 0.7384 (m-40) REVERT: B 105 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8052 (tttm) REVERT: B 145 SER cc_start: 0.8380 (t) cc_final: 0.8044 (m) REVERT: B 162 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: C 146 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6758 (tp) REVERT: C 314 MET cc_start: 0.5495 (tpt) cc_final: 0.5207 (tpt) REVERT: C 355 LYS cc_start: 0.6988 (tptt) cc_final: 0.6244 (tptp) REVERT: C 408 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: C 432 MET cc_start: 0.6648 (tpp) cc_final: 0.5578 (ttp) REVERT: C 810 PHE cc_start: 0.6775 (m-10) cc_final: 0.6479 (m-10) REVERT: C 878 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.5851 (t70) REVERT: C 1010 LYS cc_start: 0.8192 (tptt) cc_final: 0.7781 (ttmt) REVERT: F 321 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.5344 (mttp) REVERT: F 408 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: F 878 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.5809 (t70) REVERT: F 1010 LYS cc_start: 0.8214 (tptt) cc_final: 0.7819 (ttmt) outliers start: 59 outliers final: 19 residues processed: 234 average time/residue: 0.5944 time to fit residues: 159.4534 Evaluate side-chains 209 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 862 MET Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1062 ASP Chi-restraints excluded: chain F residue 1066 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 138 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN C 178 HIS ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1112 ASN F 178 HIS F 348 HIS ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 832 GLN F 944 ASN F1112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.200040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167896 restraints weight = 24075.990| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.29 r_work: 0.3338 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21136 Z= 0.164 Angle : 0.673 12.230 29302 Z= 0.323 Chirality : 0.052 0.505 3318 Planarity : 0.004 0.033 3048 Dihedral : 13.576 138.009 4486 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.56 % Allowed : 18.50 % Favored : 77.94 % 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: -0.56 (0.18), residues: 1960 helix: 1.33 (0.18), residues: 832 sheet: -0.15 (0.33), residues: 230 loop : -2.19 (0.17), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.020 0.002 TYR F 162 PHE 0.017 0.001 PHE C 420 TRP 0.004 0.001 TRP B 106 HIS 0.004 0.001 HIS C 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (21136) covalent geometry : angle 0.67272 / 0.32 (29302) hydrogen bonds : bond 0.04701 / 3.03 ( 872) hydrogen bonds : angle 4.10884 / 2.88 ( 2410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.702 Fit side-chains REVERT: A 43 ASN cc_start: 0.7872 (m110) cc_final: 0.7563 (m-40) REVERT: A 105 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8067 (tttm) REVERT: A 162 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: B 105 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8140 (tttm) REVERT: B 162 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7746 (pp20) REVERT: C 355 LYS cc_start: 0.7027 (tptt) cc_final: 0.6295 (tptp) REVERT: C 408 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: C 432 MET cc_start: 0.6680 (tpp) cc_final: 0.5575 (ttp) REVERT: C 878 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.5924 (t70) REVERT: C 1010 LYS cc_start: 0.8277 (tptt) cc_final: 0.7856 (ttmt) REVERT: F 233 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7504 (ptpt) REVERT: F 408 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: F 878 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.5747 (t70) REVERT: F 1010 LYS cc_start: 0.8247 (tptt) cc_final: 0.7850 (ttmt) outliers start: 63 outliers final: 30 residues processed: 227 average time/residue: 0.5927 time to fit residues: 154.4296 Evaluate side-chains 223 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 862 MET Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1062 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 208 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 112 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C 832 GLN C1112 ASN F 178 HIS F 348 HIS ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F 944 ASN F1112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.201603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169487 restraints weight = 24055.264| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.30 r_work: 0.3363 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21136 Z= 0.128 Angle : 0.639 11.115 29302 Z= 0.308 Chirality : 0.050 0.443 3318 Planarity : 0.003 0.033 3048 Dihedral : 13.544 137.856 4486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.34 % Allowed : 19.12 % Favored : 77.55 % 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: -0.43 (0.18), residues: 1960 helix: 1.44 (0.18), residues: 834 sheet: -0.06 (0.33), residues: 230 loop : -2.13 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 385 TYR 0.020 0.001 TYR F 162 PHE 0.016 0.001 PHE C1042 TRP 0.005 0.001 TRP A 38 HIS 0.003 0.001 HIS C 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (21136) covalent geometry : angle 0.63914 / 0.31 (29302) hydrogen bonds : bond 0.04228 / 2.72 ( 872) hydrogen bonds : angle 4.06241 / 2.85 ( 2410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.686 Fit side-chains REVERT: A 43 ASN cc_start: 0.7790 (m110) cc_final: 0.7420 (m-40) REVERT: A 105 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8041 (tttm) REVERT: A 145 SER cc_start: 0.8370 (t) cc_final: 0.8043 (m) REVERT: A 162 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7714 (pp20) REVERT: B 43 ASN cc_start: 0.7694 (m110) cc_final: 0.7288 (m-40) REVERT: B 105 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8068 (tttm) REVERT: B 162 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7729 (pp20) REVERT: C 146 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6702 (tp) REVERT: C 355 LYS cc_start: 0.7036 (tptt) cc_final: 0.6274 (tptp) REVERT: C 408 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7327 (pp20) REVERT: C 432 MET cc_start: 0.6698 (tpp) cc_final: 0.5610 (ttp) REVERT: C 810 PHE cc_start: 0.6561 (m-10) cc_final: 0.6309 (m-10) REVERT: C 878 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.5881 (t70) REVERT: C 1010 LYS cc_start: 0.8205 (tptt) cc_final: 0.7787 (ttmt) REVERT: F 233 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7492 (ptpt) REVERT: F 408 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: F 810 PHE cc_start: 0.6787 (m-80) cc_final: 0.6532 (m-10) REVERT: F 878 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.5748 (t70) REVERT: F 1010 LYS cc_start: 0.8229 (tptt) cc_final: 0.7831 (ttmt) outliers start: 59 outliers final: 28 residues processed: 226 average time/residue: 0.5740 time to fit residues: 148.2267 Evaluate side-chains 217 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 447 MET Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 862 MET Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1027 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN F 178 HIS F 348 HIS ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F 944 ASN F1112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.201373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169697 restraints weight = 23852.030| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.25 r_work: 0.3329 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21136 Z= 0.145 Angle : 0.649 11.725 29302 Z= 0.313 Chirality : 0.050 0.469 3318 Planarity : 0.003 0.032 3048 Dihedral : 13.460 137.957 4486 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.94 % Allowed : 19.46 % Favored : 77.60 % 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: -0.38 (0.18), residues: 1960 helix: 1.48 (0.18), residues: 834 sheet: -0.02 (0.33), residues: 226 loop : -2.10 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.021 0.001 TYR F 162 PHE 0.016 0.001 PHE C1042 TRP 0.004 0.001 TRP A 38 HIS 0.003 0.001 HIS F 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (21136) covalent geometry : angle 0.64905 / 0.31 (29302) hydrogen bonds : bond 0.04410 / 2.84 ( 872) hydrogen bonds : angle 4.02633 / 2.82 ( 2410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.700 Fit side-chains REVERT: A 43 ASN cc_start: 0.7730 (m110) cc_final: 0.7261 (m-40) REVERT: A 105 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8057 (tttm) REVERT: A 162 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7710 (pp20) REVERT: B 43 ASN cc_start: 0.7705 (m110) cc_final: 0.7276 (m-40) REVERT: B 105 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8077 (tttm) REVERT: B 162 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: C 355 LYS cc_start: 0.7042 (tptt) cc_final: 0.6306 (tptp) REVERT: C 408 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: C 432 MET cc_start: 0.6695 (tpp) cc_final: 0.5606 (ttp) REVERT: C 878 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.5826 (t70) REVERT: C 1010 LYS cc_start: 0.8234 (tptt) cc_final: 0.7802 (ttmt) REVERT: F 408 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7327 (pp20) REVERT: F 810 PHE cc_start: 0.6746 (m-80) cc_final: 0.6473 (m-10) REVERT: F 878 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.5702 (t70) REVERT: F 1010 LYS cc_start: 0.8200 (tptt) cc_final: 0.7798 (ttmt) outliers start: 52 outliers final: 33 residues processed: 215 average time/residue: 0.5856 time to fit residues: 144.8240 Evaluate side-chains 217 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1112 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 447 MET Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 862 MET Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1112 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 6 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN B 127 ASN C 178 HIS ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN F 178 HIS F 348 HIS ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F 944 ASN F1112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.200326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168924 restraints weight = 23973.250| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.28 r_work: 0.3344 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21136 Z= 0.156 Angle : 0.656 12.022 29302 Z= 0.317 Chirality : 0.051 0.487 3318 Planarity : 0.003 0.033 3048 Dihedral : 13.429 138.426 4486 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.66 % Allowed : 20.02 % Favored : 77.32 % 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: -0.35 (0.18), residues: 1960 helix: 1.50 (0.18), residues: 832 sheet: -0.03 (0.33), residues: 226 loop : -2.07 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.022 0.002 TYR F 162 PHE 0.016 0.001 PHE C1042 TRP 0.003 0.001 TRP A 38 HIS 0.003 0.001 HIS F 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (21136) covalent geometry : angle 0.65648 / 0.32 (29302) hydrogen bonds : bond 0.04548 / 2.93 ( 872) hydrogen bonds : angle 4.01933 / 2.81 ( 2410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.813 Fit side-chains REVERT: A 43 ASN cc_start: 0.7718 (m110) cc_final: 0.7272 (m-40) REVERT: A 105 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8075 (tttm) REVERT: A 162 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7736 (pp20) REVERT: B 43 ASN cc_start: 0.7707 (m110) cc_final: 0.7274 (m-40) REVERT: B 105 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8072 (tttm) REVERT: B 162 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: C 178 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6895 (p-80) REVERT: C 208 THR cc_start: 0.6851 (OUTLIER) cc_final: 0.6641 (m) REVERT: C 355 LYS cc_start: 0.7075 (tptt) cc_final: 0.6060 (tptp) REVERT: C 408 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7338 (pp20) REVERT: C 412 PHE cc_start: 0.7072 (t80) cc_final: 0.6734 (t80) REVERT: C 432 MET cc_start: 0.6669 (tpp) cc_final: 0.5585 (ttp) REVERT: C 810 PHE cc_start: 0.6432 (m-10) cc_final: 0.6193 (m-10) REVERT: C 878 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.5789 (t70) REVERT: C 1010 LYS cc_start: 0.8274 (tptt) cc_final: 0.7834 (ttmt) REVERT: F 355 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7006 (tptp) REVERT: F 408 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: F 810 PHE cc_start: 0.6748 (m-80) cc_final: 0.6484 (m-10) REVERT: F 878 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.5671 (t70) REVERT: F 1010 LYS cc_start: 0.8273 (tptt) cc_final: 0.7854 (ttmt) outliers start: 47 outliers final: 29 residues processed: 208 average time/residue: 0.5963 time to fit residues: 142.1876 Evaluate side-chains 215 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 447 MET Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 862 MET Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1056 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 179 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN F 178 HIS F 348 HIS ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F 944 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.200600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168464 restraints weight = 23942.720| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.28 r_work: 0.3346 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21136 Z= 0.164 Angle : 0.795 57.285 29302 Z= 0.459 Chirality : 0.051 0.559 3318 Planarity : 0.004 0.087 3048 Dihedral : 13.429 138.507 4486 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.83 % Allowed : 19.85 % Favored : 77.32 % 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: -0.35 (0.18), residues: 1960 helix: 1.51 (0.18), residues: 832 sheet: -0.08 (0.33), residues: 226 loop : -2.06 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.020 0.001 TYR F 162 PHE 0.015 0.001 PHE C1042 TRP 0.004 0.001 TRP A 38 HIS 0.127 0.003 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (21136) covalent geometry : angle 0.79532 / 0.46 (29302) hydrogen bonds : bond 0.04641 / 2.91 ( 872) hydrogen bonds : angle 4.04747 / 2.84 ( 2410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5851.38 seconds wall clock time: 100 minutes 48.32 seconds (6048.32 seconds total)