Starting phenix.real_space_refine on Sat Oct 31 02:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r8z_4763/10_2026/6r8z_4763.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r8z_4763/10_2026/6r8z_4763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r8z_4763/10_2026/6r8z_4763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r8z_4763/10_2026/6r8z_4763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r8z_4763/10_2026/6r8z_4763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r8z_4763/10_2026/6r8z_4763.map" } resolution = 3.9 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= 1.000 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: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 66 5.16 5 C 12746 2.51 5 N 3909 2.21 5 O 4608 1.98 5 H 19214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40831 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1434 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1878 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "D" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1559 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1878 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4581 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 12900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12900 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5666 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 340} Time building chain proxies: 6.31, per 1000 atoms: 0.15 Number of scatterers: 40831 At special positions: 0 Unit cell: (136.4, 183.7, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 288 15.00 O 4608 8.00 N 3909 7.00 C 12746 6.00 H 19214 1.00 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: 3.85 Conformation dependent library (CDL) restraints added in 952.7 milliseconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3690 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 34 sheets defined 33.5% alpha, 25.8% beta 141 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 4.018A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.541A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.600A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.845A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.646A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.586A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.856A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 removed outlier: 3.506A pdb=" N ALA D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.734A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.505A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.590A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.850A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.740A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.528A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.538A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.586A pdb=" N VAL H 42 " --> pdb=" O TYR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.644A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.514A pdb=" N SER H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 256 removed outlier: 4.009A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 755 through 759 Processing helix chain 'K' and resid 985 through 990 Processing helix chain 'K' and resid 1044 through 1062 Processing helix chain 'K' and resid 1069 through 1075 Processing helix chain 'K' and resid 1091 through 1096 Processing helix chain 'K' and resid 1097 through 1100 removed outlier: 3.544A pdb=" N ILE K1100 " --> pdb=" O PHE K1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1097 through 1100' Processing helix chain 'K' and resid 1101 through 1110 Processing helix chain 'K' and resid 1125 through 1138 removed outlier: 3.527A pdb=" N ARG K1138 " --> pdb=" O GLU K1134 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 78 Processing helix chain 'L' and resid 82 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.167A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.619A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 removed outlier: 7.106A pdb=" N THR B 97 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.495A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.382A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.502A pdb=" N ILE E 120 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.999A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 1004 through 1009 removed outlier: 3.710A pdb=" N VAL K1006 " --> pdb=" O GLY K1031 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER K1027 " --> pdb=" O VAL K1040 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL K1040 " --> pdb=" O SER K1027 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU K1029 " --> pdb=" O GLY K1038 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY K1038 " --> pdb=" O LEU K1029 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 17 through 21 removed outlier: 6.374A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 61 through 67 removed outlier: 4.275A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA K 86 " --> pdb=" O HIS K 105 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N HIS K 105 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE K 88 " --> pdb=" O ARG K 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 121 through 124 Processing sheet with id=AB6, first strand: chain 'K' and resid 164 through 169 removed outlier: 6.285A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 164 through 169 removed outlier: 6.285A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 218 through 221 Processing sheet with id=AB9, first strand: chain 'K' and resid 258 through 263 removed outlier: 6.943A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU K 280 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU K 304 " --> pdb=" O LEU K 280 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET K 282 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL K 302 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU K 284 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU K 300 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU K 286 " --> pdb=" O LYS K 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 313 through 318 removed outlier: 6.636A pdb=" N VAL K 321 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER K 331 " --> pdb=" O THR K 352 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR K 352 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU K 333 " --> pdb=" O MET K 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 361 through 369 removed outlier: 3.983A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU K 367 " --> pdb=" O GLN K 372 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLN K 372 " --> pdb=" O LEU K 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.626A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.626A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 811 through 819 removed outlier: 5.345A pdb=" N ALA K 813 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 834 " --> pdb=" O ALA K 813 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY K 846 " --> pdb=" O GLU K 865 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU K 865 " --> pdb=" O GLY K 846 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 848 " --> pdb=" O GLU K 863 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU K 863 " --> pdb=" O ILE K 848 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL K 850 " --> pdb=" O VAL K 861 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 870 through 876 removed outlier: 6.668A pdb=" N VAL K 888 " --> pdb=" O ASN K 904 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN K 904 " --> pdb=" O VAL K 888 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU K 890 " --> pdb=" O GLU K 902 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 911 through 917 removed outlier: 4.998A pdb=" N VAL K 930 " --> pdb=" O ASP K 948 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP K 948 " --> pdb=" O VAL K 930 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU K 992 " --> pdb=" O ILE K 945 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG K 947 " --> pdb=" O LEU K 992 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU K 994 " --> pdb=" O ARG K 947 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL K 976 " --> pdb=" O VAL K 995 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU K 997 " --> pdb=" O LEU K 974 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU K 974 " --> pdb=" O LEU K 997 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN K 964 " --> pdb=" O LEU K 960 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA K 956 " --> pdb=" O ALA K 968 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 1076 through 1077 Processing sheet with id=AC9, first strand: chain 'K' and resid 1113 through 1114 Processing sheet with id=AD1, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'L' and resid 114 through 119 Processing sheet with id=AD3, first strand: chain 'L' and resid 159 through 161 removed outlier: 6.451A pdb=" N SER L 175 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 204 through 210 removed outlier: 6.542A pdb=" N GLY L 219 " --> pdb=" O CYS L 205 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU L 207 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL L 217 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL L 209 " --> pdb=" O MET L 215 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET L 215 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 247 through 250 removed outlier: 4.098A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 291 through 296 removed outlier: 3.863A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 343 through 344 removed outlier: 5.737A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 678 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 218 stacking parallelities Total time for adding SS restraints: 11.11 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19172 1.03 - 1.22: 199 1.22 - 1.42: 9843 1.42 - 1.62: 12510 1.62 - 1.82: 108 Bond restraints: 41832 Sorted by residual: bond pdb=" C2' 3DR J 96 " pdb="H2'' 3DR J 96 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C5' 3DR J 96 " pdb=" H5' 3DR J 96 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C1' 3DR J 96 " pdb="H1'1 3DR J 96 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C1' 3DR J 96 " pdb="H1'2 3DR J 96 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C5' 3DR J 95 " pdb="H5'' 3DR J 95 " ideal model delta sigma weight residual 0.970 1.088 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 41827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.05: 75737 7.05 - 14.09: 17 14.09 - 21.14: 0 21.14 - 28.18: 1 28.18 - 35.23: 2 Bond angle restraints: 75757 Sorted by residual: angle pdb=" CB SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 109.00 73.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 109.00 74.33 34.67 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 110.00 82.76 27.24 3.00e+00 1.11e-01 8.24e+01 angle pdb=" O4' DC J 87 " pdb=" C4' DC J 87 " pdb=" C3' DC J 87 " ideal model delta sigma weight residual 106.00 101.98 4.02 6.00e-01 2.78e+00 4.48e+01 angle pdb=" O4' DT J 79 " pdb=" C1' DT J 79 " pdb=" N1 DT J 79 " ideal model delta sigma weight residual 108.00 112.50 -4.50 7.00e-01 2.04e+00 4.14e+01 ... (remaining 75752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 16650 35.28 - 70.56: 1839 70.56 - 105.83: 47 105.83 - 141.11: 5 141.11 - 176.39: 5 Dihedral angle restraints: 18546 sinusoidal: 12003 harmonic: 6543 Sorted by residual: dihedral pdb=" CA ARG K 928 " pdb=" C ARG K 928 " pdb=" N SER K 929 " pdb=" CA SER K 929 " ideal model delta harmonic sigma weight residual -180.00 -133.27 -46.73 0 5.00e+00 4.00e-02 8.74e+01 dihedral pdb=" CA LYS B 21 " pdb=" C LYS B 21 " pdb=" N VAL B 22 " pdb=" CA VAL B 22 " ideal model delta harmonic sigma weight residual -180.00 -136.85 -43.15 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" CA LEU B 23 " pdb=" C LEU B 23 " pdb=" N ARG B 24 " pdb=" CA ARG B 24 " ideal model delta harmonic sigma weight residual 180.00 144.22 35.78 0 5.00e+00 4.00e-02 5.12e+01 ... (remaining 18543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3230 0.116 - 0.231: 351 0.231 - 0.347: 4 0.347 - 0.462: 0 0.462 - 0.578: 1 Chirality restraints: 3586 Sorted by residual: chirality pdb=" CA SER L 68 " pdb=" N SER L 68 " pdb=" C SER L 68 " pdb=" CB SER L 68 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" C3' DC I 50 " pdb=" C4' DC I 50 " pdb=" O3' DC I 50 " pdb=" C2' DC I 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' DT I 70 " pdb=" C4' DT I 70 " pdb=" O3' DT I 70 " pdb=" C2' DT I 70 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3583 not shown) Planarity restraints: 5162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 382 " -0.028 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C PHE K 382 " 0.094 2.00e-02 2.50e+03 pdb=" O PHE K 382 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS K 383 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 381 " 0.026 2.00e-02 2.50e+03 5.25e-02 2.75e+01 pdb=" C ALA K 381 " -0.091 2.00e-02 2.50e+03 pdb=" O ALA K 381 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE K 382 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 146 " 0.061 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO L 147 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO L 147 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO L 147 " 0.050 5.00e-02 4.00e+02 ... (remaining 5159 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 3739 2.23 - 2.82: 83264 2.82 - 3.41: 100871 3.41 - 4.01: 145297 4.01 - 4.60: 214826 Nonbonded interactions: 547997 Sorted by model distance: nonbonded pdb=" HG1 THR L 371 " pdb=" O LEU L 386 " model vdw 1.634 2.450 nonbonded pdb=" OD1 ASN K 36 " pdb=" HZ2 LYS K 60 " model vdw 1.635 2.450 nonbonded pdb=" H ARG A 43 " pdb=" OP1 DG I 143 " model vdw 1.639 2.450 nonbonded pdb=" O LEU A 104 " pdb=" HG1 THR A 108 " model vdw 1.663 2.450 nonbonded pdb=" OD1 ASN C 69 " pdb="HH22 ARG C 72 " model vdw 1.667 2.450 ... (remaining 547992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 22 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 23 through 103)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 30 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB o \ r name HG21 or name HG22 or name HG23)) or resid 90 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 94 or resid 97 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 94 or resid 97 through 14 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.470 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: 0.130 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 43.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.174 22618 Z= 0.798 Angle : 1.045 12.510 31802 Z= 0.807 Chirality : 0.067 0.578 3586 Planarity : 0.007 0.092 3059 Dihedral : 22.932 175.472 9295 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.64 % Favored : 95.01 % Rotamer: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.17), residues: 1962 helix: 0.53 (0.19), residues: 616 sheet: -0.68 (0.23), residues: 451 loop : -2.09 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 313 TYR 0.030 0.003 TYR G 51 PHE 0.023 0.003 PHE K 382 TRP 0.015 0.003 TRP K 207 HIS 0.014 0.002 HIS L 333 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.80 (22618) covalent geometry : angle 1.04459 / 0.81 (31802) hydrogen bonds : bond 0.14111 / 9.35 ( 1065) hydrogen bonds : angle 5.68905 / 4.13 ( 2745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 442 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.9013 (t) cc_final: 0.8694 (m) REVERT: B 80 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7699 (mttm) REVERT: C 57 GLU cc_start: 0.7632 (tt0) cc_final: 0.7418 (tm-30) REVERT: D 35 LYS cc_start: 0.8602 (tppt) cc_final: 0.8333 (tptm) REVERT: D 121 LYS cc_start: 0.8986 (tttm) cc_final: 0.8744 (ttpp) REVERT: E 56 GLN cc_start: 0.8385 (mt0) cc_final: 0.7887 (mt0) REVERT: E 121 MET cc_start: 0.7994 (mtp) cc_final: 0.7706 (mtp) REVERT: F 45 LYS cc_start: 0.7824 (tttt) cc_final: 0.7610 (tttp) REVERT: H 44 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7539 (ttmm) REVERT: K 6 VAL cc_start: 0.8274 (t) cc_final: 0.7966 (m) REVERT: K 15 VAL cc_start: 0.8567 (t) cc_final: 0.8294 (t) REVERT: K 215 GLU cc_start: 0.8747 (tp30) cc_final: 0.7876 (tm-30) REVERT: K 271 TYR cc_start: 0.7223 (m-80) cc_final: 0.6382 (m-80) REVERT: K 277 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7654 (tt0) REVERT: K 933 LEU cc_start: 0.7622 (mt) cc_final: 0.7275 (tt) REVERT: K 1072 PHE cc_start: 0.7404 (t80) cc_final: 0.6971 (t80) REVERT: L 88 GLN cc_start: 0.7882 (tp40) cc_final: 0.7499 (tm-30) REVERT: L 243 LYS cc_start: 0.8716 (mttt) cc_final: 0.8404 (mttm) outliers start: 3 outliers final: 1 residues processed: 445 average time/residue: 0.4296 time to fit residues: 268.8290 Evaluate side-chains 315 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 421 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN G 111 ASN H 96 GLN K 93 GLN ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 907 ASN K 950 ASN K1055 GLN K1059 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.189229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.150343 restraints weight = 124518.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.156673 restraints weight = 48104.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.160465 restraints weight = 26138.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.162747 restraints weight = 18142.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.164015 restraints weight = 14725.301| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22618 Z= 0.180 Angle : 0.721 9.272 31802 Z= 0.434 Chirality : 0.047 0.484 3586 Planarity : 0.005 0.084 3059 Dihedral : 26.436 176.802 5448 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.18 % Favored : 95.57 % Rotamer: Outliers : 1.00 % Allowed : 10.48 % Favored : 88.52 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 1962 helix: 1.57 (0.20), residues: 621 sheet: -0.41 (0.23), residues: 454 loop : -1.94 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 54 TYR 0.029 0.002 TYR D 84 PHE 0.017 0.002 PHE K 323 TRP 0.012 0.001 TRP L 418 HIS 0.014 0.001 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (22618) covalent geometry : angle 0.72092 / 0.43 (31802) hydrogen bonds : bond 0.07695 / 5.09 ( 1065) hydrogen bonds : angle 4.85913 / 3.50 ( 2745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 346 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 329 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.9204 (t) cc_final: 0.8836 (m) REVERT: B 75 GLU cc_start: 0.8114 (tt0) cc_final: 0.7907 (tt0) REVERT: B 80 LYS cc_start: 0.8337 (mtpp) cc_final: 0.8075 (mttp) REVERT: B 85 MET cc_start: 0.7477 (mmm) cc_final: 0.7207 (mmm) REVERT: C 57 GLU cc_start: 0.7823 (tt0) cc_final: 0.7420 (tm-30) REVERT: D 63 MET cc_start: 0.8286 (mmm) cc_final: 0.7931 (mmp) REVERT: D 84 TYR cc_start: 0.7099 (m-10) cc_final: 0.6891 (m-10) REVERT: D 121 LYS cc_start: 0.9182 (tttm) cc_final: 0.8844 (ttpp) REVERT: E 56 GLN cc_start: 0.8763 (mt0) cc_final: 0.8167 (mt0) REVERT: E 121 MET cc_start: 0.8101 (mtp) cc_final: 0.7711 (mtp) REVERT: F 45 LYS cc_start: 0.7970 (tttt) cc_final: 0.7622 (tttp) REVERT: F 92 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7595 (tptt) REVERT: G 20 SER cc_start: 0.8277 (m) cc_final: 0.8037 (p) REVERT: G 58 TYR cc_start: 0.8354 (t80) cc_final: 0.8059 (t80) REVERT: H 37 SER cc_start: 0.8077 (t) cc_final: 0.7653 (m) REVERT: H 44 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7650 (ttmm) REVERT: H 84 TYR cc_start: 0.7695 (m-80) cc_final: 0.7418 (m-80) REVERT: K 6 VAL cc_start: 0.8531 (t) cc_final: 0.8263 (m) REVERT: K 215 GLU cc_start: 0.8807 (tp30) cc_final: 0.7912 (tm-30) REVERT: K 271 TYR cc_start: 0.7339 (m-80) cc_final: 0.6477 (m-80) REVERT: K 277 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7652 (tt0) REVERT: K 790 ASN cc_start: 0.4206 (m-40) cc_final: 0.3986 (t0) REVERT: K 933 LEU cc_start: 0.7682 (mt) cc_final: 0.7325 (tt) REVERT: K 1072 PHE cc_start: 0.7363 (t80) cc_final: 0.7045 (t80) REVERT: L 88 GLN cc_start: 0.7846 (tp40) cc_final: 0.7436 (tm-30) REVERT: L 172 PHE cc_start: 0.6065 (p90) cc_final: 0.5444 (p90) REVERT: L 184 GLN cc_start: 0.7209 (tt0) cc_final: 0.6929 (tt0) REVERT: L 239 ARG cc_start: 0.6104 (ttt180) cc_final: 0.5868 (ttt180) outliers start: 17 outliers final: 11 residues processed: 335 average time/residue: 0.4175 time to fit residues: 198.7445 Evaluate side-chains 320 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 309 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [145, 18, 57, 44, 179, 35, 165, 54, 199, 95, 133] chunk 145 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 199 optimal weight: 0.0010 chunk 95 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 111 ASN ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.186124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.149939 restraints weight = 119486.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.155798 restraints weight = 47046.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.159401 restraints weight = 25964.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.161580 restraints weight = 18193.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.162820 restraints weight = 14823.270| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22618 Z= 0.173 Angle : 0.666 8.851 31802 Z= 0.408 Chirality : 0.044 0.443 3586 Planarity : 0.005 0.075 3059 Dihedral : 26.380 175.504 5445 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.59 % Favored : 95.21 % Rotamer: Outliers : 1.65 % Allowed : 11.01 % Favored : 87.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.42 (0.18), residues: 1962 helix: 1.87 (0.20), residues: 621 sheet: -0.38 (0.24), residues: 454 loop : -1.86 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 54 TYR 0.014 0.001 TYR G 51 PHE 0.022 0.001 PHE K1030 TRP 0.013 0.001 TRP L 418 HIS 0.007 0.001 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (22618) covalent geometry : angle 0.66627 / 0.41 (31802) hydrogen bonds : bond 0.06843 / 4.53 ( 1065) hydrogen bonds : angle 4.64088 / 3.32 ( 2745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.9179 (t) cc_final: 0.8896 (m) REVERT: B 75 GLU cc_start: 0.8137 (tt0) cc_final: 0.7936 (tt0) REVERT: B 80 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8048 (mttp) REVERT: B 89 TYR cc_start: 0.7977 (m-10) cc_final: 0.7671 (m-80) REVERT: C 57 GLU cc_start: 0.7698 (tt0) cc_final: 0.7309 (tm-30) REVERT: D 121 LYS cc_start: 0.9167 (tttm) cc_final: 0.8806 (ttpp) REVERT: E 56 GLN cc_start: 0.8716 (mt0) cc_final: 0.8145 (mt0) REVERT: E 121 MET cc_start: 0.8195 (mtp) cc_final: 0.7693 (mtp) REVERT: F 45 LYS cc_start: 0.7843 (tttt) cc_final: 0.7523 (tttp) REVERT: G 20 SER cc_start: 0.8127 (m) cc_final: 0.7867 (p) REVERT: G 51 TYR cc_start: 0.8685 (t80) cc_final: 0.8116 (t80) REVERT: G 58 TYR cc_start: 0.8391 (t80) cc_final: 0.8098 (t80) REVERT: H 44 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7775 (ttmm) REVERT: H 84 TYR cc_start: 0.7821 (m-80) cc_final: 0.7553 (m-80) REVERT: H 109 LYS cc_start: 0.8828 (mttt) cc_final: 0.8554 (mtpt) REVERT: K 6 VAL cc_start: 0.8692 (t) cc_final: 0.8440 (m) REVERT: K 215 GLU cc_start: 0.8792 (tp30) cc_final: 0.7895 (tm-30) REVERT: K 271 TYR cc_start: 0.7276 (m-80) cc_final: 0.6450 (m-80) REVERT: K 277 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7617 (tt0) REVERT: K 933 LEU cc_start: 0.7642 (mt) cc_final: 0.7319 (tt) REVERT: K 1072 PHE cc_start: 0.7346 (t80) cc_final: 0.7039 (t80) REVERT: L 172 PHE cc_start: 0.6285 (p90) cc_final: 0.5624 (p90) REVERT: L 184 GLN cc_start: 0.7005 (tt0) cc_final: 0.6589 (tt0) outliers start: 28 outliers final: 22 residues processed: 334 average time/residue: 0.4153 time to fit residues: 198.1317 Evaluate side-chains 325 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 966 LEU Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 398 ASN Chi-restraints excluded: chain L residue 421 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [168, 114, 19, 164, 191, 96, 137, 8, 17, 196, 199] chunk 168 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 109 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 ASN ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.181486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.140608 restraints weight = 122693.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.146777 restraints weight = 47678.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.150541 restraints weight = 26245.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.152817 restraints weight = 18420.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.154054 restraints weight = 15047.180| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 22618 Z= 0.235 Angle : 0.706 9.049 31802 Z= 0.425 Chirality : 0.045 0.426 3586 Planarity : 0.005 0.066 3059 Dihedral : 26.377 175.367 5445 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.40 % Favored : 94.39 % Rotamer: Outliers : 1.94 % Allowed : 11.18 % Favored : 86.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 1962 helix: 1.58 (0.20), residues: 620 sheet: -0.44 (0.24), residues: 450 loop : -1.92 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 93 TYR 0.014 0.002 TYR G 51 PHE 0.022 0.002 PHE L 361 TRP 0.016 0.002 TRP L 418 HIS 0.007 0.001 HIS K1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.24 (22618) covalent geometry : angle 0.70556 / 0.42 (31802) hydrogen bonds : bond 0.07437 / 4.91 ( 1065) hydrogen bonds : angle 4.86057 / 3.46 ( 2745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7743 (t70) cc_final: 0.7517 (t70) REVERT: A 58 SER cc_start: 0.9042 (t) cc_final: 0.8742 (m) REVERT: B 75 GLU cc_start: 0.8176 (tt0) cc_final: 0.7960 (tt0) REVERT: B 80 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8132 (mttp) REVERT: B 89 TYR cc_start: 0.8210 (m-10) cc_final: 0.7865 (m-80) REVERT: C 37 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7562 (mtmt) REVERT: C 57 GLU cc_start: 0.7980 (tt0) cc_final: 0.7191 (tt0) REVERT: D 109 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8428 (tptp) REVERT: D 121 LYS cc_start: 0.9223 (tttm) cc_final: 0.8844 (ttpp) REVERT: E 56 GLN cc_start: 0.8840 (mt0) cc_final: 0.8312 (mt0) REVERT: E 121 MET cc_start: 0.8321 (mtp) cc_final: 0.7867 (mtp) REVERT: F 45 LYS cc_start: 0.7913 (tttt) cc_final: 0.7614 (tttp) REVERT: F 80 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7739 (mtmt) REVERT: G 20 SER cc_start: 0.8212 (m) cc_final: 0.8007 (p) REVERT: G 51 TYR cc_start: 0.8950 (t80) cc_final: 0.8052 (t80) REVERT: G 58 TYR cc_start: 0.8356 (t80) cc_final: 0.8042 (t80) REVERT: H 84 TYR cc_start: 0.8174 (m-10) cc_final: 0.7913 (m-80) REVERT: H 109 LYS cc_start: 0.8901 (mttt) cc_final: 0.8619 (mtpt) REVERT: K 6 VAL cc_start: 0.8538 (t) cc_final: 0.8297 (m) REVERT: K 215 GLU cc_start: 0.8873 (tp30) cc_final: 0.7750 (tm-30) REVERT: K 271 TYR cc_start: 0.7579 (m-80) cc_final: 0.6688 (m-80) REVERT: K 736 LEU cc_start: 0.7518 (mt) cc_final: 0.7300 (mm) REVERT: K 1072 PHE cc_start: 0.7399 (t80) cc_final: 0.7112 (t80) REVERT: L 184 GLN cc_start: 0.7032 (tt0) cc_final: 0.6821 (tt0) REVERT: L 239 ARG cc_start: 0.6657 (ttt180) cc_final: 0.6243 (mmm160) REVERT: L 405 ASP cc_start: 0.8766 (p0) cc_final: 0.8406 (p0) outliers start: 33 outliers final: 31 residues processed: 325 average time/residue: 0.3815 time to fit residues: 180.0451 Evaluate side-chains 330 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 910 MET Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 966 LEU Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [204, 205, 209, 177, 13, 220, 35, 44, 158, 61, 191] chunk 204 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN C 74 ASN E 109 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.183884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.143190 restraints weight = 123187.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.149430 restraints weight = 48028.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.153154 restraints weight = 26510.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.155395 restraints weight = 18719.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.156732 restraints weight = 15336.253| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22618 Z= 0.165 Angle : 0.642 10.126 31802 Z= 0.393 Chirality : 0.044 0.428 3586 Planarity : 0.004 0.060 3059 Dihedral : 26.316 173.683 5445 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.30 % Favored : 94.50 % Rotamer: Outliers : 1.82 % Allowed : 12.18 % Favored : 85.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1962 helix: 1.83 (0.20), residues: 625 sheet: -0.46 (0.25), residues: 445 loop : -1.89 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 188 TYR 0.013 0.001 TYR G 51 PHE 0.019 0.001 PHE K1030 TRP 0.012 0.001 TRP L 418 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (22618) covalent geometry : angle 0.64151 / 0.39 (31802) hydrogen bonds : bond 0.06213 / 4.13 ( 1065) hydrogen bonds : angle 4.49393 / 3.21 ( 2745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 316 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7712 (t70) cc_final: 0.7490 (t70) REVERT: A 58 SER cc_start: 0.9016 (t) cc_final: 0.8714 (m) REVERT: A 98 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: B 80 LYS cc_start: 0.8274 (mtpp) cc_final: 0.8037 (mttp) REVERT: C 37 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7498 (mtmt) REVERT: C 57 GLU cc_start: 0.7859 (tt0) cc_final: 0.7319 (tm-30) REVERT: C 62 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 109 LYS cc_start: 0.8707 (tmtt) cc_final: 0.8383 (tptp) REVERT: D 121 LYS cc_start: 0.9214 (tttm) cc_final: 0.8826 (ttpp) REVERT: E 56 GLN cc_start: 0.8700 (mt0) cc_final: 0.8179 (mt0) REVERT: E 82 ASP cc_start: 0.7622 (p0) cc_final: 0.6853 (t0) REVERT: F 45 LYS cc_start: 0.7946 (tttt) cc_final: 0.7696 (tttp) REVERT: F 85 MET cc_start: 0.6980 (mmm) cc_final: 0.6493 (tpt) REVERT: G 51 TYR cc_start: 0.8905 (t80) cc_final: 0.8005 (t80) REVERT: G 58 TYR cc_start: 0.8316 (t80) cc_final: 0.8003 (t80) REVERT: H 44 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7851 (ttmm) REVERT: H 84 TYR cc_start: 0.7983 (m-10) cc_final: 0.7770 (m-80) REVERT: H 109 LYS cc_start: 0.8875 (mttt) cc_final: 0.8600 (mtpt) REVERT: K 6 VAL cc_start: 0.8561 (t) cc_final: 0.8322 (m) REVERT: K 215 GLU cc_start: 0.8655 (tp30) cc_final: 0.7612 (tm-30) REVERT: K 271 TYR cc_start: 0.7512 (m-80) cc_final: 0.6624 (m-80) REVERT: K 1072 PHE cc_start: 0.7368 (t80) cc_final: 0.7104 (t80) REVERT: L 172 PHE cc_start: 0.6490 (p90) cc_final: 0.5777 (p90) REVERT: L 184 GLN cc_start: 0.7020 (tt0) cc_final: 0.6724 (tt0) REVERT: L 239 ARG cc_start: 0.6542 (ttt180) cc_final: 0.6307 (ttt180) REVERT: L 403 MET cc_start: 0.8863 (tpt) cc_final: 0.8335 (tpp) REVERT: L 405 ASP cc_start: 0.8720 (p0) cc_final: 0.8323 (p0) outliers start: 31 outliers final: 26 residues processed: 331 average time/residue: 0.3826 time to fit residues: 185.6615 Evaluate side-chains 328 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 910 MET Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 966 LEU Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 398 ASN Chi-restraints excluded: chain L residue 421 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [67, 22, 42, 196, 116, 187, 151, 9, 108, 129, 130] chunk 67 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN E 109 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.182615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.141571 restraints weight = 123634.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.147751 restraints weight = 48361.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.151570 restraints weight = 26740.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.153754 restraints weight = 18874.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.155042 restraints weight = 15461.795| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22618 Z= 0.178 Angle : 0.649 8.921 31802 Z= 0.393 Chirality : 0.043 0.422 3586 Planarity : 0.004 0.058 3059 Dihedral : 26.292 173.931 5445 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 1.77 % Allowed : 13.24 % Favored : 84.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.42 (0.19), residues: 1962 helix: 1.90 (0.20), residues: 620 sheet: -0.43 (0.25), residues: 440 loop : -1.84 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 188 TYR 0.030 0.001 TYR D 84 PHE 0.012 0.001 PHE K 323 TRP 0.013 0.001 TRP L 418 HIS 0.007 0.001 HIS K1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.18 (22618) covalent geometry : angle 0.64852 / 0.39 (31802) hydrogen bonds : bond 0.06158 / 4.08 ( 1065) hydrogen bonds : angle 4.45862 / 3.18 ( 2745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 306 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7724 (t70) cc_final: 0.7495 (t70) REVERT: A 58 SER cc_start: 0.9008 (t) cc_final: 0.8730 (m) REVERT: B 80 LYS cc_start: 0.8313 (mtpp) cc_final: 0.8087 (mttp) REVERT: C 37 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7473 (mtmt) REVERT: C 57 GLU cc_start: 0.7856 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 72 ARG cc_start: 0.7169 (mtm110) cc_final: 0.6898 (mtm110) REVERT: D 43 TYR cc_start: 0.7669 (t80) cc_final: 0.7265 (t80) REVERT: D 109 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8371 (tptp) REVERT: D 121 LYS cc_start: 0.9201 (tttm) cc_final: 0.8808 (ttpp) REVERT: E 56 GLN cc_start: 0.8700 (mt0) cc_final: 0.8175 (mt0) REVERT: E 82 ASP cc_start: 0.7525 (p0) cc_final: 0.7259 (p0) REVERT: F 45 LYS cc_start: 0.7923 (tttt) cc_final: 0.7663 (tttp) REVERT: F 85 MET cc_start: 0.6972 (mmm) cc_final: 0.6494 (tpt) REVERT: F 92 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7796 (tptt) REVERT: G 51 TYR cc_start: 0.8940 (t80) cc_final: 0.7990 (t80) REVERT: G 58 TYR cc_start: 0.8350 (t80) cc_final: 0.8044 (t80) REVERT: H 44 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7824 (ttmm) REVERT: H 84 TYR cc_start: 0.8008 (m-10) cc_final: 0.7771 (m-80) REVERT: H 109 LYS cc_start: 0.8887 (mttt) cc_final: 0.8623 (mtpt) REVERT: K 6 VAL cc_start: 0.8594 (t) cc_final: 0.8349 (m) REVERT: K 215 GLU cc_start: 0.8636 (tp30) cc_final: 0.7678 (tm-30) REVERT: K 271 TYR cc_start: 0.7539 (m-80) cc_final: 0.6771 (m-80) REVERT: K 736 LEU cc_start: 0.7545 (mt) cc_final: 0.7323 (mm) REVERT: K 1072 PHE cc_start: 0.7388 (t80) cc_final: 0.7127 (t80) REVERT: L 172 PHE cc_start: 0.6612 (p90) cc_final: 0.5980 (p90) REVERT: L 184 GLN cc_start: 0.7033 (tt0) cc_final: 0.6799 (tt0) REVERT: L 214 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7748 (mtp85) REVERT: L 239 ARG cc_start: 0.6598 (ttt180) cc_final: 0.6380 (ttt180) REVERT: L 403 MET cc_start: 0.8856 (tpt) cc_final: 0.8331 (tpp) REVERT: L 405 ASP cc_start: 0.8744 (p0) cc_final: 0.8361 (p0) outliers start: 30 outliers final: 28 residues processed: 321 average time/residue: 0.3856 time to fit residues: 181.3066 Evaluate side-chains 325 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 966 LEU Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [176, 0, 51, 14, 65, 148, 112, 185, 192, 164, 113] chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 0.0470 chunk 112 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN E 109 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.181548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.140257 restraints weight = 123544.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.146426 restraints weight = 48382.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.150203 restraints weight = 26816.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.152129 restraints weight = 18938.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.153611 restraints weight = 15834.847| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22618 Z= 0.185 Angle : 0.654 8.698 31802 Z= 0.395 Chirality : 0.043 0.418 3586 Planarity : 0.004 0.055 3059 Dihedral : 26.278 173.988 5445 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.68 % Rotamer: Outliers : 1.65 % Allowed : 14.01 % Favored : 84.34 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.44 (0.19), residues: 1962 helix: 1.85 (0.20), residues: 620 sheet: -0.38 (0.25), residues: 429 loop : -1.84 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.043 0.002 TYR D 84 PHE 0.012 0.001 PHE K 323 TRP 0.014 0.001 TRP L 418 HIS 0.008 0.001 HIS K1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (22618) covalent geometry : angle 0.65377 / 0.39 (31802) hydrogen bonds : bond 0.06143 / 4.08 ( 1065) hydrogen bonds : angle 4.48201 / 3.20 ( 2745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 303 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.7780 (t70) cc_final: 0.7565 (t70) REVERT: A 58 SER cc_start: 0.8980 (t) cc_final: 0.8682 (m) REVERT: A 62 LEU cc_start: 0.8643 (mt) cc_final: 0.8439 (mp) REVERT: A 98 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: B 54 GLU cc_start: 0.7941 (tp30) cc_final: 0.7601 (tp30) REVERT: B 80 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8118 (mttp) REVERT: C 57 GLU cc_start: 0.7829 (tt0) cc_final: 0.7277 (tm-30) REVERT: C 72 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6895 (mtm110) REVERT: D 43 TYR cc_start: 0.7718 (t80) cc_final: 0.7272 (t80) REVERT: D 109 LYS cc_start: 0.8727 (tmtt) cc_final: 0.8406 (tptp) REVERT: D 121 LYS cc_start: 0.9186 (tttm) cc_final: 0.8797 (ttpp) REVERT: E 56 GLN cc_start: 0.8715 (mt0) cc_final: 0.8177 (mt0) REVERT: F 45 LYS cc_start: 0.7915 (tttt) cc_final: 0.7664 (tttp) REVERT: F 80 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7727 (mtmt) REVERT: G 51 TYR cc_start: 0.8973 (t80) cc_final: 0.8034 (t80) REVERT: G 58 TYR cc_start: 0.8356 (t80) cc_final: 0.8035 (t80) REVERT: H 44 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7862 (ttmm) REVERT: H 84 TYR cc_start: 0.8066 (m-10) cc_final: 0.7826 (m-80) REVERT: H 109 LYS cc_start: 0.8905 (mttt) cc_final: 0.8625 (mtpt) REVERT: K 6 VAL cc_start: 0.8615 (t) cc_final: 0.8380 (m) REVERT: K 215 GLU cc_start: 0.8639 (tp30) cc_final: 0.7570 (tm-30) REVERT: K 271 TYR cc_start: 0.7567 (m-80) cc_final: 0.6713 (m-80) REVERT: K 1036 MET cc_start: 0.7044 (tmm) cc_final: 0.6705 (tmm) REVERT: K 1072 PHE cc_start: 0.7392 (t80) cc_final: 0.7156 (t80) REVERT: L 239 ARG cc_start: 0.6658 (ttt180) cc_final: 0.6438 (ttt180) REVERT: L 403 MET cc_start: 0.8927 (tpt) cc_final: 0.8623 (tpp) REVERT: L 405 ASP cc_start: 0.8727 (p0) cc_final: 0.8376 (p0) outliers start: 28 outliers final: 26 residues processed: 316 average time/residue: 0.3777 time to fit residues: 175.2175 Evaluate side-chains 327 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 910 MET Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 966 LEU Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [61, 57, 19, 15, 3, 51, 157, 183, 77, 53, 40] chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN E 109 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.180401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.138717 restraints weight = 122784.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.144887 restraints weight = 48146.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.148568 restraints weight = 26781.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.150750 restraints weight = 19040.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.152030 restraints weight = 15755.172| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22618 Z= 0.193 Angle : 0.667 9.297 31802 Z= 0.399 Chirality : 0.043 0.425 3586 Planarity : 0.004 0.052 3059 Dihedral : 26.290 174.427 5445 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.91 % Favored : 93.88 % Rotamer: Outliers : 1.77 % Allowed : 13.77 % Favored : 84.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.19), residues: 1962 helix: 1.85 (0.20), residues: 618 sheet: -0.36 (0.26), residues: 428 loop : -1.82 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.019 0.002 TYR D 84 PHE 0.048 0.002 PHE L 172 TRP 0.017 0.001 TRP L 418 HIS 0.009 0.001 HIS L 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (22618) covalent geometry : angle 0.66722 / 0.40 (31802) hydrogen bonds : bond 0.06146 / 4.08 ( 1065) hydrogen bonds : angle 4.47315 / 3.18 ( 2745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 346 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 316 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8959 (t) cc_final: 0.8680 (m) REVERT: A 62 LEU cc_start: 0.8675 (mt) cc_final: 0.8462 (mp) REVERT: A 98 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: B 80 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8168 (mttp) REVERT: C 57 GLU cc_start: 0.7780 (tt0) cc_final: 0.7169 (tm-30) REVERT: C 62 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7481 (tm-30) REVERT: D 43 TYR cc_start: 0.7832 (t80) cc_final: 0.7300 (t80) REVERT: D 109 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8446 (tptp) REVERT: D 121 LYS cc_start: 0.9148 (tttm) cc_final: 0.8712 (ttpp) REVERT: E 56 GLN cc_start: 0.8729 (mt0) cc_final: 0.8139 (mt0) REVERT: E 91 MET cc_start: 0.7661 (mmt) cc_final: 0.7460 (mmm) REVERT: F 45 LYS cc_start: 0.7828 (tttt) cc_final: 0.7601 (tttp) REVERT: F 80 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7730 (mtmt) REVERT: F 85 MET cc_start: 0.6995 (tpp) cc_final: 0.6623 (tpp) REVERT: F 92 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7866 (tptt) REVERT: G 51 TYR cc_start: 0.8997 (t80) cc_final: 0.8072 (t80) REVERT: G 58 TYR cc_start: 0.8364 (t80) cc_final: 0.8050 (t80) REVERT: H 109 LYS cc_start: 0.8928 (mttt) cc_final: 0.8653 (mtpt) REVERT: K 6 VAL cc_start: 0.8566 (t) cc_final: 0.8331 (m) REVERT: K 215 GLU cc_start: 0.8662 (tp30) cc_final: 0.7582 (tm-30) REVERT: K 271 TYR cc_start: 0.7575 (m-80) cc_final: 0.6711 (m-80) REVERT: K 1036 MET cc_start: 0.7052 (tmm) cc_final: 0.6685 (tmm) REVERT: K 1070 HIS cc_start: 0.8034 (t70) cc_final: 0.7131 (t70) REVERT: K 1072 PHE cc_start: 0.7398 (t80) cc_final: 0.7143 (t80) REVERT: L 177 MET cc_start: 0.5282 (tpp) cc_final: 0.5037 (mmm) REVERT: L 184 GLN cc_start: 0.7430 (pt0) cc_final: 0.7158 (pt0) REVERT: L 239 ARG cc_start: 0.6770 (ttt180) cc_final: 0.6569 (ttt180) REVERT: L 403 MET cc_start: 0.9031 (tpt) cc_final: 0.8748 (tpp) REVERT: L 405 ASP cc_start: 0.8773 (p0) cc_final: 0.8452 (p0) outliers start: 30 outliers final: 23 residues processed: 330 average time/residue: 0.3764 time to fit residues: 183.4203 Evaluate side-chains 326 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 794 ILE Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [123, 190, 111, 91, 217, 49, 24, 142, 10, 39, 71] chunk 123 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN E 109 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1059 ASN L 237 ASN ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.178783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.136833 restraints weight = 123769.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.142907 restraints weight = 48431.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.146644 restraints weight = 26981.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.148830 restraints weight = 19246.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.150096 restraints weight = 15826.671| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 22618 Z= 0.213 Angle : 0.674 8.377 31802 Z= 0.404 Chirality : 0.043 0.402 3586 Planarity : 0.004 0.051 3059 Dihedral : 26.308 175.203 5445 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.32 % Favored : 93.53 % Rotamer: Outliers : 1.71 % Allowed : 14.30 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.51 (0.19), residues: 1962 helix: 1.72 (0.20), residues: 617 sheet: -0.35 (0.26), residues: 425 loop : -1.84 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 100 TYR 0.020 0.002 TYR E 42 PHE 0.014 0.001 PHE K 323 TRP 0.016 0.002 TRP L 418 HIS 0.010 0.001 HIS L 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 (22618) covalent geometry : angle 0.67379 / 0.40 (31802) hydrogen bonds : bond 0.06406 / 4.25 ( 1065) hydrogen bonds : angle 4.56858 / 3.25 ( 2745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 311 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8903 (t) cc_final: 0.8639 (m) REVERT: A 65 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7911 (mmmm) REVERT: A 98 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: A 130 ARG cc_start: 0.8083 (tpt90) cc_final: 0.7564 (tpm170) REVERT: B 80 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8190 (mttp) REVERT: C 57 GLU cc_start: 0.7794 (tt0) cc_final: 0.7200 (tm-30) REVERT: D 43 TYR cc_start: 0.7894 (t80) cc_final: 0.7265 (t80) REVERT: D 109 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8541 (tptp) REVERT: D 121 LYS cc_start: 0.9180 (tttm) cc_final: 0.8740 (ttpp) REVERT: E 56 GLN cc_start: 0.8766 (mt0) cc_final: 0.8191 (mt0) REVERT: E 74 GLU cc_start: 0.7889 (tp30) cc_final: 0.7586 (tp30) REVERT: F 45 LYS cc_start: 0.7846 (tttt) cc_final: 0.7617 (tttp) REVERT: F 80 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7775 (mtmt) REVERT: F 85 MET cc_start: 0.6892 (tpp) cc_final: 0.6523 (tpp) REVERT: F 93 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7303 (mtp85) REVERT: G 51 TYR cc_start: 0.9039 (t80) cc_final: 0.8381 (t80) REVERT: G 58 TYR cc_start: 0.8401 (t80) cc_final: 0.8096 (t80) REVERT: H 109 LYS cc_start: 0.8927 (mttt) cc_final: 0.8666 (mtpt) REVERT: K 6 VAL cc_start: 0.8578 (t) cc_final: 0.8346 (m) REVERT: K 215 GLU cc_start: 0.8681 (tp30) cc_final: 0.7568 (tm-30) REVERT: K 271 TYR cc_start: 0.7529 (m-80) cc_final: 0.6547 (m-80) REVERT: K 1036 MET cc_start: 0.7065 (tmm) cc_final: 0.6728 (tmm) REVERT: K 1070 HIS cc_start: 0.7915 (t70) cc_final: 0.7222 (t70) REVERT: K 1072 PHE cc_start: 0.7433 (t80) cc_final: 0.7202 (t80) REVERT: L 178 GLU cc_start: 0.8022 (mp0) cc_final: 0.7626 (mp0) REVERT: L 239 ARG cc_start: 0.6826 (ttt180) cc_final: 0.6607 (ttt180) REVERT: L 403 MET cc_start: 0.9109 (tpt) cc_final: 0.8804 (tpp) REVERT: L 405 ASP cc_start: 0.8796 (p0) cc_final: 0.8476 (p0) outliers start: 29 outliers final: 25 residues processed: 323 average time/residue: 0.3902 time to fit residues: 183.8846 Evaluate side-chains 335 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 794 ILE Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [64, 191, 188, 82, 138, 176, 171, 172, 79, 37, 96] chunk 64 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 176 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.179065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.137211 restraints weight = 122908.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.143298 restraints weight = 48287.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.146990 restraints weight = 27003.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.149187 restraints weight = 19312.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.150410 restraints weight = 15938.826| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.254 22618 Z= 0.222 Angle : 0.791 59.200 31802 Z= 0.481 Chirality : 0.043 0.390 3586 Planarity : 0.004 0.051 3059 Dihedral : 26.312 175.210 5445 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.27 % Favored : 93.58 % Rotamer: Outliers : 1.65 % Allowed : 14.30 % Favored : 84.05 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.53 (0.19), residues: 1962 helix: 1.69 (0.20), residues: 617 sheet: -0.36 (0.26), residues: 425 loop : -1.85 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 332 TYR 0.016 0.001 TYR E 42 PHE 0.014 0.001 PHE K 323 TRP 0.013 0.001 TRP L 418 HIS 0.009 0.001 HIS L 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (22618) covalent geometry : angle 0.79076 / 0.48 (31802) hydrogen bonds : bond 0.06327 / 4.19 ( 1065) hydrogen bonds : angle 4.54711 / 3.23 ( 2745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8899 (t) cc_final: 0.8637 (m) REVERT: A 65 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7891 (mmmm) REVERT: A 98 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: A 130 ARG cc_start: 0.8076 (tpt90) cc_final: 0.7559 (tpm170) REVERT: C 57 GLU cc_start: 0.7781 (tt0) cc_final: 0.7191 (tm-30) REVERT: D 43 TYR cc_start: 0.7883 (t80) cc_final: 0.7258 (t80) REVERT: D 109 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8530 (tptp) REVERT: D 121 LYS cc_start: 0.9182 (tttm) cc_final: 0.8737 (ttpp) REVERT: E 56 GLN cc_start: 0.8767 (mt0) cc_final: 0.8180 (mt0) REVERT: E 74 GLU cc_start: 0.7880 (tp30) cc_final: 0.7574 (tp30) REVERT: F 45 LYS cc_start: 0.7860 (tttt) cc_final: 0.7613 (tttp) REVERT: F 80 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7772 (mtmt) REVERT: F 85 MET cc_start: 0.6888 (tpp) cc_final: 0.6517 (tpp) REVERT: F 93 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7292 (mtp85) REVERT: G 51 TYR cc_start: 0.9041 (t80) cc_final: 0.8370 (t80) REVERT: G 58 TYR cc_start: 0.8391 (t80) cc_final: 0.8089 (t80) REVERT: H 109 LYS cc_start: 0.8922 (mttt) cc_final: 0.8662 (mtpt) REVERT: K 6 VAL cc_start: 0.8577 (t) cc_final: 0.8343 (m) REVERT: K 215 GLU cc_start: 0.8683 (tp30) cc_final: 0.7564 (tm-30) REVERT: K 271 TYR cc_start: 0.7531 (m-80) cc_final: 0.6553 (m-80) REVERT: K 1036 MET cc_start: 0.7057 (tmm) cc_final: 0.6719 (tmm) REVERT: K 1070 HIS cc_start: 0.7902 (t70) cc_final: 0.7213 (t70) REVERT: K 1072 PHE cc_start: 0.7429 (t80) cc_final: 0.7199 (t80) REVERT: L 178 GLU cc_start: 0.7871 (mp0) cc_final: 0.7639 (mp0) REVERT: L 239 ARG cc_start: 0.6822 (ttt180) cc_final: 0.6599 (ttt180) REVERT: L 403 MET cc_start: 0.9099 (tpt) cc_final: 0.8796 (tpp) REVERT: L 405 ASP cc_start: 0.8788 (p0) cc_final: 0.8469 (p0) outliers start: 28 outliers final: 24 residues processed: 318 average time/residue: 0.3970 time to fit residues: 185.1272 Evaluate side-chains 333 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 18 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 794 ILE Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [220, 179, 9, 35, 37, 117, 26, 27, 2, 6, 115] chunk 220 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 115 optimal weight: 0.0470 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.178998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.137107 restraints weight = 123545.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.143259 restraints weight = 48285.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.146961 restraints weight = 26893.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.149180 restraints weight = 19112.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.150340 restraints weight = 15791.064| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.254 22618 Z= 0.222 Angle : 0.791 59.200 31802 Z= 0.481 Chirality : 0.043 0.390 3586 Planarity : 0.004 0.051 3059 Dihedral : 26.312 175.210 5445 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.27 % Favored : 93.58 % Rotamer: Outliers : 1.53 % Allowed : 14.48 % Favored : 83.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.53 (0.19), residues: 1962 helix: 1.69 (0.20), residues: 617 sheet: -0.36 (0.26), residues: 425 loop : -1.85 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 332 TYR 0.016 0.001 TYR E 42 PHE 0.014 0.001 PHE K 323 TRP 0.013 0.001 TRP L 418 HIS 0.009 0.001 HIS L 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (22618) covalent geometry : angle 0.79076 / 0.48 (31802) hydrogen bonds : bond 0.06327 / 4.19 ( 1065) hydrogen bonds : angle 4.54711 / 3.23 ( 2745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8018.31 seconds wall clock time: 136 minutes 48.87 seconds (8208.87 seconds total)