Starting phenix.real_space_refine on Fri Jul 3 15:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy9_11555/07_2026/6zy9_11555.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9647 2.51 5 N 2513 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14973 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 966 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 801 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 957 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1041 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 966 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 925 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 712 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1954 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 240} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1971 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1927 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "H" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1946 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.27, per 1000 atoms: 0.22 Number of scatterers: 14973 At special positions: 0 Unit cell: (99.372, 130.806, 147.03, 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 69 16.00 P 6 15.00 Mg 2 11.99 O 2736 8.00 N 2513 7.00 C 9647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 700.2 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 20 sheets defined 40.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 removed outlier: 4.077A pdb=" N GLU A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.873A pdb=" N GLN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.620A pdb=" N ILE D 8 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'I' and resid 5 through 24 removed outlier: 4.263A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 147 removed outlier: 3.632A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 147' Processing helix chain 'J' and resid 5 through 29 removed outlier: 3.692A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA J 29 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.585A pdb=" N LEU J 146 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 24 removed outlier: 3.636A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 151 removed outlier: 3.605A pdb=" N LEU K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 19 removed outlier: 4.181A pdb=" N TRP L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 10 " --> pdb=" O ASN L 6 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 23 Processing helix chain 'L' and resid 142 through 152 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.805A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 4.358A pdb=" N LEU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 4.240A pdb=" N TYR B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 51 through 69 removed outlier: 3.670A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.795A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 removed outlier: 3.994A pdb=" N LEU F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.513A pdb=" N ARG F 86 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.736A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.674A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.160A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.911A pdb=" N ARG F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.580A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.561A pdb=" N PHE F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 244' Processing helix chain 'G' and resid 47 through 56 removed outlier: 4.014A pdb=" N LEU G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.679A pdb=" N TYR G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 101 through 107 removed outlier: 3.553A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 107 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 133 removed outlier: 3.709A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 145 removed outlier: 3.691A pdb=" N LEU G 145 " --> pdb=" O PRO G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 159 removed outlier: 4.088A pdb=" N ARG G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 159 " --> pdb=" O LEU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 189 removed outlier: 3.848A pdb=" N VAL G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 Processing helix chain 'G' and resid 239 through 244 removed outlier: 4.212A pdb=" N PHE G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 244' Processing helix chain 'E' and resid 10 through 30 removed outlier: 3.781A pdb=" N LYS E 15 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 removed outlier: 3.969A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 56 through 78 removed outlier: 3.675A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.752A pdb=" N LEU E 106 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 126 removed outlier: 4.358A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.583A pdb=" N SER E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.631A pdb=" N ARG E 141 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 142 " --> pdb=" O PRO E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.538A pdb=" N TRP E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 167 removed outlier: 3.804A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.628A pdb=" N SER E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA E 188 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 221 removed outlier: 3.699A pdb=" N THR E 212 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE E 219 " --> pdb=" O TRP E 215 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 247 removed outlier: 3.648A pdb=" N SER E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 removed outlier: 4.089A pdb=" N PHE E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 252' Processing helix chain 'E' and resid 253 through 256 removed outlier: 3.617A pdb=" N LEU E 256 " --> pdb=" O LEU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'H' and resid 3 through 30 removed outlier: 3.867A pdb=" N SER H 8 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 9 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.856A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN H 50 " --> pdb=" O ARG H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 55 Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.558A pdb=" N VAL H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 78 removed outlier: 3.566A pdb=" N MET H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 98 removed outlier: 3.502A pdb=" N LEU H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H 93 " --> pdb=" O MET H 89 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 126 removed outlier: 3.625A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 143 removed outlier: 3.750A pdb=" N ARG H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 153 removed outlier: 3.717A pdb=" N GLY H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE H 153 " --> pdb=" O TRP H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 176 removed outlier: 3.794A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 removed outlier: 3.686A pdb=" N TRP H 186 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 199 through 223 removed outlier: 3.576A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 208 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE H 211 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR H 222 " --> pdb=" O LEU H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 245 removed outlier: 3.541A pdb=" N THR H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 255 removed outlier: 3.737A pdb=" N PHE H 251 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL H 252 " --> pdb=" O GLY H 248 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 255 " --> pdb=" O PHE H 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.529A pdb=" N LEU A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.668A pdb=" N SER A 100 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 99 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 41 through 45 removed outlier: 7.116A pdb=" N ARG D 81 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE D 71 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR D 83 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 67 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 58 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.872A pdb=" N SER D 98 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU D 99 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 41 through 45 removed outlier: 3.540A pdb=" N LEU I 84 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG I 102 " --> pdb=" O TYR I 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 42 through 45 Processing sheet with id=AA7, first strand: chain 'J' and resid 63 through 66 removed outlier: 6.267A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU J 99 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.574A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.574A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG K 81 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE K 71 " --> pdb=" O ARG K 81 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR K 83 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 58 through 59 removed outlier: 7.064A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 109 through 116 removed outlier: 4.566A pdb=" N GLU K 109 " --> pdb=" O SER K 104 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS K 138 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 43 through 45 removed outlier: 3.802A pdb=" N ALA L 44 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.889A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER L 100 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.760A pdb=" N LEU B 14 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 75 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.735A pdb=" N GLY B 18 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG B 49 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 20 " --> pdb=" O ARG B 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 41 through 43 removed outlier: 5.618A pdb=" N ILE C 42 " --> pdb=" O GLN C 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 29 removed outlier: 4.849A pdb=" N LEU F 29 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG F 12 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG F 12 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU F 64 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 165 through 167 removed outlier: 4.109A pdb=" N THR F 37 " --> pdb=" O CYS F 198 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 217 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 165 through 168 removed outlier: 6.497A pdb=" N ILE G 166 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE G 36 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TRP G 216 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA G 38 " --> pdb=" O TRP G 216 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU G 218 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET G 40 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 66 through 67 removed outlier: 3.924A pdb=" N GLU G 70 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4778 1.34 - 1.46: 3228 1.46 - 1.58: 7089 1.58 - 1.70: 10 1.70 - 1.81: 126 Bond restraints: 15231 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O3A ANP G 401 " pdb=" PB ANP G 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5' ANP G 401 " pdb=" PA ANP G 401 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 15226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 20511 3.25 - 6.50: 171 6.50 - 9.74: 36 9.74 - 12.99: 4 12.99 - 16.24: 4 Bond angle restraints: 20726 Sorted by residual: angle pdb=" C ASP G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.03e+01 angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 110.71 16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" PB ANP G 401 " pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 126.95 110.72 16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" C ASP G 10 " pdb=" N MET G 11 " pdb=" CA MET G 11 " ideal model delta sigma weight residual 122.46 129.52 -7.06 1.41e+00 5.03e-01 2.50e+01 angle pdb=" C ASP F 204 " pdb=" N VAL F 205 " pdb=" CA VAL F 205 " ideal model delta sigma weight residual 120.33 124.27 -3.94 8.00e-01 1.56e+00 2.42e+01 ... (remaining 20721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8212 16.92 - 33.83: 635 33.83 - 50.75: 143 50.75 - 67.67: 24 67.67 - 84.58: 5 Dihedral angle restraints: 9019 sinusoidal: 3368 harmonic: 5651 Sorted by residual: dihedral pdb=" CA GLN C 68 " pdb=" C GLN C 68 " pdb=" N GLY C 69 " pdb=" CA GLY C 69 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN C 22 " pdb=" C GLN C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP C 93 " pdb=" CB ASP C 93 " pdb=" CG ASP C 93 " pdb=" OD1 ASP C 93 " ideal model delta sinusoidal sigma weight residual -30.00 -90.53 60.53 1 2.00e+01 2.50e-03 1.22e+01 ... (remaining 9016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2123 0.060 - 0.119: 352 0.119 - 0.179: 56 0.179 - 0.238: 3 0.238 - 0.298: 4 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' ANP G 401 " pdb=" C2' ANP G 401 " pdb=" C4' ANP G 401 " pdb=" O3' ANP G 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2535 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 176 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO G 177 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 118 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO G 119 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 119 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 119 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 155 " -0.035 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO H 156 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " -0.029 5.00e-02 4.00e+02 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 459 2.72 - 3.26: 13437 3.26 - 3.81: 22671 3.81 - 4.35: 28163 4.35 - 4.90: 46516 Nonbonded interactions: 111246 Sorted by model distance: nonbonded pdb=" OG1 THR G 48 " pdb="MG MG G 402 " model vdw 2.174 2.170 nonbonded pdb=" OG1 THR F 48 " pdb="MG MG F 402 " model vdw 2.259 2.170 nonbonded pdb=" OH TYR J 40 " pdb=" OD1 ASN J 91 " model vdw 2.319 3.040 nonbonded pdb=" O SER H 86 " pdb=" OG SER H 86 " model vdw 2.331 3.040 nonbonded pdb=" O ALA E 234 " pdb=" OG1 THR E 238 " model vdw 2.338 3.040 ... (remaining 111241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 69 or (resid \ 70 through 71 and (name N or name CA or name C or name O or name CB )) or resid \ 72 through 80 or (resid 81 and (name N or name CA or name C or name O or name C \ B )) or resid 82 through 88 or (resid 89 and (name N or name CA or name C or nam \ e O or name CB )) or resid 90 or (resid 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 and (name N or name CA o \ r name C or name O or name CB )) or resid 96 through 115 or (resid 127 through 1 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 133 or (resid 134 through 135 and (name N or name CA or name C or name O or nam \ e CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 142 or (resid 143 through 145 and ( \ name N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 a \ nd (name N or name CA or name C or name O or name CB )) or resid 148 through 150 \ or (resid 151 and (name N or name CA or name C or name O or name CB )) or resid \ 152)) selection = (chain 'I' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 72 or (resid \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 94 or (resid 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 98 or (resid 99 and (name N or name CA or name C or n \ ame O or name CB )) or resid 100 through 106 or (resid 107 and (name N or name C \ A or name C or name O or name CB )) or resid 108 through 115 or (resid 127 throu \ gh 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thr \ ough 134 or (resid 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 through 142 or (resid 143 through 145 and (name N or name CA or nam \ e C or name O or name CB )) or resid 146 or (resid 147 and (name N or name CA or \ name C or name O or name CB )) or resid 148 through 150 or (resid 151 and (name \ N or name CA or name C or name O or name CB )) or resid 152)) selection = (chain 'J' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 54 or (resid \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or res \ id 68 through 69 or (resid 70 through 71 and (name N or name CA or name C or nam \ e O or name CB )) or resid 72 or (resid 73 and (name N or name CA or name C or n \ ame O or name CB )) or resid 74 through 75 or (resid 76 and (name N or name CA o \ r name C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N \ or name CA or name C or name O or name CB )) or resid 82 through 84 or (resid 8 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 86 or (resid \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 or (res \ id 89 and (name N or name CA or name C or name O or name CB )) or resid 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or (resid 109 and (name N or name CA or \ name C or name O or name CB )) or resid 110 through 115 or (resid 127 through 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 133 or (resid 134 through 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 142 or (resid 143 through 145 and (n \ ame N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 an \ d (name N or name CA or name C or name O or name CB )) or resid 148 through 150 \ or (resid 151 and (name N or name CA or name C or name O or name CB )) or resid \ 152)) selection = (chain 'K' and (resid 4 through 24 or resid 40 through 52 or (resid 53 through 5 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 56 through 6 \ 6 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resid \ 68 through 69 or (resid 70 through 71 and (name N or name CA or name C or name \ O or name CB )) or resid 72 or (resid 73 and (name N or name CA or name C or nam \ e O or name CB )) or resid 74 through 80 or (resid 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N o \ r name CA or name C or name O or name CB )) or resid 86 or (resid 87 and (name N \ or name CA or name C or name O or name CB )) or resid 88 or (resid 89 and (name \ N or name CA or name C or name O or name CB )) or resid 90 or (resid 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 or (resid 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 through 115 or (resid 127 through 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 133 or (resid 1 \ 34 through 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 137 or (resid 138 and (name N or name CA or name C or name O or nam \ e CB )) or resid 139 through 142 or (resid 143 through 145 and (name N or name C \ A or name C or name O or name CB )) or resid 146 or (resid 147 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152)) selection = (chain 'L' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 72 or (resid \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 88 or (resid 89 and (name N or name CA or name C or name O or name \ CB )) or resid 90 or (resid 91 and (name N or name CA or name C or name O or na \ me CB )) or resid 92 through 98 or (resid 99 and (name N or name CA or name C or \ name O or name CB )) or resid 100 through 127 or (resid 128 through 130 and (na \ me N or name CA or name C or name O or name CB )) or resid 131 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 137 or (resid 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 152)) } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 5 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 2 through 97 or (resid 98 and (name N or name CA or name C \ or name O or name CB )) or resid 99 through 257)) selection = (chain 'H' and resid 2 through 257) } ncs_group { reference = (chain 'F' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 402)) selection = (chain 'G' and (resid 7 through 129 or (resid 130 through 131 and (name N or nam \ e CA or name C or name O or name CB )) or resid 132 through 259 or (resid 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 264 \ or resid 401 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.004 0.142 15231 Z= 0.200 Angle : 0.806 16.239 20726 Z= 0.403 Chirality : 0.047 0.298 2538 Planarity : 0.005 0.063 2570 Dihedral : 12.811 84.584 5383 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.76 (0.13), residues: 1935 helix: -4.94 (0.05), residues: 713 sheet: -2.09 (0.32), residues: 220 loop : -3.37 (0.15), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 49 TYR 0.012 0.001 TYR L 40 PHE 0.018 0.001 PHE F 254 TRP 0.010 0.001 TRP E 168 HIS 0.003 0.000 HIS G 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (15231) covalent geometry : angle 0.80616 / 0.40 (20726) hydrogen bonds : bond 0.32078 / 20.94 ( 440) hydrogen bonds : angle 10.69657 / 7.38 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 375 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: J 14 LEU cc_start: 0.7140 (mt) cc_final: 0.6916 (mt) REVERT: L 59 SER cc_start: 0.4315 (t) cc_final: 0.4095 (t) REVERT: L 99 LEU cc_start: 0.6691 (tp) cc_final: 0.6206 (mp) REVERT: B 95 LEU cc_start: 0.6860 (mm) cc_final: 0.6642 (tp) REVERT: F 207 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5820 (mt-10) outliers start: 4 outliers final: 2 residues processed: 377 average time/residue: 0.1286 time to fit residues: 68.7506 Evaluate side-chains 264 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0060 chunk 149 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 91 ASN K 91 ASN L 88 GLN L 110 GLN C 9 GLN F 7 ASN F 175 GLN F 191 ASN G 57 GLN G 175 GLN E 11 HIS E 191 ASN H 241 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.214968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170609 restraints weight = 18722.146| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.43 r_work: 0.3489 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15231 Z= 0.142 Angle : 0.597 7.481 20726 Z= 0.300 Chirality : 0.043 0.211 2538 Planarity : 0.005 0.062 2570 Dihedral : 4.283 37.574 2111 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.09 % Allowed : 15.63 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.15), residues: 1935 helix: -3.04 (0.13), residues: 739 sheet: -1.55 (0.34), residues: 222 loop : -2.84 (0.16), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 102 TYR 0.016 0.001 TYR H 49 PHE 0.022 0.002 PHE J 23 TRP 0.008 0.001 TRP E 168 HIS 0.007 0.001 HIS H 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15231) covalent geometry : angle 0.59697 / 0.30 (20726) hydrogen bonds : bond 0.03748 / 2.51 ( 440) hydrogen bonds : angle 5.15140 / 3.56 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 99 LEU cc_start: 0.5465 (mt) cc_final: 0.5242 (tp) REVERT: J 7 GLU cc_start: 0.7790 (tp30) cc_final: 0.7440 (mt-10) REVERT: J 14 LEU cc_start: 0.8171 (mt) cc_final: 0.7882 (mt) REVERT: L 99 LEU cc_start: 0.6880 (tp) cc_final: 0.6356 (mp) REVERT: B 12 ASP cc_start: 0.8188 (p0) cc_final: 0.7964 (p0) REVERT: B 43 ASP cc_start: 0.7892 (t70) cc_final: 0.7559 (t70) REVERT: C 59 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8476 (mp) REVERT: F 29 LEU cc_start: 0.8852 (mp) cc_final: 0.8579 (mm) REVERT: F 100 MET cc_start: 0.9164 (ptp) cc_final: 0.8901 (ptp) REVERT: F 220 ASP cc_start: 0.4544 (OUTLIER) cc_final: 0.3995 (p0) REVERT: F 232 LEU cc_start: 0.7567 (mt) cc_final: 0.7282 (mp) REVERT: E 47 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8480 (mm-40) REVERT: E 233 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8077 (mtp-110) outliers start: 33 outliers final: 24 residues processed: 288 average time/residue: 0.1173 time to fit residues: 50.1018 Evaluate side-chains 261 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 252 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 ASN I 135 GLN J 91 ASN G 113 HIS E 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.199991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142186 restraints weight = 18728.383| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.78 r_work: 0.3314 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 15231 Z= 0.200 Angle : 0.668 7.639 20726 Z= 0.336 Chirality : 0.045 0.171 2538 Planarity : 0.005 0.069 2570 Dihedral : 4.779 38.047 2111 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.35 % Allowed : 18.29 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.17), residues: 1935 helix: -1.76 (0.17), residues: 777 sheet: -1.40 (0.33), residues: 244 loop : -2.61 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 18 TYR 0.020 0.001 TYR F 261 PHE 0.028 0.002 PHE G 172 TRP 0.023 0.002 TRP I 9 HIS 0.008 0.002 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (15231) covalent geometry : angle 0.66799 / 0.34 (20726) hydrogen bonds : bond 0.04266 / 2.82 ( 440) hydrogen bonds : angle 4.68346 / 3.24 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7218 (mptt) cc_final: 0.6688 (mmtt) REVERT: A 49 ILE cc_start: 0.7421 (tp) cc_final: 0.6982 (pt) REVERT: J 79 LEU cc_start: 0.5528 (mp) cc_final: 0.4600 (pp) REVERT: J 102 ARG cc_start: 0.6231 (mtt180) cc_final: 0.5422 (mmt180) REVERT: K 71 ILE cc_start: 0.6139 (mm) cc_final: 0.5828 (mm) REVERT: L 5 LYS cc_start: 0.7968 (tttt) cc_final: 0.7578 (ttpt) REVERT: L 99 LEU cc_start: 0.6855 (tp) cc_final: 0.6273 (mp) REVERT: B 43 ASP cc_start: 0.8028 (t70) cc_final: 0.7739 (t70) REVERT: C 66 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7568 (mmtp) REVERT: F 180 MET cc_start: 0.8963 (ttm) cc_final: 0.8674 (ttm) REVERT: F 207 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: E 46 ARG cc_start: 0.8310 (tpt170) cc_final: 0.8101 (tpt170) REVERT: E 197 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6898 (ttp) REVERT: E 233 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8204 (mtp-110) REVERT: H 56 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8210 (mtt) REVERT: H 72 LEU cc_start: 0.8201 (mt) cc_final: 0.7976 (mp) REVERT: H 134 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7244 (ttm) REVERT: H 250 ASP cc_start: 0.8442 (t0) cc_final: 0.8204 (t0) REVERT: H 257 MET cc_start: 0.5282 (mmt) cc_final: 0.4911 (mmt) outliers start: 53 outliers final: 32 residues processed: 287 average time/residue: 0.1119 time to fit residues: 47.7375 Evaluate side-chains 267 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 ASN F 191 ASN G 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.200721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143505 restraints weight = 18590.726| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.80 r_work: 0.3273 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15231 Z= 0.125 Angle : 0.548 7.157 20726 Z= 0.274 Chirality : 0.041 0.160 2538 Planarity : 0.004 0.074 2570 Dihedral : 4.412 40.233 2111 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.35 % Allowed : 19.24 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.18), residues: 1935 helix: -0.95 (0.19), residues: 774 sheet: -1.17 (0.34), residues: 236 loop : -2.37 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.009 0.001 TYR H 49 PHE 0.015 0.001 PHE F 254 TRP 0.009 0.001 TRP I 9 HIS 0.003 0.001 HIS H 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 (15231) covalent geometry : angle 0.54825 / 0.27 (20726) hydrogen bonds : bond 0.02849 / 1.92 ( 440) hydrogen bonds : angle 4.24579 / 2.93 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7182 (mptt) cc_final: 0.6669 (mmtt) REVERT: A 102 ARG cc_start: 0.2751 (mmt90) cc_final: 0.2271 (mmp80) REVERT: D 141 MET cc_start: 0.5817 (tpt) cc_final: 0.5095 (tpt) REVERT: I 92 HIS cc_start: 0.6760 (t70) cc_final: 0.6393 (t-90) REVERT: J 79 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.4607 (pp) REVERT: J 102 ARG cc_start: 0.6161 (mtt180) cc_final: 0.5380 (mmt180) REVERT: L 5 LYS cc_start: 0.7866 (tttt) cc_final: 0.7437 (ttpt) REVERT: L 99 LEU cc_start: 0.6791 (tp) cc_final: 0.6307 (mp) REVERT: B 43 ASP cc_start: 0.8054 (t70) cc_final: 0.7752 (t70) REVERT: B 50 VAL cc_start: 0.8727 (t) cc_final: 0.8418 (p) REVERT: F 40 MET cc_start: 0.9039 (mpp) cc_final: 0.8656 (mtm) REVERT: G 208 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8868 (p) REVERT: E 46 ARG cc_start: 0.8397 (tpt170) cc_final: 0.8098 (tpt170) REVERT: E 167 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7626 (tt) REVERT: E 194 ASP cc_start: 0.5311 (OUTLIER) cc_final: 0.4170 (p0) REVERT: E 197 MET cc_start: 0.7085 (ttp) cc_final: 0.6849 (ttp) REVERT: E 233 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8064 (mtp-110) REVERT: H 134 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6877 (ttm) REVERT: H 249 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8368 (mp) REVERT: H 257 MET cc_start: 0.4963 (mmt) cc_final: 0.4598 (mmt) outliers start: 53 outliers final: 34 residues processed: 278 average time/residue: 0.1051 time to fit residues: 43.2984 Evaluate side-chains 270 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 202 CYS Chi-restraints excluded: chain H residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 191 ASN E 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.194647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128339 restraints weight = 18491.532| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.19 r_work: 0.3125 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15231 Z= 0.205 Angle : 0.632 8.365 20726 Z= 0.316 Chirality : 0.044 0.154 2538 Planarity : 0.005 0.069 2570 Dihedral : 4.753 39.888 2111 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.43 % Allowed : 20.13 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.18), residues: 1935 helix: -0.86 (0.19), residues: 787 sheet: -1.23 (0.33), residues: 251 loop : -2.27 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.009 0.001 TYR F 261 PHE 0.031 0.002 PHE J 23 TRP 0.021 0.002 TRP C 7 HIS 0.006 0.001 HIS H 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (15231) covalent geometry : angle 0.63172 / 0.32 (20726) hydrogen bonds : bond 0.03628 / 2.42 ( 440) hydrogen bonds : angle 4.32294 / 2.98 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7130 (mptt) cc_final: 0.6570 (mmtt) REVERT: I 92 HIS cc_start: 0.6789 (t70) cc_final: 0.6411 (t-90) REVERT: J 79 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.4542 (pp) REVERT: J 102 ARG cc_start: 0.6067 (mtt180) cc_final: 0.5355 (mmt180) REVERT: K 60 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6578 (tp) REVERT: L 5 LYS cc_start: 0.7722 (tttt) cc_final: 0.7503 (tttm) REVERT: L 99 LEU cc_start: 0.6684 (tp) cc_final: 0.6125 (mp) REVERT: B 43 ASP cc_start: 0.8119 (t70) cc_final: 0.7800 (t70) REVERT: B 50 VAL cc_start: 0.8848 (t) cc_final: 0.8582 (p) REVERT: C 41 CYS cc_start: 0.7733 (m) cc_final: 0.7171 (t) REVERT: F 40 MET cc_start: 0.9062 (mpp) cc_final: 0.8795 (mtm) REVERT: F 66 LEU cc_start: 0.7258 (pt) cc_final: 0.6848 (mt) REVERT: E 111 ARG cc_start: 0.8587 (tpt90) cc_final: 0.8308 (tpt90) REVERT: E 167 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7782 (tt) REVERT: E 197 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6894 (ttp) REVERT: E 233 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8158 (mtp-110) REVERT: E 250 ASP cc_start: 0.8511 (t0) cc_final: 0.8114 (t0) REVERT: H 56 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: H 72 LEU cc_start: 0.8021 (mt) cc_final: 0.7783 (mp) REVERT: H 134 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7618 (ttm) REVERT: H 249 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8430 (mp) REVERT: H 257 MET cc_start: 0.4978 (mmt) cc_final: 0.4544 (mmt) outliers start: 70 outliers final: 45 residues processed: 288 average time/residue: 0.1191 time to fit residues: 51.0850 Evaluate side-chains 283 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Chi-restraints excluded: chain H residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.194546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129796 restraints weight = 18533.524| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.08 r_work: 0.3125 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15231 Z= 0.174 Angle : 0.608 10.973 20726 Z= 0.302 Chirality : 0.043 0.149 2538 Planarity : 0.004 0.065 2570 Dihedral : 4.672 39.962 2109 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.68 % Allowed : 21.14 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.19), residues: 1935 helix: -0.60 (0.19), residues: 790 sheet: -1.13 (0.34), residues: 242 loop : -2.21 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.007 0.001 TYR H 49 PHE 0.020 0.002 PHE F 172 TRP 0.014 0.001 TRP I 9 HIS 0.005 0.001 HIS H 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.17 (15231) covalent geometry : angle 0.60806 / 0.30 (20726) hydrogen bonds : bond 0.03153 / 2.11 ( 440) hydrogen bonds : angle 4.16143 / 2.87 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7194 (mptt) cc_final: 0.6635 (mmtt) REVERT: A 102 ARG cc_start: 0.2885 (mmt90) cc_final: 0.2497 (mmp80) REVERT: D 7 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 141 MET cc_start: 0.5868 (tpt) cc_final: 0.5106 (tpt) REVERT: I 92 HIS cc_start: 0.6772 (t70) cc_final: 0.6389 (t-90) REVERT: J 5 LYS cc_start: 0.7800 (tptm) cc_final: 0.7056 (ttmt) REVERT: J 79 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.4699 (pp) REVERT: J 102 ARG cc_start: 0.6176 (mtt180) cc_final: 0.5450 (mmt180) REVERT: K 60 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6498 (tp) REVERT: L 5 LYS cc_start: 0.7810 (tttt) cc_final: 0.7552 (tttm) REVERT: L 99 LEU cc_start: 0.6661 (tp) cc_final: 0.6056 (mp) REVERT: B 43 ASP cc_start: 0.8074 (t70) cc_final: 0.7825 (t70) REVERT: B 50 VAL cc_start: 0.8929 (t) cc_final: 0.8718 (p) REVERT: B 75 GLN cc_start: 0.7643 (mm110) cc_final: 0.7290 (pt0) REVERT: C 41 CYS cc_start: 0.7563 (m) cc_final: 0.7047 (t) REVERT: F 40 MET cc_start: 0.9066 (mpp) cc_final: 0.8829 (mtm) REVERT: F 66 LEU cc_start: 0.7486 (pt) cc_final: 0.7085 (mt) REVERT: F 208 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8627 (t) REVERT: E 167 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7563 (tt) REVERT: E 171 SER cc_start: 0.8579 (m) cc_final: 0.8145 (t) REVERT: E 233 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8150 (mtp-110) REVERT: E 250 ASP cc_start: 0.8593 (t0) cc_final: 0.8318 (t0) REVERT: H 56 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8382 (mtm) REVERT: H 134 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7576 (ttm) outliers start: 74 outliers final: 46 residues processed: 296 average time/residue: 0.1159 time to fit residues: 51.0547 Evaluate side-chains 283 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 GLN F 191 ASN E 47 GLN E 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.197560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130577 restraints weight = 18174.584| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.02 r_work: 0.3186 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15231 Z= 0.104 Angle : 0.546 11.659 20726 Z= 0.270 Chirality : 0.041 0.147 2538 Planarity : 0.004 0.058 2570 Dihedral : 4.347 38.852 2109 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.48 % Allowed : 22.66 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1935 helix: -0.21 (0.19), residues: 794 sheet: -1.08 (0.34), residues: 243 loop : -2.10 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.007 0.001 TYR H 81 PHE 0.018 0.001 PHE J 23 TRP 0.011 0.001 TRP C 7 HIS 0.004 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 (15231) covalent geometry : angle 0.54560 / 0.27 (20726) hydrogen bonds : bond 0.02616 / 1.75 ( 440) hydrogen bonds : angle 3.96563 / 2.72 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 0.513 Fit side-chains REVERT: A 27 LYS cc_start: 0.7055 (mptt) cc_final: 0.6516 (mmtt) REVERT: A 102 ARG cc_start: 0.2754 (mmt90) cc_final: 0.2472 (mmp80) REVERT: D 141 MET cc_start: 0.5548 (tpt) cc_final: 0.4793 (tpt) REVERT: I 92 HIS cc_start: 0.6765 (t70) cc_final: 0.6380 (t-90) REVERT: J 5 LYS cc_start: 0.7707 (tptm) cc_final: 0.6938 (ttmt) REVERT: J 79 LEU cc_start: 0.5614 (OUTLIER) cc_final: 0.4670 (pp) REVERT: J 102 ARG cc_start: 0.6141 (mtt180) cc_final: 0.5355 (mmt180) REVERT: K 60 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6492 (tp) REVERT: L 5 LYS cc_start: 0.7753 (tttt) cc_final: 0.7504 (tttm) REVERT: L 99 LEU cc_start: 0.6610 (tp) cc_final: 0.6072 (mp) REVERT: B 43 ASP cc_start: 0.8050 (t70) cc_final: 0.7785 (t70) REVERT: B 50 VAL cc_start: 0.8844 (t) cc_final: 0.8562 (p) REVERT: B 59 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 75 GLN cc_start: 0.7700 (mm110) cc_final: 0.7331 (pt0) REVERT: C 22 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6942 (mm-40) REVERT: C 41 CYS cc_start: 0.7489 (m) cc_final: 0.6928 (t) REVERT: F 66 LEU cc_start: 0.7264 (pt) cc_final: 0.6968 (mt) REVERT: F 180 MET cc_start: 0.8806 (ttm) cc_final: 0.8237 (ttp) REVERT: F 207 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7255 (mt-10) REVERT: F 221 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7916 (mtpp) REVERT: E 46 ARG cc_start: 0.8462 (tpt170) cc_final: 0.8203 (tpt-90) REVERT: E 167 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7453 (tt) REVERT: E 171 SER cc_start: 0.8414 (m) cc_final: 0.8018 (t) REVERT: E 194 ASP cc_start: 0.5193 (OUTLIER) cc_final: 0.4108 (p0) REVERT: E 197 MET cc_start: 0.7065 (ttp) cc_final: 0.6772 (ttp) REVERT: H 134 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7095 (ttm) outliers start: 55 outliers final: 39 residues processed: 281 average time/residue: 0.1040 time to fit residues: 43.7350 Evaluate side-chains 281 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 CYS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 152 optimal weight: 0.0570 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 136 optimal weight: 0.0070 chunk 124 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.198146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142326 restraints weight = 18354.053| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.73 r_work: 0.3329 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15231 Z= 0.095 Angle : 0.533 11.505 20726 Z= 0.262 Chirality : 0.040 0.145 2538 Planarity : 0.004 0.055 2570 Dihedral : 4.151 38.403 2109 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.54 % Allowed : 22.34 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.19), residues: 1935 helix: 0.11 (0.20), residues: 794 sheet: -0.93 (0.35), residues: 233 loop : -2.03 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.007 0.001 TYR H 81 PHE 0.016 0.001 PHE J 23 TRP 0.008 0.001 TRP B 7 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.09 (15231) covalent geometry : angle 0.53296 / 0.26 (20726) hydrogen bonds : bond 0.02434 / 1.63 ( 440) hydrogen bonds : angle 3.86866 / 2.64 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7289 (mptt) cc_final: 0.6826 (mmtt) REVERT: A 102 ARG cc_start: 0.3052 (mmt90) cc_final: 0.2633 (mmp80) REVERT: D 141 MET cc_start: 0.5867 (tpt) cc_final: 0.5000 (tpt) REVERT: I 92 HIS cc_start: 0.6640 (t70) cc_final: 0.6286 (t-90) REVERT: J 79 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.4782 (pp) REVERT: J 102 ARG cc_start: 0.6317 (mtt180) cc_final: 0.5493 (mmt180) REVERT: L 5 LYS cc_start: 0.7840 (tttt) cc_final: 0.7629 (tttm) REVERT: L 99 LEU cc_start: 0.6604 (tp) cc_final: 0.6023 (mp) REVERT: B 8 MET cc_start: 0.7112 (ppp) cc_final: 0.6805 (ppp) REVERT: B 43 ASP cc_start: 0.8131 (t70) cc_final: 0.7928 (t70) REVERT: B 50 VAL cc_start: 0.8869 (t) cc_final: 0.8632 (p) REVERT: B 59 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8303 (mp) REVERT: C 41 CYS cc_start: 0.7702 (m) cc_final: 0.7194 (t) REVERT: F 66 LEU cc_start: 0.7484 (pt) cc_final: 0.7204 (mt) REVERT: F 180 MET cc_start: 0.8634 (ttm) cc_final: 0.8259 (ttp) REVERT: F 221 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7813 (mtpt) REVERT: E 46 ARG cc_start: 0.8586 (tpt170) cc_final: 0.8161 (tpt170) REVERT: E 76 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7974 (tt) REVERT: E 167 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7571 (tt) REVERT: E 194 ASP cc_start: 0.5341 (OUTLIER) cc_final: 0.4562 (p0) REVERT: H 36 GLU cc_start: 0.7752 (pm20) cc_final: 0.7452 (pm20) REVERT: H 56 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8263 (mtm) REVERT: H 134 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6954 (ttp) REVERT: H 257 MET cc_start: 0.5232 (mmt) cc_final: 0.4701 (mmt) outliers start: 56 outliers final: 37 residues processed: 283 average time/residue: 0.1035 time to fit residues: 44.4953 Evaluate side-chains 280 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 CYS Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 88 GLN F 175 GLN G 57 GLN E 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.191033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124463 restraints weight = 18386.985| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.06 r_work: 0.3075 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15231 Z= 0.251 Angle : 0.703 12.769 20726 Z= 0.347 Chirality : 0.047 0.165 2538 Planarity : 0.005 0.065 2570 Dihedral : 4.966 36.955 2109 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.30 % Rotamer: Outliers : 4.05 % Allowed : 22.85 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.19), residues: 1935 helix: -0.39 (0.19), residues: 803 sheet: -1.14 (0.34), residues: 250 loop : -2.04 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.011 0.001 TYR C 88 PHE 0.028 0.002 PHE G 172 TRP 0.029 0.002 TRP I 9 HIS 0.008 0.002 HIS F 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.25 (15231) covalent geometry : angle 0.70329 / 0.35 (20726) hydrogen bonds : bond 0.03880 / 2.59 ( 440) hydrogen bonds : angle 4.44557 / 3.04 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7193 (mptt) cc_final: 0.6676 (mmtt) REVERT: D 141 MET cc_start: 0.5446 (tpt) cc_final: 0.4665 (tpt) REVERT: I 92 HIS cc_start: 0.6814 (t70) cc_final: 0.6440 (t-90) REVERT: J 5 LYS cc_start: 0.7814 (tptm) cc_final: 0.7269 (ttmt) REVERT: J 79 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.4789 (pp) REVERT: J 102 ARG cc_start: 0.6262 (mtt180) cc_final: 0.5472 (mmt180) REVERT: L 5 LYS cc_start: 0.7818 (tttt) cc_final: 0.7570 (tttm) REVERT: L 99 LEU cc_start: 0.6465 (tp) cc_final: 0.5763 (mp) REVERT: B 8 MET cc_start: 0.7560 (ppp) cc_final: 0.7268 (ppp) REVERT: B 43 ASP cc_start: 0.8251 (t70) cc_final: 0.7960 (t70) REVERT: B 59 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 37 LYS cc_start: 0.7312 (ptpp) cc_final: 0.7075 (mtmm) REVERT: C 41 CYS cc_start: 0.7447 (m) cc_final: 0.6953 (t) REVERT: F 66 LEU cc_start: 0.7504 (pt) cc_final: 0.7265 (mt) REVERT: F 221 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (mtpp) REVERT: G 47 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8745 (mtmt) REVERT: E 167 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7694 (tt) REVERT: E 171 SER cc_start: 0.8861 (m) cc_final: 0.8458 (t) REVERT: E 233 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8123 (mtp-110) REVERT: H 56 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: H 72 LEU cc_start: 0.8035 (mt) cc_final: 0.7812 (mp) outliers start: 64 outliers final: 46 residues processed: 286 average time/residue: 0.1165 time to fit residues: 50.1158 Evaluate side-chains 288 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 180 MET Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 202 CYS Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 16 optimal weight: 0.0020 chunk 94 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 0.0060 chunk 109 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 ASN B 75 GLN E 50 ASN E 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.197027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130575 restraints weight = 18338.516| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.02 r_work: 0.3173 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15231 Z= 0.100 Angle : 0.564 12.480 20726 Z= 0.279 Chirality : 0.041 0.147 2538 Planarity : 0.004 0.059 2570 Dihedral : 4.372 38.617 2109 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.97 % Allowed : 23.99 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1935 helix: 0.13 (0.20), residues: 802 sheet: -0.84 (0.35), residues: 238 loop : -1.97 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.008 0.001 TYR H 81 PHE 0.014 0.001 PHE F 254 TRP 0.011 0.001 TRP B 7 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (15231) covalent geometry : angle 0.56416 / 0.28 (20726) hydrogen bonds : bond 0.02502 / 1.66 ( 440) hydrogen bonds : angle 3.99768 / 2.72 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.662 Fit side-chains REVERT: A 27 LYS cc_start: 0.7153 (mptt) cc_final: 0.6653 (mmtt) REVERT: A 141 MET cc_start: 0.3099 (tpp) cc_final: 0.2799 (tpp) REVERT: D 141 MET cc_start: 0.5464 (tpt) cc_final: 0.4759 (tpt) REVERT: I 92 HIS cc_start: 0.6771 (t70) cc_final: 0.6384 (t-90) REVERT: J 79 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.4790 (pp) REVERT: J 102 ARG cc_start: 0.6175 (mtt180) cc_final: 0.5422 (mmt180) REVERT: L 5 LYS cc_start: 0.7783 (tttt) cc_final: 0.7545 (tttm) REVERT: L 99 LEU cc_start: 0.6508 (tp) cc_final: 0.5881 (mp) REVERT: B 8 MET cc_start: 0.7496 (ppp) cc_final: 0.7184 (ppp) REVERT: B 43 ASP cc_start: 0.8204 (t70) cc_final: 0.7902 (t70) REVERT: B 59 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 22 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6971 (mm110) REVERT: C 41 CYS cc_start: 0.7459 (m) cc_final: 0.6907 (t) REVERT: F 66 LEU cc_start: 0.7370 (pt) cc_final: 0.7142 (mt) REVERT: F 180 MET cc_start: 0.8743 (ttm) cc_final: 0.8310 (ttp) REVERT: F 221 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7820 (mtpt) REVERT: E 46 ARG cc_start: 0.8648 (tpt170) cc_final: 0.7870 (tpt170) REVERT: E 76 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7681 (tt) REVERT: E 171 SER cc_start: 0.8691 (m) cc_final: 0.8355 (t) REVERT: E 194 ASP cc_start: 0.5559 (OUTLIER) cc_final: 0.4558 (p0) REVERT: E 233 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8068 (mtp-110) REVERT: H 56 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8309 (mtm) outliers start: 47 outliers final: 38 residues processed: 270 average time/residue: 0.1048 time to fit residues: 42.4227 Evaluate side-chains 283 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 202 CYS Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Chi-restraints excluded: chain H residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 117 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 chunk 184 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** G 57 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.197005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131201 restraints weight = 18231.195| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.00 r_work: 0.3178 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 15231 Z= 0.141 Angle : 0.768 59.198 20726 Z= 0.428 Chirality : 0.041 0.373 2538 Planarity : 0.004 0.058 2570 Dihedral : 4.389 38.607 2109 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.97 % Allowed : 23.80 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1935 helix: 0.16 (0.20), residues: 802 sheet: -0.84 (0.35), residues: 238 loop : -1.97 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.008 0.001 TYR H 81 PHE 0.014 0.001 PHE F 254 TRP 0.009 0.001 TRP B 7 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (15231) covalent geometry : angle 0.76804 / 0.43 (20726) hydrogen bonds : bond 0.02514 / 1.67 ( 440) hydrogen bonds : angle 3.99760 / 2.72 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4518.78 seconds wall clock time: 77 minutes 41.20 seconds (4661.20 seconds total)