Starting phenix.real_space_refine on Fri Feb 6 08:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui9_64188/02_2026/9ui9_64188.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui9_64188/02_2026/9ui9_64188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ui9_64188/02_2026/9ui9_64188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui9_64188/02_2026/9ui9_64188.map" model { file = "/net/cci-nas-00/data/ceres_data/9ui9_64188/02_2026/9ui9_64188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui9_64188/02_2026/9ui9_64188.cif" } resolution = 3.42 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= 0.004 sd= 0.046 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 114 5.49 5 Mg 9 5.21 5 S 122 5.16 5 C 14439 2.51 5 N 4124 2.21 5 O 4805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23613 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "F" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "G" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "U" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "T" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 622 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "H" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "I" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "L" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "E" 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: "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} Chain: "H" 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: "I" 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: "A" 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: "B" 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: "C" 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: "D" 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: 5.75, per 1000 atoms: 0.24 Number of scatterers: 23613 At special positions: 0 Unit cell: (122.84, 116.2, 195.88, 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 122 16.00 P 114 15.00 Mg 9 11.99 O 4805 8.00 N 4124 7.00 C 14439 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 27 sheets defined 45.0% alpha, 8.8% beta 6 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'E' and resid 25 through 31 removed outlier: 3.761A pdb=" N CYS E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 44 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.799A pdb=" N ILE E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.861A pdb=" N HIS E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA E 141 " --> pdb=" O CYS E 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.704A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 removed outlier: 3.706A pdb=" N LEU E 186 " --> pdb=" O GLY E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 214 removed outlier: 4.322A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET E 210 " --> pdb=" O GLN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 245 removed outlier: 3.939A pdb=" N MET E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 260 removed outlier: 4.214A pdb=" N MET E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.547A pdb=" N VAL F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.528A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.551A pdb=" N LYS F 80 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 94 removed outlier: 3.505A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.780A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 187 Processing helix chain 'F' and resid 198 through 212 removed outlier: 3.505A pdb=" N GLU F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 237 through 260 removed outlier: 3.939A pdb=" N MET F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA F 246 " --> pdb=" O GLN F 242 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 247 " --> pdb=" O MET F 243 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'G' and resid 34 through 42 removed outlier: 4.091A pdb=" N VAL G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 54 removed outlier: 4.186A pdb=" N VAL G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 89 through 95 Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 167 through 178 removed outlier: 3.998A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 188 removed outlier: 3.541A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.552A pdb=" N GLN G 200 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 227 removed outlier: 4.062A pdb=" N LEU G 227 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 260 Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.735A pdb=" N HIS G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 36 through 43 removed outlier: 4.148A pdb=" N LYS H 40 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.620A pdb=" N VAL H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 63 removed outlier: 3.852A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 88 through 96 Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 135 through 145 removed outlier: 3.563A pdb=" N ALA H 141 " --> pdb=" O CYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 178 removed outlier: 4.017A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 189 Processing helix chain 'H' and resid 196 through 213 removed outlier: 3.832A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU H 213 " --> pdb=" O ASP H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 232 removed outlier: 3.593A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 260 Processing helix chain 'H' and resid 272 through 277 removed outlier: 3.571A pdb=" N ALA H 276 " --> pdb=" O VAL H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 294 Processing helix chain 'I' and resid 34 through 44 removed outlier: 4.189A pdb=" N VAL I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 removed outlier: 4.042A pdb=" N VAL I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 63 removed outlier: 3.985A pdb=" N ILE I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.687A pdb=" N THR I 76 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 98 removed outlier: 4.044A pdb=" N GLN I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 132 through 143 removed outlier: 3.845A pdb=" N CYS I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS I 138 " --> pdb=" O THR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.645A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'I' and resid 197 through 208 Processing helix chain 'I' and resid 223 through 232 removed outlier: 4.207A pdb=" N LEU I 227 " --> pdb=" O SER I 223 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 259 removed outlier: 3.854A pdb=" N ALA I 240 " --> pdb=" O GLY I 236 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET I 251 " --> pdb=" O ARG I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 296 Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.770A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.530A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.756A pdb=" N ILE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 4.117A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.963A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.578A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.877A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 181 through 189 Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.530A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.689A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.528A pdb=" N ARG B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.510A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 82 removed outlier: 3.670A pdb=" N ILE B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.677A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 189 removed outlier: 4.123A pdb=" N VAL B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.746A pdb=" N ASP B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.565A pdb=" N GLN B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 4.018A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 296' Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.055A pdb=" N GLN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.871A pdb=" N ILE C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.571A pdb=" N LYS C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 135 through 144 removed outlier: 4.034A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.801A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 198 through 214 removed outlier: 4.057A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.524A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 255 Processing helix chain 'C' and resid 291 through 296 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 62 Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.678A pdb=" N LYS D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 173 through 179 removed outlier: 3.695A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.764A pdb=" N LEU D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 202 Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.648A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.689A pdb=" N ASP D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 259 removed outlier: 3.888A pdb=" N ARG D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.556A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 293' Processing sheet with id=AA1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'E' and resid 324 through 328 removed outlier: 6.420A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA E 157 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA E 192 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR E 159 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'F' and resid 87 through 88 removed outlier: 5.967A pdb=" N ALA G 157 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'F' and resid 125 through 127 removed outlier: 6.435A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 221 through 222 removed outlier: 7.550A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.188A pdb=" N ILE H 160 " --> pdb=" O ASP H 222 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA H 224 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'G' and resid 301 through 306 removed outlier: 5.330A pdb=" N LEU G 302 " --> pdb=" O LYS G 313 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS G 313 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS G 304 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE G 311 " --> pdb=" O LYS G 304 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR G 309 " --> pdb=" O ARG G 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 328 through 329 Processing sheet with id=AB4, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'H' and resid 299 through 302 removed outlier: 6.484A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 327 " --> pdb=" O ARG H 310 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 325 " --> pdb=" O CYS H 312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 190 through 191 removed outlier: 7.322A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 303 through 304 Processing sheet with id=AB8, first strand: chain 'I' and resid 328 through 330 removed outlier: 3.512A pdb=" N GLY I 333 " --> pdb=" O ASN I 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'A' and resid 218 through 221 removed outlier: 6.126A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 87 through 88 removed outlier: 7.213A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 263 through 265 removed outlier: 5.808A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.589A pdb=" N ALA D 190 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AC6, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AC7, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.954A pdb=" N GLY C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.496A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 312 " --> pdb=" O ALA D 325 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN D 330 " --> pdb=" O GLY D 333 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 269 through 271 775 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3901 1.31 - 1.44: 6327 1.44 - 1.57: 13496 1.57 - 1.69: 198 1.69 - 1.82: 217 Bond restraints: 24139 Sorted by residual: bond pdb=" C ILE A 136 " pdb=" O ILE A 136 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C LYS C 70 " pdb=" O LYS C 70 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.19e-02 7.06e+03 1.53e+01 bond pdb=" CA SER B 223 " pdb=" CB SER B 223 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.24e-02 6.50e+03 1.45e+01 bond pdb=" C LYS I 70 " pdb=" O LYS I 70 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N ILE A 291 " pdb=" CA ILE A 291 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.40e+01 ... (remaining 24134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 31001 2.41 - 4.81: 1795 4.81 - 7.22: 173 7.22 - 9.63: 25 9.63 - 12.04: 4 Bond angle restraints: 32998 Sorted by residual: angle pdb=" CA HIS G 294 " pdb=" CB HIS G 294 " pdb=" CG HIS G 294 " ideal model delta sigma weight residual 113.80 105.41 8.39 1.00e+00 1.00e+00 7.03e+01 angle pdb=" N ILE A 291 " pdb=" CA ILE A 291 " pdb=" C ILE A 291 " ideal model delta sigma weight residual 112.96 104.90 8.06 1.00e+00 1.00e+00 6.50e+01 angle pdb=" N MET E 243 " pdb=" CA MET E 243 " pdb=" C MET E 243 " ideal model delta sigma weight residual 114.56 104.88 9.68 1.27e+00 6.20e-01 5.81e+01 angle pdb=" N SER F 26 " pdb=" CA SER F 26 " pdb=" C SER F 26 " ideal model delta sigma weight residual 114.75 106.13 8.62 1.26e+00 6.30e-01 4.68e+01 angle pdb=" CA THR A 139 " pdb=" C THR A 139 " pdb=" O THR A 139 " ideal model delta sigma weight residual 120.70 114.07 6.63 1.03e+00 9.43e-01 4.15e+01 ... (remaining 32993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 13308 35.74 - 71.49: 1124 71.49 - 107.23: 80 107.23 - 142.98: 2 142.98 - 178.72: 8 Dihedral angle restraints: 14522 sinusoidal: 6519 harmonic: 8003 Sorted by residual: dihedral pdb=" CD ARG C 229 " pdb=" NE ARG C 229 " pdb=" CZ ARG C 229 " pdb=" NH1 ARG C 229 " ideal model delta sinusoidal sigma weight residual 0.00 88.55 -88.55 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CD ARG G 27 " pdb=" NE ARG G 27 " pdb=" CZ ARG G 27 " pdb=" NH1 ARG G 27 " ideal model delta sinusoidal sigma weight residual 0.00 -86.17 86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CD ARG A 130 " pdb=" NE ARG A 130 " pdb=" CZ ARG A 130 " pdb=" NH1 ARG A 130 " ideal model delta sinusoidal sigma weight residual 0.00 -76.72 76.72 1 1.00e+01 1.00e-02 7.39e+01 ... (remaining 14519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3497 0.120 - 0.240: 239 0.240 - 0.359: 7 0.359 - 0.479: 2 0.479 - 0.599: 4 Chirality restraints: 3749 Sorted by residual: chirality pdb=" P DT U 22 " pdb=" OP1 DT U 22 " pdb=" OP2 DT U 22 " pdb=" O5' DT U 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" P DG T 27 " pdb=" OP1 DG T 27 " pdb=" OP2 DG T 27 " pdb=" O5' DG T 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.47e+00 chirality pdb=" P DT L 29 " pdb=" OP1 DT L 29 " pdb=" OP2 DT L 29 " pdb=" O5' DT L 29 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.26e+00 ... (remaining 3746 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 27 " 1.105 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG G 27 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG G 27 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 27 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 27 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 229 " 1.092 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG C 229 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C 229 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 229 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 229 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 310 " -1.083 9.50e-02 1.11e+02 4.85e-01 1.43e+02 pdb=" NE ARG I 310 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG I 310 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG I 310 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG I 310 " -0.026 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 59 2.46 - 3.07: 16409 3.07 - 3.68: 38640 3.68 - 4.29: 58243 4.29 - 4.90: 91638 Nonbonded interactions: 204989 Sorted by model distance: nonbonded pdb=" O3G ANP B 600 " pdb="MG MG B 601 " model vdw 1.853 2.170 nonbonded pdb=" O1A ANP B 600 " pdb="MG MG B 601 " model vdw 1.866 2.170 nonbonded pdb=" C THR G 134 " pdb="MG MG G 601 " model vdw 1.872 2.400 nonbonded pdb=" O3G ANP D 600 " pdb="MG MG D 601 " model vdw 1.904 2.170 nonbonded pdb=" O2B ANP A 600 " pdb="MG MG A 601 " model vdw 1.907 2.170 ... (remaining 204984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 22 through 275 or resid 283 through 601)) selection = (chain 'F' and (resid 22 through 275 or resid 283 through 601)) selection = (chain 'G' and (resid 22 through 275 or resid 283 through 601)) selection = (chain 'H' and (resid 22 through 275 or resid 283 through 601)) selection = (chain 'I' and (resid 22 through 275 or resid 283 through 601)) } 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: 4.250 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.750 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.008 0.058 24139 Z= 0.529 Angle : 1.185 12.036 32998 Z= 0.813 Chirality : 0.065 0.599 3749 Planarity : 0.029 0.495 3940 Dihedral : 23.255 178.725 9412 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.82 % Favored : 89.75 % Rotamer: Outliers : 11.75 % Allowed : 29.17 % Favored : 59.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.14), residues: 2781 helix: -2.02 (0.14), residues: 1192 sheet: -3.58 (0.25), residues: 352 loop : -2.88 (0.15), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 310 TYR 0.020 0.001 TYR G 232 PHE 0.031 0.002 PHE G 195 HIS 0.013 0.002 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00759 (24139) covalent geometry : angle 1.18549 (32998) hydrogen bonds : bond 0.21227 ( 790) hydrogen bonds : angle 9.17826 ( 2233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 287 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: E 77 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6293 (mm-30) REVERT: E 211 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: E 213 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: E 242 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: E 278 MET cc_start: 0.3491 (OUTLIER) cc_final: 0.2749 (pmm) REVERT: G 290 ASN cc_start: 0.8618 (m110) cc_final: 0.8322 (m-40) REVERT: H 73 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6604 (pttt) REVERT: H 107 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8441 (mmtt) REVERT: H 191 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7094 (t80) REVERT: H 195 PHE cc_start: 0.8419 (m-80) cc_final: 0.8131 (m-80) REVERT: H 223 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.7896 (p) REVERT: H 306 ARG cc_start: 0.8545 (ttp-170) cc_final: 0.7931 (mpp80) REVERT: H 326 MET cc_start: 0.8358 (mmp) cc_final: 0.7996 (mmm) REVERT: I 43 GLU cc_start: 0.4564 (OUTLIER) cc_final: 0.3666 (mm-30) REVERT: I 59 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.4515 (tm-30) REVERT: I 64 LYS cc_start: -0.0275 (OUTLIER) cc_final: -0.0506 (mmtm) REVERT: I 107 LYS cc_start: 0.8647 (tttt) cc_final: 0.8308 (mmtt) REVERT: I 138 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5680 (m170) REVERT: I 199 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.5902 (t-90) REVERT: I 265 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7500 (mm) REVERT: I 284 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6052 (mttp) REVERT: A 130 ARG cc_start: 0.7592 (mtp-110) cc_final: 0.7086 (mmt90) REVERT: A 131 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7677 (m) REVERT: A 191 TYR cc_start: 0.6925 (t80) cc_final: 0.6600 (t80) REVERT: A 310 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5507 (ptt90) REVERT: B 125 MET cc_start: 0.8779 (mtp) cc_final: 0.8512 (mtp) REVERT: B 272 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: B 315 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 39 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7858 (tptp) REVERT: D 23 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: D 223 SER cc_start: 0.6603 (OUTLIER) cc_final: 0.5486 (p) REVERT: D 268 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7507 (mt0) outliers start: 265 outliers final: 99 residues processed: 494 average time/residue: 0.1821 time to fit residues: 138.6104 Evaluate side-chains 333 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 210 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 259 PHE Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 284 LYS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 138 HIS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 199 HIS Chi-restraints excluded: chain I residue 243 MET Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN E 34 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN G 196 ASN G 242 GLN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN I 267 ASN A 23 GLN A 242 GLN A 290 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN C 36 ASN D 294 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.126469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088850 restraints weight = 56825.497| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.29 r_work: 0.3354 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 24139 Z= 0.244 Angle : 0.726 9.423 32998 Z= 0.384 Chirality : 0.045 0.253 3749 Planarity : 0.005 0.068 3940 Dihedral : 20.742 176.573 4543 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.88 % Favored : 91.01 % Rotamer: Outliers : 8.24 % Allowed : 28.59 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.34 (0.14), residues: 2781 helix: -1.41 (0.14), residues: 1205 sheet: -3.19 (0.26), residues: 342 loop : -2.68 (0.15), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 27 TYR 0.024 0.002 TYR E 232 PHE 0.023 0.002 PHE I 259 HIS 0.007 0.001 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00564 (24139) covalent geometry : angle 0.72616 (32998) hydrogen bonds : bond 0.04819 ( 790) hydrogen bonds : angle 6.27722 ( 2233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 214 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3364 (mpm) cc_final: 0.2593 (pmm) REVERT: F 135 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: F 332 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8232 (p0) REVERT: G 59 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: G 92 PHE cc_start: 0.6540 (t80) cc_final: 0.6249 (t80) REVERT: G 284 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7862 (mttt) REVERT: H 50 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: H 73 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6224 (pttt) REVERT: H 158 MET cc_start: 0.8989 (mtm) cc_final: 0.8580 (mpp) REVERT: H 159 TYR cc_start: 0.6319 (t80) cc_final: 0.5719 (t80) REVERT: H 191 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7134 (t80) REVERT: H 195 PHE cc_start: 0.8419 (m-80) cc_final: 0.8120 (m-80) REVERT: H 303 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.6097 (ptm160) REVERT: H 306 ARG cc_start: 0.8724 (ttp-170) cc_final: 0.8177 (mpp80) REVERT: H 308 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: H 313 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5788 (tttm) REVERT: H 326 MET cc_start: 0.8251 (mmp) cc_final: 0.7879 (mmm) REVERT: I 43 GLU cc_start: 0.4523 (OUTLIER) cc_final: 0.3708 (mm-30) REVERT: I 59 GLU cc_start: 0.4784 (OUTLIER) cc_final: 0.4473 (tm-30) REVERT: I 64 LYS cc_start: -0.0293 (OUTLIER) cc_final: -0.0526 (mmtm) REVERT: I 235 ARG cc_start: 0.5437 (mmm160) cc_final: 0.3624 (ptt180) REVERT: I 284 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5971 (mmtp) REVERT: B 125 MET cc_start: 0.8750 (mtp) cc_final: 0.8466 (mtp) REVERT: B 315 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7926 (t80) REVERT: C 39 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7926 (tptp) REVERT: C 107 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8270 (tppt) REVERT: C 222 ASP cc_start: 0.8298 (t70) cc_final: 0.8043 (t0) REVERT: C 235 ARG cc_start: 0.3986 (OUTLIER) cc_final: 0.3653 (ptt180) REVERT: D 73 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7999 (tptp) outliers start: 186 outliers final: 99 residues processed: 374 average time/residue: 0.1655 time to fit residues: 98.5167 Evaluate side-chains 308 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 190 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 303 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 312 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 62 optimal weight: 7.9990 chunk 250 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN F 62 ASN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.126701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089015 restraints weight = 56814.249| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.02 r_work: 0.3356 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24139 Z= 0.199 Angle : 0.655 7.907 32998 Z= 0.347 Chirality : 0.044 0.204 3749 Planarity : 0.004 0.068 3940 Dihedral : 20.287 176.063 4424 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.49 % Favored : 91.41 % Rotamer: Outliers : 8.47 % Allowed : 28.24 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.06 (0.15), residues: 2781 helix: -1.14 (0.14), residues: 1250 sheet: -3.00 (0.25), residues: 366 loop : -2.59 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.015 0.001 TYR I 54 PHE 0.018 0.002 PHE H 259 HIS 0.006 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00459 (24139) covalent geometry : angle 0.65454 (32998) hydrogen bonds : bond 0.04315 ( 790) hydrogen bonds : angle 5.87567 ( 2233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 209 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3185 (OUTLIER) cc_final: 0.2419 (pmm) REVERT: F 135 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: F 235 ARG cc_start: 0.7420 (ttp-170) cc_final: 0.7198 (ttp-170) REVERT: F 253 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8506 (tt) REVERT: F 282 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.5430 (m-30) REVERT: F 332 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8226 (p0) REVERT: G 59 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: G 284 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8372 (mmmt) REVERT: H 73 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5926 (pttt) REVERT: H 158 MET cc_start: 0.9008 (mtm) cc_final: 0.8512 (mpp) REVERT: H 159 TYR cc_start: 0.6334 (t80) cc_final: 0.5688 (t80) REVERT: H 191 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7029 (t80) REVERT: H 195 PHE cc_start: 0.8416 (m-80) cc_final: 0.8065 (m-80) REVERT: H 284 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5329 (mttm) REVERT: H 306 ARG cc_start: 0.8766 (ttp-170) cc_final: 0.8205 (mpp80) REVERT: I 43 GLU cc_start: 0.4539 (OUTLIER) cc_final: 0.3726 (mm-30) REVERT: I 64 LYS cc_start: -0.0304 (OUTLIER) cc_final: -0.0540 (mmtm) REVERT: I 113 LEU cc_start: 0.4097 (OUTLIER) cc_final: 0.3866 (pp) REVERT: I 235 ARG cc_start: 0.5253 (mmm160) cc_final: 0.3430 (ptt180) REVERT: I 284 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5676 (mmtp) REVERT: I 326 MET cc_start: 0.7226 (tmm) cc_final: 0.6186 (mpp) REVERT: A 176 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: A 251 MET cc_start: 0.8586 (tpp) cc_final: 0.8360 (tpp) REVERT: B 125 MET cc_start: 0.8676 (mtp) cc_final: 0.8373 (mtp) REVERT: B 315 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7821 (t80) REVERT: C 39 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7896 (tptp) REVERT: C 107 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8187 (tppt) REVERT: C 167 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8493 (mpt180) REVERT: C 235 ARG cc_start: 0.3885 (OUTLIER) cc_final: 0.3567 (ptt180) REVERT: C 315 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8926 (t80) outliers start: 191 outliers final: 113 residues processed: 373 average time/residue: 0.1612 time to fit residues: 96.1734 Evaluate side-chains 322 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 188 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 284 LYS Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 312 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 139 optimal weight: 50.0000 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 GLN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 36 ASN C 36 ASN D 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.127581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091279 restraints weight = 56367.331| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.97 r_work: 0.3356 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24139 Z= 0.160 Angle : 0.614 10.053 32998 Z= 0.327 Chirality : 0.042 0.186 3749 Planarity : 0.004 0.064 3940 Dihedral : 20.083 177.994 4397 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.13 % Favored : 91.73 % Rotamer: Outliers : 6.91 % Allowed : 28.99 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.81 (0.15), residues: 2781 helix: -0.97 (0.14), residues: 1247 sheet: -2.85 (0.24), residues: 413 loop : -2.39 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 299 TYR 0.015 0.001 TYR I 54 PHE 0.022 0.002 PHE H 259 HIS 0.013 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00364 (24139) covalent geometry : angle 0.61393 (32998) hydrogen bonds : bond 0.03930 ( 790) hydrogen bonds : angle 5.55373 ( 2233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 214 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3186 (OUTLIER) cc_final: 0.2427 (pmm) REVERT: F 135 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: F 235 ARG cc_start: 0.7356 (ttp-170) cc_final: 0.6976 (ttp-110) REVERT: F 332 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8233 (p0) REVERT: G 156 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7672 (mtmt) REVERT: H 46 TYR cc_start: 0.6921 (m-80) cc_final: 0.6604 (m-80) REVERT: H 73 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5948 (pttt) REVERT: H 158 MET cc_start: 0.8869 (mtm) cc_final: 0.8291 (mpp) REVERT: H 159 TYR cc_start: 0.6534 (t80) cc_final: 0.6284 (t80) REVERT: H 195 PHE cc_start: 0.8438 (m-80) cc_final: 0.8063 (m-80) REVERT: H 210 MET cc_start: 0.8492 (mtt) cc_final: 0.8118 (ppp) REVERT: H 284 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5469 (mttm) REVERT: I 43 GLU cc_start: 0.4572 (OUTLIER) cc_final: 0.3812 (mm-30) REVERT: I 113 LEU cc_start: 0.4238 (OUTLIER) cc_final: 0.4007 (pp) REVERT: I 235 ARG cc_start: 0.5228 (mmm160) cc_final: 0.3309 (ptt180) REVERT: I 284 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5735 (mmtp) REVERT: I 294 HIS cc_start: 0.3209 (OUTLIER) cc_final: 0.2836 (t-90) REVERT: I 326 MET cc_start: 0.7241 (tmm) cc_final: 0.6257 (mpp) REVERT: A 121 SER cc_start: 0.8428 (p) cc_final: 0.8211 (p) REVERT: A 158 MET cc_start: 0.7991 (tmm) cc_final: 0.7733 (ppp) REVERT: A 176 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: B 125 MET cc_start: 0.8656 (mtp) cc_final: 0.8415 (mtp) REVERT: B 315 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7779 (t80) REVERT: C 39 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7947 (tptp) REVERT: C 107 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8065 (tppt) REVERT: C 235 ARG cc_start: 0.3720 (OUTLIER) cc_final: 0.3479 (ptt180) REVERT: C 315 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.8876 (t80) outliers start: 156 outliers final: 99 residues processed: 344 average time/residue: 0.1605 time to fit residues: 88.2813 Evaluate side-chains 300 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 185 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 294 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 312 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 79 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 chunk 8 optimal weight: 0.0870 chunk 127 optimal weight: 8.9990 chunk 276 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 HIS E 145 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 GLN G 268 GLN ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS A 93 HIS B 36 ASN C 47 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.132608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.095814 restraints weight = 55675.024| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.01 r_work: 0.3416 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24139 Z= 0.134 Angle : 0.590 8.496 32998 Z= 0.313 Chirality : 0.041 0.182 3749 Planarity : 0.004 0.123 3940 Dihedral : 19.953 179.940 4379 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.55 % Favored : 92.30 % Rotamer: Outliers : 6.74 % Allowed : 29.43 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.55 (0.15), residues: 2781 helix: -0.71 (0.15), residues: 1229 sheet: -2.66 (0.26), residues: 381 loop : -2.34 (0.16), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 310 TYR 0.013 0.001 TYR I 54 PHE 0.029 0.002 PHE H 259 HIS 0.012 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00301 (24139) covalent geometry : angle 0.58998 (32998) hydrogen bonds : bond 0.03641 ( 790) hydrogen bonds : angle 5.30203 ( 2233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 208 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3209 (OUTLIER) cc_final: 0.2481 (ptp) REVERT: F 135 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: F 235 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6932 (ttp-110) REVERT: F 253 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8438 (tt) REVERT: F 332 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8284 (p0) REVERT: G 145 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8178 (mp10) REVERT: G 322 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: H 73 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5867 (pttt) REVERT: H 118 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8397 (pp20) REVERT: H 158 MET cc_start: 0.8726 (mtm) cc_final: 0.8396 (mpp) REVERT: H 195 PHE cc_start: 0.8413 (m-80) cc_final: 0.8067 (m-80) REVERT: H 284 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5739 (mttm) REVERT: I 43 GLU cc_start: 0.4471 (OUTLIER) cc_final: 0.3772 (mm-30) REVERT: I 113 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.4252 (pp) REVERT: I 235 ARG cc_start: 0.5238 (mmm160) cc_final: 0.3349 (ptt180) REVERT: I 284 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5753 (mmtp) REVERT: I 294 HIS cc_start: 0.3428 (OUTLIER) cc_final: 0.2938 (t-90) REVERT: I 326 MET cc_start: 0.7340 (tmm) cc_final: 0.6508 (mpp) REVERT: A 125 MET cc_start: 0.8426 (mpp) cc_final: 0.8143 (mpp) REVERT: A 158 MET cc_start: 0.8000 (tmm) cc_final: 0.7784 (ppp) REVERT: A 210 MET cc_start: 0.7567 (tpp) cc_final: 0.7363 (tpp) REVERT: B 125 MET cc_start: 0.8609 (mtp) cc_final: 0.8352 (mtp) REVERT: C 39 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7965 (tptp) REVERT: C 107 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8296 (tppt) REVERT: C 235 ARG cc_start: 0.3684 (OUTLIER) cc_final: 0.3387 (ptt180) REVERT: C 315 TYR cc_start: 0.9266 (OUTLIER) cc_final: 0.8712 (t80) outliers start: 152 outliers final: 93 residues processed: 334 average time/residue: 0.1557 time to fit residues: 84.5841 Evaluate side-chains 301 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 191 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 294 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 312 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN G 145 GLN H 138 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS B 34 ASN B 36 ASN D 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094122 restraints weight = 56201.056| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.99 r_work: 0.3366 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24139 Z= 0.183 Angle : 0.617 7.708 32998 Z= 0.327 Chirality : 0.042 0.183 3749 Planarity : 0.004 0.082 3940 Dihedral : 19.895 179.809 4362 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.20 % Favored : 91.66 % Rotamer: Outliers : 6.78 % Allowed : 28.95 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.54 (0.15), residues: 2781 helix: -0.68 (0.15), residues: 1237 sheet: -2.75 (0.24), residues: 420 loop : -2.28 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 250 TYR 0.019 0.001 TYR H 216 PHE 0.031 0.002 PHE G 259 HIS 0.013 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00420 (24139) covalent geometry : angle 0.61695 (32998) hydrogen bonds : bond 0.03819 ( 790) hydrogen bonds : angle 5.33551 ( 2233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 196 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3344 (OUTLIER) cc_final: 0.2617 (ptp) REVERT: E 316 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8513 (t70) REVERT: F 135 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: F 235 ARG cc_start: 0.7114 (ttp-170) cc_final: 0.6809 (ttp-110) REVERT: F 253 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8478 (tt) REVERT: F 332 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8279 (p0) REVERT: G 145 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: G 306 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6549 (mmp-170) REVERT: G 322 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: H 73 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5909 (pttt) REVERT: H 158 MET cc_start: 0.8746 (mtm) cc_final: 0.8399 (mmm) REVERT: H 195 PHE cc_start: 0.8436 (m-80) cc_final: 0.8017 (m-80) REVERT: H 210 MET cc_start: 0.8516 (mtt) cc_final: 0.8154 (ppp) REVERT: H 216 TYR cc_start: 0.7005 (m-10) cc_final: 0.6179 (m-10) REVERT: H 284 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5843 (mttm) REVERT: I 43 GLU cc_start: 0.4339 (OUTLIER) cc_final: 0.3631 (mm-30) REVERT: I 126 PHE cc_start: 0.3278 (OUTLIER) cc_final: 0.2088 (t80) REVERT: I 235 ARG cc_start: 0.5178 (mmm160) cc_final: 0.3330 (ptt180) REVERT: I 284 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5314 (mmtp) REVERT: I 294 HIS cc_start: 0.3519 (OUTLIER) cc_final: 0.2992 (t-90) REVERT: I 326 MET cc_start: 0.7366 (tmm) cc_final: 0.6665 (mpp) REVERT: A 158 MET cc_start: 0.7876 (tmm) cc_final: 0.7452 (tmm) REVERT: A 186 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 210 MET cc_start: 0.7615 (tpp) cc_final: 0.7380 (tpp) REVERT: B 315 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7855 (t80) REVERT: C 39 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7944 (tptp) REVERT: C 84 MET cc_start: 0.7080 (mtp) cc_final: 0.6665 (mtt) REVERT: C 107 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8303 (tppt) REVERT: C 235 ARG cc_start: 0.3718 (OUTLIER) cc_final: 0.3405 (ptt180) REVERT: C 315 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8847 (t80) REVERT: D 247 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8132 (ttp-170) REVERT: D 322 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: D 329 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8126 (mm) outliers start: 153 outliers final: 101 residues processed: 321 average time/residue: 0.1554 time to fit residues: 80.1664 Evaluate side-chains 306 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 182 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 145 GLN Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 294 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 312 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 329 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 149 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 184 optimal weight: 0.2980 chunk 221 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.133780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097395 restraints weight = 55904.498| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.06 r_work: 0.3430 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24139 Z= 0.120 Angle : 0.582 10.175 32998 Z= 0.309 Chirality : 0.041 0.177 3749 Planarity : 0.004 0.078 3940 Dihedral : 19.744 179.585 4361 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.26 % Favored : 92.59 % Rotamer: Outliers : 5.45 % Allowed : 30.14 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.32 (0.15), residues: 2781 helix: -0.52 (0.15), residues: 1224 sheet: -2.49 (0.26), residues: 394 loop : -2.23 (0.16), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 130 TYR 0.017 0.001 TYR H 216 PHE 0.049 0.002 PHE G 259 HIS 0.013 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00267 (24139) covalent geometry : angle 0.58243 (32998) hydrogen bonds : bond 0.03433 ( 790) hydrogen bonds : angle 5.11421 ( 2233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 216 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3208 (OUTLIER) cc_final: 0.2552 (ptp) REVERT: E 316 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8464 (t70) REVERT: F 135 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: F 332 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8284 (p0) REVERT: G 29 GLU cc_start: 0.8076 (mt-10) cc_final: 0.6259 (pp20) REVERT: G 81 LEU cc_start: 0.8429 (mt) cc_final: 0.8119 (pp) REVERT: G 259 PHE cc_start: 0.7789 (m-10) cc_final: 0.7221 (m-10) REVERT: G 306 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6509 (mmp-170) REVERT: G 322 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: H 73 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.5887 (pttt) REVERT: H 158 MET cc_start: 0.8745 (mtm) cc_final: 0.8441 (mmm) REVERT: H 195 PHE cc_start: 0.8380 (m-80) cc_final: 0.7975 (m-80) REVERT: H 210 MET cc_start: 0.8452 (mtt) cc_final: 0.8190 (ppp) REVERT: H 216 TYR cc_start: 0.6855 (m-10) cc_final: 0.6339 (m-80) REVERT: H 284 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5636 (mptm) REVERT: H 308 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: I 43 GLU cc_start: 0.4284 (OUTLIER) cc_final: 0.3608 (mm-30) REVERT: I 126 PHE cc_start: 0.3031 (OUTLIER) cc_final: 0.2246 (t80) REVERT: I 235 ARG cc_start: 0.5187 (mmm160) cc_final: 0.3381 (ptt180) REVERT: I 284 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5341 (mmtp) REVERT: I 294 HIS cc_start: 0.3400 (OUTLIER) cc_final: 0.2747 (t-90) REVERT: I 326 MET cc_start: 0.7474 (tmm) cc_final: 0.6774 (mpp) REVERT: A 158 MET cc_start: 0.7931 (tmm) cc_final: 0.7670 (ppp) REVERT: A 186 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8405 (mt) REVERT: A 210 MET cc_start: 0.7627 (tpp) cc_final: 0.7414 (tpp) REVERT: B 315 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7722 (t80) REVERT: C 84 MET cc_start: 0.6846 (mtp) cc_final: 0.6432 (mtt) REVERT: C 107 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8222 (tppt) REVERT: C 235 ARG cc_start: 0.3556 (OUTLIER) cc_final: 0.3169 (ptt180) outliers start: 123 outliers final: 84 residues processed: 311 average time/residue: 0.1555 time to fit residues: 78.5965 Evaluate side-chains 290 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 189 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 205 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 294 HIS Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 315 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 247 optimal weight: 0.0010 chunk 87 optimal weight: 6.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 GLN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS B 34 ASN B 36 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.129222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091745 restraints weight = 54449.054| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.06 r_work: 0.3280 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24139 Z= 0.196 Angle : 0.637 10.514 32998 Z= 0.335 Chirality : 0.043 0.181 3749 Planarity : 0.004 0.063 3940 Dihedral : 19.804 179.122 4349 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.38 % Favored : 91.48 % Rotamer: Outliers : 5.19 % Allowed : 31.07 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.30 (0.16), residues: 2781 helix: -0.48 (0.15), residues: 1219 sheet: -2.53 (0.25), residues: 422 loop : -2.19 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.019 0.001 TYR G 159 PHE 0.030 0.002 PHE G 259 HIS 0.014 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00453 (24139) covalent geometry : angle 0.63716 (32998) hydrogen bonds : bond 0.03824 ( 790) hydrogen bonds : angle 5.25005 ( 2233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 189 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3387 (OUTLIER) cc_final: 0.2669 (ptp) REVERT: E 316 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8657 (t70) REVERT: F 135 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: F 332 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8154 (p0) REVERT: G 29 GLU cc_start: 0.8041 (mt-10) cc_final: 0.6161 (pp20) REVERT: G 81 LEU cc_start: 0.8477 (mt) cc_final: 0.8145 (pp) REVERT: G 306 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6649 (mmp-170) REVERT: G 322 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: H 73 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5920 (pttt) REVERT: H 158 MET cc_start: 0.8624 (mtm) cc_final: 0.8397 (mmm) REVERT: H 195 PHE cc_start: 0.8423 (m-80) cc_final: 0.8007 (m-80) REVERT: H 210 MET cc_start: 0.8414 (mtt) cc_final: 0.8191 (ppp) REVERT: H 216 TYR cc_start: 0.6896 (m-10) cc_final: 0.6441 (m-80) REVERT: H 284 LYS cc_start: 0.6380 (OUTLIER) cc_final: 0.5848 (mttm) REVERT: H 308 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: I 43 GLU cc_start: 0.4545 (OUTLIER) cc_final: 0.3844 (mm-30) REVERT: I 177 ARG cc_start: 0.4171 (OUTLIER) cc_final: 0.3762 (ptm160) REVERT: I 235 ARG cc_start: 0.5099 (mmm160) cc_final: 0.3260 (ptt180) REVERT: I 284 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6052 (mmtp) REVERT: I 326 MET cc_start: 0.7507 (tmm) cc_final: 0.6788 (mpp) REVERT: A 158 MET cc_start: 0.7860 (tmm) cc_final: 0.7400 (tmm) REVERT: A 186 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 210 MET cc_start: 0.7643 (tpp) cc_final: 0.7438 (tpp) REVERT: B 315 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7874 (t80) REVERT: C 84 MET cc_start: 0.7190 (mtp) cc_final: 0.6714 (mtt) REVERT: C 107 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8265 (tppt) REVERT: C 235 ARG cc_start: 0.3732 (OUTLIER) cc_final: 0.3379 (ptt180) REVERT: D 322 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6488 (tm-30) outliers start: 117 outliers final: 89 residues processed: 285 average time/residue: 0.1541 time to fit residues: 71.5220 Evaluate side-chains 288 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 182 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 284 LYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 322 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 144 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 256 optimal weight: 0.0060 chunk 159 optimal weight: 7.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 GLN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.129680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093021 restraints weight = 56303.648| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.13 r_work: 0.3438 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24139 Z= 0.120 Angle : 0.586 11.670 32998 Z= 0.308 Chirality : 0.040 0.224 3749 Planarity : 0.004 0.063 3940 Dihedral : 19.590 179.994 4348 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.98 % Favored : 92.88 % Rotamer: Outliers : 4.34 % Allowed : 31.91 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2781 helix: -0.37 (0.15), residues: 1226 sheet: -2.28 (0.26), residues: 390 loop : -2.14 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 130 TYR 0.022 0.001 TYR F 54 PHE 0.061 0.002 PHE G 259 HIS 0.013 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00266 (24139) covalent geometry : angle 0.58601 (32998) hydrogen bonds : bond 0.03310 ( 790) hydrogen bonds : angle 5.01310 ( 2233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 209 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.3391 (OUTLIER) cc_final: 0.2717 (ptp) REVERT: E 316 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8423 (t70) REVERT: F 278 MET cc_start: 0.3178 (ptt) cc_final: 0.2943 (ptp) REVERT: F 332 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (p0) REVERT: G 81 LEU cc_start: 0.8382 (mt) cc_final: 0.8069 (pp) REVERT: G 279 PHE cc_start: 0.5932 (m-80) cc_final: 0.4740 (t80) REVERT: G 306 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6456 (mmp-170) REVERT: G 322 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: H 73 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5883 (pttt) REVERT: H 195 PHE cc_start: 0.8360 (m-80) cc_final: 0.7925 (m-80) REVERT: H 216 TYR cc_start: 0.6722 (m-10) cc_final: 0.6458 (m-80) REVERT: H 308 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: I 43 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.3684 (mm-30) REVERT: I 177 ARG cc_start: 0.4044 (OUTLIER) cc_final: 0.3810 (ptm160) REVERT: I 210 MET cc_start: 0.6231 (pmm) cc_final: 0.5869 (pmm) REVERT: I 235 ARG cc_start: 0.5180 (mmm160) cc_final: 0.3358 (ptt180) REVERT: I 284 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6163 (mmtm) REVERT: I 294 HIS cc_start: 0.3422 (OUTLIER) cc_final: 0.2779 (t-90) REVERT: I 326 MET cc_start: 0.7588 (tmm) cc_final: 0.6918 (mpp) REVERT: A 158 MET cc_start: 0.7939 (tmm) cc_final: 0.7689 (ppp) REVERT: A 186 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 315 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 59 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 84 MET cc_start: 0.6841 (mtp) cc_final: 0.6406 (mtt) REVERT: D 243 MET cc_start: 0.7997 (mtp) cc_final: 0.7778 (mtp) REVERT: D 322 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6416 (tm-30) outliers start: 98 outliers final: 70 residues processed: 290 average time/residue: 0.1583 time to fit residues: 74.7281 Evaluate side-chains 272 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 188 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 294 HIS Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 322 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 257 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.130670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091861 restraints weight = 54972.195| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.09 r_work: 0.3287 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24139 Z= 0.207 Angle : 0.650 10.325 32998 Z= 0.340 Chirality : 0.043 0.211 3749 Planarity : 0.004 0.061 3940 Dihedral : 19.661 179.061 4336 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.70 % Favored : 91.12 % Rotamer: Outliers : 4.12 % Allowed : 32.31 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.18 (0.16), residues: 2781 helix: -0.44 (0.15), residues: 1235 sheet: -2.31 (0.25), residues: 414 loop : -2.15 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.019 0.002 TYR H 46 PHE 0.025 0.002 PHE G 259 HIS 0.013 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00482 (24139) covalent geometry : angle 0.64985 (32998) hydrogen bonds : bond 0.03751 ( 790) hydrogen bonds : angle 5.14600 ( 2233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 187 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6804 (mt-10) REVERT: E 278 MET cc_start: 0.3602 (OUTLIER) cc_final: 0.2875 (ptp) REVERT: E 316 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8656 (t70) REVERT: F 135 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: F 332 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8160 (p0) REVERT: G 279 PHE cc_start: 0.5806 (m-80) cc_final: 0.4671 (t80) REVERT: G 306 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6568 (mmp-170) REVERT: G 322 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: H 73 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5865 (pttt) REVERT: H 195 PHE cc_start: 0.8377 (m-80) cc_final: 0.7703 (m-80) REVERT: H 206 GLN cc_start: 0.8555 (mp10) cc_final: 0.7843 (tm-30) REVERT: H 308 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: I 43 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.3788 (mm-30) REVERT: I 177 ARG cc_start: 0.3944 (OUTLIER) cc_final: 0.3608 (ptm160) REVERT: I 210 MET cc_start: 0.6247 (pmm) cc_final: 0.5733 (pmm) REVERT: I 235 ARG cc_start: 0.5209 (mmm160) cc_final: 0.3345 (ptt180) REVERT: I 284 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.6135 (mmtp) REVERT: I 294 HIS cc_start: 0.3540 (OUTLIER) cc_final: 0.2835 (t-90) REVERT: I 326 MET cc_start: 0.7637 (tmm) cc_final: 0.6844 (mpp) REVERT: A 158 MET cc_start: 0.7891 (tmm) cc_final: 0.7349 (tmm) REVERT: A 186 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 315 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7837 (t80) REVERT: C 59 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7814 (mt-10) REVERT: D 322 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6497 (tm-30) outliers start: 93 outliers final: 74 residues processed: 266 average time/residue: 0.1482 time to fit residues: 64.8049 Evaluate side-chains 270 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 181 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 294 HIS Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 191 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 200 GLN Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 294 HIS Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 312 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 322 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 38 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.132977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097041 restraints weight = 55877.763| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.25 r_work: 0.3419 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24139 Z= 0.129 Angle : 0.604 11.438 32998 Z= 0.316 Chirality : 0.041 0.207 3749 Planarity : 0.004 0.060 3940 Dihedral : 19.498 179.571 4334 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.08 % Favored : 92.74 % Rotamer: Outliers : 4.08 % Allowed : 32.27 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.05 (0.16), residues: 2781 helix: -0.33 (0.15), residues: 1233 sheet: -2.19 (0.26), residues: 413 loop : -2.11 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.025 0.001 TYR H 216 PHE 0.019 0.002 PHE G 259 HIS 0.012 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00289 (24139) covalent geometry : angle 0.60351 (32998) hydrogen bonds : bond 0.03379 ( 790) hydrogen bonds : angle 5.01338 ( 2233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6398.34 seconds wall clock time: 110 minutes 43.95 seconds (6643.95 seconds total)