Starting phenix.real_space_refine on Fri Aug 7 19:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui8_64187/08_2026/9ui8_64187.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui8_64187/08_2026/9ui8_64187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ui8_64187/08_2026/9ui8_64187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui8_64187/08_2026/9ui8_64187.map" model { file = "/net/cci-nas-00/data/ceres_data/9ui8_64187/08_2026/9ui8_64187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui8_64187/08_2026/9ui8_64187.cif" } resolution = 3.2 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= 0.003 sd= 0.055 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 91 5.49 5 Mg 9 5.21 5 S 120 5.16 5 C 14147 2.51 5 N 4034 2.21 5 O 4640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23041 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: "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: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 394 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "U" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} 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: "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: "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: "F" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2408 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" 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: "H" 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: "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: "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: "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: "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: "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: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5.02, per 1000 atoms: 0.22 Number of scatterers: 23041 At special positions: 0 Unit cell: (124.5, 114.54, 200.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 91 15.00 Mg 9 11.99 O 4640 8.00 N 4034 7.00 C 14147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 934.8 milliseconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 26 sheets defined 40.7% alpha, 9.5% beta 13 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.626A pdb=" N ALA E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 139 through 144 removed outlier: 3.600A pdb=" N THR E 143 " --> pdb=" O THR E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 179 removed outlier: 3.700A pdb=" N TYR E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 214 removed outlier: 3.791A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 208 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 210 " --> pdb=" O GLN E 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 226 removed outlier: 3.711A pdb=" N ALA E 226 " --> pdb=" O SER E 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 223 through 226' Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.629A pdb=" N ASP E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 246 Processing helix chain 'E' and resid 247 through 260 removed outlier: 3.872A pdb=" N MET E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 45 removed outlier: 4.216A pdb=" N LYS G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY G 45 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.528A pdb=" N VAL G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.639A pdb=" N GLU G 59 " --> pdb=" O PRO G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.753A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 removed outlier: 4.066A pdb=" N ARG G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 114 Processing helix chain 'G' and resid 135 through 144 removed outlier: 3.542A pdb=" N ALA G 141 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL G 142 " --> pdb=" O HIS G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 178 removed outlier: 3.834A pdb=" N GLU G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.905A pdb=" N VAL G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 208 removed outlier: 3.716A pdb=" N THR G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU G 208 " --> pdb=" O LEU G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.700A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 removed outlier: 3.575A pdb=" N HIS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA G 256 " --> pdb=" O LEU G 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.570A pdb=" N GLN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 removed outlier: 3.818A pdb=" N LYS C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.995A pdb=" N LYS C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.640A pdb=" N ILE C 99 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.754A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.704A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 198 through 212 removed outlier: 4.152A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.512A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.766A pdb=" N ARG C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.905A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 291 through 296 removed outlier: 3.771A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.588A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.665A pdb=" N ALA B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 146 removed outlier: 4.311A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.592A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.835A pdb=" N ASP B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.557A pdb=" N GLU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 removed outlier: 4.499A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 259 removed outlier: 4.029A pdb=" N ALA B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.811A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 56 through 63 removed outlier: 4.204A pdb=" N ILE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 88 through 98 removed outlier: 4.215A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.534A pdb=" N ASP A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.635A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 removed outlier: 4.247A pdb=" N VAL A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.268A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'F' and resid 35 through 45 removed outlier: 3.519A pdb=" N LYS F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.550A pdb=" N VAL F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 53' Processing helix chain 'F' and resid 56 through 62 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.879A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 144 removed outlier: 3.915A pdb=" N ALA F 141 " --> pdb=" O CYS F 137 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 175 removed outlier: 3.721A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 196 through 202 removed outlier: 4.120A pdb=" N THR F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 211 removed outlier: 4.015A pdb=" N ASP F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 230 removed outlier: 4.000A pdb=" N ARG F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 225 through 230' Processing helix chain 'F' and resid 241 through 252 removed outlier: 4.049A pdb=" N ARG F 247 " --> pdb=" O MET F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 removed outlier: 3.732A pdb=" N ALA F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 30 removed outlier: 4.025A pdb=" N GLN I 30 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 59 through 63 removed outlier: 3.644A pdb=" N ILE I 63 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.811A pdb=" N THR I 76 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 97 removed outlier: 3.853A pdb=" N HIS I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 113 removed outlier: 3.927A pdb=" N LEU I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.967A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA I 173 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU I 176 " --> pdb=" O LEU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 187 Processing helix chain 'I' and resid 196 through 212 removed outlier: 3.797A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 removed outlier: 3.511A pdb=" N THR I 230 " --> pdb=" O ALA I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 259 removed outlier: 3.968A pdb=" N ALA I 246 " --> pdb=" O GLN I 242 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE I 259 " --> pdb=" O LEU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.609A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.606A pdb=" N ARG H 27 " --> pdb=" O PRO H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 42 removed outlier: 3.523A pdb=" N VAL H 38 " --> pdb=" O ASN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 55 removed outlier: 3.809A pdb=" N VAL H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 62 removed outlier: 3.816A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.832A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 96 removed outlier: 3.672A pdb=" N PHE H 92 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 106 through 112 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 181 through 188 Processing helix chain 'H' and resid 203 through 212 removed outlier: 4.278A pdb=" N ASP H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 232 removed outlier: 4.072A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 258 removed outlier: 3.795A pdb=" N MET H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG H 247 " --> pdb=" O MET H 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET H 251 " --> pdb=" O ARG H 247 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 253 " --> pdb=" O LEU H 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 34 through 43 removed outlier: 3.734A pdb=" N GLU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.755A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 63' Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.611A pdb=" N ASP D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.668A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 187 Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.541A pdb=" N GLU D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 removed outlier: 3.705A pdb=" N PHE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.037A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP F 222 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 160 " --> pdb=" O ASP F 222 " (cutoff:3.500A) 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 263 through 266 removed outlier: 6.409A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 216 through 221 removed outlier: 5.383A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AA6, first strand: chain 'G' and resid 87 through 88 removed outlier: 7.446A pdb=" N LYS H 156 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU H 219 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET H 158 " --> pdb=" O LEU H 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 220 through 221 removed outlier: 3.577A pdb=" N THR G 266 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR G 301 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE G 314 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ARG G 303 " --> pdb=" O CYS G 312 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N CYS G 312 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 158 through 159 Processing sheet with id=AA9, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.544A pdb=" N ALA D 190 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS D 156 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU D 219 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET D 158 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 218 through 219 removed outlier: 3.924A pdb=" N ALA C 192 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 301 through 304 removed outlier: 3.512A pdb=" N GLY C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.649A pdb=" N THR B 123 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 264 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.763A pdb=" N LYS B 285 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 299 through 302 removed outlier: 7.040A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 123 through 126 removed outlier: 6.481A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.061A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'F' and resid 263 through 266 removed outlier: 3.591A pdb=" N THR F 123 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 122 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU F 300 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F 333 " --> pdb=" O ASN F 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 157 through 159 removed outlier: 3.615A pdb=" N MET I 158 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE I 220 " --> pdb=" O MET I 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 269 through 270 Processing sheet with id=AC4, first strand: chain 'I' and resid 302 through 304 removed outlier: 3.727A pdb=" N ALA I 325 " --> pdb=" O CYS I 312 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 125 through 127 removed outlier: 6.358A pdb=" N PHE H 126 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N LYS H 304 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU H 302 " --> pdb=" O LYS H 313 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS H 313 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS H 304 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE H 311 " --> pdb=" O LYS H 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 328 through 330 Processing sheet with id=AC7, first strand: chain 'D' and resid 123 through 126 removed outlier: 6.345A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE D 126 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS D 304 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 328 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 269 through 271 667 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 2.52 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: 3822 1.31 - 1.44: 6074 1.44 - 1.56: 13246 1.56 - 1.69: 152 1.69 - 1.81: 213 Bond restraints: 23507 Sorted by residual: bond pdb=" C3' DG T 34 " pdb=" C2' DG T 34 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" CA THR I 297 " pdb=" C THR I 297 " ideal model delta sigma weight residual 1.533 1.514 0.019 5.60e-03 3.19e+04 1.14e+01 bond pdb=" C LEU H 112 " pdb=" O LEU H 112 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.36e-02 5.41e+03 1.14e+01 bond pdb=" CA ALA H 207 " pdb=" C ALA H 207 " ideal model delta sigma weight residual 1.522 1.477 0.046 1.36e-02 5.41e+03 1.13e+01 bond pdb=" C3' DG T 24 " pdb=" C2' DG T 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 23502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 30992 2.42 - 4.85: 931 4.85 - 7.27: 82 7.27 - 9.69: 26 9.69 - 12.11: 4 Bond angle restraints: 32035 Sorted by residual: angle pdb=" N GLY H 236 " pdb=" CA GLY H 236 " pdb=" C GLY H 236 " ideal model delta sigma weight residual 114.69 103.34 11.35 1.19e+00 7.06e-01 9.09e+01 angle pdb=" N LEU H 112 " pdb=" CA LEU H 112 " pdb=" C LEU H 112 " ideal model delta sigma weight residual 110.53 98.42 12.11 1.32e+00 5.74e-01 8.42e+01 angle pdb=" N GLY A 65 " pdb=" CA GLY A 65 " pdb=" C GLY A 65 " ideal model delta sigma weight residual 114.48 103.80 10.68 1.19e+00 7.06e-01 8.05e+01 angle pdb=" N THR E 197 " pdb=" CA THR E 197 " pdb=" C THR E 197 " ideal model delta sigma weight residual 111.14 102.21 8.93 1.08e+00 8.57e-01 6.84e+01 angle pdb=" N GLY C 236 " pdb=" CA GLY C 236 " pdb=" C GLY C 236 " ideal model delta sigma weight residual 114.69 105.06 9.63 1.19e+00 7.06e-01 6.55e+01 ... (remaining 32030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 13052 35.48 - 70.95: 1074 70.95 - 106.43: 64 106.43 - 141.90: 5 141.90 - 177.38: 9 Dihedral angle restraints: 14204 sinusoidal: 6249 harmonic: 7955 Sorted by residual: dihedral pdb=" CA GLY I 236 " pdb=" C GLY I 236 " pdb=" N GLU I 237 " pdb=" CA GLU I 237 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLY I 132 " pdb=" C GLY I 132 " pdb=" N LYS I 133 " pdb=" CA LYS I 133 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" O1B ANP A 600 " pdb=" N3B ANP A 600 " pdb=" PB ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sinusoidal sigma weight residual 35.15 -148.77 -176.08 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 14201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2543 0.043 - 0.086: 843 0.086 - 0.129: 226 0.129 - 0.172: 26 0.172 - 0.215: 4 Chirality restraints: 3642 Sorted by residual: chirality pdb=" CB ILE G 160 " pdb=" CA ILE G 160 " pdb=" CG1 ILE G 160 " pdb=" CG2 ILE G 160 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE F 265 " pdb=" N ILE F 265 " pdb=" C ILE F 265 " pdb=" CB ILE F 265 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU H 112 " pdb=" N LEU H 112 " pdb=" C LEU H 112 " pdb=" CB LEU H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 3639 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 196 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASN F 196 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN F 196 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN F 196 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 146 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO F 147 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 147 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 147 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 33 " -0.029 2.00e-02 2.50e+03 1.20e-02 4.35e+00 pdb=" N9 DG T 33 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG T 33 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DG T 33 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG T 33 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG T 33 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG T 33 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG T 33 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG T 33 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG T 33 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG T 33 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG T 33 " -0.002 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 35 2.43 - 3.05: 15314 3.05 - 3.67: 36854 3.67 - 4.28: 56647 4.28 - 4.90: 90544 Nonbonded interactions: 199394 Sorted by model distance: nonbonded pdb=" O1A ANP A 600 " pdb="MG MG A 601 " model vdw 1.816 2.170 nonbonded pdb=" O1B ANP C 600 " pdb="MG MG C 601 " model vdw 1.900 2.170 nonbonded pdb=" O1A ANP C 600 " pdb="MG MG C 601 " model vdw 1.910 2.170 nonbonded pdb=" N THR A 134 " pdb="MG MG A 601 " model vdw 1.924 2.250 nonbonded pdb=" O3G ANP D 600 " pdb="MG MG D 601 " model vdw 1.930 2.170 ... (remaining 199389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = (chain 'C' and resid 22 through 336) selection = (chain 'D' and resid 22 through 336) selection = (chain 'E' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'F' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'G' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'H' and resid 22 through 336) selection = (chain 'I' and resid 22 through 336) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.000 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.005 0.046 23507 Z= 0.339 Angle : 0.985 12.113 32035 Z= 0.675 Chirality : 0.045 0.215 3642 Planarity : 0.004 0.053 3892 Dihedral : 22.774 177.379 9124 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.33 % Favored : 89.38 % Rotamer: Outliers : 12.27 % Allowed : 29.57 % Favored : 58.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.13), residues: 2760 helix: -3.03 (0.13), residues: 1117 sheet: -4.31 (0.21), residues: 369 loop : -2.82 (0.15), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 254 TYR 0.018 0.001 TYR C 216 PHE 0.028 0.002 PHE F 195 HIS 0.008 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.34 (23507) covalent geometry : angle 0.98471 / 0.67 (32035) hydrogen bonds : bond 0.22535 / 14.95 ( 704) hydrogen bonds : angle 9.65125 / 6.77 ( 1925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 319 time to evaluate : 0.836 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: E 197 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8772 (p) REVERT: E 222 ASP cc_start: 0.8255 (t0) cc_final: 0.8039 (t0) REVERT: E 245 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8635 (tt) REVERT: E 302 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9123 (mm) REVERT: G 40 LYS cc_start: 0.7640 (tptp) cc_final: 0.7427 (tttt) REVERT: G 96 ARG cc_start: 0.7240 (tpp-160) cc_final: 0.6564 (tmt170) REVERT: G 114 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: G 118 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: G 238 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7971 (tp) REVERT: C 27 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7222 (tpp-160) REVERT: C 198 ASP cc_start: 0.8161 (t0) cc_final: 0.7850 (m-30) REVERT: C 202 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: C 210 MET cc_start: 0.7702 (mtp) cc_final: 0.7474 (mtp) REVERT: B 70 LYS cc_start: 0.4202 (OUTLIER) cc_final: 0.3888 (mmtp) REVERT: B 80 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.5835 (tttm) REVERT: B 124 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: B 199 HIS cc_start: 0.4767 (OUTLIER) cc_final: 0.4301 (p90) REVERT: B 225 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6582 (t) REVERT: B 232 TYR cc_start: 0.4882 (OUTLIER) cc_final: 0.4573 (p90) REVERT: B 244 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.5737 (t-90) REVERT: B 254 ARG cc_start: 0.6972 (ttp-170) cc_final: 0.6633 (ttp-170) REVERT: B 274 ASP cc_start: 0.2238 (OUTLIER) cc_final: 0.1668 (p0) REVERT: B 306 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6712 (mmp-170) REVERT: B 336 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.6163 (m-30) REVERT: A 30 GLN cc_start: 0.1834 (OUTLIER) cc_final: 0.1590 (pt0) REVERT: A 64 LYS cc_start: 0.4553 (OUTLIER) cc_final: 0.4282 (mmmt) REVERT: A 101 GLN cc_start: 0.5957 (OUTLIER) cc_final: 0.5277 (mm-40) REVERT: A 156 LYS cc_start: 0.4060 (mttt) cc_final: 0.3582 (mmmt) REVERT: A 214 SER cc_start: 0.3892 (OUTLIER) cc_final: 0.3466 (m) REVERT: A 219 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5052 (tt) REVERT: A 235 ARG cc_start: 0.1003 (OUTLIER) cc_final: 0.0323 (ptm160) REVERT: A 254 ARG cc_start: 0.4232 (tmt90) cc_final: 0.2994 (mmm160) REVERT: A 310 ARG cc_start: 0.5102 (ptt90) cc_final: 0.4752 (pmt-80) REVERT: A 326 MET cc_start: 0.5293 (tpp) cc_final: 0.5091 (tpp) REVERT: F 29 GLU cc_start: 0.6629 (pp20) cc_final: 0.6229 (pt0) REVERT: F 42 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7613 (mp0) REVERT: F 43 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: F 215 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7848 (tpt170) REVERT: F 235 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.6315 (ttm170) REVERT: F 278 MET cc_start: 0.4513 (OUTLIER) cc_final: 0.4243 (mtp) REVERT: I 27 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.5877 (mmt180) REVERT: I 43 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: I 57 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5177 (mptt) REVERT: I 303 ARG cc_start: 0.8182 (mtp180) cc_final: 0.7935 (mmm-85) REVERT: I 318 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7725 (Cg_endo) REVERT: H 80 LYS cc_start: 0.8035 (mttp) cc_final: 0.7594 (mtpt) REVERT: H 96 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6754 (ttm-80) REVERT: H 99 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8160 (pt) REVERT: H 311 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8833 (mm) REVERT: D 59 GLU cc_start: 0.8240 (tp30) cc_final: 0.7735 (tp30) REVERT: D 238 LEU cc_start: 0.8388 (tp) cc_final: 0.8169 (tp) REVERT: D 320 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8367 (tt) outliers start: 276 outliers final: 97 residues processed: 516 average time/residue: 0.1679 time to fit residues: 132.6177 Evaluate side-chains 391 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 260 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 317 SER Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 206 GLN A 188 ASN A 202 GLN I 62 ASN I 94 GLN H 23 GLN D 272 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.162900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107443 restraints weight = 33885.775| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.04 r_work: 0.3242 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23507 Z= 0.220 Angle : 0.735 9.441 32035 Z= 0.392 Chirality : 0.047 0.336 3642 Planarity : 0.005 0.050 3892 Dihedral : 20.256 176.280 4271 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.17 % Favored : 90.76 % Rotamer: Outliers : 9.43 % Allowed : 28.99 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.14), residues: 2760 helix: -2.77 (0.13), residues: 1183 sheet: -3.95 (0.23), residues: 350 loop : -2.61 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 130 TYR 0.021 0.002 TYR C 216 PHE 0.022 0.002 PHE B 327 HIS 0.007 0.001 HIS I 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (23507) covalent geometry : angle 0.73462 / 0.39 (32035) hydrogen bonds : bond 0.05339 / 3.55 ( 704) hydrogen bonds : angle 6.63942 / 4.66 ( 1925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 263 time to evaluate : 0.821 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: E 197 THR cc_start: 0.9065 (m) cc_final: 0.8727 (p) REVERT: E 222 ASP cc_start: 0.8217 (t0) cc_final: 0.8015 (t0) REVERT: E 245 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8755 (tt) REVERT: G 40 LYS cc_start: 0.7626 (tptp) cc_final: 0.7415 (tttt) REVERT: G 96 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.6547 (tmt170) REVERT: G 118 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: G 238 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8188 (tp) REVERT: G 251 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7931 (tpp) REVERT: C 27 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7184 (tpp-160) REVERT: C 198 ASP cc_start: 0.8185 (t0) cc_final: 0.7891 (m-30) REVERT: C 202 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: C 235 ARG cc_start: 0.8225 (mpp-170) cc_final: 0.7713 (mtm-85) REVERT: B 77 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5951 (tt0) REVERT: B 80 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.5684 (tttm) REVERT: B 82 VAL cc_start: 0.7531 (t) cc_final: 0.7227 (p) REVERT: B 124 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: B 205 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: B 244 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.5925 (t-90) REVERT: B 251 MET cc_start: 0.7535 (tpt) cc_final: 0.7136 (tpt) REVERT: B 274 ASP cc_start: 0.2528 (OUTLIER) cc_final: 0.2000 (p0) REVERT: B 306 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6720 (mmp-170) REVERT: B 336 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.6148 (m-30) REVERT: A 30 GLN cc_start: 0.1803 (OUTLIER) cc_final: 0.1578 (pt0) REVERT: A 64 LYS cc_start: 0.4776 (OUTLIER) cc_final: 0.4008 (ptpp) REVERT: A 67 SER cc_start: 0.6054 (OUTLIER) cc_final: 0.5569 (t) REVERT: A 156 LYS cc_start: 0.3898 (mttt) cc_final: 0.3419 (mmmt) REVERT: A 210 MET cc_start: 0.1061 (ptt) cc_final: 0.0838 (ptm) REVERT: A 235 ARG cc_start: 0.1755 (OUTLIER) cc_final: 0.0886 (ptm160) REVERT: A 310 ARG cc_start: 0.5084 (ptt90) cc_final: 0.4801 (pmt-80) REVERT: A 326 MET cc_start: 0.5003 (tpp) cc_final: 0.4738 (tpp) REVERT: F 43 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: F 169 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: F 215 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7884 (tpt170) REVERT: F 235 ARG cc_start: 0.7901 (tmm-80) cc_final: 0.6476 (ttm170) REVERT: F 278 MET cc_start: 0.4696 (pmm) cc_final: 0.4411 (mtt) REVERT: I 43 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: I 303 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7908 (mmm-85) REVERT: H 27 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7267 (tpt170) REVERT: H 42 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: H 80 LYS cc_start: 0.8151 (mttp) cc_final: 0.7647 (mtpp) REVERT: H 138 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8778 (m90) REVERT: H 311 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8753 (mm) REVERT: D 50 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: D 59 GLU cc_start: 0.8305 (tp30) cc_final: 0.7731 (tp30) REVERT: D 178 TYR cc_start: 0.8493 (m-80) cc_final: 0.8183 (m-80) outliers start: 212 outliers final: 119 residues processed: 429 average time/residue: 0.1440 time to fit residues: 98.2325 Evaluate side-chains 384 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 238 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain F residue 31 CYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 138 HIS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 201 optimal weight: 0.0060 chunk 72 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 178 optimal weight: 0.0870 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN E 93 HIS ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN D 268 GLN D 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110346 restraints weight = 33718.879| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.93 r_work: 0.3308 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23507 Z= 0.134 Angle : 0.640 10.454 32035 Z= 0.342 Chirality : 0.044 0.326 3642 Planarity : 0.004 0.047 3892 Dihedral : 19.662 176.052 4191 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.33 % Favored : 91.59 % Rotamer: Outliers : 7.83 % Allowed : 29.08 % Favored : 63.09 % 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: -3.95 (0.14), residues: 2760 helix: -2.36 (0.14), residues: 1165 sheet: -3.73 (0.23), residues: 385 loop : -2.32 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.021 0.001 TYR B 232 PHE 0.015 0.001 PHE F 129 HIS 0.007 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (23507) covalent geometry : angle 0.64008 / 0.34 (32035) hydrogen bonds : bond 0.04395 / 2.92 ( 704) hydrogen bonds : angle 6.01617 / 4.21 ( 1925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 261 time to evaluate : 0.780 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: E 197 THR cc_start: 0.9099 (m) cc_final: 0.8745 (p) REVERT: E 245 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8845 (tt) REVERT: G 40 LYS cc_start: 0.7613 (tptp) cc_final: 0.7402 (tttt) REVERT: G 96 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.6475 (tmt170) REVERT: G 118 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: G 251 MET cc_start: 0.8472 (ttp) cc_final: 0.8096 (tpp) REVERT: C 119 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 198 ASP cc_start: 0.8213 (t0) cc_final: 0.7933 (m-30) REVERT: C 202 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: C 235 ARG cc_start: 0.8129 (mpp-170) cc_final: 0.7838 (mtm-85) REVERT: B 80 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.5799 (tttm) REVERT: B 124 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6365 (tm-30) REVERT: B 216 TYR cc_start: 0.5875 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: B 228 TYR cc_start: 0.5730 (m-80) cc_final: 0.5077 (m-10) REVERT: B 244 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.5940 (t-90) REVERT: B 306 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6654 (mmp-170) REVERT: B 336 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.6273 (m-30) REVERT: A 64 LYS cc_start: 0.4896 (OUTLIER) cc_final: 0.4041 (ptpp) REVERT: A 156 LYS cc_start: 0.3824 (mttt) cc_final: 0.3297 (mmmt) REVERT: A 219 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5911 (mm) REVERT: A 235 ARG cc_start: 0.1985 (OUTLIER) cc_final: 0.0760 (ptm160) REVERT: A 310 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.5024 (pmt-80) REVERT: A 326 MET cc_start: 0.5322 (tpp) cc_final: 0.4931 (tpp) REVERT: F 169 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: F 215 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7996 (tpt170) REVERT: F 235 ARG cc_start: 0.7644 (tmm-80) cc_final: 0.6167 (ttm170) REVERT: F 278 MET cc_start: 0.4829 (OUTLIER) cc_final: 0.4325 (mtm) REVERT: I 43 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: I 50 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4852 (mt-10) REVERT: I 86 PHE cc_start: 0.4711 (OUTLIER) cc_final: 0.4379 (m-80) REVERT: I 158 MET cc_start: 0.8425 (mmm) cc_final: 0.8089 (ttm) REVERT: I 303 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7979 (mmm-85) REVERT: H 27 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7252 (tpt170) REVERT: H 42 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: H 80 LYS cc_start: 0.8238 (mttp) cc_final: 0.7707 (mtpp) REVERT: H 311 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8831 (mm) REVERT: D 50 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: D 59 GLU cc_start: 0.8395 (tp30) cc_final: 0.7785 (tp30) REVERT: D 213 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7635 (mp0) outliers start: 176 outliers final: 91 residues processed: 403 average time/residue: 0.1566 time to fit residues: 98.2055 Evaluate side-chains 345 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 229 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain F residue 31 CYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 86 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN E 199 HIS ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN A 145 GLN D 196 ASN D 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.160588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104576 restraints weight = 33852.385| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.99 r_work: 0.3221 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23507 Z= 0.281 Angle : 0.730 10.623 32035 Z= 0.382 Chirality : 0.048 0.357 3642 Planarity : 0.005 0.057 3892 Dihedral : 19.590 177.365 4131 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.49 % Favored : 90.43 % Rotamer: Outliers : 8.45 % Allowed : 28.77 % Favored : 62.78 % 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: -3.94 (0.14), residues: 2760 helix: -2.27 (0.14), residues: 1173 sheet: -3.75 (0.22), residues: 399 loop : -2.37 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 177 TYR 0.034 0.002 TYR C 216 PHE 0.018 0.002 PHE H 126 HIS 0.006 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.28 (23507) covalent geometry : angle 0.73041 / 0.38 (32035) hydrogen bonds : bond 0.04594 / 3.07 ( 704) hydrogen bonds : angle 5.90820 / 4.13 ( 1925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 237 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 LYS cc_start: 0.8651 (tptm) cc_final: 0.8334 (tppt) REVERT: E 138 HIS cc_start: 0.9282 (OUTLIER) cc_final: 0.9003 (m90) REVERT: E 245 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8831 (tt) REVERT: G 40 LYS cc_start: 0.7691 (tptp) cc_final: 0.7471 (tttt) REVERT: G 96 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.6539 (tmt170) REVERT: G 118 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: G 251 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8216 (tpp) REVERT: C 27 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7187 (tpp-160) REVERT: C 198 ASP cc_start: 0.8395 (t0) cc_final: 0.8109 (m-30) REVERT: C 202 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: B 80 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.5717 (tttm) REVERT: B 124 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: B 158 MET cc_start: 0.6664 (tpp) cc_final: 0.5637 (mmm) REVERT: B 216 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: B 244 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6755 (t-90) REVERT: B 336 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.6189 (m-30) REVERT: A 64 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.4101 (ptpp) REVERT: A 109 LEU cc_start: 0.6466 (mt) cc_final: 0.5768 (tp) REVERT: A 156 LYS cc_start: 0.3842 (mttt) cc_final: 0.3331 (mmmt) REVERT: A 235 ARG cc_start: 0.1646 (OUTLIER) cc_final: 0.0504 (ptm160) REVERT: A 310 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.4962 (pmt-80) REVERT: F 43 GLU cc_start: 0.8386 (mp0) cc_final: 0.7988 (pm20) REVERT: F 169 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: F 215 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7217 (ttp80) REVERT: F 235 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.6458 (ttm170) REVERT: F 243 MET cc_start: 0.9070 (mtp) cc_final: 0.8840 (mtt) REVERT: F 278 MET cc_start: 0.4691 (pmm) cc_final: 0.4223 (mtt) REVERT: I 39 LYS cc_start: 0.8565 (mmmm) cc_final: 0.7977 (pttt) REVERT: I 43 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: I 50 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4818 (mt-10) REVERT: I 213 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: I 303 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7976 (mmm-85) REVERT: H 42 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: H 80 LYS cc_start: 0.8235 (mttp) cc_final: 0.7721 (mtpp) REVERT: H 138 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8870 (m90) REVERT: D 50 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: D 59 GLU cc_start: 0.8480 (tp30) cc_final: 0.7883 (tp30) REVERT: D 213 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7635 (mp0) outliers start: 190 outliers final: 129 residues processed: 392 average time/residue: 0.1572 time to fit residues: 97.2324 Evaluate side-chains 369 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 217 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 315 TYR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 138 HIS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 70 optimal weight: 0.8980 chunk 192 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 199 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 HIS D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.164215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108105 restraints weight = 33342.053| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.76 r_work: 0.3291 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23507 Z= 0.134 Angle : 0.625 8.919 32035 Z= 0.332 Chirality : 0.044 0.338 3642 Planarity : 0.004 0.048 3892 Dihedral : 19.318 174.784 4122 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 6.36 % Allowed : 31.04 % Favored : 62.61 % 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: -3.63 (0.15), residues: 2760 helix: -2.03 (0.14), residues: 1170 sheet: -3.52 (0.23), residues: 384 loop : -2.25 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 177 TYR 0.020 0.001 TYR B 232 PHE 0.014 0.001 PHE F 129 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (23507) covalent geometry : angle 0.62461 / 0.33 (32035) hydrogen bonds : bond 0.03885 / 2.60 ( 704) hydrogen bonds : angle 5.57075 / 3.90 ( 1925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 239 time to evaluate : 0.919 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: E 245 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8754 (tt) REVERT: G 96 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.6391 (ttt180) REVERT: G 118 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: G 251 MET cc_start: 0.8435 (ttp) cc_final: 0.8162 (tpp) REVERT: C 198 ASP cc_start: 0.8302 (t0) cc_final: 0.7976 (m-30) REVERT: C 202 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: C 243 MET cc_start: 0.8744 (mtt) cc_final: 0.8341 (mtm) REVERT: B 80 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.5792 (tttm) REVERT: B 124 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6333 (tm-30) REVERT: B 216 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.5781 (m-80) REVERT: B 244 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.5990 (t-90) REVERT: B 336 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: A 64 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4121 (ptpp) REVERT: A 109 LEU cc_start: 0.6566 (mt) cc_final: 0.5813 (tp) REVERT: A 156 LYS cc_start: 0.3872 (mttt) cc_final: 0.3579 (tttt) REVERT: A 158 MET cc_start: 0.4643 (ttt) cc_final: 0.3374 (mmt) REVERT: A 167 ARG cc_start: 0.2356 (ttt90) cc_final: 0.1948 (mtt90) REVERT: A 235 ARG cc_start: 0.1558 (OUTLIER) cc_final: 0.0323 (ptm160) REVERT: A 310 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.4959 (pmt-80) REVERT: F 43 GLU cc_start: 0.8359 (mp0) cc_final: 0.7966 (pm20) REVERT: F 169 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: F 215 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8019 (tpt170) REVERT: F 235 ARG cc_start: 0.7766 (tmm-80) cc_final: 0.6225 (ttm170) REVERT: F 243 MET cc_start: 0.9003 (mtp) cc_final: 0.8795 (mtt) REVERT: F 278 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.4259 (mtp) REVERT: I 39 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7968 (pttt) REVERT: I 43 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: I 50 GLU cc_start: 0.5223 (OUTLIER) cc_final: 0.5000 (mt-10) REVERT: I 158 MET cc_start: 0.8363 (mmm) cc_final: 0.8112 (ttm) REVERT: I 213 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: I 303 ARG cc_start: 0.8245 (mtp180) cc_final: 0.8012 (mmm-85) REVERT: H 42 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: H 80 LYS cc_start: 0.8271 (mttp) cc_final: 0.7740 (mtpp) REVERT: H 138 HIS cc_start: 0.9068 (OUTLIER) cc_final: 0.8765 (m90) REVERT: H 326 MET cc_start: 0.8633 (ttm) cc_final: 0.8312 (ttt) REVERT: D 30 GLN cc_start: 0.7439 (pm20) cc_final: 0.7112 (pm20) REVERT: D 50 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: D 59 GLU cc_start: 0.8432 (tp30) cc_final: 0.7854 (tp30) REVERT: D 213 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7599 (mp0) outliers start: 143 outliers final: 100 residues processed: 356 average time/residue: 0.1715 time to fit residues: 94.8631 Evaluate side-chains 345 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 224 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 138 HIS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 254 optimal weight: 0.0000 chunk 241 optimal weight: 0.9990 chunk 64 optimal weight: 30.0000 chunk 222 optimal weight: 0.0030 chunk 75 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110048 restraints weight = 33417.282| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.85 r_work: 0.3310 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23507 Z= 0.121 Angle : 0.597 8.812 32035 Z= 0.319 Chirality : 0.044 0.348 3642 Planarity : 0.004 0.043 3892 Dihedral : 19.132 177.147 4118 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.15 % Favored : 91.78 % Rotamer: Outliers : 6.45 % Allowed : 30.77 % Favored : 62.78 % 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: -3.43 (0.15), residues: 2760 helix: -1.85 (0.14), residues: 1180 sheet: -3.33 (0.24), residues: 364 loop : -2.22 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 95 TYR 0.021 0.001 TYR E 205 PHE 0.014 0.001 PHE B 327 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (23507) covalent geometry : angle 0.59654 / 0.32 (32035) hydrogen bonds : bond 0.03572 / 2.40 ( 704) hydrogen bonds : angle 5.36076 / 3.76 ( 1925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 250 time to evaluate : 0.920 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 245 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8780 (tt) REVERT: G 96 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.6406 (ttt180) REVERT: G 118 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: G 251 MET cc_start: 0.8449 (ttp) cc_final: 0.8220 (tpp) REVERT: G 285 LYS cc_start: 0.8038 (tttp) cc_final: 0.7794 (pttt) REVERT: C 198 ASP cc_start: 0.8243 (t0) cc_final: 0.7949 (m-30) REVERT: C 202 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: C 210 MET cc_start: 0.7310 (mtp) cc_final: 0.7076 (mtp) REVERT: C 243 MET cc_start: 0.8709 (mtt) cc_final: 0.8305 (mtm) REVERT: B 25 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7177 (pt) REVERT: B 80 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.5836 (tttm) REVERT: B 124 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6361 (tm-30) REVERT: B 228 TYR cc_start: 0.5554 (m-10) cc_final: 0.5061 (m-10) REVERT: B 244 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.5847 (t-90) REVERT: B 336 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.6358 (m-30) REVERT: A 58 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.4964 (pttt) REVERT: A 64 LYS cc_start: 0.5052 (OUTLIER) cc_final: 0.4336 (mtpt) REVERT: A 91 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 109 LEU cc_start: 0.6699 (mt) cc_final: 0.5990 (tp) REVERT: A 156 LYS cc_start: 0.3838 (mttt) cc_final: 0.3531 (tttt) REVERT: A 158 MET cc_start: 0.4749 (ttt) cc_final: 0.3410 (mmt) REVERT: A 167 ARG cc_start: 0.2426 (ttt90) cc_final: 0.2016 (mtt90) REVERT: A 235 ARG cc_start: 0.1519 (OUTLIER) cc_final: 0.0389 (ptm160) REVERT: A 310 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4419 (pmt-80) REVERT: F 43 GLU cc_start: 0.8361 (mp0) cc_final: 0.7971 (pm20) REVERT: F 169 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: F 215 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8072 (tpt170) REVERT: F 235 ARG cc_start: 0.7709 (tmm-80) cc_final: 0.6287 (ttm170) REVERT: F 278 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4275 (mtp) REVERT: I 39 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8029 (pttt) REVERT: I 43 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: I 124 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6787 (mm-30) REVERT: I 213 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: I 303 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7969 (mmm-85) REVERT: H 42 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: H 80 LYS cc_start: 0.8312 (mttp) cc_final: 0.7771 (mtpp) REVERT: H 138 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.8783 (m90) REVERT: H 311 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8872 (mm) REVERT: H 326 MET cc_start: 0.8598 (ttm) cc_final: 0.8280 (ttt) REVERT: D 30 GLN cc_start: 0.7440 (pm20) cc_final: 0.7098 (pm20) REVERT: D 50 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: D 59 GLU cc_start: 0.8369 (tp30) cc_final: 0.7898 (tp30) REVERT: D 95 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8360 (ttm-80) REVERT: D 213 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7611 (mp0) outliers start: 145 outliers final: 97 residues processed: 365 average time/residue: 0.1721 time to fit residues: 97.9423 Evaluate side-chains 345 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 225 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 138 HIS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 98 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 258 optimal weight: 0.0870 chunk 151 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.162599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107085 restraints weight = 33521.523| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.17 r_work: 0.3236 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23507 Z= 0.198 Angle : 0.640 9.040 32035 Z= 0.338 Chirality : 0.045 0.347 3642 Planarity : 0.004 0.067 3892 Dihedral : 19.187 177.225 4113 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.84 % Favored : 91.09 % Rotamer: Outliers : 6.85 % Allowed : 30.68 % Favored : 62.47 % 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: -3.39 (0.15), residues: 2760 helix: -1.76 (0.14), residues: 1173 sheet: -3.34 (0.24), residues: 381 loop : -2.22 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 95 TYR 0.015 0.001 TYR B 232 PHE 0.013 0.002 PHE B 327 HIS 0.006 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (23507) covalent geometry : angle 0.64024 / 0.34 (32035) hydrogen bonds : bond 0.03817 / 2.55 ( 704) hydrogen bonds : angle 5.32602 / 3.73 ( 1925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 219 time to evaluate : 0.873 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 39 LYS cc_start: 0.8647 (tptm) cc_final: 0.8335 (tppt) REVERT: E 245 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8650 (tt) REVERT: G 96 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.6500 (tmt170) REVERT: G 118 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: C 198 ASP cc_start: 0.8211 (t0) cc_final: 0.7932 (m-30) REVERT: C 202 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: C 243 MET cc_start: 0.8599 (mtt) cc_final: 0.8191 (mtm) REVERT: B 80 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.5860 (tttm) REVERT: B 124 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: B 176 GLU cc_start: 0.8169 (tp30) cc_final: 0.7450 (mm-30) REVERT: B 211 MET cc_start: 0.7803 (ppp) cc_final: 0.7017 (ptm) REVERT: B 244 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.5804 (t-90) REVERT: B 336 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.6254 (m-30) REVERT: A 64 LYS cc_start: 0.4966 (OUTLIER) cc_final: 0.4592 (mmmt) REVERT: A 109 LEU cc_start: 0.6755 (mt) cc_final: 0.6062 (tp) REVERT: A 156 LYS cc_start: 0.3886 (mttt) cc_final: 0.3599 (tttt) REVERT: A 158 MET cc_start: 0.4621 (ttt) cc_final: 0.3350 (mmt) REVERT: A 235 ARG cc_start: 0.1322 (OUTLIER) cc_final: 0.0219 (ptm160) REVERT: A 326 MET cc_start: 0.2744 (ttt) cc_final: 0.1743 (tpp) REVERT: F 43 GLU cc_start: 0.8347 (mp0) cc_final: 0.7918 (pm20) REVERT: F 169 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: F 215 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8007 (tpt170) REVERT: F 235 ARG cc_start: 0.7808 (tmm-80) cc_final: 0.6423 (ttm170) REVERT: F 243 MET cc_start: 0.8988 (mtt) cc_final: 0.8771 (mtm) REVERT: I 39 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8006 (pttt) REVERT: I 43 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: I 124 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6991 (mm-30) REVERT: I 213 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: I 303 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7962 (mmm-85) REVERT: H 42 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: H 80 LYS cc_start: 0.8332 (mttp) cc_final: 0.7810 (mtpp) REVERT: H 138 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8765 (m90) REVERT: H 308 GLU cc_start: 0.8216 (pm20) cc_final: 0.7757 (pt0) REVERT: H 311 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8826 (mm) REVERT: H 326 MET cc_start: 0.8617 (ttm) cc_final: 0.8269 (ttt) REVERT: D 30 GLN cc_start: 0.7516 (pm20) cc_final: 0.7154 (pm20) REVERT: D 50 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: D 59 GLU cc_start: 0.8333 (tp30) cc_final: 0.7893 (tp30) REVERT: D 213 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7496 (mp0) outliers start: 154 outliers final: 116 residues processed: 340 average time/residue: 0.1649 time to fit residues: 88.4328 Evaluate side-chains 354 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 220 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 138 HIS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 271 optimal weight: 0.5980 chunk 72 optimal weight: 0.0070 chunk 141 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.166026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110124 restraints weight = 33331.423| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.88 r_work: 0.3309 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23507 Z= 0.117 Angle : 0.592 8.586 32035 Z= 0.315 Chirality : 0.043 0.357 3642 Planarity : 0.004 0.107 3892 Dihedral : 18.989 175.798 4109 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer: Outliers : 5.82 % Allowed : 31.48 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.15), residues: 2760 helix: -1.58 (0.15), residues: 1175 sheet: -3.17 (0.24), residues: 372 loop : -2.10 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG A 310 TYR 0.016 0.001 TYR B 232 PHE 0.012 0.001 PHE A 248 HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (23507) covalent geometry : angle 0.59203 / 0.32 (32035) hydrogen bonds : bond 0.03457 / 2.33 ( 704) hydrogen bonds : angle 5.13371 / 3.60 ( 1925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 242 time to evaluate : 0.893 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: E 228 TYR cc_start: 0.8581 (m-80) cc_final: 0.8327 (m-80) REVERT: E 245 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8674 (tt) REVERT: G 96 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.6490 (tmt170) REVERT: G 118 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: G 285 LYS cc_start: 0.8108 (tttp) cc_final: 0.7645 (pttt) REVERT: C 198 ASP cc_start: 0.8239 (t0) cc_final: 0.7926 (m-30) REVERT: C 202 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: C 210 MET cc_start: 0.7381 (mtp) cc_final: 0.7148 (mtp) REVERT: C 243 MET cc_start: 0.8695 (mtt) cc_final: 0.8304 (mtm) REVERT: B 80 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6053 (tttm) REVERT: B 124 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: B 176 GLU cc_start: 0.8184 (tp30) cc_final: 0.7475 (mm-30) REVERT: B 210 MET cc_start: 0.7002 (tmm) cc_final: 0.6795 (tmm) REVERT: B 211 MET cc_start: 0.7837 (ppp) cc_final: 0.7636 (ppp) REVERT: B 244 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.5831 (t-90) REVERT: B 327 PHE cc_start: 0.7889 (p90) cc_final: 0.7644 (p90) REVERT: A 64 LYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4251 (mtpt) REVERT: A 67 SER cc_start: 0.5792 (m) cc_final: 0.5424 (t) REVERT: A 91 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 124 GLU cc_start: 0.6766 (mt-10) cc_final: 0.5735 (tm-30) REVERT: A 125 MET cc_start: 0.5508 (tpp) cc_final: 0.4800 (tpp) REVERT: A 156 LYS cc_start: 0.3791 (mttt) cc_final: 0.3505 (tttt) REVERT: A 158 MET cc_start: 0.4502 (ttt) cc_final: 0.3321 (mmt) REVERT: A 235 ARG cc_start: 0.1239 (OUTLIER) cc_final: 0.0196 (ptm160) REVERT: A 326 MET cc_start: 0.2875 (ttt) cc_final: 0.1781 (tpp) REVERT: F 43 GLU cc_start: 0.8381 (mp0) cc_final: 0.7944 (pm20) REVERT: F 68 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7065 (tm-30) REVERT: F 169 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: F 215 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8066 (tpt170) REVERT: F 235 ARG cc_start: 0.7626 (tmm-80) cc_final: 0.6251 (ttm170) REVERT: I 39 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8094 (pttt) REVERT: I 43 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: I 213 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: H 42 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: H 80 LYS cc_start: 0.8342 (mttp) cc_final: 0.7809 (mtpp) REVERT: H 114 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7484 (mm110) REVERT: H 308 GLU cc_start: 0.8394 (pm20) cc_final: 0.7837 (pt0) REVERT: H 311 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8844 (mm) REVERT: H 326 MET cc_start: 0.8686 (ttm) cc_final: 0.8360 (ttt) REVERT: D 30 GLN cc_start: 0.7535 (pm20) cc_final: 0.7240 (pm20) REVERT: D 50 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: D 59 GLU cc_start: 0.8384 (tp30) cc_final: 0.7902 (tp30) REVERT: D 95 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8326 (ttm-80) REVERT: D 213 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7502 (mp0) outliers start: 131 outliers final: 97 residues processed: 346 average time/residue: 0.1728 time to fit residues: 92.7456 Evaluate side-chains 344 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 230 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 112 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 65 optimal weight: 40.0000 chunk 189 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN A 242 GLN F 200 GLN D 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.159819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104450 restraints weight = 33799.568| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.22 r_work: 0.3180 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 23507 Z= 0.312 Angle : 0.729 9.362 32035 Z= 0.378 Chirality : 0.049 0.391 3642 Planarity : 0.005 0.087 3892 Dihedral : 19.204 176.679 4099 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 6.22 % Allowed : 31.30 % Favored : 62.47 % 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: -3.33 (0.15), residues: 2760 helix: -1.69 (0.14), residues: 1173 sheet: -3.21 (0.25), residues: 367 loop : -2.28 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 130 TYR 0.035 0.002 TYR E 228 PHE 0.030 0.002 PHE A 327 HIS 0.010 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.31 (23507) covalent geometry : angle 0.72924 / 0.38 (32035) hydrogen bonds : bond 0.04246 / 2.83 ( 704) hydrogen bonds : angle 5.36126 / 3.75 ( 1925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 232 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 LYS cc_start: 0.8704 (tptm) cc_final: 0.8380 (tppt) REVERT: E 245 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8691 (tt) REVERT: G 96 ARG cc_start: 0.7503 (tpp-160) cc_final: 0.6532 (tmt170) REVERT: G 118 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: G 285 LYS cc_start: 0.8206 (tttp) cc_final: 0.7685 (pttt) REVERT: C 27 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7164 (tpp-160) REVERT: C 195 PHE cc_start: 0.7787 (m-80) cc_final: 0.7552 (m-80) REVERT: C 198 ASP cc_start: 0.8378 (t0) cc_final: 0.8072 (m-30) REVERT: C 202 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: C 206 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: C 243 MET cc_start: 0.8585 (mtt) cc_final: 0.8176 (mtm) REVERT: B 80 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6055 (tttm) REVERT: B 124 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: B 176 GLU cc_start: 0.8149 (tp30) cc_final: 0.7443 (mm-30) REVERT: B 244 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.5903 (t-90) REVERT: A 64 LYS cc_start: 0.4901 (OUTLIER) cc_final: 0.4543 (mmmt) REVERT: A 67 SER cc_start: 0.5976 (m) cc_final: 0.5547 (t) REVERT: A 91 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 124 GLU cc_start: 0.6854 (mt-10) cc_final: 0.5762 (tm-30) REVERT: A 125 MET cc_start: 0.5520 (tpp) cc_final: 0.4862 (tpp) REVERT: A 156 LYS cc_start: 0.3912 (mttt) cc_final: 0.3552 (mmmt) REVERT: A 158 MET cc_start: 0.4387 (ttt) cc_final: 0.3251 (mmt) REVERT: A 235 ARG cc_start: 0.1037 (OUTLIER) cc_final: 0.0041 (ptm160) REVERT: A 326 MET cc_start: 0.3503 (ttt) cc_final: 0.2535 (tpp) REVERT: F 43 GLU cc_start: 0.8368 (mp0) cc_final: 0.7925 (pm20) REVERT: F 68 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7442 (tm-30) REVERT: F 169 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: F 215 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7005 (ttp80) REVERT: F 235 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.6580 (ttm110) REVERT: I 39 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8076 (mtmt) REVERT: I 43 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: I 213 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: I 232 TYR cc_start: 0.8202 (m-80) cc_final: 0.7811 (m-80) REVERT: H 42 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: H 80 LYS cc_start: 0.8388 (mttp) cc_final: 0.7905 (mtpp) REVERT: H 138 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8843 (m90) REVERT: H 311 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8829 (mm) REVERT: D 30 GLN cc_start: 0.7687 (pm20) cc_final: 0.7323 (pm20) REVERT: D 50 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7352 (mm-30) REVERT: D 59 GLU cc_start: 0.8425 (tp30) cc_final: 0.8003 (tp30) REVERT: D 213 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7448 (mp0) outliers start: 140 outliers final: 105 residues processed: 344 average time/residue: 0.1780 time to fit residues: 95.4667 Evaluate side-chains 346 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 221 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 138 HIS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 29 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107714 restraints weight = 33827.102| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.05 r_work: 0.3250 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23507 Z= 0.149 Angle : 0.627 9.464 32035 Z= 0.332 Chirality : 0.044 0.356 3642 Planarity : 0.004 0.083 3892 Dihedral : 19.046 173.995 4097 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.22 % Favored : 91.67 % Rotamer: Outliers : 5.20 % Allowed : 32.01 % Favored : 62.78 % 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: -3.13 (0.15), residues: 2760 helix: -1.53 (0.15), residues: 1160 sheet: -3.10 (0.25), residues: 369 loop : -2.15 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 130 TYR 0.018 0.001 TYR E 228 PHE 0.026 0.001 PHE A 327 HIS 0.006 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (23507) covalent geometry : angle 0.62704 / 0.33 (32035) hydrogen bonds : bond 0.03663 / 2.46 ( 704) hydrogen bonds : angle 5.19297 / 3.64 ( 1925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 232 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8712 (tt) REVERT: G 96 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.6533 (tmt170) REVERT: G 118 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: G 285 LYS cc_start: 0.8303 (tttp) cc_final: 0.7785 (pttt) REVERT: C 198 ASP cc_start: 0.8434 (t0) cc_final: 0.8093 (m-30) REVERT: C 202 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: C 243 MET cc_start: 0.8705 (mtt) cc_final: 0.8304 (mtm) REVERT: B 80 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6044 (tttm) REVERT: B 124 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6394 (tm-30) REVERT: B 244 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.5881 (t-90) REVERT: A 64 LYS cc_start: 0.4920 (OUTLIER) cc_final: 0.4578 (mmmt) REVERT: A 67 SER cc_start: 0.5964 (m) cc_final: 0.5614 (t) REVERT: A 124 GLU cc_start: 0.6805 (mt-10) cc_final: 0.5768 (tm-30) REVERT: A 125 MET cc_start: 0.5436 (tpp) cc_final: 0.4753 (tpp) REVERT: A 156 LYS cc_start: 0.3877 (mttt) cc_final: 0.3485 (mmmt) REVERT: A 158 MET cc_start: 0.4259 (ttt) cc_final: 0.3176 (mmt) REVERT: A 167 ARG cc_start: 0.2621 (ttt90) cc_final: 0.2177 (mtt90) REVERT: A 235 ARG cc_start: 0.1097 (OUTLIER) cc_final: 0.0141 (ptm160) REVERT: A 326 MET cc_start: 0.3766 (ttt) cc_final: 0.2844 (tpp) REVERT: F 43 GLU cc_start: 0.8387 (mp0) cc_final: 0.7946 (pm20) REVERT: F 68 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7423 (tm-30) REVERT: F 169 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: F 215 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8079 (tpt170) REVERT: F 235 ARG cc_start: 0.7947 (tmm-80) cc_final: 0.6290 (ttm170) REVERT: F 278 MET cc_start: 0.4337 (pmm) cc_final: 0.3489 (pmm) REVERT: I 39 LYS cc_start: 0.8528 (mmmm) cc_final: 0.7929 (pttt) REVERT: I 43 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: I 213 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: I 232 TYR cc_start: 0.8213 (m-80) cc_final: 0.7805 (m-80) REVERT: H 42 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: H 80 LYS cc_start: 0.8355 (mttp) cc_final: 0.7852 (mtpp) REVERT: H 114 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7599 (mm110) REVERT: H 308 GLU cc_start: 0.8359 (pm20) cc_final: 0.7875 (pt0) REVERT: H 311 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8862 (mm) REVERT: H 326 MET cc_start: 0.8703 (ttm) cc_final: 0.8361 (ttt) REVERT: D 30 GLN cc_start: 0.7675 (pm20) cc_final: 0.7303 (pm20) REVERT: D 50 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: D 59 GLU cc_start: 0.8492 (tp30) cc_final: 0.8016 (tp30) REVERT: D 95 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8356 (ttm-80) REVERT: D 213 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7441 (mp0) outliers start: 117 outliers final: 96 residues processed: 327 average time/residue: 0.1726 time to fit residues: 87.5266 Evaluate side-chains 335 residues out of total 2250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 223 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 312 CYS Chi-restraints excluded: chain I residue 324 GLU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 237 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 0.0070 chunk 125 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 226 optimal weight: 0.3980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.163919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108187 restraints weight = 33534.424| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.86 r_work: 0.3260 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23507 Z= 0.142 Angle : 0.611 9.151 32035 Z= 0.323 Chirality : 0.044 0.358 3642 Planarity : 0.004 0.072 3892 Dihedral : 18.925 175.520 4095 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.37 % Favored : 91.52 % Rotamer: Outliers : 5.16 % Allowed : 32.24 % Favored : 62.61 % 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: -3.02 (0.15), residues: 2760 helix: -1.43 (0.15), residues: 1176 sheet: -2.96 (0.26), residues: 355 loop : -2.17 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 130 TYR 0.017 0.001 TYR E 228 PHE 0.032 0.001 PHE C 195 HIS 0.005 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (23507) covalent geometry : angle 0.61123 / 0.32 (32035) hydrogen bonds : bond 0.03540 / 2.36 ( 704) hydrogen bonds : angle 5.08827 / 3.57 ( 1925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7239.93 seconds wall clock time: 124 minutes 21.55 seconds (7461.55 seconds total)