Starting phenix.real_space_refine on Sun Aug 24 18:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fs8_29417/08_2025/8fs8_29417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs8_29417/08_2025/8fs8_29417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2025/8fs8_29417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2025/8fs8_29417.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2025/8fs8_29417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2025/8fs8_29417.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 68 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13702 2.51 5 N 3764 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21906 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3489 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 409} 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: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 317} Chain breaks: 2 Chain: "F" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2216 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 7 Chain: "G" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2303 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 4, 'TRANS': 285} Chain breaks: 2 Chain: "H" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2296 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 5 Chain: "I" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "J" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.24 Number of scatterers: 21906 At special positions: 0 Unit cell: (122.544, 129.996, 139.932, 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 114 16.00 P 68 15.00 Mg 4 11.99 O 4254 8.00 N 3764 7.00 C 13702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 916.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 15 sheets defined 51.2% alpha, 14.3% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.835A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 173 removed outlier: 4.162A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.502A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.143A pdb=" N LEU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.105A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 6.081A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.654A pdb=" N LEU A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 497 Proline residue: A 489 - end of helix removed outlier: 4.479A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.861A pdb=" N VAL B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.912A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.287A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.507A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.534A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.598A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.971A pdb=" N ILE C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.838A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.753A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.596A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.522A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 240 through 253 Processing helix chain 'C' and resid 255 through 270 removed outlier: 3.862A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.301A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 4.133A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.716A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.540A pdb=" N THR D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.074A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.992A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 294 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.237A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.170A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.087A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.579A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 30 Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.323A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 425 removed outlier: 3.780A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 94 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 317 through 329 removed outlier: 4.175A pdb=" N GLN G 321 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 removed outlier: 3.521A pdb=" N GLN H 13 " --> pdb=" O GLU H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 234 through 244 Processing helix chain 'H' and resid 326 through 336 removed outlier: 3.522A pdb=" N ASN H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 339 No H-bonds generated for 'chain 'H' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.339A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.869A pdb=" N GLY A 109 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 7.093A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 161 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.081A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.475A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 72 removed outlier: 4.078A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.559A pdb=" N PHE F 160 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.145A pdb=" N LYS F 206 " --> pdb=" O SER H 283 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER H 283 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 3.913A pdb=" N ILE F 44 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 70 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 463 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 405 through 411 removed outlier: 3.521A pdb=" N ILE F 284 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 267 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 280 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU G 131 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE G 120 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 36 through 41 Processing sheet with id=AB3, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.549A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.959A pdb=" N GLU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 78 through 79 removed outlier: 4.355A pdb=" N SER H 93 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 79 removed outlier: 7.338A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU H 38 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN H 363 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN H 228 " --> pdb=" O PHE H 353 " (cutoff:3.500A) 1074 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7083 1.36 - 1.51: 5957 1.51 - 1.65: 9184 1.65 - 1.80: 69 1.80 - 1.95: 100 Bond restraints: 22393 Sorted by residual: bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.44e+00 bond pdb=" N ASN E 103 " pdb=" CA ASN E 103 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.46e+00 bond pdb=" N LEU B 133 " pdb=" CA LEU B 133 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.27e-02 6.20e+03 6.86e+00 bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.85e+00 bond pdb=" N ASP E 100 " pdb=" CA ASP E 100 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.33e-02 5.65e+03 6.42e+00 ... (remaining 22388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 29559 1.34 - 2.68: 805 2.68 - 4.01: 98 4.01 - 5.35: 26 5.35 - 6.69: 9 Bond angle restraints: 30497 Sorted by residual: angle pdb=" N GLU C 332 " pdb=" CA GLU C 332 " pdb=" C GLU C 332 " ideal model delta sigma weight residual 113.23 107.05 6.18 1.24e+00 6.50e-01 2.49e+01 angle pdb=" CA GLY E 102 " pdb=" C GLY E 102 " pdb=" O GLY E 102 " ideal model delta sigma weight residual 121.18 117.19 3.99 8.80e-01 1.29e+00 2.05e+01 angle pdb=" N THR H 290 " pdb=" CA THR H 290 " pdb=" C THR H 290 " ideal model delta sigma weight residual 114.04 109.20 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N ASN B 136 " pdb=" CA ASN B 136 " pdb=" C ASN B 136 " ideal model delta sigma weight residual 113.28 108.61 4.67 1.22e+00 6.72e-01 1.47e+01 angle pdb=" N ASN C 333 " pdb=" CA ASN C 333 " pdb=" C ASN C 333 " ideal model delta sigma weight residual 113.18 108.65 4.53 1.21e+00 6.83e-01 1.40e+01 ... (remaining 30492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 12710 23.25 - 46.50: 615 46.50 - 69.75: 210 69.75 - 93.00: 9 93.00 - 116.25: 1 Dihedral angle restraints: 13545 sinusoidal: 5965 harmonic: 7580 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -176.26 116.25 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA ASN C 180 " pdb=" CB ASN C 180 " pdb=" CG ASN C 180 " pdb=" OD1 ASN C 180 " ideal model delta sinusoidal sigma weight residual -90.00 -159.37 69.37 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" O1B AGS D 401 " pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " pdb=" PG AGS D 401 " ideal model delta sinusoidal sigma weight residual 68.91 157.20 -88.29 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2548 0.035 - 0.071: 709 0.071 - 0.106: 216 0.106 - 0.141: 51 0.141 - 0.177: 3 Chirality restraints: 3527 Sorted by residual: chirality pdb=" CB ILE G 137 " pdb=" CA ILE G 137 " pdb=" CG1 ILE G 137 " pdb=" CG2 ILE G 137 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ASP E 100 " pdb=" N ASP E 100 " pdb=" C ASP E 100 " pdb=" CB ASP E 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 3524 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 217 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C LEU D 217 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU D 217 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU D 218 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.023 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" N9 DG I 28 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 131 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C MET B 131 " -0.030 2.00e-02 2.50e+03 pdb=" O MET B 131 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 132 " 0.010 2.00e-02 2.50e+03 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 206 2.58 - 3.16: 18227 3.16 - 3.74: 36468 3.74 - 4.32: 49106 4.32 - 4.90: 81377 Nonbonded interactions: 185384 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.218 2.170 nonbonded pdb=" O GLN A 207 " pdb=" OG SER A 211 " model vdw 2.236 3.040 ... (remaining 185379 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.800 Find NCS groups from input model: 0.220 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 : 0.002 0.039 22393 Z= 0.151 Angle : 0.534 6.692 30497 Z= 0.330 Chirality : 0.038 0.177 3527 Planarity : 0.003 0.044 3643 Dihedral : 14.335 116.254 8601 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.29 % Allowed : 7.31 % Favored : 89.40 % 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 aren not related in a simple way. whole: 0.66 (0.18), residues: 2532 helix: 1.71 (0.16), residues: 1165 sheet: -0.66 (0.24), residues: 525 loop : -0.53 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.009 0.001 TYR A 67 PHE 0.010 0.001 PHE A 201 TRP 0.009 0.001 TRP E 259 HIS 0.004 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00240 (22393) covalent geometry : angle 0.53372 (30497) hydrogen bonds : bond 0.16803 ( 1118) hydrogen bonds : angle 6.76185 ( 3195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 554 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7846 (tt0) cc_final: 0.7187 (tm-30) REVERT: A 163 MET cc_start: 0.6551 (mtm) cc_final: 0.5838 (mtm) REVERT: A 174 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5957 (ptm160) REVERT: A 196 ASP cc_start: 0.7677 (t0) cc_final: 0.7442 (t0) REVERT: A 225 GLU cc_start: 0.7597 (tt0) cc_final: 0.6987 (mp0) REVERT: A 289 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6540 (mtmm) REVERT: A 374 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6510 (tp30) REVERT: A 436 HIS cc_start: 0.4305 (m-70) cc_final: 0.3830 (m-70) REVERT: A 443 PHE cc_start: 0.7430 (t80) cc_final: 0.7159 (t80) REVERT: B 38 LYS cc_start: 0.7533 (tmmm) cc_final: 0.7069 (mtmt) REVERT: B 146 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7183 (mt0) REVERT: B 152 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 272 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mmm160) REVERT: C 250 SER cc_start: 0.7262 (m) cc_final: 0.6947 (p) REVERT: C 256 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.6405 (t60) REVERT: D 83 TYR cc_start: 0.7239 (m-80) cc_final: 0.6940 (m-80) REVERT: E 19 ASN cc_start: 0.6100 (m110) cc_final: 0.5825 (m-40) REVERT: E 32 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6421 (mp10) REVERT: E 34 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6107 (ptm160) REVERT: E 68 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7142 (tm) REVERT: E 221 ARG cc_start: 0.6469 (mtp180) cc_final: 0.6129 (mtp-110) REVERT: E 329 ASP cc_start: 0.8077 (p0) cc_final: 0.7867 (p0) REVERT: F 109 ARG cc_start: 0.7665 (mpt90) cc_final: 0.7442 (mmt180) REVERT: F 120 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6259 (m) REVERT: F 162 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6173 (tm-30) REVERT: F 293 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6872 (tt0) REVERT: F 422 TYR cc_start: 0.7459 (t80) cc_final: 0.7186 (t80) REVERT: F 461 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5474 (ptm160) REVERT: G 40 PHE cc_start: 0.7072 (m-80) cc_final: 0.6499 (m-80) REVERT: G 188 ASP cc_start: 0.7642 (m-30) cc_final: 0.7349 (m-30) REVERT: G 270 LEU cc_start: 0.6031 (tt) cc_final: 0.5572 (mp) REVERT: G 321 GLN cc_start: 0.8006 (tt0) cc_final: 0.7619 (mp10) REVERT: H 158 ASP cc_start: 0.7336 (p0) cc_final: 0.7094 (p0) REVERT: H 282 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6316 (mm) REVERT: H 320 LYS cc_start: 0.7100 (mmtm) cc_final: 0.6797 (mmtm) REVERT: H 364 MET cc_start: 0.7705 (ptm) cc_final: 0.7302 (ptt) outliers start: 77 outliers final: 24 residues processed: 600 average time/residue: 0.1721 time to fit residues: 156.9195 Evaluate side-chains 391 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 282 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0170 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 355 ASN A 368 ASN A 409 ASN A 436 HIS C 96 GLN C 333 ASN D 345 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN G 9 ASN H 27 GLN H 132 ASN H 295 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.184820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148105 restraints weight = 27299.802| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.26 r_work: 0.3760 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22393 Z= 0.127 Angle : 0.544 7.776 30497 Z= 0.290 Chirality : 0.041 0.178 3527 Planarity : 0.004 0.041 3643 Dihedral : 16.424 98.144 3517 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.33 % Allowed : 11.89 % Favored : 84.78 % 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 aren not related in a simple way. whole: 0.52 (0.18), residues: 2532 helix: 1.45 (0.15), residues: 1219 sheet: -0.65 (0.24), residues: 513 loop : -0.57 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 297 TYR 0.024 0.001 TYR A 67 PHE 0.021 0.001 PHE B 96 TRP 0.015 0.001 TRP H 42 HIS 0.010 0.001 HIS F 203 Details of bonding type rmsd covalent geometry : bond 0.00278 (22393) covalent geometry : angle 0.54368 (30497) hydrogen bonds : bond 0.04078 ( 1118) hydrogen bonds : angle 5.09233 ( 3195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 385 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7908 (tt0) cc_final: 0.7250 (tm-30) REVERT: A 163 MET cc_start: 0.6739 (mtm) cc_final: 0.6069 (mtm) REVERT: A 178 MET cc_start: 0.7118 (mpp) cc_final: 0.6873 (mpp) REVERT: A 196 ASP cc_start: 0.7962 (t0) cc_final: 0.7642 (t0) REVERT: A 225 GLU cc_start: 0.7898 (tt0) cc_final: 0.7036 (mp0) REVERT: A 289 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6704 (mtmm) REVERT: A 306 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7402 (mt0) REVERT: A 374 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6414 (tp30) REVERT: A 436 HIS cc_start: 0.5021 (m90) cc_final: 0.4800 (m90) REVERT: B 27 LYS cc_start: 0.8389 (mmtm) cc_final: 0.8185 (mptt) REVERT: B 38 LYS cc_start: 0.7573 (tmmm) cc_final: 0.7127 (mtmt) REVERT: B 133 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 272 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7651 (mmm160) REVERT: C 250 SER cc_start: 0.7234 (m) cc_final: 0.6979 (p) REVERT: C 256 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.5744 (t-100) REVERT: D 207 GLN cc_start: 0.7666 (tp40) cc_final: 0.6842 (mm110) REVERT: D 227 ASP cc_start: 0.8157 (t0) cc_final: 0.7847 (t0) REVERT: E 19 ASN cc_start: 0.5946 (m110) cc_final: 0.5691 (m110) REVERT: E 32 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6606 (mp10) REVERT: E 34 ARG cc_start: 0.7457 (ptp90) cc_final: 0.6326 (ptm160) REVERT: E 221 ARG cc_start: 0.6665 (mtp180) cc_final: 0.6255 (mtp-110) REVERT: F 293 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6847 (tt0) REVERT: F 461 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5593 (ptm160) REVERT: G 66 LEU cc_start: 0.8433 (tp) cc_final: 0.8217 (tp) REVERT: G 188 ASP cc_start: 0.7601 (m-30) cc_final: 0.7331 (m-30) REVERT: G 270 LEU cc_start: 0.6133 (tt) cc_final: 0.5569 (mp) REVERT: H 158 ASP cc_start: 0.7343 (p0) cc_final: 0.7122 (p0) REVERT: H 253 LYS cc_start: 0.8184 (tmtm) cc_final: 0.7956 (tptt) REVERT: H 320 LYS cc_start: 0.7199 (mmtm) cc_final: 0.6959 (mmtm) REVERT: H 375 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6892 (mt-10) outliers start: 78 outliers final: 47 residues processed: 437 average time/residue: 0.1608 time to fit residues: 109.4324 Evaluate side-chains 384 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 215 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN D 196 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN G 218 GLN G 321 GLN H 132 ASN H 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.179916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142248 restraints weight = 27601.061| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.25 r_work: 0.3696 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22393 Z= 0.154 Angle : 0.555 7.611 30497 Z= 0.294 Chirality : 0.041 0.161 3527 Planarity : 0.004 0.046 3643 Dihedral : 16.290 104.914 3508 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.19 % Allowed : 12.36 % Favored : 83.45 % 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 aren not related in a simple way. whole: 0.26 (0.17), residues: 2532 helix: 1.24 (0.15), residues: 1215 sheet: -0.78 (0.23), residues: 517 loop : -0.66 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 165 TYR 0.024 0.002 TYR A 67 PHE 0.015 0.002 PHE F 77 TRP 0.013 0.001 TRP H 42 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00357 (22393) covalent geometry : angle 0.55479 (30497) hydrogen bonds : bond 0.03980 ( 1118) hydrogen bonds : angle 4.86091 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7966 (tt0) cc_final: 0.7205 (tm-30) REVERT: A 163 MET cc_start: 0.6986 (mtm) cc_final: 0.6288 (mtm) REVERT: A 178 MET cc_start: 0.7320 (mpp) cc_final: 0.7015 (mpp) REVERT: A 196 ASP cc_start: 0.8025 (t0) cc_final: 0.7603 (t0) REVERT: A 223 ILE cc_start: 0.8685 (mt) cc_final: 0.8427 (mt) REVERT: A 225 GLU cc_start: 0.8020 (tt0) cc_final: 0.7059 (mp0) REVERT: A 289 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6818 (mtmm) REVERT: A 290 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8033 (pt0) REVERT: A 436 HIS cc_start: 0.5239 (m90) cc_final: 0.4663 (m90) REVERT: B 38 LYS cc_start: 0.7608 (tmmm) cc_final: 0.7025 (mtmt) REVERT: B 119 MET cc_start: 0.8823 (ttp) cc_final: 0.8582 (ttp) REVERT: B 133 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 272 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7777 (mmm160) REVERT: C 250 SER cc_start: 0.7268 (m) cc_final: 0.6870 (p) REVERT: D 207 GLN cc_start: 0.7898 (tp40) cc_final: 0.7350 (tp40) REVERT: D 353 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7605 (mp) REVERT: E 32 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6596 (mp10) REVERT: E 34 ARG cc_start: 0.7579 (ptp90) cc_final: 0.6440 (ptm160) REVERT: E 52 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5296 (mpt90) REVERT: E 210 ARG cc_start: 0.6286 (tpp80) cc_final: 0.5784 (mmt180) REVERT: E 221 ARG cc_start: 0.7008 (mtp180) cc_final: 0.6586 (mtp-110) REVERT: E 311 GLU cc_start: 0.7350 (mp0) cc_final: 0.7029 (tp30) REVERT: F 159 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7160 (m) REVERT: F 293 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7037 (tt0) REVERT: F 461 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5608 (ptm160) REVERT: F 472 LYS cc_start: 0.7396 (mtmm) cc_final: 0.7181 (mtmm) REVERT: G 9 ASN cc_start: 0.8529 (m-40) cc_final: 0.8304 (m-40) REVERT: G 66 LEU cc_start: 0.8551 (tp) cc_final: 0.8282 (tp) REVERT: G 96 MET cc_start: 0.7050 (tpt) cc_final: 0.6796 (tpt) REVERT: G 188 ASP cc_start: 0.7627 (m-30) cc_final: 0.7353 (m-30) REVERT: G 206 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8056 (tttm) REVERT: H 158 ASP cc_start: 0.7553 (p0) cc_final: 0.7289 (p0) REVERT: H 274 ASN cc_start: 0.7750 (t0) cc_final: 0.7517 (t0) REVERT: H 320 LYS cc_start: 0.7272 (mmtm) cc_final: 0.6941 (mmtm) REVERT: H 375 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 98 outliers final: 63 residues processed: 423 average time/residue: 0.1613 time to fit residues: 106.6142 Evaluate side-chains 386 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 47 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 224 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS H 27 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.176801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138838 restraints weight = 27816.257| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.28 r_work: 0.3651 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22393 Z= 0.172 Angle : 0.567 7.809 30497 Z= 0.300 Chirality : 0.042 0.162 3527 Planarity : 0.004 0.051 3643 Dihedral : 16.229 113.992 3504 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.79 % Allowed : 13.30 % Favored : 81.92 % 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 aren not related in a simple way. whole: 0.05 (0.17), residues: 2532 helix: 1.03 (0.15), residues: 1221 sheet: -0.88 (0.23), residues: 532 loop : -0.69 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 165 TYR 0.021 0.002 TYR A 67 PHE 0.029 0.002 PHE A 443 TRP 0.012 0.002 TRP F 415 HIS 0.010 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00405 (22393) covalent geometry : angle 0.56708 (30497) hydrogen bonds : bond 0.04011 ( 1118) hydrogen bonds : angle 4.79970 ( 3195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 337 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: A 150 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 163 MET cc_start: 0.7090 (mtm) cc_final: 0.6401 (mtm) REVERT: A 184 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 196 ASP cc_start: 0.7989 (t0) cc_final: 0.7556 (t0) REVERT: A 225 GLU cc_start: 0.8062 (tt0) cc_final: 0.7199 (mp0) REVERT: A 306 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7464 (mt0) REVERT: B 38 LYS cc_start: 0.7663 (tmmm) cc_final: 0.7017 (mtmt) REVERT: B 67 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6167 (mm) REVERT: B 129 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7431 (tpp80) REVERT: B 133 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7900 (mt) REVERT: B 272 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7743 (mmm160) REVERT: C 98 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7651 (ttpt) REVERT: C 250 SER cc_start: 0.7433 (m) cc_final: 0.6932 (p) REVERT: D 207 GLN cc_start: 0.7888 (tp40) cc_final: 0.7317 (tp40) REVERT: D 353 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7637 (mp) REVERT: E 32 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6683 (mt0) REVERT: E 34 ARG cc_start: 0.7729 (ptp90) cc_final: 0.6583 (ptm160) REVERT: E 52 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5089 (mpt90) REVERT: E 104 ASN cc_start: 0.6441 (p0) cc_final: 0.5906 (t0) REVERT: E 210 ARG cc_start: 0.6315 (tpp80) cc_final: 0.5906 (mmt180) REVERT: E 221 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6669 (mtm110) REVERT: E 311 GLU cc_start: 0.7362 (mp0) cc_final: 0.7047 (tp30) REVERT: F 162 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6464 (tm-30) REVERT: F 228 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5755 (tp) REVERT: F 293 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7065 (tt0) REVERT: F 461 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5377 (ptm160) REVERT: F 472 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7303 (mtmm) REVERT: G 9 ASN cc_start: 0.8617 (m-40) cc_final: 0.8326 (m-40) REVERT: G 168 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7705 (ttpt) REVERT: G 188 ASP cc_start: 0.7662 (m-30) cc_final: 0.7392 (m-30) REVERT: G 206 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8133 (tttm) REVERT: H 158 ASP cc_start: 0.7515 (p0) cc_final: 0.7277 (p0) REVERT: H 375 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7358 (mt-10) outliers start: 112 outliers final: 72 residues processed: 412 average time/residue: 0.1611 time to fit residues: 103.4901 Evaluate side-chains 397 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 315 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 260 ASN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.178730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140731 restraints weight = 27395.195| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.27 r_work: 0.3670 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22393 Z= 0.124 Angle : 0.528 7.747 30497 Z= 0.278 Chirality : 0.040 0.144 3527 Planarity : 0.004 0.047 3643 Dihedral : 16.121 118.383 3502 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.89 % Allowed : 15.13 % Favored : 80.97 % 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 aren not related in a simple way. whole: 0.20 (0.17), residues: 2532 helix: 1.17 (0.15), residues: 1218 sheet: -0.85 (0.23), residues: 532 loop : -0.64 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 450 TYR 0.021 0.001 TYR A 67 PHE 0.019 0.001 PHE A 279 TRP 0.010 0.001 TRP D 324 HIS 0.011 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00279 (22393) covalent geometry : angle 0.52762 (30497) hydrogen bonds : bond 0.03524 ( 1118) hydrogen bonds : angle 4.64348 ( 3195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 340 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7029 (mtm) cc_final: 0.6303 (mtm) REVERT: A 178 MET cc_start: 0.7064 (mpp) cc_final: 0.6779 (mpp) REVERT: A 184 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 196 ASP cc_start: 0.8005 (t0) cc_final: 0.7536 (t0) REVERT: A 225 GLU cc_start: 0.8093 (tt0) cc_final: 0.7256 (mp0) REVERT: A 306 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 13 GLU cc_start: 0.6615 (tp30) cc_final: 0.6268 (tp30) REVERT: B 38 LYS cc_start: 0.7641 (tmmm) cc_final: 0.7046 (mtmt) REVERT: B 129 ARG cc_start: 0.7850 (tpt170) cc_final: 0.7564 (tpp80) REVERT: B 182 GLU cc_start: 0.6782 (tp30) cc_final: 0.6002 (tm-30) REVERT: B 272 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7797 (mmm160) REVERT: C 98 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7738 (ttpt) REVERT: C 250 SER cc_start: 0.7362 (m) cc_final: 0.6924 (p) REVERT: D 207 GLN cc_start: 0.7885 (tp40) cc_final: 0.7340 (tp40) REVERT: E 32 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6618 (mt0) REVERT: E 34 ARG cc_start: 0.7764 (ptp90) cc_final: 0.5941 (ptm160) REVERT: E 104 ASN cc_start: 0.6575 (p0) cc_final: 0.6017 (t0) REVERT: E 135 TYR cc_start: 0.5402 (OUTLIER) cc_final: 0.4591 (m-80) REVERT: E 210 ARG cc_start: 0.6374 (tpp80) cc_final: 0.5962 (mmt180) REVERT: E 221 ARG cc_start: 0.7182 (mtp180) cc_final: 0.6552 (mtp-110) REVERT: E 311 GLU cc_start: 0.7331 (mp0) cc_final: 0.7072 (tp30) REVERT: F 162 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6584 (tm-30) REVERT: F 228 ILE cc_start: 0.5951 (OUTLIER) cc_final: 0.5682 (tp) REVERT: F 293 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7068 (tt0) REVERT: F 461 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5242 (ptm160) REVERT: G 9 ASN cc_start: 0.8665 (m-40) cc_final: 0.8374 (m-40) REVERT: G 168 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7782 (ttpt) REVERT: G 188 ASP cc_start: 0.7643 (m-30) cc_final: 0.7384 (m-30) REVERT: H 158 ASP cc_start: 0.7474 (p0) cc_final: 0.7221 (p0) REVERT: H 322 ILE cc_start: 0.8389 (tp) cc_final: 0.8065 (tt) REVERT: H 375 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7241 (mt-10) outliers start: 91 outliers final: 66 residues processed: 403 average time/residue: 0.1635 time to fit residues: 102.9228 Evaluate side-chains 392 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 321 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 2 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 260 ASN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141367 restraints weight = 27674.869| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.27 r_work: 0.3673 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22393 Z= 0.126 Angle : 0.527 7.784 30497 Z= 0.277 Chirality : 0.040 0.144 3527 Planarity : 0.004 0.077 3643 Dihedral : 16.058 122.861 3501 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.89 % Allowed : 15.90 % Favored : 80.21 % 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 aren not related in a simple way. whole: 0.27 (0.17), residues: 2532 helix: 1.23 (0.15), residues: 1215 sheet: -0.76 (0.23), residues: 527 loop : -0.62 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.020 0.001 TYR A 67 PHE 0.022 0.001 PHE A 279 TRP 0.011 0.001 TRP F 415 HIS 0.010 0.001 HIS F 203 Details of bonding type rmsd covalent geometry : bond 0.00286 (22393) covalent geometry : angle 0.52726 (30497) hydrogen bonds : bond 0.03469 ( 1118) hydrogen bonds : angle 4.58579 ( 3195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 342 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7020 (mtm) cc_final: 0.6396 (ttp) REVERT: A 164 GLU cc_start: 0.7214 (mp0) cc_final: 0.6965 (tp30) REVERT: A 178 MET cc_start: 0.7166 (mpp) cc_final: 0.6830 (mpp) REVERT: A 184 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 196 ASP cc_start: 0.7990 (t0) cc_final: 0.7655 (t0) REVERT: A 306 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7527 (mt0) REVERT: B 38 LYS cc_start: 0.7595 (tmmm) cc_final: 0.7006 (mtmt) REVERT: B 67 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6181 (mm) REVERT: B 129 ARG cc_start: 0.7821 (tpt170) cc_final: 0.7488 (tpp80) REVERT: B 182 GLU cc_start: 0.6750 (tp30) cc_final: 0.5964 (tm-30) REVERT: B 272 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7703 (mmm160) REVERT: C 98 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7668 (ttpt) REVERT: C 250 SER cc_start: 0.7349 (m) cc_final: 0.6857 (p) REVERT: D 207 GLN cc_start: 0.7870 (tp40) cc_final: 0.7311 (tp40) REVERT: D 353 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7569 (mp) REVERT: E 32 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6457 (mt0) REVERT: E 34 ARG cc_start: 0.7739 (ptp90) cc_final: 0.5904 (ptm160) REVERT: E 104 ASN cc_start: 0.6485 (p0) cc_final: 0.5864 (t0) REVERT: E 135 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4561 (m-80) REVERT: E 210 ARG cc_start: 0.6415 (tpp80) cc_final: 0.5970 (mmt180) REVERT: E 221 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6647 (mtp-110) REVERT: E 311 GLU cc_start: 0.7405 (mp0) cc_final: 0.7059 (tp30) REVERT: F 119 MET cc_start: 0.5757 (tmm) cc_final: 0.5447 (tmm) REVERT: F 162 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6398 (tm-30) REVERT: F 228 ILE cc_start: 0.5932 (OUTLIER) cc_final: 0.5624 (tp) REVERT: F 246 PHE cc_start: 0.7147 (t80) cc_final: 0.6710 (t80) REVERT: F 293 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7077 (tt0) REVERT: F 461 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.5150 (ptm160) REVERT: F 472 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7722 (mtmm) REVERT: G 9 ASN cc_start: 0.8637 (m-40) cc_final: 0.8307 (m-40) REVERT: G 168 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7703 (ttpt) REVERT: G 188 ASP cc_start: 0.7710 (m-30) cc_final: 0.7453 (m-30) REVERT: G 223 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7441 (p0) REVERT: H 158 ASP cc_start: 0.7490 (p0) cc_final: 0.7231 (p0) REVERT: H 322 ILE cc_start: 0.8424 (tp) cc_final: 0.8056 (tt) REVERT: H 375 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7295 (mt-10) outliers start: 91 outliers final: 62 residues processed: 407 average time/residue: 0.1648 time to fit residues: 104.5149 Evaluate side-chains 389 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 237 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN H 295 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.180007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143039 restraints weight = 27525.482| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.32 r_work: 0.3676 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22393 Z= 0.115 Angle : 0.523 7.970 30497 Z= 0.276 Chirality : 0.040 0.143 3527 Planarity : 0.004 0.044 3643 Dihedral : 15.969 125.427 3498 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.98 % Allowed : 16.12 % Favored : 79.91 % 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 aren not related in a simple way. whole: 0.37 (0.17), residues: 2532 helix: 1.29 (0.15), residues: 1219 sheet: -0.68 (0.23), residues: 531 loop : -0.57 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.019 0.001 TYR A 67 PHE 0.018 0.001 PHE A 279 TRP 0.012 0.001 TRP F 415 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00255 (22393) covalent geometry : angle 0.52288 (30497) hydrogen bonds : bond 0.03290 ( 1118) hydrogen bonds : angle 4.48834 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 344 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6797 (mtm) cc_final: 0.6277 (ttp) REVERT: A 178 MET cc_start: 0.7007 (mpp) cc_final: 0.6705 (mpp) REVERT: A 184 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 196 ASP cc_start: 0.7937 (t0) cc_final: 0.7665 (t0) REVERT: A 250 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6654 (mmt) REVERT: A 306 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7550 (mt0) REVERT: B 38 LYS cc_start: 0.7647 (tmmm) cc_final: 0.7076 (mtmt) REVERT: B 67 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6118 (mm) REVERT: B 129 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7349 (tpp80) REVERT: B 182 GLU cc_start: 0.6539 (tp30) cc_final: 0.5915 (tm-30) REVERT: B 272 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7690 (mmm160) REVERT: C 98 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7677 (ttpt) REVERT: C 250 SER cc_start: 0.7186 (m) cc_final: 0.6787 (p) REVERT: D 207 GLN cc_start: 0.7668 (tp40) cc_final: 0.7179 (tp40) REVERT: D 318 PHE cc_start: 0.7013 (t80) cc_final: 0.6787 (t80) REVERT: E 32 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6106 (mt0) REVERT: E 34 ARG cc_start: 0.7638 (ptp90) cc_final: 0.5923 (ptm160) REVERT: E 104 ASN cc_start: 0.6607 (p0) cc_final: 0.5867 (t0) REVERT: E 135 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.4364 (m-80) REVERT: E 210 ARG cc_start: 0.6263 (tpp80) cc_final: 0.5868 (mmt180) REVERT: E 221 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6462 (mtp-110) REVERT: F 119 MET cc_start: 0.5753 (tmm) cc_final: 0.5471 (tmm) REVERT: F 162 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6323 (tm-30) REVERT: F 228 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5629 (tp) REVERT: F 246 PHE cc_start: 0.7054 (t80) cc_final: 0.6659 (t80) REVERT: F 293 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6978 (tt0) REVERT: F 413 LYS cc_start: 0.7850 (mptt) cc_final: 0.7611 (mtpp) REVERT: F 461 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5013 (ptm160) REVERT: F 472 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7724 (mtmm) REVERT: G 9 ASN cc_start: 0.8621 (m-40) cc_final: 0.8280 (m-40) REVERT: G 168 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7681 (ttpt) REVERT: G 188 ASP cc_start: 0.7693 (m-30) cc_final: 0.7452 (m-30) REVERT: G 223 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7448 (p0) REVERT: H 158 ASP cc_start: 0.7297 (p0) cc_final: 0.7050 (p0) REVERT: H 322 ILE cc_start: 0.8313 (tp) cc_final: 0.7977 (tt) REVERT: H 375 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7053 (mt-10) outliers start: 93 outliers final: 64 residues processed: 407 average time/residue: 0.1587 time to fit residues: 101.5863 Evaluate side-chains 399 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 148 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN E 19 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140736 restraints weight = 27661.579| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.27 r_work: 0.3651 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22393 Z= 0.139 Angle : 0.545 8.260 30497 Z= 0.287 Chirality : 0.041 0.141 3527 Planarity : 0.004 0.045 3643 Dihedral : 15.941 126.954 3496 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.76 % Allowed : 16.59 % Favored : 79.65 % 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 aren not related in a simple way. whole: 0.31 (0.17), residues: 2532 helix: 1.24 (0.15), residues: 1213 sheet: -0.68 (0.23), residues: 531 loop : -0.62 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.017 0.001 TYR D 83 PHE 0.021 0.002 PHE F 77 TRP 0.013 0.001 TRP F 69 HIS 0.006 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00323 (22393) covalent geometry : angle 0.54476 (30497) hydrogen bonds : bond 0.03512 ( 1118) hydrogen bonds : angle 4.50565 ( 3195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 334 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6762 (mtm) cc_final: 0.6398 (ttp) REVERT: A 184 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 196 ASP cc_start: 0.7978 (t0) cc_final: 0.7700 (t0) REVERT: A 250 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6517 (mmt) REVERT: A 252 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7639 (mmtp) REVERT: A 306 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7449 (mt0) REVERT: A 307 GLU cc_start: 0.7128 (tp30) cc_final: 0.6914 (tp30) REVERT: B 38 LYS cc_start: 0.7597 (tmmm) cc_final: 0.7035 (mtmt) REVERT: B 67 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6195 (mm) REVERT: B 129 ARG cc_start: 0.7663 (tpt170) cc_final: 0.7343 (tpp80) REVERT: B 272 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7677 (mmm160) REVERT: B 321 ASN cc_start: 0.7595 (m110) cc_final: 0.7261 (m-40) REVERT: C 98 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7655 (ttpt) REVERT: C 250 SER cc_start: 0.7266 (m) cc_final: 0.6789 (p) REVERT: D 51 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8350 (mmtt) REVERT: D 207 GLN cc_start: 0.7747 (tp40) cc_final: 0.7232 (tp40) REVERT: D 318 PHE cc_start: 0.7071 (t80) cc_final: 0.6792 (t80) REVERT: D 353 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7387 (mp) REVERT: E 32 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6274 (mt0) REVERT: E 34 ARG cc_start: 0.7678 (ptp90) cc_final: 0.5999 (ptm160) REVERT: E 82 LYS cc_start: 0.6229 (ptmm) cc_final: 0.5785 (ttpp) REVERT: E 104 ASN cc_start: 0.6581 (p0) cc_final: 0.5888 (t0) REVERT: E 135 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4422 (m-80) REVERT: E 197 GLU cc_start: 0.6358 (mt-10) cc_final: 0.6078 (mp0) REVERT: E 221 ARG cc_start: 0.7060 (mtp180) cc_final: 0.6464 (mtp-110) REVERT: F 119 MET cc_start: 0.5742 (tmm) cc_final: 0.5378 (tmm) REVERT: F 162 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6304 (tm-30) REVERT: F 228 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5589 (tp) REVERT: F 246 PHE cc_start: 0.7109 (t80) cc_final: 0.6716 (t80) REVERT: F 293 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6996 (tt0) REVERT: F 461 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.4899 (ptm160) REVERT: F 472 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7660 (mtmm) REVERT: G 9 ASN cc_start: 0.8616 (m-40) cc_final: 0.8282 (m-40) REVERT: G 168 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7614 (ttpt) REVERT: G 188 ASP cc_start: 0.7695 (m-30) cc_final: 0.7452 (m-30) REVERT: G 223 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7440 (p0) REVERT: H 158 ASP cc_start: 0.7342 (p0) cc_final: 0.7086 (p0) REVERT: H 322 ILE cc_start: 0.8342 (tp) cc_final: 0.7997 (tt) REVERT: H 375 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7108 (mt-10) outliers start: 88 outliers final: 68 residues processed: 391 average time/residue: 0.1600 time to fit residues: 98.1075 Evaluate side-chains 400 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 323 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 ASN E 224 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 HIS ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141101 restraints weight = 27658.121| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.27 r_work: 0.3666 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22393 Z= 0.128 Angle : 0.545 12.398 30497 Z= 0.284 Chirality : 0.040 0.150 3527 Planarity : 0.004 0.045 3643 Dihedral : 15.922 127.380 3496 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.51 % Allowed : 16.80 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2532 helix: 1.24 (0.15), residues: 1218 sheet: -0.65 (0.23), residues: 531 loop : -0.64 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 450 TYR 0.023 0.001 TYR A 67 PHE 0.016 0.001 PHE H 240 TRP 0.014 0.001 TRP F 69 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00294 (22393) covalent geometry : angle 0.54499 (30497) hydrogen bonds : bond 0.03404 ( 1118) hydrogen bonds : angle 4.46313 ( 3195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 327 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6624 (mtm) cc_final: 0.6221 (ttp) REVERT: A 184 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 196 ASP cc_start: 0.7964 (t0) cc_final: 0.7670 (t0) REVERT: A 250 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6377 (mmt) REVERT: A 252 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7652 (mmtp) REVERT: A 306 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7459 (mt0) REVERT: A 307 GLU cc_start: 0.7089 (tp30) cc_final: 0.6888 (tp30) REVERT: B 27 LYS cc_start: 0.8296 (mptt) cc_final: 0.8034 (mptt) REVERT: B 38 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7014 (mtmt) REVERT: B 67 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6204 (mm) REVERT: B 129 ARG cc_start: 0.7658 (tpt170) cc_final: 0.7346 (tpp80) REVERT: B 272 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7602 (mmm160) REVERT: C 98 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7637 (ttpt) REVERT: C 250 SER cc_start: 0.7244 (m) cc_final: 0.6786 (p) REVERT: D 207 GLN cc_start: 0.7704 (tp40) cc_final: 0.7199 (tp40) REVERT: D 252 THR cc_start: 0.8059 (p) cc_final: 0.7748 (m) REVERT: D 318 PHE cc_start: 0.7048 (t80) cc_final: 0.6829 (t80) REVERT: D 353 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7392 (mp) REVERT: E 32 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6256 (mt0) REVERT: E 34 ARG cc_start: 0.7657 (ptp90) cc_final: 0.5952 (ptm160) REVERT: E 82 LYS cc_start: 0.6223 (ptmm) cc_final: 0.5768 (ttpp) REVERT: E 104 ASN cc_start: 0.6623 (p0) cc_final: 0.5931 (t0) REVERT: E 135 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4390 (m-80) REVERT: E 221 ARG cc_start: 0.7028 (mtp180) cc_final: 0.6546 (mtp-110) REVERT: F 118 ASN cc_start: 0.7357 (p0) cc_final: 0.7155 (p0) REVERT: F 119 MET cc_start: 0.5692 (tmm) cc_final: 0.5475 (tmm) REVERT: F 162 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6334 (tm-30) REVERT: F 228 ILE cc_start: 0.6017 (OUTLIER) cc_final: 0.5607 (tp) REVERT: F 246 PHE cc_start: 0.7079 (t80) cc_final: 0.6660 (t80) REVERT: F 293 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6951 (tt0) REVERT: F 413 LYS cc_start: 0.7826 (mptt) cc_final: 0.7590 (mtpp) REVERT: F 461 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.4872 (ptm160) REVERT: F 472 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7691 (mtmm) REVERT: G 9 ASN cc_start: 0.8609 (m-40) cc_final: 0.8271 (m-40) REVERT: G 168 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7616 (ttpt) REVERT: G 188 ASP cc_start: 0.7819 (m-30) cc_final: 0.7597 (m-30) REVERT: G 223 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7437 (p0) REVERT: H 158 ASP cc_start: 0.7300 (p0) cc_final: 0.7066 (p0) REVERT: H 322 ILE cc_start: 0.8331 (tp) cc_final: 0.7980 (tt) REVERT: H 375 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7114 (mt-10) outliers start: 82 outliers final: 64 residues processed: 378 average time/residue: 0.1627 time to fit residues: 96.0690 Evaluate side-chains 394 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 320 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 202 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 176 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 chunk 220 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 HIS H 122 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.178990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139776 restraints weight = 27695.276| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.32 r_work: 0.3676 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22393 Z= 0.122 Angle : 0.541 13.023 30497 Z= 0.281 Chirality : 0.040 0.149 3527 Planarity : 0.004 0.045 3643 Dihedral : 15.899 128.388 3496 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.33 % Allowed : 17.02 % Favored : 79.65 % 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 aren not related in a simple way. whole: 0.40 (0.17), residues: 2532 helix: 1.32 (0.15), residues: 1210 sheet: -0.63 (0.23), residues: 531 loop : -0.58 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 450 TYR 0.022 0.001 TYR A 67 PHE 0.020 0.001 PHE H 240 TRP 0.016 0.001 TRP F 69 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00276 (22393) covalent geometry : angle 0.54068 (30497) hydrogen bonds : bond 0.03306 ( 1118) hydrogen bonds : angle 4.41259 ( 3195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 326 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6579 (mtm) cc_final: 0.6125 (ttp) REVERT: A 175 TYR cc_start: 0.7781 (m-80) cc_final: 0.7223 (m-80) REVERT: A 184 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 196 ASP cc_start: 0.7944 (t0) cc_final: 0.7641 (t0) REVERT: A 250 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6404 (mmt) REVERT: A 252 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7726 (mmtp) REVERT: A 289 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6800 (mttp) REVERT: A 306 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7479 (mt0) REVERT: B 27 LYS cc_start: 0.8315 (mptt) cc_final: 0.8033 (mptt) REVERT: B 38 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7023 (mtmt) REVERT: B 67 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6183 (mm) REVERT: B 129 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7302 (tpp80) REVERT: B 272 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7623 (mmm160) REVERT: C 74 ASN cc_start: 0.7924 (m110) cc_final: 0.7721 (m110) REVERT: C 98 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7596 (ttpt) REVERT: C 250 SER cc_start: 0.7239 (m) cc_final: 0.6781 (p) REVERT: D 207 GLN cc_start: 0.7715 (tp40) cc_final: 0.7200 (tp40) REVERT: D 252 THR cc_start: 0.8013 (p) cc_final: 0.7703 (m) REVERT: D 318 PHE cc_start: 0.7030 (t80) cc_final: 0.6785 (t80) REVERT: D 353 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7337 (mp) REVERT: E 32 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6369 (mp10) REVERT: E 34 ARG cc_start: 0.7689 (ptp90) cc_final: 0.5979 (ptm160) REVERT: E 82 LYS cc_start: 0.6183 (ptmm) cc_final: 0.5748 (ttpp) REVERT: E 104 ASN cc_start: 0.6630 (p0) cc_final: 0.5935 (t0) REVERT: E 135 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4344 (m-80) REVERT: E 221 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6441 (mtp-110) REVERT: F 40 GLU cc_start: 0.5322 (pm20) cc_final: 0.4712 (mp0) REVERT: F 118 ASN cc_start: 0.7354 (p0) cc_final: 0.7122 (p0) REVERT: F 119 MET cc_start: 0.5681 (tmm) cc_final: 0.5457 (tmm) REVERT: F 162 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6269 (tm-30) REVERT: F 228 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5624 (tp) REVERT: F 246 PHE cc_start: 0.7070 (t80) cc_final: 0.6662 (t80) REVERT: F 293 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6947 (tt0) REVERT: F 413 LYS cc_start: 0.7853 (mptt) cc_final: 0.7605 (mtpp) REVERT: F 461 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.4894 (ptt180) REVERT: F 472 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7658 (mtmm) REVERT: G 9 ASN cc_start: 0.8584 (m-40) cc_final: 0.8245 (m-40) REVERT: G 168 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7573 (ttpt) REVERT: G 188 ASP cc_start: 0.7877 (m-30) cc_final: 0.7674 (m-30) REVERT: G 206 LYS cc_start: 0.7954 (tttm) cc_final: 0.7719 (pttm) REVERT: G 223 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7433 (p0) REVERT: H 158 ASP cc_start: 0.7265 (p0) cc_final: 0.7045 (p0) REVERT: H 322 ILE cc_start: 0.8335 (tp) cc_final: 0.7975 (tt) REVERT: H 352 TRP cc_start: 0.7952 (m-90) cc_final: 0.7599 (m-90) REVERT: H 375 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7096 (mt-10) outliers start: 78 outliers final: 62 residues processed: 379 average time/residue: 0.1613 time to fit residues: 95.7953 Evaluate side-chains 388 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 HIS ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141368 restraints weight = 27718.235| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.31 r_work: 0.3665 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22393 Z= 0.128 Angle : 0.551 12.931 30497 Z= 0.286 Chirality : 0.040 0.150 3527 Planarity : 0.004 0.045 3643 Dihedral : 15.883 128.765 3494 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.46 % Allowed : 16.97 % Favored : 79.56 % 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 aren not related in a simple way. whole: 0.36 (0.17), residues: 2532 helix: 1.27 (0.15), residues: 1217 sheet: -0.63 (0.23), residues: 530 loop : -0.61 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.023 0.001 TYR A 67 PHE 0.033 0.001 PHE H 240 TRP 0.020 0.001 TRP F 69 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00295 (22393) covalent geometry : angle 0.55119 (30497) hydrogen bonds : bond 0.03359 ( 1118) hydrogen bonds : angle 4.42529 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6044.33 seconds wall clock time: 104 minutes 50.77 seconds (6290.77 seconds total)