Starting phenix.real_space_refine on Sat Aug 23 18:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t42_41018/08_2025/8t42_41018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t42_41018/08_2025/8t42_41018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t42_41018/08_2025/8t42_41018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t42_41018/08_2025/8t42_41018.map" model { file = "/net/cci-nas-00/data/ceres_data/8t42_41018/08_2025/8t42_41018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t42_41018/08_2025/8t42_41018.cif" } resolution = 3.6 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= 0.016 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 12 5.49 5 Mg 4 5.21 5 S 94 5.16 5 C 8703 2.51 5 N 2363 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s 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: 13854 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3348 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3371 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "F" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3401 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Chain: "N" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 208 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.26, per 1000 atoms: 0.24 Number of scatterers: 13854 At special positions: 0 Unit cell: (74.75, 85.1, 196.65, 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 94 16.00 P 12 15.00 Mg 4 11.99 O 2678 8.00 N 2363 7.00 C 8703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 640.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 52.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.579A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 4.341A pdb=" N PHE A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.794A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.523A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.017A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.787A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.632A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.975A pdb=" N PHE A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.053A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.511A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.942A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.484A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.881A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.359A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.370A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 removed outlier: 3.518A pdb=" N GLY B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 127 removed outlier: 4.442A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.557A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 4.254A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.693A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.650A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.587A pdb=" N ASP B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.637A pdb=" N HIS B 307 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.371A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 4.196A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.625A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 46 through 49 removed outlier: 3.581A pdb=" N VAL E 49 " --> pdb=" O ARG E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 69 through 78 removed outlier: 4.668A pdb=" N MET E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 108 through 127 removed outlier: 4.042A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 159 removed outlier: 4.553A pdb=" N MET E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 removed outlier: 3.515A pdb=" N ASN E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.974A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR E 237 " --> pdb=" O MET E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.898A pdb=" N ARG E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.804A pdb=" N PHE E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 299 removed outlier: 4.033A pdb=" N MET E 299 " --> pdb=" O ALA E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 374 through 388 removed outlier: 3.616A pdb=" N ILE E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 400 removed outlier: 3.905A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY E 400 " --> pdb=" O HIS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 426 removed outlier: 4.029A pdb=" N PHE E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 45 through 51 removed outlier: 4.417A pdb=" N PHE F 49 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR F 51 " --> pdb=" O SER F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.353A pdb=" N ILE F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.582A pdb=" N ASP F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 removed outlier: 4.410A pdb=" N THR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 190 through 197 removed outlier: 3.709A pdb=" N HIS F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 239 Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.838A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.595A pdb=" N PHE F 296 " --> pdb=" O THR F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 337 removed outlier: 3.515A pdb=" N VAL F 328 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 400 removed outlier: 4.109A pdb=" N ALA F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 removed outlier: 3.611A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 436 removed outlier: 4.353A pdb=" N SER F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 436 " --> pdb=" O TYR F 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 480 through 499 removed outlier: 3.748A pdb=" N GLN N 489 " --> pdb=" O GLN N 485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.871A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.697A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.084A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 198 " --> pdb=" O MET B 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 271 removed outlier: 4.078A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 92 removed outlier: 8.013A pdb=" N VAL E 91 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 65 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU E 3 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE E 133 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL E 5 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU E 135 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE E 7 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 198 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR E 199 " --> pdb=" O PHE E 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 68 removed outlier: 8.662A pdb=" N VAL F 66 " --> pdb=" O CYS F 4 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER F 6 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL F 68 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER F 140 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE F 135 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 171 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N HIS F 139 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS F 200 " --> pdb=" O LYS F 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'F' and resid 269 through 273 658 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2642 1.33 - 1.46: 4025 1.46 - 1.59: 7326 1.59 - 1.71: 18 1.71 - 1.84: 152 Bond restraints: 14163 Sorted by residual: bond pdb=" C ILE F 171 " pdb=" N TYR F 172 " ideal model delta sigma weight residual 1.331 1.275 0.056 2.07e-02 2.33e+03 7.42e+00 bond pdb=" CB ILE A 7 " pdb=" CG2 ILE A 7 " ideal model delta sigma weight residual 1.521 1.608 -0.087 3.30e-02 9.18e+02 7.00e+00 bond pdb=" CG LYS B 324 " pdb=" CD LYS B 324 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.64e+00 bond pdb=" C ARG A 221 " pdb=" N PRO A 222 " ideal model delta sigma weight residual 1.334 1.393 -0.060 2.34e-02 1.83e+03 6.48e+00 bond pdb=" C ARG F 221 " pdb=" N PRO F 222 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.99e+00 ... (remaining 14158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 18583 2.74 - 5.47: 527 5.47 - 8.21: 107 8.21 - 10.94: 16 10.94 - 13.68: 4 Bond angle restraints: 19237 Sorted by residual: angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 104.43 7.57 1.40e+00 5.10e-01 2.92e+01 angle pdb=" CB ARG F 221 " pdb=" CG ARG F 221 " pdb=" CD ARG F 221 " ideal model delta sigma weight residual 111.30 122.78 -11.48 2.30e+00 1.89e-01 2.49e+01 angle pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " pdb=" CD GLU B 108 " ideal model delta sigma weight residual 112.60 121.00 -8.40 1.70e+00 3.46e-01 2.44e+01 angle pdb=" CA GLN E 291 " pdb=" CB GLN E 291 " pdb=" CG GLN E 291 " ideal model delta sigma weight residual 114.10 123.33 -9.23 2.00e+00 2.50e-01 2.13e+01 angle pdb=" CB MET F 36 " pdb=" CG MET F 36 " pdb=" SD MET F 36 " ideal model delta sigma weight residual 112.70 126.38 -13.68 3.00e+00 1.11e-01 2.08e+01 ... (remaining 19232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 8179 32.81 - 65.62: 259 65.62 - 98.43: 14 98.43 - 131.23: 0 131.23 - 164.04: 4 Dihedral angle restraints: 8456 sinusoidal: 3404 harmonic: 5052 Sorted by residual: dihedral pdb=" C8 GTP F 501 " pdb=" C1' GTP F 501 " pdb=" N9 GTP F 501 " pdb=" O4' GTP F 501 " ideal model delta sinusoidal sigma weight residual 104.59 -59.45 164.04 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -137.13 -153.60 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" CA SER B 322 " pdb=" C SER B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual -180.00 -147.63 -32.37 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 8453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1690 0.064 - 0.128: 360 0.128 - 0.192: 50 0.192 - 0.256: 5 0.256 - 0.320: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CB ILE A 7 " pdb=" CA ILE A 7 " pdb=" CG1 ILE A 7 " pdb=" CG2 ILE A 7 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB THR A 239 " pdb=" CA THR A 239 " pdb=" OG1 THR A 239 " pdb=" CG2 THR A 239 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLN B 329 " pdb=" N GLN B 329 " pdb=" C GLN B 329 " pdb=" CB GLN B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2103 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 297 " -0.093 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO A 298 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 121 " 0.339 9.50e-02 1.11e+02 1.52e-01 1.55e+01 pdb=" NE ARG B 121 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 121 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 121 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 221 " -0.326 9.50e-02 1.11e+02 1.46e-01 1.33e+01 pdb=" NE ARG A 221 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 221 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 221 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 221 " -0.009 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 145 2.58 - 3.16: 11652 3.16 - 3.74: 22616 3.74 - 4.32: 30765 4.32 - 4.90: 51225 Nonbonded interactions: 116403 Sorted by model distance: nonbonded pdb=" O3G G2P E 501 " pdb="MG MG E 502 " model vdw 1.998 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 1.999 2.170 nonbonded pdb=" O1G GTP F 501 " pdb="MG MG F 502 " model vdw 2.006 2.170 nonbonded pdb=" O3G G2P B 501 " pdb="MG MG B 502 " model vdw 2.015 2.170 nonbonded pdb=" OE1 GLU F 71 " pdb="MG MG F 502 " model vdw 2.024 2.170 ... (remaining 116398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 44 or resid 46 through 502)) selection = (chain 'F' and (resid 1 through 325 or (resid 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 through 439 or resid 501 through 502)) } ncs_group { reference = chain 'B' selection = (chain 'E' and (resid 1 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB )) or resid 391 through 427 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 : 0.007 0.087 14163 Z= 0.290 Angle : 1.110 13.675 19237 Z= 0.581 Chirality : 0.054 0.320 2106 Planarity : 0.009 0.152 2502 Dihedral : 16.003 164.042 5218 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.13 % Allowed : 14.40 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.35 (0.19), residues: 1738 helix: 0.12 (0.17), residues: 750 sheet: -2.25 (0.27), residues: 277 loop : -1.29 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG F 214 TYR 0.044 0.002 TYR B 159 PHE 0.020 0.002 PHE F 149 TRP 0.048 0.002 TRP A 407 HIS 0.039 0.003 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00685 (14163) covalent geometry : angle 1.10957 (19237) hydrogen bonds : bond 0.17012 ( 658) hydrogen bonds : angle 6.76064 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 565 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.6888 (mp0) cc_final: 0.6549 (mp0) REVERT: A 8 HIS cc_start: 0.7666 (m-70) cc_final: 0.7381 (m170) REVERT: A 26 LEU cc_start: 0.8267 (mp) cc_final: 0.8051 (mt) REVERT: A 47 ASP cc_start: 0.7806 (p0) cc_final: 0.7424 (p0) REVERT: A 91 GLN cc_start: 0.7981 (pt0) cc_final: 0.7696 (pt0) REVERT: A 154 MET cc_start: 0.7926 (mmm) cc_final: 0.7573 (mmm) REVERT: A 166 LYS cc_start: 0.7372 (mtmm) cc_final: 0.7097 (mttp) REVERT: A 181 VAL cc_start: 0.8509 (m) cc_final: 0.8308 (p) REVERT: A 187 SER cc_start: 0.8149 (m) cc_final: 0.7797 (p) REVERT: A 203 MET cc_start: 0.7412 (mmp) cc_final: 0.7067 (mmp) REVERT: A 215 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6898 (mtt180) REVERT: A 237 SER cc_start: 0.8445 (m) cc_final: 0.8069 (p) REVERT: A 243 ARG cc_start: 0.8281 (ptt90) cc_final: 0.8040 (ptt180) REVERT: A 254 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 259 LEU cc_start: 0.7732 (tp) cc_final: 0.7518 (mp) REVERT: A 276 ILE cc_start: 0.8579 (tp) cc_final: 0.8177 (tp) REVERT: A 284 GLU cc_start: 0.7794 (tt0) cc_final: 0.7299 (tt0) REVERT: A 290 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 304 LYS cc_start: 0.8316 (tppt) cc_final: 0.8094 (tppt) REVERT: A 309 HIS cc_start: 0.6596 (m-70) cc_final: 0.6189 (m-70) REVERT: A 311 LYS cc_start: 0.8277 (mttp) cc_final: 0.7792 (mtpp) REVERT: A 312 TYR cc_start: 0.7479 (m-80) cc_final: 0.7183 (m-80) REVERT: A 376 CYS cc_start: 0.8033 (t) cc_final: 0.7485 (t) REVERT: A 391 LEU cc_start: 0.7596 (mm) cc_final: 0.7385 (mt) REVERT: A 405 VAL cc_start: 0.7851 (m) cc_final: 0.7622 (t) REVERT: A 433 GLU cc_start: 0.7315 (tp30) cc_final: 0.7040 (pt0) REVERT: B 35 THR cc_start: 0.8342 (p) cc_final: 0.8114 (p) REVERT: B 44 LEU cc_start: 0.8499 (mt) cc_final: 0.8269 (mt) REVERT: B 53 GLU cc_start: 0.6489 (tp30) cc_final: 0.6180 (tp30) REVERT: B 74 ASP cc_start: 0.7173 (m-30) cc_final: 0.6972 (m-30) REVERT: B 86 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6276 (mmp80) REVERT: B 99 ASN cc_start: 0.7631 (m-40) cc_final: 0.7181 (m-40) REVERT: B 122 LYS cc_start: 0.7538 (tttt) cc_final: 0.7250 (tmtt) REVERT: B 209 ASP cc_start: 0.7650 (t70) cc_final: 0.7075 (t0) REVERT: B 221 THR cc_start: 0.8287 (t) cc_final: 0.8074 (p) REVERT: B 247 ASN cc_start: 0.7947 (m110) cc_final: 0.7707 (m-40) REVERT: B 280 GLN cc_start: 0.7487 (mt0) cc_final: 0.6995 (mt0) REVERT: B 298 ASN cc_start: 0.6609 (t0) cc_final: 0.6339 (t0) REVERT: B 318 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7423 (mtp-110) REVERT: B 362 LYS cc_start: 0.8378 (tttt) cc_final: 0.8150 (tttt) REVERT: B 381 ILE cc_start: 0.7763 (mm) cc_final: 0.7538 (tt) REVERT: B 415 MET cc_start: 0.7867 (mmm) cc_final: 0.7287 (tpt) REVERT: E 1 MET cc_start: 0.6013 (ptm) cc_final: 0.5674 (ptm) REVERT: E 3 GLU cc_start: 0.6937 (mp0) cc_final: 0.6097 (mp0) REVERT: E 35 THR cc_start: 0.8128 (p) cc_final: 0.7829 (p) REVERT: E 51 TYR cc_start: 0.8076 (m-80) cc_final: 0.7803 (m-80) REVERT: E 59 TYR cc_start: 0.8187 (m-80) cc_final: 0.7562 (m-80) REVERT: E 65 LEU cc_start: 0.8376 (mp) cc_final: 0.8113 (mt) REVERT: E 69 GLU cc_start: 0.6656 (tt0) cc_final: 0.6313 (tt0) REVERT: E 86 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6062 (tpm170) REVERT: E 137 HIS cc_start: 0.7533 (p90) cc_final: 0.7314 (p90) REVERT: E 154 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7363 (mmtm) REVERT: E 164 MET cc_start: 0.5874 (mpp) cc_final: 0.5524 (mpp) REVERT: E 174 LYS cc_start: 0.8049 (mptt) cc_final: 0.7694 (mptt) REVERT: E 175 VAL cc_start: 0.7853 (m) cc_final: 0.7266 (t) REVERT: E 203 ASP cc_start: 0.7432 (t0) cc_final: 0.7158 (t0) REVERT: E 209 ASP cc_start: 0.7414 (t0) cc_final: 0.5367 (t0) REVERT: E 213 ARG cc_start: 0.6519 (mtm180) cc_final: 0.6009 (mtm180) REVERT: E 216 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7863 (mmtt) REVERT: E 265 PHE cc_start: 0.8046 (m-80) cc_final: 0.7839 (m-80) REVERT: E 279 GLN cc_start: 0.7891 (pt0) cc_final: 0.7500 (pt0) REVERT: E 280 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7716 (mm-40) REVERT: E 284 LEU cc_start: 0.8644 (tp) cc_final: 0.8286 (tt) REVERT: E 288 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6302 (tm-30) REVERT: E 299 MET cc_start: 0.6110 (mmm) cc_final: 0.5655 (mmm) REVERT: E 338 SER cc_start: 0.8195 (t) cc_final: 0.7821 (p) REVERT: E 385 PHE cc_start: 0.7761 (t80) cc_final: 0.7546 (t80) REVERT: E 394 PHE cc_start: 0.8003 (m-80) cc_final: 0.7572 (m-80) REVERT: E 405 GLU cc_start: 0.7140 (tt0) cc_final: 0.6480 (mt-10) REVERT: E 413 SER cc_start: 0.8074 (m) cc_final: 0.7508 (p) REVERT: F 3 GLU cc_start: 0.6198 (mp0) cc_final: 0.5984 (mp0) REVERT: F 18 ASN cc_start: 0.7413 (m-40) cc_final: 0.7187 (m-40) REVERT: F 24 TYR cc_start: 0.7817 (m-10) cc_final: 0.7583 (m-10) REVERT: F 49 PHE cc_start: 0.7365 (p90) cc_final: 0.7105 (p90) REVERT: F 67 PHE cc_start: 0.7778 (m-80) cc_final: 0.7553 (m-10) REVERT: F 70 LEU cc_start: 0.7252 (mm) cc_final: 0.7041 (mt) REVERT: F 129 CYS cc_start: 0.7556 (m) cc_final: 0.7124 (m) REVERT: F 160 ASP cc_start: 0.7310 (t0) cc_final: 0.6526 (t0) REVERT: F 166 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6785 (mtmm) REVERT: F 179 THR cc_start: 0.7729 (m) cc_final: 0.7507 (m) REVERT: F 248 LEU cc_start: 0.7730 (mp) cc_final: 0.7522 (mt) REVERT: F 264 ARG cc_start: 0.7638 (mtp85) cc_final: 0.6777 (mpt180) REVERT: F 276 ILE cc_start: 0.8299 (tp) cc_final: 0.7725 (tp) REVERT: F 280 LYS cc_start: 0.5034 (tptt) cc_final: 0.4603 (ttpp) REVERT: F 285 GLN cc_start: 0.7804 (mt0) cc_final: 0.7520 (mt0) REVERT: F 295 CYS cc_start: 0.7089 (m) cc_final: 0.6871 (m) REVERT: F 320 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7636 (mtt-85) REVERT: F 342 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7685 (mm110) REVERT: F 376 CYS cc_start: 0.7759 (t) cc_final: 0.7545 (t) REVERT: F 380 ASN cc_start: 0.7470 (t0) cc_final: 0.7000 (t0) REVERT: F 392 ASP cc_start: 0.6809 (m-30) cc_final: 0.6479 (m-30) REVERT: F 425 MET cc_start: 0.7510 (tpp) cc_final: 0.7231 (tpt) outliers start: 2 outliers final: 1 residues processed: 566 average time/residue: 0.1498 time to fit residues: 115.2703 Evaluate side-chains 517 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 424 GLN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 245 GLN E 292 GLN E 298 ASN E 307 HIS F 31 GLN F 91 GLN F 233 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.133129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118447 restraints weight = 19458.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.122758 restraints weight = 8646.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.125568 restraints weight = 4617.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.127367 restraints weight = 2759.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.128612 restraints weight = 1789.276| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14163 Z= 0.161 Angle : 0.633 8.670 19237 Z= 0.324 Chirality : 0.046 0.153 2106 Planarity : 0.005 0.088 2502 Dihedral : 9.842 162.943 1994 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.57 % Allowed : 15.34 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.62 (0.20), residues: 1738 helix: 0.79 (0.18), residues: 774 sheet: -1.92 (0.28), residues: 289 loop : -1.02 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 422 TYR 0.024 0.002 TYR E 36 PHE 0.013 0.001 PHE E 266 TRP 0.020 0.002 TRP A 407 HIS 0.008 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00356 (14163) covalent geometry : angle 0.63337 (19237) hydrogen bonds : bond 0.04718 ( 658) hydrogen bonds : angle 4.89899 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 545 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7771 (p0) cc_final: 0.7508 (p0) REVERT: A 67 PHE cc_start: 0.8243 (m-80) cc_final: 0.7888 (m-80) REVERT: A 71 GLU cc_start: 0.6841 (tt0) cc_final: 0.6534 (tt0) REVERT: A 91 GLN cc_start: 0.8075 (pt0) cc_final: 0.7792 (pt0) REVERT: A 154 MET cc_start: 0.7709 (mmm) cc_final: 0.7271 (mmm) REVERT: A 164 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7828 (mmtp) REVERT: A 166 LYS cc_start: 0.7441 (mtmm) cc_final: 0.7155 (mttp) REVERT: A 179 THR cc_start: 0.8177 (p) cc_final: 0.7858 (t) REVERT: A 187 SER cc_start: 0.8121 (m) cc_final: 0.7730 (p) REVERT: A 209 ILE cc_start: 0.8277 (mm) cc_final: 0.7730 (mt) REVERT: A 226 ASN cc_start: 0.7051 (m110) cc_final: 0.6802 (m-40) REVERT: A 237 SER cc_start: 0.8583 (m) cc_final: 0.8100 (p) REVERT: A 239 THR cc_start: 0.7895 (p) cc_final: 0.7557 (t) REVERT: A 284 GLU cc_start: 0.7516 (tt0) cc_final: 0.7037 (tm-30) REVERT: A 290 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6959 (mt-10) REVERT: A 302 MET cc_start: 0.7911 (mmm) cc_final: 0.7499 (mmm) REVERT: A 304 LYS cc_start: 0.8185 (tppt) cc_final: 0.7892 (tppt) REVERT: A 309 HIS cc_start: 0.6576 (m-70) cc_final: 0.6229 (m-70) REVERT: A 311 LYS cc_start: 0.8254 (mttp) cc_final: 0.7867 (mtpp) REVERT: A 370 LYS cc_start: 0.8217 (tptp) cc_final: 0.8010 (tptp) REVERT: A 373 ARG cc_start: 0.8077 (mtm180) cc_final: 0.7810 (mtm-85) REVERT: A 376 CYS cc_start: 0.8097 (t) cc_final: 0.7810 (t) REVERT: A 402 ARG cc_start: 0.7117 (mpt180) cc_final: 0.6876 (mmt-90) REVERT: A 405 VAL cc_start: 0.8147 (m) cc_final: 0.7888 (t) REVERT: B 53 GLU cc_start: 0.6800 (tp30) cc_final: 0.6590 (tp30) REVERT: B 73 MET cc_start: 0.7487 (mmm) cc_final: 0.6935 (mmm) REVERT: B 86 ARG cc_start: 0.7660 (mtt180) cc_final: 0.6718 (mmp-170) REVERT: B 99 ASN cc_start: 0.7924 (m-40) cc_final: 0.7385 (m-40) REVERT: B 122 LYS cc_start: 0.7775 (tttt) cc_final: 0.7331 (tmtt) REVERT: B 164 MET cc_start: 0.6563 (tpp) cc_final: 0.5958 (tpp) REVERT: B 174 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7946 (mmmt) REVERT: B 209 ASP cc_start: 0.7680 (t70) cc_final: 0.7316 (t0) REVERT: B 213 ARG cc_start: 0.7269 (ptm160) cc_final: 0.6957 (ptm160) REVERT: B 221 THR cc_start: 0.8347 (t) cc_final: 0.8095 (p) REVERT: B 233 MET cc_start: 0.7368 (mmt) cc_final: 0.7119 (mmt) REVERT: B 237 THR cc_start: 0.8095 (p) cc_final: 0.7622 (t) REVERT: B 241 ARG cc_start: 0.8687 (mtp180) cc_final: 0.7910 (mtp180) REVERT: B 247 ASN cc_start: 0.7850 (m110) cc_final: 0.7644 (m-40) REVERT: B 280 GLN cc_start: 0.7488 (mt0) cc_final: 0.7220 (mt0) REVERT: B 298 ASN cc_start: 0.6861 (t0) cc_final: 0.6522 (t0) REVERT: B 299 MET cc_start: 0.6404 (tpt) cc_final: 0.6174 (tpt) REVERT: B 309 ARG cc_start: 0.7253 (mtt-85) cc_final: 0.6457 (mtt-85) REVERT: B 318 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7550 (mtp-110) REVERT: B 415 MET cc_start: 0.8031 (mmm) cc_final: 0.7807 (tpt) REVERT: E 3 GLU cc_start: 0.6881 (mp0) cc_final: 0.6380 (mp0) REVERT: E 19 LYS cc_start: 0.7582 (tptm) cc_final: 0.7262 (tptm) REVERT: E 41 ASP cc_start: 0.7291 (t0) cc_final: 0.7015 (t0) REVERT: E 53 GLU cc_start: 0.6739 (tp30) cc_final: 0.6514 (tp30) REVERT: E 86 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.6470 (tpm170) REVERT: E 108 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6834 (tm-30) REVERT: E 164 MET cc_start: 0.5872 (mpp) cc_final: 0.5307 (mpp) REVERT: E 174 LYS cc_start: 0.7858 (mptt) cc_final: 0.7638 (mptt) REVERT: E 175 VAL cc_start: 0.7980 (m) cc_final: 0.7537 (t) REVERT: E 192 LEU cc_start: 0.8115 (tp) cc_final: 0.7914 (tp) REVERT: E 209 ASP cc_start: 0.7791 (t0) cc_final: 0.5526 (t0) REVERT: E 213 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6381 (mtm180) REVERT: E 216 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7998 (mmtt) REVERT: E 225 LEU cc_start: 0.8312 (mp) cc_final: 0.8007 (mp) REVERT: E 279 GLN cc_start: 0.7747 (pt0) cc_final: 0.7521 (pt0) REVERT: E 299 MET cc_start: 0.6034 (mmm) cc_final: 0.5798 (mmm) REVERT: E 380 ARG cc_start: 0.7206 (ptm160) cc_final: 0.6712 (ptm160) REVERT: E 385 PHE cc_start: 0.7868 (t80) cc_final: 0.7651 (t80) REVERT: E 391 ARG cc_start: 0.4445 (ptt180) cc_final: 0.3588 (mtp180) REVERT: E 394 PHE cc_start: 0.8107 (m-80) cc_final: 0.7789 (m-80) REVERT: E 405 GLU cc_start: 0.7238 (tt0) cc_final: 0.6666 (mt-10) REVERT: E 413 SER cc_start: 0.8157 (m) cc_final: 0.7951 (p) REVERT: F 24 TYR cc_start: 0.8067 (m-10) cc_final: 0.7752 (m-10) REVERT: F 50 ASN cc_start: 0.8009 (t0) cc_final: 0.7691 (t0) REVERT: F 51 THR cc_start: 0.8361 (p) cc_final: 0.8152 (t) REVERT: F 70 LEU cc_start: 0.7858 (mm) cc_final: 0.7534 (mt) REVERT: F 102 ASN cc_start: 0.6867 (t0) cc_final: 0.6492 (t0) REVERT: F 123 ARG cc_start: 0.6828 (tpp-160) cc_final: 0.6038 (tpp-160) REVERT: F 154 MET cc_start: 0.7125 (mmm) cc_final: 0.6884 (mmm) REVERT: F 216 ASN cc_start: 0.8203 (m-40) cc_final: 0.7967 (m-40) REVERT: F 280 LYS cc_start: 0.5719 (tptt) cc_final: 0.4227 (tptt) REVERT: F 295 CYS cc_start: 0.7393 (m) cc_final: 0.6983 (m) REVERT: F 304 LYS cc_start: 0.7707 (tppp) cc_final: 0.7371 (tppp) REVERT: F 380 ASN cc_start: 0.7827 (t0) cc_final: 0.7593 (t0) REVERT: F 395 PHE cc_start: 0.7778 (t80) cc_final: 0.7541 (t80) REVERT: F 425 MET cc_start: 0.7631 (tpp) cc_final: 0.7274 (tpt) outliers start: 53 outliers final: 33 residues processed: 563 average time/residue: 0.1453 time to fit residues: 112.4966 Evaluate side-chains 535 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 502 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 134 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 156 optimal weight: 0.0970 chunk 106 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 83 GLN B 137 HIS B 424 GLN E 131 GLN F 329 ASN F 393 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.116252 restraints weight = 19661.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120340 restraints weight = 8818.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.122972 restraints weight = 4710.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.124710 restraints weight = 2824.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.125861 restraints weight = 1830.044| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14163 Z= 0.192 Angle : 0.623 8.434 19237 Z= 0.322 Chirality : 0.047 0.174 2106 Planarity : 0.005 0.064 2502 Dihedral : 9.937 165.166 1994 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.36 % Allowed : 18.84 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.48 (0.20), residues: 1738 helix: 0.83 (0.18), residues: 781 sheet: -1.53 (0.28), residues: 286 loop : -1.01 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 214 TYR 0.015 0.002 TYR A 224 PHE 0.016 0.002 PHE B 133 TRP 0.014 0.002 TRP A 407 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00423 (14163) covalent geometry : angle 0.62315 (19237) hydrogen bonds : bond 0.04767 ( 658) hydrogen bonds : angle 4.62772 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 539 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7808 (m-80) cc_final: 0.7468 (m-80) REVERT: A 91 GLN cc_start: 0.8088 (pt0) cc_final: 0.7858 (pt0) REVERT: A 120 ASP cc_start: 0.7223 (m-30) cc_final: 0.6839 (t0) REVERT: A 154 MET cc_start: 0.7723 (mmm) cc_final: 0.7119 (mmm) REVERT: A 166 LYS cc_start: 0.7603 (mtmm) cc_final: 0.7343 (mttp) REVERT: A 168 GLU cc_start: 0.6170 (mp0) cc_final: 0.5909 (mp0) REVERT: A 175 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8022 (Cg_endo) REVERT: A 176 GLN cc_start: 0.7010 (pm20) cc_final: 0.6570 (pm20) REVERT: A 187 SER cc_start: 0.8221 (m) cc_final: 0.7800 (p) REVERT: A 209 ILE cc_start: 0.8374 (mm) cc_final: 0.7785 (mt) REVERT: A 226 ASN cc_start: 0.7283 (m110) cc_final: 0.6994 (m110) REVERT: A 237 SER cc_start: 0.8550 (m) cc_final: 0.8264 (t) REVERT: A 239 THR cc_start: 0.7899 (p) cc_final: 0.7669 (t) REVERT: A 254 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 284 GLU cc_start: 0.7489 (tt0) cc_final: 0.7251 (tt0) REVERT: A 290 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6933 (mt-10) REVERT: A 302 MET cc_start: 0.7982 (mmm) cc_final: 0.7558 (mmm) REVERT: A 304 LYS cc_start: 0.8140 (tppt) cc_final: 0.7913 (tppt) REVERT: A 309 HIS cc_start: 0.6656 (m-70) cc_final: 0.6273 (m-70) REVERT: A 342 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8137 (mm-40) REVERT: A 373 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7960 (mtm-85) REVERT: A 376 CYS cc_start: 0.8164 (t) cc_final: 0.7927 (t) REVERT: A 420 GLU cc_start: 0.6155 (tm-30) cc_final: 0.5770 (tm-30) REVERT: A 424 ASP cc_start: 0.7168 (m-30) cc_final: 0.6604 (m-30) REVERT: B 73 MET cc_start: 0.7473 (mmm) cc_final: 0.6988 (mmm) REVERT: B 86 ARG cc_start: 0.7773 (mtt180) cc_final: 0.6761 (tpm170) REVERT: B 122 LYS cc_start: 0.7774 (tttt) cc_final: 0.7415 (tmtt) REVERT: B 164 MET cc_start: 0.6960 (tpp) cc_final: 0.6740 (tpp) REVERT: B 194 GLU cc_start: 0.6698 (tp30) cc_final: 0.6478 (tp30) REVERT: B 209 ASP cc_start: 0.7662 (t70) cc_final: 0.7312 (t0) REVERT: B 213 ARG cc_start: 0.7314 (ptm160) cc_final: 0.6996 (ptm160) REVERT: B 247 ASN cc_start: 0.7958 (m110) cc_final: 0.7545 (m-40) REVERT: B 279 GLN cc_start: 0.7898 (pm20) cc_final: 0.7312 (pp30) REVERT: B 298 ASN cc_start: 0.7076 (t0) cc_final: 0.6861 (t0) REVERT: B 318 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7431 (mtm-85) REVERT: B 415 MET cc_start: 0.8082 (mmm) cc_final: 0.7847 (tpt) REVERT: B 418 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8114 (tp) REVERT: E 3 GLU cc_start: 0.6917 (mp0) cc_final: 0.6390 (mp0) REVERT: E 4 ILE cc_start: 0.8640 (mm) cc_final: 0.8416 (mt) REVERT: E 19 LYS cc_start: 0.7683 (tptm) cc_final: 0.7400 (tptm) REVERT: E 39 ASP cc_start: 0.7578 (p0) cc_final: 0.7337 (p0) REVERT: E 41 ASP cc_start: 0.7477 (t0) cc_final: 0.7109 (t0) REVERT: E 86 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.6696 (tpm170) REVERT: E 108 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6927 (tm-30) REVERT: E 117 LEU cc_start: 0.8181 (mm) cc_final: 0.7898 (mt) REVERT: E 123 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 174 LYS cc_start: 0.7980 (mptt) cc_final: 0.7687 (mptt) REVERT: E 175 VAL cc_start: 0.7967 (m) cc_final: 0.7667 (t) REVERT: E 197 ASP cc_start: 0.7707 (m-30) cc_final: 0.7123 (m-30) REVERT: E 216 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7982 (mmtt) REVERT: E 257 MET cc_start: 0.6832 (mpp) cc_final: 0.6334 (mpp) REVERT: E 265 PHE cc_start: 0.8010 (m-80) cc_final: 0.7725 (m-80) REVERT: E 279 GLN cc_start: 0.7718 (pt0) cc_final: 0.7464 (pt0) REVERT: E 366 THR cc_start: 0.8350 (m) cc_final: 0.8082 (t) REVERT: E 380 ARG cc_start: 0.7270 (ptm160) cc_final: 0.6661 (ptm160) REVERT: E 385 PHE cc_start: 0.7906 (t80) cc_final: 0.7694 (t80) REVERT: E 392 LYS cc_start: 0.6833 (mmtp) cc_final: 0.6571 (mmtt) REVERT: E 399 THR cc_start: 0.7879 (m) cc_final: 0.6878 (t) REVERT: E 413 SER cc_start: 0.8132 (m) cc_final: 0.7873 (p) REVERT: F 3 GLU cc_start: 0.6662 (mp0) cc_final: 0.6145 (mp0) REVERT: F 24 TYR cc_start: 0.8052 (m-10) cc_final: 0.7742 (m-10) REVERT: F 50 ASN cc_start: 0.8202 (t0) cc_final: 0.7697 (t0) REVERT: F 69 ASP cc_start: 0.7831 (t0) cc_final: 0.7385 (t0) REVERT: F 70 LEU cc_start: 0.7812 (mm) cc_final: 0.7421 (mt) REVERT: F 77 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6743 (tm-30) REVERT: F 97 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6600 (tm-30) REVERT: F 102 ASN cc_start: 0.7222 (t0) cc_final: 0.6741 (t0) REVERT: F 123 ARG cc_start: 0.6949 (tpp-160) cc_final: 0.6538 (tpp-160) REVERT: F 155 GLU cc_start: 0.6693 (tp30) cc_final: 0.6037 (tp30) REVERT: F 248 LEU cc_start: 0.8075 (mp) cc_final: 0.7820 (mt) REVERT: F 280 LYS cc_start: 0.5771 (tptt) cc_final: 0.4272 (tptt) REVERT: F 295 CYS cc_start: 0.7380 (m) cc_final: 0.7007 (m) REVERT: F 301 GLN cc_start: 0.6913 (mm-40) cc_final: 0.6694 (mp10) REVERT: F 304 LYS cc_start: 0.7795 (tppp) cc_final: 0.7315 (tppp) REVERT: F 306 ASP cc_start: 0.7691 (t0) cc_final: 0.7340 (t0) REVERT: F 352 LYS cc_start: 0.8038 (tptt) cc_final: 0.6298 (mmtt) REVERT: F 367 ASP cc_start: 0.7303 (t0) cc_final: 0.6969 (t0) REVERT: F 415 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7330 (tm-30) outliers start: 50 outliers final: 35 residues processed: 555 average time/residue: 0.1264 time to fit residues: 96.4602 Evaluate side-chains 558 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 522 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 167 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 154 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 102 ASN A 107 HIS ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 423 GLN E 52 ASN E 99 ASN E 100 ASN E 191 GLN E 245 GLN E 396 HIS F 88 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.128016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.114453 restraints weight = 19771.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118435 restraints weight = 8894.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.121018 restraints weight = 4779.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.122700 restraints weight = 2872.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.123823 restraints weight = 1859.614| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14163 Z= 0.210 Angle : 0.620 8.089 19237 Z= 0.321 Chirality : 0.047 0.177 2106 Planarity : 0.005 0.060 2502 Dihedral : 9.922 164.512 1994 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.97 % Allowed : 21.06 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.20), residues: 1738 helix: 0.93 (0.19), residues: 774 sheet: -1.29 (0.29), residues: 283 loop : -0.87 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 320 TYR 0.016 0.002 TYR F 312 PHE 0.014 0.002 PHE F 255 TRP 0.011 0.002 TRP E 101 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00458 (14163) covalent geometry : angle 0.62001 (19237) hydrogen bonds : bond 0.04750 ( 658) hydrogen bonds : angle 4.50238 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 542 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7811 (m-80) cc_final: 0.7381 (m-80) REVERT: A 67 PHE cc_start: 0.8293 (m-80) cc_final: 0.7952 (m-80) REVERT: A 103 TYR cc_start: 0.7353 (t80) cc_final: 0.7068 (t80) REVERT: A 120 ASP cc_start: 0.7204 (m-30) cc_final: 0.6773 (t0) REVERT: A 154 MET cc_start: 0.7713 (mmm) cc_final: 0.7187 (mmm) REVERT: A 166 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7099 (mttp) REVERT: A 175 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8040 (Cg_endo) REVERT: A 176 GLN cc_start: 0.6925 (pm20) cc_final: 0.6559 (pm20) REVERT: A 179 THR cc_start: 0.8306 (p) cc_final: 0.7884 (t) REVERT: A 187 SER cc_start: 0.8312 (m) cc_final: 0.7892 (p) REVERT: A 209 ILE cc_start: 0.8391 (mm) cc_final: 0.7890 (mt) REVERT: A 226 ASN cc_start: 0.7423 (m110) cc_final: 0.7174 (m110) REVERT: A 237 SER cc_start: 0.8624 (m) cc_final: 0.8236 (t) REVERT: A 239 THR cc_start: 0.7884 (p) cc_final: 0.7660 (t) REVERT: A 254 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6834 (mt-10) REVERT: A 284 GLU cc_start: 0.7544 (tt0) cc_final: 0.7010 (tm-30) REVERT: A 290 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6829 (mt-10) REVERT: A 297 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 302 MET cc_start: 0.7943 (mmm) cc_final: 0.7574 (mmm) REVERT: A 304 LYS cc_start: 0.8199 (tppt) cc_final: 0.7880 (tppt) REVERT: A 309 HIS cc_start: 0.6692 (m-70) cc_final: 0.6297 (m-70) REVERT: A 373 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7980 (mtm-85) REVERT: A 376 CYS cc_start: 0.8156 (t) cc_final: 0.7924 (t) REVERT: A 420 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5831 (tm-30) REVERT: A 424 ASP cc_start: 0.7346 (m-30) cc_final: 0.6730 (m-30) REVERT: B 73 MET cc_start: 0.7522 (mmm) cc_final: 0.7215 (mmm) REVERT: B 86 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6736 (tpm170) REVERT: B 122 LYS cc_start: 0.7908 (tttt) cc_final: 0.7561 (tmtt) REVERT: B 194 GLU cc_start: 0.6698 (tp30) cc_final: 0.6490 (tp30) REVERT: B 209 ASP cc_start: 0.7713 (t70) cc_final: 0.7353 (t0) REVERT: B 213 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6977 (ptm160) REVERT: B 237 THR cc_start: 0.8182 (p) cc_final: 0.7851 (t) REVERT: B 247 ASN cc_start: 0.7965 (m110) cc_final: 0.7573 (m-40) REVERT: B 250 LEU cc_start: 0.7961 (tp) cc_final: 0.7659 (tp) REVERT: B 279 GLN cc_start: 0.7815 (pm20) cc_final: 0.7251 (pp30) REVERT: B 280 GLN cc_start: 0.7496 (mt0) cc_final: 0.6974 (mt0) REVERT: B 297 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7281 (mtmm) REVERT: B 318 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7900 (mtm-85) REVERT: B 380 ARG cc_start: 0.7104 (ptp-170) cc_final: 0.6800 (ptp-170) REVERT: B 418 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8150 (tp) REVERT: E 3 GLU cc_start: 0.7026 (mp0) cc_final: 0.6250 (mp0) REVERT: E 19 LYS cc_start: 0.7653 (tptm) cc_final: 0.7357 (tptm) REVERT: E 41 ASP cc_start: 0.7459 (t0) cc_final: 0.7008 (t0) REVERT: E 62 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7177 (mtt90) REVERT: E 108 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7047 (tm-30) REVERT: E 123 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7423 (mm-30) REVERT: E 174 LYS cc_start: 0.8041 (mptt) cc_final: 0.7661 (mptt) REVERT: E 175 VAL cc_start: 0.7961 (m) cc_final: 0.7379 (t) REVERT: E 197 ASP cc_start: 0.7724 (m-30) cc_final: 0.7277 (m-30) REVERT: E 199 THR cc_start: 0.8046 (m) cc_final: 0.7773 (p) REVERT: E 225 LEU cc_start: 0.8285 (mp) cc_final: 0.8060 (mp) REVERT: E 251 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7449 (tpp80) REVERT: E 257 MET cc_start: 0.6907 (mpp) cc_final: 0.6104 (mpp) REVERT: E 265 PHE cc_start: 0.8030 (m-80) cc_final: 0.7771 (m-80) REVERT: E 279 GLN cc_start: 0.7682 (pt0) cc_final: 0.7292 (pt0) REVERT: E 366 THR cc_start: 0.8326 (m) cc_final: 0.8017 (t) REVERT: E 380 ARG cc_start: 0.7346 (ptm160) cc_final: 0.6726 (ptm160) REVERT: E 391 ARG cc_start: 0.4818 (ptt180) cc_final: 0.4355 (ptt180) REVERT: E 392 LYS cc_start: 0.7249 (mmtp) cc_final: 0.6582 (mptt) REVERT: E 399 THR cc_start: 0.7825 (m) cc_final: 0.6838 (t) REVERT: E 405 GLU cc_start: 0.7198 (tt0) cc_final: 0.6979 (mt-10) REVERT: E 413 SER cc_start: 0.8134 (m) cc_final: 0.7897 (p) REVERT: F 3 GLU cc_start: 0.6584 (mp0) cc_final: 0.6046 (mp0) REVERT: F 24 TYR cc_start: 0.7972 (m-10) cc_final: 0.7551 (m-10) REVERT: F 50 ASN cc_start: 0.7964 (t0) cc_final: 0.7127 (t0) REVERT: F 69 ASP cc_start: 0.7943 (t0) cc_final: 0.7506 (t0) REVERT: F 70 LEU cc_start: 0.7854 (mm) cc_final: 0.7475 (mt) REVERT: F 77 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6813 (tm-30) REVERT: F 97 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6880 (tm-30) REVERT: F 102 ASN cc_start: 0.7146 (t0) cc_final: 0.6694 (t0) REVERT: F 123 ARG cc_start: 0.7090 (tpp-160) cc_final: 0.6539 (tpp-160) REVERT: F 154 MET cc_start: 0.7070 (mmm) cc_final: 0.6776 (mmm) REVERT: F 155 GLU cc_start: 0.6799 (tp30) cc_final: 0.6155 (tp30) REVERT: F 164 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7906 (mmtp) REVERT: F 248 LEU cc_start: 0.8024 (mp) cc_final: 0.7744 (mt) REVERT: F 301 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6759 (mp10) REVERT: F 306 ASP cc_start: 0.7732 (t0) cc_final: 0.7322 (t0) REVERT: F 326 LYS cc_start: 0.5248 (mttt) cc_final: 0.5008 (mttp) REVERT: F 352 LYS cc_start: 0.8031 (tptt) cc_final: 0.6275 (mmtt) REVERT: F 367 ASP cc_start: 0.7329 (t0) cc_final: 0.7027 (t0) REVERT: F 398 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6862 (mpp) REVERT: F 404 PHE cc_start: 0.7956 (m-80) cc_final: 0.7697 (m-10) REVERT: F 425 MET cc_start: 0.8186 (mmm) cc_final: 0.7604 (tpt) REVERT: F 432 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6035 (t80) REVERT: F 434 GLU cc_start: 0.8083 (tt0) cc_final: 0.7861 (tt0) outliers start: 59 outliers final: 39 residues processed: 560 average time/residue: 0.1306 time to fit residues: 102.1190 Evaluate side-chains 567 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 525 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 76 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS E 52 ASN E 99 ASN F 88 HIS F 101 ASN F 342 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113829 restraints weight = 19921.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117862 restraints weight = 8822.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.120453 restraints weight = 4674.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122146 restraints weight = 2787.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.123144 restraints weight = 1799.818| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14163 Z= 0.199 Angle : 0.611 9.801 19237 Z= 0.316 Chirality : 0.046 0.166 2106 Planarity : 0.004 0.054 2502 Dihedral : 9.875 165.688 1994 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.24 % Allowed : 22.41 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.20), residues: 1738 helix: 0.96 (0.19), residues: 775 sheet: -1.15 (0.29), residues: 284 loop : -0.85 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 84 TYR 0.015 0.002 TYR A 432 PHE 0.018 0.002 PHE A 267 TRP 0.014 0.001 TRP E 101 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00433 (14163) covalent geometry : angle 0.61080 (19237) hydrogen bonds : bond 0.04618 ( 658) hydrogen bonds : angle 4.46340 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 517 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7287 (m-30) cc_final: 0.6791 (t0) REVERT: A 154 MET cc_start: 0.7701 (mmm) cc_final: 0.7182 (mmm) REVERT: A 166 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7114 (mttp) REVERT: A 179 THR cc_start: 0.8302 (p) cc_final: 0.7896 (t) REVERT: A 187 SER cc_start: 0.8257 (m) cc_final: 0.7821 (p) REVERT: A 209 ILE cc_start: 0.8395 (mm) cc_final: 0.7876 (mt) REVERT: A 226 ASN cc_start: 0.7359 (m110) cc_final: 0.7111 (m110) REVERT: A 237 SER cc_start: 0.8606 (m) cc_final: 0.8238 (t) REVERT: A 254 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6774 (mt-10) REVERT: A 284 GLU cc_start: 0.7534 (tt0) cc_final: 0.7259 (tt0) REVERT: A 290 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6903 (mt-10) REVERT: A 297 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 302 MET cc_start: 0.7972 (mmm) cc_final: 0.7605 (mmm) REVERT: A 304 LYS cc_start: 0.8052 (tppt) cc_final: 0.7797 (tppt) REVERT: A 309 HIS cc_start: 0.6723 (m-70) cc_final: 0.6295 (m-70) REVERT: A 376 CYS cc_start: 0.8158 (t) cc_final: 0.7874 (t) REVERT: A 420 GLU cc_start: 0.6361 (tm-30) cc_final: 0.5924 (tm-30) REVERT: A 424 ASP cc_start: 0.7388 (m-30) cc_final: 0.6757 (m-30) REVERT: A 434 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7874 (tt0) REVERT: B 73 MET cc_start: 0.7513 (mmm) cc_final: 0.7274 (mmm) REVERT: B 86 ARG cc_start: 0.7812 (mtt180) cc_final: 0.6777 (tpm170) REVERT: B 194 GLU cc_start: 0.6682 (tp30) cc_final: 0.6205 (tp30) REVERT: B 195 ASN cc_start: 0.7819 (m-40) cc_final: 0.7588 (m-40) REVERT: B 209 ASP cc_start: 0.7725 (t70) cc_final: 0.7380 (t0) REVERT: B 213 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6858 (ptm160) REVERT: B 247 ASN cc_start: 0.7964 (m110) cc_final: 0.7565 (m-40) REVERT: B 250 LEU cc_start: 0.7905 (tp) cc_final: 0.7694 (tp) REVERT: B 279 GLN cc_start: 0.7798 (pm20) cc_final: 0.7222 (pp30) REVERT: B 280 GLN cc_start: 0.7519 (mt0) cc_final: 0.6980 (mt0) REVERT: B 297 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7241 (mtmm) REVERT: B 318 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7822 (mtp-110) REVERT: B 323 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6799 (mtm) REVERT: B 329 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7092 (mm-40) REVERT: B 380 ARG cc_start: 0.7115 (ptp-170) cc_final: 0.6804 (ptp-170) REVERT: B 391 ARG cc_start: 0.6835 (tpp80) cc_final: 0.6455 (mpt180) REVERT: B 418 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8213 (tp) REVERT: E 3 GLU cc_start: 0.7057 (mp0) cc_final: 0.6409 (mp0) REVERT: E 19 LYS cc_start: 0.7613 (tptm) cc_final: 0.7376 (tptm) REVERT: E 67 ASP cc_start: 0.6653 (t0) cc_final: 0.6254 (t0) REVERT: E 108 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6970 (tm-30) REVERT: E 123 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7492 (mm-30) REVERT: E 174 LYS cc_start: 0.8103 (mptt) cc_final: 0.7880 (mptt) REVERT: E 175 VAL cc_start: 0.7962 (m) cc_final: 0.7635 (t) REVERT: E 197 ASP cc_start: 0.7778 (m-30) cc_final: 0.7458 (m-30) REVERT: E 199 THR cc_start: 0.8086 (m) cc_final: 0.7854 (p) REVERT: E 203 ASP cc_start: 0.7686 (t0) cc_final: 0.7440 (t0) REVERT: E 225 LEU cc_start: 0.8336 (mp) cc_final: 0.8087 (mp) REVERT: E 257 MET cc_start: 0.6808 (mpp) cc_final: 0.5945 (mpp) REVERT: E 265 PHE cc_start: 0.8087 (m-80) cc_final: 0.7869 (m-80) REVERT: E 279 GLN cc_start: 0.7665 (pt0) cc_final: 0.7291 (pt0) REVERT: E 366 THR cc_start: 0.8328 (m) cc_final: 0.8025 (t) REVERT: E 391 ARG cc_start: 0.5114 (ptt180) cc_final: 0.3561 (ptt90) REVERT: E 399 THR cc_start: 0.7848 (m) cc_final: 0.6833 (t) REVERT: F 3 GLU cc_start: 0.6639 (mp0) cc_final: 0.6207 (mp0) REVERT: F 24 TYR cc_start: 0.7959 (m-10) cc_final: 0.7579 (m-10) REVERT: F 69 ASP cc_start: 0.7890 (t0) cc_final: 0.7459 (t0) REVERT: F 70 LEU cc_start: 0.7871 (mm) cc_final: 0.7480 (mt) REVERT: F 77 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6803 (tm-30) REVERT: F 78 VAL cc_start: 0.8032 (t) cc_final: 0.7672 (t) REVERT: F 123 ARG cc_start: 0.7112 (tpp-160) cc_final: 0.6608 (tpp-160) REVERT: F 155 GLU cc_start: 0.6787 (tp30) cc_final: 0.6203 (tp30) REVERT: F 164 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7917 (mmtp) REVERT: F 237 SER cc_start: 0.8507 (m) cc_final: 0.8258 (t) REVERT: F 248 LEU cc_start: 0.7995 (mp) cc_final: 0.7733 (mt) REVERT: F 301 GLN cc_start: 0.6999 (mm-40) cc_final: 0.6760 (mp10) REVERT: F 306 ASP cc_start: 0.7739 (t0) cc_final: 0.7305 (t0) REVERT: F 326 LYS cc_start: 0.5278 (mttt) cc_final: 0.5053 (mttp) REVERT: F 342 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7771 (mm110) REVERT: F 352 LYS cc_start: 0.7958 (tptt) cc_final: 0.7063 (tppt) REVERT: F 367 ASP cc_start: 0.7374 (t0) cc_final: 0.7096 (t0) REVERT: F 398 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6933 (mpp) REVERT: F 404 PHE cc_start: 0.7909 (m-80) cc_final: 0.7697 (m-10) REVERT: F 422 ARG cc_start: 0.7727 (tpt90) cc_final: 0.7513 (tpt170) REVERT: F 432 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.5937 (t80) REVERT: F 434 GLU cc_start: 0.8071 (tt0) cc_final: 0.7818 (tt0) outliers start: 63 outliers final: 46 residues processed: 539 average time/residue: 0.1493 time to fit residues: 111.2235 Evaluate side-chains 563 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 513 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 137 HIS E 52 ASN E 99 ASN ** F 91 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 = 0.3902 r_free = 0.3902 target = 0.127318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113897 restraints weight = 19836.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117811 restraints weight = 8866.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.120345 restraints weight = 4736.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.122022 restraints weight = 2840.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123115 restraints weight = 1837.630| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14163 Z= 0.205 Angle : 0.624 9.754 19237 Z= 0.323 Chirality : 0.047 0.169 2106 Planarity : 0.005 0.051 2502 Dihedral : 9.885 166.031 1994 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.91 % Allowed : 23.22 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.12 (0.20), residues: 1738 helix: 0.97 (0.19), residues: 775 sheet: -1.04 (0.30), residues: 284 loop : -0.77 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 262 TYR 0.014 0.002 TYR A 83 PHE 0.015 0.002 PHE A 267 TRP 0.018 0.002 TRP E 101 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00446 (14163) covalent geometry : angle 0.62406 (19237) hydrogen bonds : bond 0.04657 ( 658) hydrogen bonds : angle 4.42534 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 536 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7292 (m-30) cc_final: 0.6801 (t0) REVERT: A 145 THR cc_start: 0.7828 (m) cc_final: 0.7601 (p) REVERT: A 154 MET cc_start: 0.7703 (mmm) cc_final: 0.7181 (mmm) REVERT: A 166 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7120 (mttp) REVERT: A 176 GLN cc_start: 0.6974 (pm20) cc_final: 0.6549 (pm20) REVERT: A 179 THR cc_start: 0.8325 (p) cc_final: 0.7923 (t) REVERT: A 187 SER cc_start: 0.8286 (m) cc_final: 0.7870 (p) REVERT: A 207 GLU cc_start: 0.6697 (tt0) cc_final: 0.6162 (tt0) REVERT: A 209 ILE cc_start: 0.8396 (mm) cc_final: 0.7871 (mt) REVERT: A 211 ASP cc_start: 0.7964 (m-30) cc_final: 0.7588 (m-30) REVERT: A 226 ASN cc_start: 0.7368 (m110) cc_final: 0.7153 (m110) REVERT: A 237 SER cc_start: 0.8593 (m) cc_final: 0.8235 (t) REVERT: A 254 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 286 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8026 (mm) REVERT: A 290 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6816 (mt-10) REVERT: A 297 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 302 MET cc_start: 0.8027 (mmm) cc_final: 0.7624 (mmm) REVERT: A 309 HIS cc_start: 0.6770 (m-70) cc_final: 0.6351 (m-70) REVERT: A 373 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7994 (mtm-85) REVERT: A 376 CYS cc_start: 0.8170 (t) cc_final: 0.7843 (t) REVERT: A 420 GLU cc_start: 0.6387 (tm-30) cc_final: 0.5967 (tm-30) REVERT: A 424 ASP cc_start: 0.7437 (m-30) cc_final: 0.6736 (m-30) REVERT: A 434 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7675 (tt0) REVERT: B 53 GLU cc_start: 0.7067 (tp30) cc_final: 0.6702 (tp30) REVERT: B 68 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6774 (mp) REVERT: B 73 MET cc_start: 0.7528 (mmm) cc_final: 0.7269 (mmm) REVERT: B 86 ARG cc_start: 0.7766 (mtt180) cc_final: 0.6755 (tpm170) REVERT: B 122 LYS cc_start: 0.8007 (tmtt) cc_final: 0.7671 (tmtt) REVERT: B 194 GLU cc_start: 0.6720 (tp30) cc_final: 0.6240 (tp30) REVERT: B 195 ASN cc_start: 0.7845 (m-40) cc_final: 0.7620 (m-40) REVERT: B 197 ASP cc_start: 0.7532 (m-30) cc_final: 0.7183 (m-30) REVERT: B 209 ASP cc_start: 0.7764 (t70) cc_final: 0.7391 (t0) REVERT: B 213 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6866 (ptm160) REVERT: B 247 ASN cc_start: 0.7964 (m110) cc_final: 0.7566 (m-40) REVERT: B 297 LYS cc_start: 0.7588 (mtmm) cc_final: 0.7216 (mtmm) REVERT: B 318 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7811 (mtp-110) REVERT: B 320 ARG cc_start: 0.6758 (tpt90) cc_final: 0.6480 (tpt90) REVERT: B 376 GLU cc_start: 0.7169 (mp0) cc_final: 0.6758 (mp0) REVERT: B 380 ARG cc_start: 0.7127 (ptp-170) cc_final: 0.6823 (ptp-170) REVERT: B 391 ARG cc_start: 0.6969 (tpp80) cc_final: 0.6338 (mpt180) REVERT: B 412 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 415 MET cc_start: 0.8062 (tpt) cc_final: 0.7813 (tpt) REVERT: B 418 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8247 (tp) REVERT: E 3 GLU cc_start: 0.7079 (mp0) cc_final: 0.6391 (mp0) REVERT: E 67 ASP cc_start: 0.6640 (t0) cc_final: 0.6221 (t0) REVERT: E 108 GLU cc_start: 0.7614 (tm-30) cc_final: 0.6805 (tm-30) REVERT: E 123 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 174 LYS cc_start: 0.8088 (mptt) cc_final: 0.7858 (mptt) REVERT: E 175 VAL cc_start: 0.7952 (m) cc_final: 0.7413 (t) REVERT: E 197 ASP cc_start: 0.7777 (m-30) cc_final: 0.7452 (m-30) REVERT: E 199 THR cc_start: 0.8067 (m) cc_final: 0.7857 (p) REVERT: E 203 ASP cc_start: 0.7622 (t0) cc_final: 0.7355 (t0) REVERT: E 225 LEU cc_start: 0.8355 (mp) cc_final: 0.8114 (mp) REVERT: E 251 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7597 (tpp80) REVERT: E 257 MET cc_start: 0.6835 (mpp) cc_final: 0.5940 (mpp) REVERT: E 265 PHE cc_start: 0.8111 (m-80) cc_final: 0.7799 (m-80) REVERT: E 279 GLN cc_start: 0.7632 (pt0) cc_final: 0.7258 (pt0) REVERT: E 298 ASN cc_start: 0.7235 (t0) cc_final: 0.7010 (t0) REVERT: E 366 THR cc_start: 0.8320 (m) cc_final: 0.8019 (t) REVERT: E 391 ARG cc_start: 0.5116 (ptt180) cc_final: 0.4308 (ptt180) REVERT: E 405 GLU cc_start: 0.7470 (tt0) cc_final: 0.6884 (mt-10) REVERT: F 3 GLU cc_start: 0.6658 (mp0) cc_final: 0.6172 (mp0) REVERT: F 24 TYR cc_start: 0.7942 (m-10) cc_final: 0.7560 (m-10) REVERT: F 69 ASP cc_start: 0.7871 (t0) cc_final: 0.7477 (t0) REVERT: F 70 LEU cc_start: 0.7874 (mm) cc_final: 0.7487 (mt) REVERT: F 77 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6778 (tm-30) REVERT: F 78 VAL cc_start: 0.8035 (t) cc_final: 0.7651 (t) REVERT: F 123 ARG cc_start: 0.7149 (tpp-160) cc_final: 0.6616 (tpp-160) REVERT: F 155 GLU cc_start: 0.6783 (tp30) cc_final: 0.6225 (tp30) REVERT: F 237 SER cc_start: 0.8496 (m) cc_final: 0.8233 (t) REVERT: F 248 LEU cc_start: 0.8038 (mp) cc_final: 0.7802 (mt) REVERT: F 254 GLU cc_start: 0.1771 (OUTLIER) cc_final: -0.1224 (mt-10) REVERT: F 301 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6777 (mp10) REVERT: F 306 ASP cc_start: 0.7746 (t0) cc_final: 0.7310 (t0) REVERT: F 326 LYS cc_start: 0.5237 (mttt) cc_final: 0.5013 (mttp) REVERT: F 342 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7745 (mm-40) REVERT: F 352 LYS cc_start: 0.7985 (tptt) cc_final: 0.7099 (tppt) REVERT: F 367 ASP cc_start: 0.7380 (t0) cc_final: 0.7118 (t0) REVERT: F 398 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6890 (mpp) REVERT: F 404 PHE cc_start: 0.7922 (m-80) cc_final: 0.7709 (m-10) REVERT: F 432 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.5839 (t80) REVERT: F 434 GLU cc_start: 0.8090 (tt0) cc_final: 0.7816 (tt0) outliers start: 73 outliers final: 54 residues processed: 561 average time/residue: 0.1515 time to fit residues: 116.9858 Evaluate side-chains 588 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 528 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 130 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 131 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 170 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN B 137 HIS B 280 GLN E 52 ASN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113880 restraints weight = 19916.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117866 restraints weight = 8859.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.120457 restraints weight = 4722.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.122172 restraints weight = 2816.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123261 restraints weight = 1812.866| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14163 Z= 0.197 Angle : 0.617 9.728 19237 Z= 0.319 Chirality : 0.046 0.170 2106 Planarity : 0.004 0.049 2502 Dihedral : 9.885 166.453 1994 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.18 % Allowed : 24.83 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.20), residues: 1738 helix: 0.98 (0.19), residues: 776 sheet: -1.04 (0.30), residues: 277 loop : -0.76 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 282 TYR 0.016 0.001 TYR A 432 PHE 0.021 0.002 PHE F 351 TRP 0.018 0.002 TRP E 101 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00430 (14163) covalent geometry : angle 0.61685 (19237) hydrogen bonds : bond 0.04563 ( 658) hydrogen bonds : angle 4.42052 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 548 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7828 (m-80) cc_final: 0.7473 (m-80) REVERT: A 91 GLN cc_start: 0.8155 (pt0) cc_final: 0.7806 (pt0) REVERT: A 108 TYR cc_start: 0.7855 (m-80) cc_final: 0.7532 (m-80) REVERT: A 120 ASP cc_start: 0.7286 (m-30) cc_final: 0.6793 (t0) REVERT: A 145 THR cc_start: 0.7805 (m) cc_final: 0.7558 (p) REVERT: A 154 MET cc_start: 0.7696 (mmm) cc_final: 0.7184 (mmm) REVERT: A 166 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7112 (mttp) REVERT: A 179 THR cc_start: 0.8333 (p) cc_final: 0.7931 (t) REVERT: A 187 SER cc_start: 0.8254 (m) cc_final: 0.7833 (p) REVERT: A 237 SER cc_start: 0.8601 (m) cc_final: 0.8249 (t) REVERT: A 254 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 284 GLU cc_start: 0.7401 (tt0) cc_final: 0.7027 (tm-30) REVERT: A 290 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6631 (mt-10) REVERT: A 297 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 302 MET cc_start: 0.7968 (mmm) cc_final: 0.7364 (mmm) REVERT: A 304 LYS cc_start: 0.8178 (tppt) cc_final: 0.7857 (tppt) REVERT: A 309 HIS cc_start: 0.6745 (m-70) cc_final: 0.6481 (m-70) REVERT: A 349 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 376 CYS cc_start: 0.8116 (t) cc_final: 0.7898 (t) REVERT: A 420 GLU cc_start: 0.6408 (tm-30) cc_final: 0.6150 (tm-30) REVERT: A 434 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7777 (tt0) REVERT: B 53 GLU cc_start: 0.7095 (tp30) cc_final: 0.6713 (tp30) REVERT: B 68 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6843 (mp) REVERT: B 73 MET cc_start: 0.7530 (mmm) cc_final: 0.7282 (mmm) REVERT: B 86 ARG cc_start: 0.7766 (mtt180) cc_final: 0.6799 (tpm170) REVERT: B 122 LYS cc_start: 0.8003 (tmtt) cc_final: 0.7658 (tmtt) REVERT: B 194 GLU cc_start: 0.6716 (tp30) cc_final: 0.6199 (tp30) REVERT: B 195 ASN cc_start: 0.7846 (m-40) cc_final: 0.7595 (m-40) REVERT: B 197 ASP cc_start: 0.7573 (m-30) cc_final: 0.7169 (m-30) REVERT: B 209 ASP cc_start: 0.7768 (t70) cc_final: 0.7400 (t0) REVERT: B 213 ARG cc_start: 0.7319 (ptm160) cc_final: 0.6880 (ptm160) REVERT: B 241 ARG cc_start: 0.8706 (mtm-85) cc_final: 0.8486 (mtm-85) REVERT: B 247 ASN cc_start: 0.7926 (m110) cc_final: 0.7551 (m-40) REVERT: B 265 PHE cc_start: 0.8512 (m-80) cc_final: 0.8268 (m-80) REVERT: B 297 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7227 (mtmm) REVERT: B 318 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7816 (mtp-110) REVERT: B 320 ARG cc_start: 0.6767 (tpt90) cc_final: 0.6510 (tpt90) REVERT: B 376 GLU cc_start: 0.7192 (mp0) cc_final: 0.6747 (mp0) REVERT: B 380 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6830 (ptp-170) REVERT: B 391 ARG cc_start: 0.7007 (tpp80) cc_final: 0.6453 (mpt180) REVERT: B 412 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 415 MET cc_start: 0.8110 (tpt) cc_final: 0.7826 (tpt) REVERT: B 418 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8241 (tp) REVERT: E 3 GLU cc_start: 0.7123 (mp0) cc_final: 0.6459 (mp0) REVERT: E 67 ASP cc_start: 0.6680 (t0) cc_final: 0.6307 (t0) REVERT: E 73 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6843 (mtm) REVERT: E 108 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6792 (tm-30) REVERT: E 123 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7531 (mm-30) REVERT: E 197 ASP cc_start: 0.7785 (m-30) cc_final: 0.7482 (m-30) REVERT: E 199 THR cc_start: 0.8075 (m) cc_final: 0.7874 (p) REVERT: E 203 ASP cc_start: 0.7642 (t0) cc_final: 0.7338 (t0) REVERT: E 225 LEU cc_start: 0.8335 (mp) cc_final: 0.8100 (mp) REVERT: E 251 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7600 (tpp80) REVERT: E 257 MET cc_start: 0.6851 (mpp) cc_final: 0.5975 (mpp) REVERT: E 265 PHE cc_start: 0.8044 (m-80) cc_final: 0.7709 (m-80) REVERT: E 279 GLN cc_start: 0.7592 (pt0) cc_final: 0.7289 (pt0) REVERT: E 285 THR cc_start: 0.7710 (t) cc_final: 0.7417 (p) REVERT: E 298 ASN cc_start: 0.7253 (t0) cc_final: 0.7011 (t0) REVERT: E 366 THR cc_start: 0.8306 (m) cc_final: 0.8022 (t) REVERT: E 391 ARG cc_start: 0.5149 (ptt180) cc_final: 0.4434 (ptt180) REVERT: F 3 GLU cc_start: 0.6678 (mp0) cc_final: 0.6043 (mp0) REVERT: F 24 TYR cc_start: 0.7919 (m-10) cc_final: 0.7559 (m-10) REVERT: F 50 ASN cc_start: 0.8094 (t0) cc_final: 0.7163 (t0) REVERT: F 69 ASP cc_start: 0.7864 (t0) cc_final: 0.7463 (t0) REVERT: F 70 LEU cc_start: 0.7863 (mm) cc_final: 0.7497 (mt) REVERT: F 77 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6767 (tm-30) REVERT: F 78 VAL cc_start: 0.8020 (t) cc_final: 0.7569 (t) REVERT: F 97 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6693 (tm-30) REVERT: F 123 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6650 (tpp-160) REVERT: F 237 SER cc_start: 0.8493 (m) cc_final: 0.8236 (t) REVERT: F 248 LEU cc_start: 0.8027 (mp) cc_final: 0.7787 (mt) REVERT: F 254 GLU cc_start: 0.1754 (OUTLIER) cc_final: -0.1183 (mt-10) REVERT: F 301 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6894 (mp10) REVERT: F 306 ASP cc_start: 0.7730 (t0) cc_final: 0.7293 (t0) REVERT: F 342 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7873 (mm-40) REVERT: F 352 LYS cc_start: 0.7985 (tptt) cc_final: 0.7090 (tppt) REVERT: F 367 ASP cc_start: 0.7406 (t0) cc_final: 0.7148 (t0) REVERT: F 398 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6967 (mpp) REVERT: F 404 PHE cc_start: 0.7883 (m-80) cc_final: 0.7676 (m-10) REVERT: F 422 ARG cc_start: 0.7727 (tpt90) cc_final: 0.7512 (tpt170) REVERT: F 432 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.5826 (t80) REVERT: F 434 GLU cc_start: 0.8084 (tt0) cc_final: 0.7791 (tt0) outliers start: 77 outliers final: 57 residues processed: 580 average time/residue: 0.1500 time to fit residues: 119.5682 Evaluate side-chains 599 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 535 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 143 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN A 285 GLN B 137 HIS E 52 ASN E 99 ASN F 88 HIS F 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113677 restraints weight = 19730.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117620 restraints weight = 8813.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.120186 restraints weight = 4715.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.121876 restraints weight = 2824.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.122839 restraints weight = 1818.307| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14163 Z= 0.196 Angle : 0.631 9.652 19237 Z= 0.328 Chirality : 0.047 0.176 2106 Planarity : 0.005 0.046 2502 Dihedral : 9.876 167.265 1994 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.45 % Allowed : 24.83 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.07 (0.20), residues: 1738 helix: 1.03 (0.19), residues: 774 sheet: -1.06 (0.31), residues: 267 loop : -0.76 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 282 TYR 0.015 0.001 TYR A 312 PHE 0.028 0.002 PHE F 351 TRP 0.019 0.002 TRP E 101 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00431 (14163) covalent geometry : angle 0.63090 (19237) hydrogen bonds : bond 0.04535 ( 658) hydrogen bonds : angle 4.39258 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 549 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7811 (m-80) cc_final: 0.7442 (m-80) REVERT: A 91 GLN cc_start: 0.8125 (pt0) cc_final: 0.7817 (pt0) REVERT: A 108 TYR cc_start: 0.7856 (m-80) cc_final: 0.7524 (m-80) REVERT: A 120 ASP cc_start: 0.7282 (m-30) cc_final: 0.6796 (t0) REVERT: A 145 THR cc_start: 0.7862 (m) cc_final: 0.7631 (p) REVERT: A 154 MET cc_start: 0.7708 (mmm) cc_final: 0.7123 (mmm) REVERT: A 166 LYS cc_start: 0.7555 (mtmm) cc_final: 0.7125 (mttp) REVERT: A 179 THR cc_start: 0.8350 (p) cc_final: 0.7943 (t) REVERT: A 187 SER cc_start: 0.8286 (m) cc_final: 0.7863 (p) REVERT: A 209 ILE cc_start: 0.8384 (mm) cc_final: 0.7834 (mt) REVERT: A 237 SER cc_start: 0.8611 (m) cc_final: 0.8265 (t) REVERT: A 254 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6849 (mt-10) REVERT: A 284 GLU cc_start: 0.7383 (tt0) cc_final: 0.6994 (tm-30) REVERT: A 290 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6922 (mt-10) REVERT: A 297 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 302 MET cc_start: 0.7952 (mmm) cc_final: 0.7472 (mmm) REVERT: A 309 HIS cc_start: 0.6741 (m-70) cc_final: 0.6510 (m-70) REVERT: A 349 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8111 (p) REVERT: A 376 CYS cc_start: 0.8131 (t) cc_final: 0.7871 (t) REVERT: A 381 THR cc_start: 0.8151 (m) cc_final: 0.7588 (p) REVERT: A 420 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5954 (tm-30) REVERT: A 424 ASP cc_start: 0.7354 (m-30) cc_final: 0.6740 (m-30) REVERT: A 434 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7752 (tt0) REVERT: B 53 GLU cc_start: 0.7105 (tp30) cc_final: 0.6728 (tp30) REVERT: B 68 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6909 (mp) REVERT: B 73 MET cc_start: 0.7596 (mmm) cc_final: 0.7371 (mmm) REVERT: B 86 ARG cc_start: 0.7769 (mtt180) cc_final: 0.6889 (tpm170) REVERT: B 194 GLU cc_start: 0.6729 (tp30) cc_final: 0.6243 (tp30) REVERT: B 195 ASN cc_start: 0.7845 (m-40) cc_final: 0.7570 (m-40) REVERT: B 197 ASP cc_start: 0.7559 (m-30) cc_final: 0.7353 (m-30) REVERT: B 209 ASP cc_start: 0.7766 (t70) cc_final: 0.7371 (t0) REVERT: B 213 ARG cc_start: 0.7319 (ptm160) cc_final: 0.7063 (ptm160) REVERT: B 237 THR cc_start: 0.8202 (p) cc_final: 0.7894 (t) REVERT: B 297 LYS cc_start: 0.7628 (mtmm) cc_final: 0.7233 (mtmm) REVERT: B 318 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7795 (mtp-110) REVERT: B 320 ARG cc_start: 0.6753 (tpt90) cc_final: 0.6508 (tpt90) REVERT: B 376 GLU cc_start: 0.7203 (mp0) cc_final: 0.6748 (mp0) REVERT: B 380 ARG cc_start: 0.7154 (ptp-170) cc_final: 0.6825 (ptp-170) REVERT: B 391 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6466 (mpt180) REVERT: B 407 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: B 412 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 415 MET cc_start: 0.8127 (tpt) cc_final: 0.7804 (tpt) REVERT: B 418 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8270 (tp) REVERT: E 3 GLU cc_start: 0.7082 (mp0) cc_final: 0.6413 (mp0) REVERT: E 67 ASP cc_start: 0.6709 (t0) cc_final: 0.6306 (t0) REVERT: E 73 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6838 (mtm) REVERT: E 108 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6793 (tm-30) REVERT: E 137 HIS cc_start: 0.7577 (p90) cc_final: 0.7294 (p90) REVERT: E 203 ASP cc_start: 0.7572 (t0) cc_final: 0.7292 (t0) REVERT: E 216 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8041 (mmtt) REVERT: E 225 LEU cc_start: 0.8346 (mp) cc_final: 0.8117 (mp) REVERT: E 251 ARG cc_start: 0.7819 (tpp80) cc_final: 0.7611 (tpp80) REVERT: E 257 MET cc_start: 0.6851 (mpp) cc_final: 0.5966 (mpp) REVERT: E 265 PHE cc_start: 0.8018 (m-80) cc_final: 0.7673 (m-80) REVERT: E 279 GLN cc_start: 0.7616 (pt0) cc_final: 0.7259 (pt0) REVERT: E 285 THR cc_start: 0.7782 (t) cc_final: 0.7420 (p) REVERT: E 366 THR cc_start: 0.8303 (m) cc_final: 0.8023 (t) REVERT: E 391 ARG cc_start: 0.5144 (ptt180) cc_final: 0.4477 (ptt180) REVERT: E 405 GLU cc_start: 0.7203 (tt0) cc_final: 0.6799 (tt0) REVERT: E 418 LEU cc_start: 0.8523 (tp) cc_final: 0.8306 (tp) REVERT: F 3 GLU cc_start: 0.6726 (mp0) cc_final: 0.6084 (mp0) REVERT: F 24 TYR cc_start: 0.7947 (m-10) cc_final: 0.7550 (m-10) REVERT: F 50 ASN cc_start: 0.8106 (t0) cc_final: 0.7145 (t0) REVERT: F 69 ASP cc_start: 0.7869 (t0) cc_final: 0.7481 (t0) REVERT: F 70 LEU cc_start: 0.7893 (mm) cc_final: 0.7511 (mt) REVERT: F 77 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6776 (tm-30) REVERT: F 78 VAL cc_start: 0.7972 (t) cc_final: 0.7514 (t) REVERT: F 97 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6606 (tm-30) REVERT: F 123 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6600 (tpp-160) REVERT: F 199 ASP cc_start: 0.7844 (t0) cc_final: 0.7574 (t0) REVERT: F 237 SER cc_start: 0.8522 (m) cc_final: 0.8265 (t) REVERT: F 248 LEU cc_start: 0.8018 (mp) cc_final: 0.7801 (mt) REVERT: F 254 GLU cc_start: 0.1862 (OUTLIER) cc_final: -0.1122 (mt-10) REVERT: F 301 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6823 (mp10) REVERT: F 306 ASP cc_start: 0.7725 (t0) cc_final: 0.7299 (t0) REVERT: F 326 LYS cc_start: 0.5214 (mttp) cc_final: 0.4854 (mttm) REVERT: F 342 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7930 (mm-40) REVERT: F 351 PHE cc_start: 0.7448 (m-80) cc_final: 0.7230 (m-80) REVERT: F 352 LYS cc_start: 0.7971 (tptt) cc_final: 0.7089 (tppt) REVERT: F 367 ASP cc_start: 0.7444 (t0) cc_final: 0.7182 (t0) REVERT: F 404 PHE cc_start: 0.7879 (m-80) cc_final: 0.7652 (m-10) REVERT: F 413 MET cc_start: 0.7237 (tpp) cc_final: 0.6796 (mmp) REVERT: F 417 GLU cc_start: 0.6652 (tt0) cc_final: 0.6119 (tt0) REVERT: F 432 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.5761 (t80) REVERT: F 434 GLU cc_start: 0.8093 (tt0) cc_final: 0.7769 (tt0) outliers start: 81 outliers final: 63 residues processed: 584 average time/residue: 0.1541 time to fit residues: 124.0909 Evaluate side-chains 608 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 538 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 16 optimal weight: 0.1980 chunk 126 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 146 optimal weight: 0.4980 chunk 133 optimal weight: 0.0370 chunk 63 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 285 GLN B 8 GLN B 137 HIS B 256 ASN E 52 ASN E 99 ASN F 88 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.128822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115111 restraints weight = 19843.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.119129 restraints weight = 8907.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.121750 restraints weight = 4775.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123454 restraints weight = 2861.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.124561 restraints weight = 1848.805| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14163 Z= 0.153 Angle : 0.613 9.647 19237 Z= 0.317 Chirality : 0.045 0.173 2106 Planarity : 0.004 0.045 2502 Dihedral : 9.780 168.329 1994 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.85 % Allowed : 25.77 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.02 (0.20), residues: 1738 helix: 1.08 (0.19), residues: 776 sheet: -1.11 (0.30), residues: 271 loop : -0.70 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 84 TYR 0.013 0.001 TYR F 432 PHE 0.021 0.001 PHE F 351 TRP 0.020 0.002 TRP E 101 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00339 (14163) covalent geometry : angle 0.61313 (19237) hydrogen bonds : bond 0.04137 ( 658) hydrogen bonds : angle 4.33491 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 542 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7802 (m-80) cc_final: 0.7459 (m-80) REVERT: A 27 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 91 GLN cc_start: 0.8138 (pt0) cc_final: 0.7847 (pt0) REVERT: A 118 VAL cc_start: 0.8304 (p) cc_final: 0.8097 (m) REVERT: A 120 ASP cc_start: 0.7262 (m-30) cc_final: 0.6784 (t0) REVERT: A 145 THR cc_start: 0.7857 (m) cc_final: 0.7587 (p) REVERT: A 154 MET cc_start: 0.7683 (mmm) cc_final: 0.7199 (mmm) REVERT: A 166 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7125 (mttp) REVERT: A 187 SER cc_start: 0.8217 (m) cc_final: 0.7800 (p) REVERT: A 209 ILE cc_start: 0.8384 (mm) cc_final: 0.7806 (mt) REVERT: A 211 ASP cc_start: 0.8028 (m-30) cc_final: 0.7756 (m-30) REVERT: A 215 ARG cc_start: 0.7527 (mtt180) cc_final: 0.6862 (mtt180) REVERT: A 229 ARG cc_start: 0.7799 (mpt-90) cc_final: 0.7483 (mmt90) REVERT: A 237 SER cc_start: 0.8564 (m) cc_final: 0.8224 (t) REVERT: A 254 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6695 (mt-10) REVERT: A 284 GLU cc_start: 0.7339 (tt0) cc_final: 0.6929 (tm-30) REVERT: A 290 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 297 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 302 MET cc_start: 0.7993 (mmm) cc_final: 0.7517 (mmm) REVERT: A 309 HIS cc_start: 0.6697 (m-70) cc_final: 0.6444 (m-70) REVERT: A 349 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 352 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8038 (tptm) REVERT: A 376 CYS cc_start: 0.8110 (t) cc_final: 0.7891 (t) REVERT: A 420 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5896 (tm-30) REVERT: A 424 ASP cc_start: 0.7321 (m-30) cc_final: 0.6718 (m-30) REVERT: A 434 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7844 (tt0) REVERT: B 53 GLU cc_start: 0.7108 (tp30) cc_final: 0.6730 (tp30) REVERT: B 68 LEU cc_start: 0.7335 (mp) cc_final: 0.6785 (mp) REVERT: B 86 ARG cc_start: 0.7774 (mtt180) cc_final: 0.6868 (tpm170) REVERT: B 194 GLU cc_start: 0.6731 (tp30) cc_final: 0.6235 (tp30) REVERT: B 195 ASN cc_start: 0.7853 (m-40) cc_final: 0.7565 (m-40) REVERT: B 197 ASP cc_start: 0.7516 (m-30) cc_final: 0.7156 (m-30) REVERT: B 209 ASP cc_start: 0.7772 (t70) cc_final: 0.7358 (t0) REVERT: B 213 ARG cc_start: 0.7321 (ptm160) cc_final: 0.7073 (ptm160) REVERT: B 237 THR cc_start: 0.8203 (p) cc_final: 0.7889 (t) REVERT: B 297 LYS cc_start: 0.7639 (mtmm) cc_final: 0.7306 (mtmm) REVERT: B 309 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.6578 (mtt-85) REVERT: B 318 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7853 (mtm-85) REVERT: B 320 ARG cc_start: 0.6734 (tpt90) cc_final: 0.6492 (tpt90) REVERT: B 338 SER cc_start: 0.8395 (p) cc_final: 0.8147 (t) REVERT: B 380 ARG cc_start: 0.7132 (ptp-170) cc_final: 0.6825 (ptp-170) REVERT: B 391 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6506 (mpt180) REVERT: B 407 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: B 412 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 415 MET cc_start: 0.8092 (tpt) cc_final: 0.7815 (tpt) REVERT: B 418 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8278 (tp) REVERT: E 3 GLU cc_start: 0.7064 (mp0) cc_final: 0.6304 (mp0) REVERT: E 67 ASP cc_start: 0.6741 (t0) cc_final: 0.6331 (t0) REVERT: E 73 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6801 (mtm) REVERT: E 203 ASP cc_start: 0.7549 (t0) cc_final: 0.7239 (t0) REVERT: E 216 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8030 (mmtt) REVERT: E 225 LEU cc_start: 0.8342 (mp) cc_final: 0.8104 (mp) REVERT: E 257 MET cc_start: 0.6787 (mpp) cc_final: 0.5880 (mpp) REVERT: E 265 PHE cc_start: 0.7903 (m-80) cc_final: 0.7631 (m-80) REVERT: E 279 GLN cc_start: 0.7609 (pt0) cc_final: 0.7220 (pt0) REVERT: E 366 THR cc_start: 0.8257 (m) cc_final: 0.8018 (t) REVERT: E 391 ARG cc_start: 0.5099 (ptt180) cc_final: 0.4459 (ptt180) REVERT: E 405 GLU cc_start: 0.7134 (tt0) cc_final: 0.6640 (tt0) REVERT: F 3 GLU cc_start: 0.6723 (mp0) cc_final: 0.6213 (mp0) REVERT: F 24 TYR cc_start: 0.7940 (m-10) cc_final: 0.7668 (m-10) REVERT: F 69 ASP cc_start: 0.7855 (t0) cc_final: 0.7490 (t0) REVERT: F 70 LEU cc_start: 0.7923 (mm) cc_final: 0.7497 (mt) REVERT: F 77 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6761 (tm-30) REVERT: F 78 VAL cc_start: 0.7922 (t) cc_final: 0.7420 (t) REVERT: F 91 GLN cc_start: 0.7918 (pt0) cc_final: 0.7609 (pt0) REVERT: F 97 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6566 (tm-30) REVERT: F 123 ARG cc_start: 0.7162 (tpp-160) cc_final: 0.6805 (tpp-160) REVERT: F 161 TYR cc_start: 0.8255 (m-80) cc_final: 0.7817 (m-10) REVERT: F 237 SER cc_start: 0.8493 (m) cc_final: 0.8282 (t) REVERT: F 248 LEU cc_start: 0.7998 (mp) cc_final: 0.7764 (mt) REVERT: F 254 GLU cc_start: 0.1605 (OUTLIER) cc_final: -0.1384 (mt-10) REVERT: F 301 GLN cc_start: 0.6894 (mm-40) cc_final: 0.6610 (mt0) REVERT: F 306 ASP cc_start: 0.7733 (t0) cc_final: 0.7306 (t0) REVERT: F 326 LYS cc_start: 0.5363 (mttp) cc_final: 0.5066 (mttm) REVERT: F 342 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7932 (mm-40) REVERT: F 351 PHE cc_start: 0.7454 (m-80) cc_final: 0.7235 (m-80) REVERT: F 352 LYS cc_start: 0.7921 (tptt) cc_final: 0.7025 (tppt) REVERT: F 367 ASP cc_start: 0.7426 (t0) cc_final: 0.7201 (t0) REVERT: F 404 PHE cc_start: 0.7827 (m-80) cc_final: 0.7624 (m-10) REVERT: F 413 MET cc_start: 0.7158 (tpp) cc_final: 0.6405 (mmp) REVERT: F 417 GLU cc_start: 0.6578 (tt0) cc_final: 0.5946 (tt0) REVERT: F 432 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.5852 (t80) REVERT: F 434 GLU cc_start: 0.8071 (tt0) cc_final: 0.7721 (tt0) outliers start: 72 outliers final: 56 residues processed: 575 average time/residue: 0.1509 time to fit residues: 119.4577 Evaluate side-chains 589 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 526 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 75 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 285 GLN B 8 GLN B 43 GLN B 137 HIS E 99 ASN F 88 HIS F 192 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.114155 restraints weight = 19944.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118146 restraints weight = 8929.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.120715 restraints weight = 4782.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.122415 restraints weight = 2870.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.123519 restraints weight = 1855.497| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14163 Z= 0.188 Angle : 0.657 10.159 19237 Z= 0.338 Chirality : 0.046 0.187 2106 Planarity : 0.005 0.062 2502 Dihedral : 9.848 168.311 1994 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.64 % Allowed : 26.78 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.04 (0.20), residues: 1738 helix: 1.05 (0.19), residues: 774 sheet: -1.03 (0.30), residues: 274 loop : -0.74 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 84 TYR 0.015 0.001 TYR A 432 PHE 0.025 0.002 PHE F 351 TRP 0.019 0.002 TRP E 101 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00416 (14163) covalent geometry : angle 0.65696 (19237) hydrogen bonds : bond 0.04417 ( 658) hydrogen bonds : angle 4.33647 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 536 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7827 (m-80) cc_final: 0.7451 (m-80) REVERT: A 27 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 91 GLN cc_start: 0.8091 (pt0) cc_final: 0.7806 (pt0) REVERT: A 118 VAL cc_start: 0.8324 (p) cc_final: 0.8095 (m) REVERT: A 120 ASP cc_start: 0.7276 (m-30) cc_final: 0.6798 (t0) REVERT: A 141 PHE cc_start: 0.8267 (m-10) cc_final: 0.7873 (m-10) REVERT: A 154 MET cc_start: 0.7703 (mmm) cc_final: 0.7142 (mmm) REVERT: A 166 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7128 (mttp) REVERT: A 187 SER cc_start: 0.8250 (m) cc_final: 0.7808 (p) REVERT: A 211 ASP cc_start: 0.8033 (m-30) cc_final: 0.7761 (m-30) REVERT: A 215 ARG cc_start: 0.7518 (mtt180) cc_final: 0.6888 (mtt180) REVERT: A 219 ILE cc_start: 0.8886 (tp) cc_final: 0.8304 (pt) REVERT: A 229 ARG cc_start: 0.7814 (mpt-90) cc_final: 0.7491 (mmt90) REVERT: A 237 SER cc_start: 0.8655 (m) cc_final: 0.8318 (t) REVERT: A 254 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 284 GLU cc_start: 0.7309 (tt0) cc_final: 0.6976 (tm-30) REVERT: A 290 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 297 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7317 (mm-30) REVERT: A 302 MET cc_start: 0.8014 (mmm) cc_final: 0.7450 (mmm) REVERT: A 309 HIS cc_start: 0.6705 (m-70) cc_final: 0.6433 (m-70) REVERT: A 349 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 352 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8048 (tptm) REVERT: A 434 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7620 (tt0) REVERT: B 53 GLU cc_start: 0.7113 (tp30) cc_final: 0.6710 (tp30) REVERT: B 68 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6923 (mp) REVERT: B 86 ARG cc_start: 0.7832 (mtt180) cc_final: 0.6881 (tpm170) REVERT: B 194 GLU cc_start: 0.6739 (tp30) cc_final: 0.5528 (tp30) REVERT: B 195 ASN cc_start: 0.7853 (m-40) cc_final: 0.6474 (m-40) REVERT: B 197 ASP cc_start: 0.7527 (m-30) cc_final: 0.7315 (m-30) REVERT: B 209 ASP cc_start: 0.7767 (t70) cc_final: 0.7369 (t0) REVERT: B 213 ARG cc_start: 0.7322 (ptm160) cc_final: 0.7072 (ptm160) REVERT: B 237 THR cc_start: 0.8220 (p) cc_final: 0.7906 (t) REVERT: B 267 MET cc_start: 0.7589 (ptm) cc_final: 0.7257 (ppp) REVERT: B 297 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7285 (mtmm) REVERT: B 318 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7785 (mtp-110) REVERT: B 376 GLU cc_start: 0.7229 (mp0) cc_final: 0.6709 (mp0) REVERT: B 380 ARG cc_start: 0.7154 (ptp-170) cc_final: 0.6842 (ptp-170) REVERT: B 391 ARG cc_start: 0.7069 (tpp80) cc_final: 0.6537 (mpt180) REVERT: B 407 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: B 412 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 415 MET cc_start: 0.8126 (tpt) cc_final: 0.7790 (tpt) REVERT: E 35 THR cc_start: 0.8710 (p) cc_final: 0.8507 (p) REVERT: E 62 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7189 (mtt90) REVERT: E 67 ASP cc_start: 0.6838 (t0) cc_final: 0.6391 (t0) REVERT: E 73 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6839 (mtm) REVERT: E 108 GLU cc_start: 0.7653 (tm-30) cc_final: 0.6866 (tm-30) REVERT: E 137 HIS cc_start: 0.7562 (p90) cc_final: 0.7312 (p90) REVERT: E 203 ASP cc_start: 0.7562 (t0) cc_final: 0.7257 (t0) REVERT: E 216 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8040 (mmtt) REVERT: E 225 LEU cc_start: 0.8335 (mp) cc_final: 0.8107 (mp) REVERT: E 257 MET cc_start: 0.6851 (mpp) cc_final: 0.5945 (mpp) REVERT: E 265 PHE cc_start: 0.7953 (m-80) cc_final: 0.7611 (m-80) REVERT: E 279 GLN cc_start: 0.7605 (pt0) cc_final: 0.7225 (pt0) REVERT: E 285 THR cc_start: 0.7716 (t) cc_final: 0.7287 (p) REVERT: E 366 THR cc_start: 0.8263 (m) cc_final: 0.8029 (t) REVERT: E 391 ARG cc_start: 0.5182 (ptt180) cc_final: 0.4451 (ptt180) REVERT: E 405 GLU cc_start: 0.7269 (tt0) cc_final: 0.6792 (tt0) REVERT: F 3 GLU cc_start: 0.6749 (mp0) cc_final: 0.6237 (mp0) REVERT: F 24 TYR cc_start: 0.7987 (m-10) cc_final: 0.7748 (m-10) REVERT: F 69 ASP cc_start: 0.7855 (t0) cc_final: 0.7501 (t0) REVERT: F 70 LEU cc_start: 0.7922 (mm) cc_final: 0.7504 (mt) REVERT: F 77 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6748 (tm-30) REVERT: F 78 VAL cc_start: 0.7951 (t) cc_final: 0.7445 (t) REVERT: F 97 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6577 (tm-30) REVERT: F 123 ARG cc_start: 0.7166 (tpp-160) cc_final: 0.6797 (tpp-160) REVERT: F 154 MET cc_start: 0.7103 (mmm) cc_final: 0.6722 (tmm) REVERT: F 155 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6628 (mm-30) REVERT: F 161 TYR cc_start: 0.8235 (m-80) cc_final: 0.7830 (m-10) REVERT: F 237 SER cc_start: 0.8517 (m) cc_final: 0.8226 (t) REVERT: F 239 THR cc_start: 0.8040 (m) cc_final: 0.7613 (t) REVERT: F 248 LEU cc_start: 0.7996 (mp) cc_final: 0.7753 (mt) REVERT: F 272 TYR cc_start: 0.8496 (t80) cc_final: 0.8084 (t80) REVERT: F 301 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6497 (mp10) REVERT: F 306 ASP cc_start: 0.7733 (t0) cc_final: 0.7304 (t0) REVERT: F 326 LYS cc_start: 0.5118 (mttp) cc_final: 0.4729 (mttm) REVERT: F 332 ILE cc_start: 0.8278 (mm) cc_final: 0.8003 (tp) REVERT: F 342 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7885 (mm-40) REVERT: F 352 LYS cc_start: 0.7933 (tptt) cc_final: 0.7062 (tppt) REVERT: F 367 ASP cc_start: 0.7465 (t0) cc_final: 0.7239 (t0) REVERT: F 404 PHE cc_start: 0.7832 (m-80) cc_final: 0.7596 (m-10) REVERT: F 413 MET cc_start: 0.7203 (tpp) cc_final: 0.6444 (mmp) REVERT: F 417 GLU cc_start: 0.6662 (tt0) cc_final: 0.6031 (tt0) REVERT: F 432 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.5811 (t80) REVERT: F 434 GLU cc_start: 0.8088 (tt0) cc_final: 0.7774 (tt0) outliers start: 69 outliers final: 56 residues processed: 567 average time/residue: 0.1573 time to fit residues: 123.0552 Evaluate side-chains 597 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 535 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 117 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 107 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.0970 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 285 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS E 99 ASN F 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.130546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116674 restraints weight = 19871.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120740 restraints weight = 8940.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.123333 restraints weight = 4810.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.124996 restraints weight = 2899.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.126154 restraints weight = 1901.490| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14163 Z= 0.131 Angle : 0.628 9.986 19237 Z= 0.321 Chirality : 0.045 0.176 2106 Planarity : 0.005 0.051 2502 Dihedral : 9.645 169.373 1994 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.04 % Allowed : 27.52 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.00 (0.20), residues: 1738 helix: 1.06 (0.19), residues: 781 sheet: -0.96 (0.30), residues: 272 loop : -0.72 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 84 TYR 0.012 0.001 TYR F 432 PHE 0.018 0.001 PHE F 351 TRP 0.017 0.001 TRP E 101 HIS 0.004 0.001 HIS F 393 Details of bonding type rmsd covalent geometry : bond 0.00297 (14163) covalent geometry : angle 0.62754 (19237) hydrogen bonds : bond 0.03781 ( 658) hydrogen bonds : angle 4.24525 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.44 seconds wall clock time: 53 minutes 48.35 seconds (3228.35 seconds total)