Starting phenix.real_space_refine on Fri May 16 02:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t42_41018/05_2025/8t42_41018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t42_41018/05_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_41018/05_2025/8t42_41018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t42_41018/05_2025/8t42_41018.map" model { file = "/net/cci-nas-00/data/ceres_data/8t42_41018/05_2025/8t42_41018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t42_41018/05_2025/8t42_41018.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.81, per 1000 atoms: 0.78 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.39 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: 4.21 Time building geometry restraints manager: 3.66 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 439 or resid 501 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: 21.340 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 34.030 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.048 0.002 TRP A 407 HIS 0.039 0.003 HIS E 190 PHE 0.020 0.002 PHE F 149 TYR 0.044 0.002 TYR B 159 ARG 0.034 0.001 ARG F 214 Details of bonding type rmsd hydrogen bonds : bond 0.17012 ( 658) hydrogen bonds : angle 6.76064 ( 1911) covalent geometry : bond 0.00685 (14163) covalent geometry : angle 1.10957 (19237) *********************** 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 : 1.696 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: 0.6550 (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: 0.8049 (mt) REVERT: A 47 ASP cc_start: 0.7806 (p0) cc_final: 0.7425 (p0) REVERT: A 91 GLN cc_start: 0.7981 (pt0) cc_final: 0.7693 (pt0) REVERT: A 154 MET cc_start: 0.7926 (mmm) cc_final: 0.7575 (mmm) REVERT: A 166 LYS cc_start: 0.7372 (mtmm) cc_final: 0.7122 (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: 0.7068 (mmp) REVERT: A 215 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6899 (mtt180) REVERT: A 237 SER cc_start: 0.8445 (m) cc_final: 0.8068 (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: 0.7514 (mp) REVERT: A 276 ILE cc_start: 0.8579 (tp) cc_final: 0.8179 (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: 0.8095 (tppt) REVERT: A 309 HIS cc_start: 0.6596 (m-70) cc_final: 0.6187 (m-70) REVERT: A 311 LYS cc_start: 0.8277 (mttp) cc_final: 0.7794 (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: 0.7493 (t) REVERT: A 391 LEU cc_start: 0.7596 (mm) cc_final: 0.7384 (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: 0.7039 (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: 0.6970 (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: 0.7173 (m-40) REVERT: B 122 LYS cc_start: 0.7538 (tttt) cc_final: 0.7249 (tmtt) REVERT: B 209 ASP cc_start: 0.7650 (t70) cc_final: 0.7074 (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: 0.7706 (m-40) REVERT: B 280 GLN cc_start: 0.7487 (mt0) cc_final: 0.6996 (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: 0.7422 (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: 0.7535 (tt) REVERT: B 415 MET cc_start: 0.7867 (mmm) cc_final: 0.7286 (tpt) REVERT: E 1 MET cc_start: 0.6013 (ptm) cc_final: 0.5676 (ptm) REVERT: E 3 GLU cc_start: 0.6937 (mp0) cc_final: 0.6098 (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: 0.7804 (m-80) REVERT: E 59 TYR cc_start: 0.8187 (m-80) cc_final: 0.7561 (m-80) REVERT: E 65 LEU cc_start: 0.8376 (mp) cc_final: 0.8114 (mt) REVERT: E 69 GLU cc_start: 0.6656 (tt0) cc_final: 0.6312 (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: 0.7364 (mmtm) REVERT: E 164 MET cc_start: 0.5874 (mpp) cc_final: 0.5525 (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: 0.7161 (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: 0.6007 (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: 0.7503 (pt0) REVERT: E 280 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7714 (mm-40) REVERT: E 288 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6325 (tm-30) REVERT: E 299 MET cc_start: 0.6110 (mmm) cc_final: 0.5656 (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: 0.7547 (t80) REVERT: E 394 PHE cc_start: 0.8003 (m-80) cc_final: 0.7573 (m-80) REVERT: E 405 GLU cc_start: 0.7140 (tt0) cc_final: 0.6479 (mt-10) REVERT: E 413 SER cc_start: 0.8074 (m) cc_final: 0.7507 (p) REVERT: F 3 GLU cc_start: 0.6198 (mp0) cc_final: 0.5983 (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: 0.7554 (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: 0.7509 (m) REVERT: F 248 LEU cc_start: 0.7730 (mp) cc_final: 0.7523 (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: 0.6872 (m) REVERT: F 320 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7635 (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: 0.6478 (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: 0.3244 time to fit residues: 248.4833 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 : 1.348 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN B 6 HIS 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 227 HIS E 245 GLN E 292 GLN E 298 ASN E 307 HIS F 31 GLN F 91 GLN F 197 HIS F 233 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.131128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117070 restraints weight = 19348.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.121167 restraints weight = 8697.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.123867 restraints weight = 4672.968| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14163 Z= 0.229 Angle : 0.686 9.179 19237 Z= 0.353 Chirality : 0.049 0.178 2106 Planarity : 0.006 0.092 2502 Dihedral : 10.070 163.206 1994 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.90 % Allowed : 15.34 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1738 helix: 0.68 (0.18), residues: 769 sheet: -1.86 (0.28), residues: 284 loop : -1.05 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 407 HIS 0.008 0.001 HIS E 190 PHE 0.017 0.002 PHE F 267 TYR 0.024 0.002 TYR E 36 ARG 0.006 0.001 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.05465 ( 658) hydrogen bonds : angle 4.98982 ( 1911) covalent geometry : bond 0.00501 (14163) covalent geometry : angle 0.68596 (19237) *********************** 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 601 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 543 time to evaluate : 1.426 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 47 ASP cc_start: 0.7795 (p0) cc_final: 0.7585 (p0) REVERT: A 67 PHE cc_start: 0.8266 (m-80) cc_final: 0.8055 (m-80) REVERT: A 91 GLN cc_start: 0.8116 (pt0) cc_final: 0.7839 (pt0) REVERT: A 154 MET cc_start: 0.7742 (mmm) cc_final: 0.7018 (mmm) REVERT: A 166 LYS cc_start: 0.7611 (mtmm) cc_final: 0.7377 (mttp) REVERT: A 168 GLU cc_start: 0.6145 (mp0) cc_final: 0.5926 (mp0) REVERT: A 176 GLN cc_start: 0.7212 (pm20) cc_final: 0.6748 (pm20) REVERT: A 187 SER cc_start: 0.8252 (m) cc_final: 0.7790 (p) REVERT: A 215 ARG cc_start: 0.7268 (mtt180) cc_final: 0.7018 (mtt180) REVERT: A 226 ASN cc_start: 0.7341 (m110) cc_final: 0.7030 (m110) REVERT: A 237 SER cc_start: 0.8635 (m) cc_final: 0.8358 (t) REVERT: A 239 THR cc_start: 0.8012 (p) cc_final: 0.7652 (t) REVERT: A 254 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6652 (mt-10) REVERT: A 259 LEU cc_start: 0.7870 (tp) cc_final: 0.7585 (tt) REVERT: A 284 GLU cc_start: 0.7544 (tt0) cc_final: 0.7074 (tm-30) REVERT: A 290 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 304 LYS cc_start: 0.8157 (tppt) cc_final: 0.7894 (tppt) REVERT: A 309 HIS cc_start: 0.6684 (m-70) cc_final: 0.6325 (m-70) REVERT: A 311 LYS cc_start: 0.8222 (mttp) cc_final: 0.7973 (mttt) REVERT: A 370 LYS cc_start: 0.8293 (tptp) cc_final: 0.8073 (tptp) REVERT: A 376 CYS cc_start: 0.8113 (t) cc_final: 0.7866 (t) REVERT: A 401 LYS cc_start: 0.6328 (ptpp) cc_final: 0.6065 (ptpp) REVERT: A 402 ARG cc_start: 0.7189 (mpt180) cc_final: 0.6963 (mmt-90) REVERT: A 405 VAL cc_start: 0.8235 (m) cc_final: 0.7966 (t) REVERT: A 424 ASP cc_start: 0.6516 (m-30) cc_final: 0.6281 (m-30) REVERT: B 73 MET cc_start: 0.7489 (mmm) cc_final: 0.6953 (mmm) REVERT: B 86 ARG cc_start: 0.7722 (mtt180) cc_final: 0.6833 (tpm170) REVERT: B 99 ASN cc_start: 0.7987 (m-40) cc_final: 0.7476 (m-40) REVERT: B 108 GLU cc_start: 0.6514 (tm-30) cc_final: 0.6256 (tm-30) REVERT: B 122 LYS cc_start: 0.7765 (tttt) cc_final: 0.7388 (tmtt) REVERT: B 209 ASP cc_start: 0.7719 (t70) cc_final: 0.7380 (t0) REVERT: B 213 ARG cc_start: 0.7322 (ptm160) cc_final: 0.6990 (ptm160) REVERT: B 221 THR cc_start: 0.8356 (t) cc_final: 0.8113 (p) REVERT: B 241 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8507 (mtm-85) REVERT: B 247 ASN cc_start: 0.7897 (m110) cc_final: 0.7598 (m-40) REVERT: B 279 GLN cc_start: 0.8048 (pm20) cc_final: 0.7574 (pp30) REVERT: B 298 ASN cc_start: 0.7008 (t0) cc_final: 0.6735 (t0) REVERT: B 318 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7361 (mtp-110) REVERT: B 375 GLN cc_start: 0.7869 (pt0) cc_final: 0.7655 (pt0) REVERT: B 415 MET cc_start: 0.8080 (mmm) cc_final: 0.7850 (tpt) REVERT: E 1 MET cc_start: 0.5495 (ptm) cc_final: 0.5253 (ptm) REVERT: E 3 GLU cc_start: 0.6878 (mp0) cc_final: 0.6364 (mp0) REVERT: E 4 ILE cc_start: 0.8689 (mm) cc_final: 0.8416 (mt) REVERT: E 19 LYS cc_start: 0.7577 (tptm) cc_final: 0.7345 (tptm) REVERT: E 41 ASP cc_start: 0.7426 (t0) cc_final: 0.7125 (t0) REVERT: E 53 GLU cc_start: 0.6761 (tp30) cc_final: 0.6538 (tp30) REVERT: E 69 GLU cc_start: 0.6865 (tt0) cc_final: 0.6551 (tt0) REVERT: E 108 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6787 (tm-30) REVERT: E 123 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7359 (mm-30) REVERT: E 137 HIS cc_start: 0.7644 (p90) cc_final: 0.7417 (p90) REVERT: E 154 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7510 (mmtm) REVERT: E 175 VAL cc_start: 0.8036 (m) cc_final: 0.7709 (t) REVERT: E 192 LEU cc_start: 0.8156 (tp) cc_final: 0.7936 (tp) REVERT: E 216 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8018 (mmtt) REVERT: E 225 LEU cc_start: 0.8383 (mp) cc_final: 0.8064 (mp) REVERT: E 279 GLN cc_start: 0.7772 (pt0) cc_final: 0.7542 (pt0) REVERT: E 285 THR cc_start: 0.7720 (t) cc_final: 0.7507 (t) REVERT: E 299 MET cc_start: 0.6077 (mmm) cc_final: 0.5875 (mmm) REVERT: E 300 MET cc_start: 0.8488 (mtp) cc_final: 0.8245 (mtm) REVERT: E 368 ILE cc_start: 0.8451 (mp) cc_final: 0.8230 (mp) REVERT: E 385 PHE cc_start: 0.7904 (t80) cc_final: 0.7691 (t80) REVERT: E 391 ARG cc_start: 0.4487 (ptt180) cc_final: 0.3521 (ptt180) REVERT: E 392 LYS cc_start: 0.6948 (mmtp) cc_final: 0.6697 (mmtt) REVERT: E 413 SER cc_start: 0.8162 (m) cc_final: 0.7879 (p) REVERT: F 24 TYR cc_start: 0.8003 (m-10) cc_final: 0.7551 (m-10) REVERT: F 50 ASN cc_start: 0.8172 (t0) cc_final: 0.7850 (t0) REVERT: F 51 THR cc_start: 0.8387 (p) cc_final: 0.8166 (t) REVERT: F 70 LEU cc_start: 0.7834 (mm) cc_final: 0.7527 (mt) REVERT: F 102 ASN cc_start: 0.7165 (t0) cc_final: 0.6678 (t0) REVERT: F 123 ARG cc_start: 0.6945 (tpp-160) cc_final: 0.6507 (tpp-160) REVERT: F 154 MET cc_start: 0.7212 (mmm) cc_final: 0.6916 (mmm) REVERT: F 216 ASN cc_start: 0.8257 (m-40) cc_final: 0.7981 (m-40) REVERT: F 280 LYS cc_start: 0.5833 (tptt) cc_final: 0.4324 (tptt) REVERT: F 295 CYS cc_start: 0.7424 (m) cc_final: 0.7136 (m) REVERT: F 301 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6539 (mp10) REVERT: F 304 LYS cc_start: 0.7797 (tppp) cc_final: 0.7386 (tppp) REVERT: F 306 ASP cc_start: 0.7711 (t0) cc_final: 0.7297 (t0) REVERT: F 376 CYS cc_start: 0.7671 (t) cc_final: 0.7418 (t) REVERT: F 380 ASN cc_start: 0.8004 (t0) cc_final: 0.7728 (t0) REVERT: F 391 LEU cc_start: 0.8071 (mm) cc_final: 0.7808 (tt) REVERT: F 404 PHE cc_start: 0.7938 (m-80) cc_final: 0.7695 (m-10) REVERT: F 425 MET cc_start: 0.7784 (tpp) cc_final: 0.7325 (tpt) outliers start: 58 outliers final: 36 residues processed: 561 average time/residue: 0.3049 time to fit residues: 235.2470 Evaluate side-chains 551 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 515 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 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 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 322 SER 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 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 409 THR 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 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 160 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 107 HIS B 6 HIS B 8 GLN B 423 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 18 ASN F 101 ASN F 329 ASN F 393 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.130479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116554 restraints weight = 19524.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.120648 restraints weight = 8710.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.123309 restraints weight = 4646.694| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14163 Z= 0.166 Angle : 0.609 8.828 19237 Z= 0.313 Chirality : 0.046 0.174 2106 Planarity : 0.005 0.070 2502 Dihedral : 9.948 165.392 1994 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.57 % Allowed : 18.24 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1738 helix: 0.83 (0.18), residues: 785 sheet: -1.55 (0.28), residues: 286 loop : -1.01 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 407 HIS 0.004 0.001 HIS F 406 PHE 0.017 0.002 PHE B 133 TYR 0.014 0.001 TYR E 36 ARG 0.007 0.000 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 658) hydrogen bonds : angle 4.62866 ( 1911) covalent geometry : bond 0.00367 (14163) covalent geometry : angle 0.60881 (19237) *********************** 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 592 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 539 time to evaluate : 1.668 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: A 123 ARG cc_start: 0.7129 (ttp80) cc_final: 0.6678 (ttp80) REVERT: A 154 MET cc_start: 0.7694 (mmm) cc_final: 0.7169 (mmm) REVERT: A 166 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7197 (mttp) REVERT: A 175 PRO cc_start: 0.8488 (Cg_endo) cc_final: 0.8281 (Cg_endo) REVERT: A 187 SER cc_start: 0.8195 (m) cc_final: 0.7790 (p) REVERT: A 209 ILE cc_start: 0.8329 (mm) cc_final: 0.7715 (mt) REVERT: A 211 ASP cc_start: 0.7907 (m-30) cc_final: 0.7556 (m-30) REVERT: A 215 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6995 (mtt180) REVERT: A 226 ASN cc_start: 0.7266 (m110) cc_final: 0.6999 (m110) REVERT: A 229 ARG cc_start: 0.7640 (mpt-90) cc_final: 0.7429 (mmt90) REVERT: A 237 SER cc_start: 0.8554 (m) cc_final: 0.8270 (t) REVERT: A 239 THR cc_start: 0.7913 (p) cc_final: 0.7708 (t) REVERT: A 254 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6657 (mt-10) REVERT: A 259 LEU cc_start: 0.7892 (tp) cc_final: 0.7639 (tt) REVERT: A 265 ILE cc_start: 0.7897 (mm) cc_final: 0.7667 (mm) REVERT: A 280 LYS cc_start: 0.8547 (mtmm) cc_final: 0.8305 (ptpp) REVERT: A 284 GLU cc_start: 0.7511 (tt0) cc_final: 0.7261 (tt0) REVERT: A 290 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 302 MET cc_start: 0.7918 (mmm) cc_final: 0.7498 (mmm) REVERT: A 304 LYS cc_start: 0.8126 (tppt) cc_final: 0.7897 (tppt) REVERT: A 309 HIS cc_start: 0.6696 (m-70) cc_final: 0.6323 (m-70) REVERT: A 373 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7925 (mtm-85) REVERT: A 402 ARG cc_start: 0.7131 (mpt180) cc_final: 0.6925 (mmt-90) REVERT: A 424 ASP cc_start: 0.7378 (m-30) cc_final: 0.6879 (m-30) REVERT: B 73 MET cc_start: 0.7473 (mmm) cc_final: 0.7121 (mmt) REVERT: B 86 ARG cc_start: 0.7760 (mtt180) cc_final: 0.6768 (tpm170) REVERT: B 99 ASN cc_start: 0.8008 (m-40) cc_final: 0.7600 (m-40) REVERT: B 108 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6135 (tm-30) REVERT: B 122 LYS cc_start: 0.7772 (tttt) cc_final: 0.7414 (tmtt) REVERT: B 194 GLU cc_start: 0.6713 (tp30) cc_final: 0.6505 (tp30) REVERT: B 197 ASP cc_start: 0.7282 (m-30) cc_final: 0.7025 (m-30) REVERT: B 209 ASP cc_start: 0.7683 (t70) cc_final: 0.7297 (t0) REVERT: B 213 ARG cc_start: 0.7304 (ptm160) cc_final: 0.7019 (ptm160) REVERT: B 237 THR cc_start: 0.8165 (p) cc_final: 0.7866 (t) REVERT: B 241 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8601 (mtm-85) REVERT: B 298 ASN cc_start: 0.6981 (t0) cc_final: 0.6509 (t0) REVERT: B 318 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7652 (mtp-110) REVERT: B 415 MET cc_start: 0.8042 (mmm) cc_final: 0.7823 (tpt) REVERT: B 418 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8106 (tp) REVERT: E 3 GLU cc_start: 0.6894 (mp0) cc_final: 0.6271 (mp0) REVERT: E 4 ILE cc_start: 0.8620 (mm) cc_final: 0.8418 (mt) REVERT: E 41 ASP cc_start: 0.7428 (t0) cc_final: 0.7062 (t0) REVERT: E 108 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6905 (tm-30) REVERT: E 175 VAL cc_start: 0.7963 (m) cc_final: 0.7365 (t) REVERT: E 197 ASP cc_start: 0.7664 (m-30) cc_final: 0.7128 (m-30) REVERT: E 216 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8026 (mmtt) REVERT: E 251 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7336 (tpp80) REVERT: E 257 MET cc_start: 0.6894 (mpp) cc_final: 0.6328 (mpp) REVERT: E 279 GLN cc_start: 0.7741 (pt0) cc_final: 0.7461 (pt0) REVERT: E 300 MET cc_start: 0.8402 (mtp) cc_final: 0.8152 (mtm) REVERT: E 385 PHE cc_start: 0.7905 (t80) cc_final: 0.7689 (t80) REVERT: E 391 ARG cc_start: 0.4886 (ptt180) cc_final: 0.3616 (ptt90) REVERT: E 399 THR cc_start: 0.7924 (m) cc_final: 0.6880 (t) REVERT: E 413 SER cc_start: 0.8164 (m) cc_final: 0.7936 (p) REVERT: F 3 GLU cc_start: 0.6599 (mp0) cc_final: 0.6063 (mp0) REVERT: F 24 TYR cc_start: 0.8044 (m-10) cc_final: 0.7738 (m-10) REVERT: F 50 ASN cc_start: 0.8174 (t0) cc_final: 0.7430 (t0) REVERT: F 51 THR cc_start: 0.8333 (p) cc_final: 0.8110 (t) REVERT: F 70 LEU cc_start: 0.7862 (mm) cc_final: 0.7579 (mt) REVERT: F 77 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6734 (tm-30) REVERT: F 97 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6684 (tm-30) REVERT: F 102 ASN cc_start: 0.7094 (t0) cc_final: 0.6618 (t0) REVERT: F 123 ARG cc_start: 0.7064 (tpp-160) cc_final: 0.6472 (tpp-160) REVERT: F 248 LEU cc_start: 0.8080 (mp) cc_final: 0.7811 (mt) REVERT: F 295 CYS cc_start: 0.7348 (m) cc_final: 0.7014 (m) REVERT: F 301 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6635 (mp10) REVERT: F 306 ASP cc_start: 0.7725 (t0) cc_final: 0.7404 (t0) REVERT: F 352 LYS cc_start: 0.8026 (tptt) cc_final: 0.6275 (mmtt) REVERT: F 367 ASP cc_start: 0.7351 (t0) cc_final: 0.6958 (t0) REVERT: F 391 LEU cc_start: 0.8097 (mm) cc_final: 0.7816 (tt) outliers start: 53 outliers final: 37 residues processed: 556 average time/residue: 0.3043 time to fit residues: 231.9388 Evaluate side-chains 560 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 522 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 276 ILE Chi-restraints excluded: chain A residue 375 VAL 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 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 27 GLU 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 131 GLN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 338 SER 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 237 SER 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 37 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 176 GLN B 43 GLN B 137 HIS B 292 GLN B 334 GLN B 424 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 245 GLN E 396 HIS F 88 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.127781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.114144 restraints weight = 19662.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.118186 restraints weight = 8769.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.120799 restraints weight = 4675.113| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14163 Z= 0.217 Angle : 0.630 8.515 19237 Z= 0.325 Chirality : 0.047 0.173 2106 Planarity : 0.005 0.060 2502 Dihedral : 10.026 165.358 1994 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.77 % Allowed : 21.87 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1738 helix: 0.93 (0.19), residues: 774 sheet: -1.36 (0.29), residues: 287 loop : -0.93 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS A 107 PHE 0.013 0.002 PHE F 255 TYR 0.016 0.002 TYR F 312 ARG 0.008 0.000 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 658) hydrogen bonds : angle 4.53979 ( 1911) covalent geometry : bond 0.00474 (14163) covalent geometry : angle 0.63033 (19237) *********************** 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 591 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 535 time to evaluate : 1.619 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: 0.7871 (m-80) cc_final: 0.7509 (m-80) REVERT: A 67 PHE cc_start: 0.8298 (m-80) cc_final: 0.7959 (m-80) REVERT: A 120 ASP cc_start: 0.7197 (m-30) cc_final: 0.6806 (t0) REVERT: A 154 MET cc_start: 0.7674 (mmm) cc_final: 0.7151 (mmm) REVERT: A 166 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7141 (mttp) REVERT: A 175 PRO cc_start: 0.8537 (Cg_endo) cc_final: 0.8337 (Cg_endo) REVERT: A 187 SER cc_start: 0.8304 (m) cc_final: 0.7874 (p) REVERT: A 209 ILE cc_start: 0.8385 (mm) cc_final: 0.7898 (mt) REVERT: A 211 ASP cc_start: 0.7933 (m-30) cc_final: 0.7660 (m-30) REVERT: A 215 ARG cc_start: 0.7293 (mtt180) cc_final: 0.7019 (mtt180) REVERT: A 226 ASN cc_start: 0.7464 (m110) cc_final: 0.7166 (m110) REVERT: A 229 ARG cc_start: 0.7761 (mpt-90) cc_final: 0.7512 (mmt90) REVERT: A 237 SER cc_start: 0.8601 (m) cc_final: 0.8280 (t) REVERT: A 254 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6737 (mt-10) REVERT: A 284 GLU cc_start: 0.7551 (tt0) cc_final: 0.7015 (tm-30) REVERT: A 290 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 302 MET cc_start: 0.7948 (mmm) cc_final: 0.7567 (mmm) REVERT: A 304 LYS cc_start: 0.8158 (tppt) cc_final: 0.7916 (tppt) REVERT: A 309 HIS cc_start: 0.6720 (m-70) cc_final: 0.6293 (m-70) REVERT: A 313 MET cc_start: 0.7634 (ttm) cc_final: 0.7409 (mtp) REVERT: A 424 ASP cc_start: 0.7474 (m-30) cc_final: 0.7246 (m-30) REVERT: B 73 MET cc_start: 0.7530 (mmm) cc_final: 0.7233 (mmm) REVERT: B 86 ARG cc_start: 0.7805 (mtt180) cc_final: 0.6792 (tpm170) REVERT: B 99 ASN cc_start: 0.8089 (m-40) cc_final: 0.7716 (m-40) REVERT: B 108 GLU cc_start: 0.6561 (tm-30) cc_final: 0.6149 (tm-30) REVERT: B 164 MET cc_start: 0.6455 (tpp) cc_final: 0.6235 (tpp) REVERT: B 194 GLU cc_start: 0.6715 (tp30) cc_final: 0.6496 (tp30) REVERT: B 209 ASP cc_start: 0.7702 (t70) cc_final: 0.7315 (t0) REVERT: B 213 ARG cc_start: 0.7290 (ptm160) cc_final: 0.7009 (ptm160) REVERT: B 237 THR cc_start: 0.8189 (p) cc_final: 0.7840 (t) REVERT: B 241 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8616 (mtm-85) REVERT: B 265 PHE cc_start: 0.8505 (m-80) cc_final: 0.8295 (m-80) REVERT: B 318 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7886 (mtm-85) REVERT: B 380 ARG cc_start: 0.7109 (ptp-170) cc_final: 0.6812 (ptp-170) REVERT: B 415 MET cc_start: 0.8085 (mmm) cc_final: 0.7837 (tpt) REVERT: E 3 GLU cc_start: 0.6935 (mp0) cc_final: 0.6235 (mp0) REVERT: E 41 ASP cc_start: 0.7501 (t0) cc_final: 0.7083 (t0) REVERT: E 108 GLU cc_start: 0.7622 (tm-30) cc_final: 0.6875 (tm-30) REVERT: E 154 LYS cc_start: 0.7762 (mmtm) cc_final: 0.7554 (mmtp) REVERT: E 175 VAL cc_start: 0.7998 (m) cc_final: 0.7695 (t) REVERT: E 197 ASP cc_start: 0.7697 (m-30) cc_final: 0.7328 (m-30) REVERT: E 199 THR cc_start: 0.8020 (m) cc_final: 0.7722 (p) REVERT: E 225 LEU cc_start: 0.8371 (mp) cc_final: 0.8132 (mp) REVERT: E 251 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7346 (tpp80) REVERT: E 257 MET cc_start: 0.6843 (mpp) cc_final: 0.6146 (mpp) REVERT: E 262 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6840 (mtp180) REVERT: E 279 GLN cc_start: 0.7675 (pt0) cc_final: 0.7301 (pt0) REVERT: E 285 THR cc_start: 0.7748 (t) cc_final: 0.7379 (p) REVERT: E 391 ARG cc_start: 0.5145 (ptt180) cc_final: 0.3602 (ptt90) REVERT: E 392 LYS cc_start: 0.7017 (mptt) cc_final: 0.6400 (mptt) REVERT: E 399 THR cc_start: 0.7884 (m) cc_final: 0.6867 (t) REVERT: E 405 GLU cc_start: 0.7366 (tt0) cc_final: 0.7002 (mt-10) REVERT: E 413 SER cc_start: 0.8139 (m) cc_final: 0.7894 (p) REVERT: E 421 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6999 (mm-30) REVERT: F 3 GLU cc_start: 0.6646 (mp0) cc_final: 0.6232 (mp0) REVERT: F 24 TYR cc_start: 0.8010 (m-10) cc_final: 0.7615 (m-10) REVERT: F 69 ASP cc_start: 0.7931 (t0) cc_final: 0.7504 (t0) REVERT: F 70 LEU cc_start: 0.7872 (mm) cc_final: 0.7459 (mt) REVERT: F 77 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6808 (tm-30) REVERT: F 97 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6799 (tm-30) REVERT: F 114 ILE cc_start: 0.8197 (mm) cc_final: 0.7987 (mm) REVERT: F 123 ARG cc_start: 0.7109 (tpp-160) cc_final: 0.6569 (tpp-160) REVERT: F 164 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7917 (mmtp) REVERT: F 248 LEU cc_start: 0.8070 (mp) cc_final: 0.7789 (mt) REVERT: F 301 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6699 (mt0) REVERT: F 306 ASP cc_start: 0.7725 (t0) cc_final: 0.7308 (t0) REVERT: F 326 LYS cc_start: 0.5316 (mttt) cc_final: 0.5054 (mttp) REVERT: F 342 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7664 (mm110) REVERT: F 352 LYS cc_start: 0.7997 (tptt) cc_final: 0.6302 (mmtt) REVERT: F 367 ASP cc_start: 0.7328 (t0) cc_final: 0.7027 (t0) REVERT: F 425 MET cc_start: 0.8255 (mmm) cc_final: 0.7591 (tpt) REVERT: F 432 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.5969 (t80) REVERT: F 434 GLU cc_start: 0.7996 (tt0) cc_final: 0.7774 (tt0) outliers start: 56 outliers final: 40 residues processed: 548 average time/residue: 0.3167 time to fit residues: 236.4595 Evaluate side-chains 555 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 514 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU 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 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 375 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 31 ASP 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 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 27 GLU 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 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 330 MET 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 179 THR Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 286 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 54 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 124 optimal weight: 0.0370 chunk 19 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 143 optimal weight: 0.7980 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 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 137 HIS B 291 GLN B 329 GLN B 334 GLN B 424 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.129411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115669 restraints weight = 19817.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119748 restraints weight = 8847.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122401 restraints weight = 4730.476| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14163 Z= 0.149 Angle : 0.584 9.781 19237 Z= 0.300 Chirality : 0.045 0.170 2106 Planarity : 0.004 0.055 2502 Dihedral : 9.790 166.430 1994 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.90 % Allowed : 23.15 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1738 helix: 1.05 (0.19), residues: 781 sheet: -1.14 (0.29), residues: 283 loop : -0.85 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.018 0.001 PHE E 385 TYR 0.019 0.001 TYR A 103 ARG 0.009 0.000 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 658) hydrogen bonds : angle 4.36546 ( 1911) covalent geometry : bond 0.00330 (14163) covalent geometry : angle 0.58440 (19237) *********************** 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 586 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 528 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7793 (m-80) cc_final: 0.7354 (m-80) REVERT: A 67 PHE cc_start: 0.8259 (m-80) cc_final: 0.7880 (m-80) REVERT: A 120 ASP cc_start: 0.7225 (m-30) cc_final: 0.6695 (t0) REVERT: A 154 MET cc_start: 0.7666 (mmm) cc_final: 0.7231 (mmm) REVERT: A 166 LYS cc_start: 0.7580 (mtmm) cc_final: 0.7152 (mttp) REVERT: A 187 SER cc_start: 0.8258 (m) cc_final: 0.7811 (p) REVERT: A 209 ILE cc_start: 0.8387 (mm) cc_final: 0.7879 (mt) REVERT: A 211 ASP cc_start: 0.7878 (m-30) cc_final: 0.7596 (m-30) REVERT: A 215 ARG cc_start: 0.7289 (mtt180) cc_final: 0.7008 (mtt180) REVERT: A 226 ASN cc_start: 0.7281 (m110) cc_final: 0.7022 (m110) REVERT: A 229 ARG cc_start: 0.7713 (mpt-90) cc_final: 0.7455 (mmt90) REVERT: A 237 SER cc_start: 0.8578 (m) cc_final: 0.8260 (t) REVERT: A 254 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 265 ILE cc_start: 0.7802 (mm) cc_final: 0.7588 (mm) REVERT: A 284 GLU cc_start: 0.7544 (tt0) cc_final: 0.7267 (tt0) REVERT: A 290 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6954 (mt-10) REVERT: A 302 MET cc_start: 0.7919 (mmm) cc_final: 0.7556 (mmm) REVERT: A 304 LYS cc_start: 0.8125 (tppt) cc_final: 0.7915 (tppt) REVERT: A 309 HIS cc_start: 0.6677 (m-70) cc_final: 0.6273 (m-70) REVERT: A 313 MET cc_start: 0.7624 (ttm) cc_final: 0.7418 (mtp) REVERT: B 53 GLU cc_start: 0.6997 (tp30) cc_final: 0.6711 (tp30) REVERT: B 73 MET cc_start: 0.7542 (mmm) cc_final: 0.7273 (mmm) REVERT: B 86 ARG cc_start: 0.7742 (mtt180) cc_final: 0.6834 (tpm170) REVERT: B 99 ASN cc_start: 0.8031 (m-40) cc_final: 0.7672 (m-40) REVERT: B 108 GLU cc_start: 0.6434 (tm-30) cc_final: 0.5960 (tm-30) REVERT: B 122 LYS cc_start: 0.7843 (tmtt) cc_final: 0.7510 (tmtt) REVERT: B 194 GLU cc_start: 0.6702 (tp30) cc_final: 0.6224 (tp30) REVERT: B 195 ASN cc_start: 0.7792 (m-40) cc_final: 0.7552 (m-40) REVERT: B 197 ASP cc_start: 0.7416 (m-30) cc_final: 0.7091 (m-30) REVERT: B 209 ASP cc_start: 0.7714 (t70) cc_final: 0.7316 (t0) REVERT: B 213 ARG cc_start: 0.7260 (ptm160) cc_final: 0.7027 (ptm160) REVERT: B 237 THR cc_start: 0.8156 (p) cc_final: 0.7847 (t) REVERT: B 241 ARG cc_start: 0.8825 (mtp180) cc_final: 0.8608 (mtp180) REVERT: B 265 PHE cc_start: 0.8554 (m-80) cc_final: 0.8341 (m-80) REVERT: B 309 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6441 (mtt-85) REVERT: B 318 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7442 (mtm-85) REVERT: B 380 ARG cc_start: 0.7093 (ptp-170) cc_final: 0.6795 (ptp-170) REVERT: B 391 ARG cc_start: 0.6616 (tpp80) cc_final: 0.6300 (mmt90) REVERT: B 418 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8154 (tp) REVERT: E 3 GLU cc_start: 0.6903 (mp0) cc_final: 0.6267 (mp0) REVERT: E 108 GLU cc_start: 0.7616 (tm-30) cc_final: 0.6909 (tm-30) REVERT: E 175 VAL cc_start: 0.7936 (m) cc_final: 0.7369 (t) REVERT: E 197 ASP cc_start: 0.7750 (m-30) cc_final: 0.7464 (m-30) REVERT: E 199 THR cc_start: 0.8007 (m) cc_final: 0.7756 (p) REVERT: E 225 LEU cc_start: 0.8348 (mp) cc_final: 0.8106 (mp) REVERT: E 251 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7441 (tpp80) REVERT: E 257 MET cc_start: 0.6802 (mpp) cc_final: 0.6178 (mpp) REVERT: E 262 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6733 (mtp-110) REVERT: E 279 GLN cc_start: 0.7672 (pt0) cc_final: 0.7400 (pt0) REVERT: E 391 ARG cc_start: 0.5322 (ptt180) cc_final: 0.3839 (ptt90) REVERT: E 392 LYS cc_start: 0.6792 (mptt) cc_final: 0.6142 (mptt) REVERT: E 399 THR cc_start: 0.7853 (m) cc_final: 0.6823 (t) REVERT: E 405 GLU cc_start: 0.7305 (tt0) cc_final: 0.6740 (mt-10) REVERT: F 3 GLU cc_start: 0.6569 (mp0) cc_final: 0.6111 (mp0) REVERT: F 24 TYR cc_start: 0.7975 (m-10) cc_final: 0.7698 (m-10) REVERT: F 69 ASP cc_start: 0.7926 (t0) cc_final: 0.7466 (t0) REVERT: F 70 LEU cc_start: 0.7844 (mm) cc_final: 0.7426 (mt) REVERT: F 77 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6794 (tm-30) REVERT: F 78 VAL cc_start: 0.8029 (t) cc_final: 0.7644 (t) REVERT: F 123 ARG cc_start: 0.7079 (tpp-160) cc_final: 0.6523 (tpp-160) REVERT: F 155 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6626 (mm-30) REVERT: F 164 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7768 (mmtp) REVERT: F 248 LEU cc_start: 0.7999 (mp) cc_final: 0.7764 (mt) REVERT: F 254 GLU cc_start: 0.1523 (OUTLIER) cc_final: -0.1447 (mt-10) REVERT: F 301 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6571 (mp10) REVERT: F 306 ASP cc_start: 0.7689 (t0) cc_final: 0.7347 (t0) REVERT: F 326 LYS cc_start: 0.5243 (mttt) cc_final: 0.4994 (mttp) REVERT: F 352 LYS cc_start: 0.7988 (tptt) cc_final: 0.7042 (tppt) REVERT: F 367 ASP cc_start: 0.7335 (t0) cc_final: 0.7082 (t0) REVERT: F 432 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6017 (t80) REVERT: F 434 GLU cc_start: 0.7933 (tt0) cc_final: 0.7622 (tt0) outliers start: 58 outliers final: 38 residues processed: 546 average time/residue: 0.3216 time to fit residues: 239.5013 Evaluate side-chains 554 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 513 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU 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 375 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 218 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS 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 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 330 MET 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 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 179 THR 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 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 131 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 176 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 137 HIS B 256 ASN B 424 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 88 HIS ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.128808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.115364 restraints weight = 19784.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.119379 restraints weight = 8814.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.121972 restraints weight = 4685.458| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14163 Z= 0.164 Angle : 0.597 9.813 19237 Z= 0.307 Chirality : 0.045 0.174 2106 Planarity : 0.004 0.052 2502 Dihedral : 9.778 167.079 1994 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.51 % Allowed : 23.55 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1738 helix: 1.19 (0.19), residues: 769 sheet: -1.05 (0.28), residues: 294 loop : -0.77 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.006 0.001 HIS F 88 PHE 0.015 0.001 PHE B 367 TYR 0.015 0.001 TYR A 103 ARG 0.008 0.000 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 658) hydrogen bonds : angle 4.30222 ( 1911) covalent geometry : bond 0.00361 (14163) covalent geometry : angle 0.59656 (19237) *********************** 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 587 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 520 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8230 (m-80) cc_final: 0.7829 (m-80) REVERT: A 120 ASP cc_start: 0.7240 (m-30) cc_final: 0.6722 (t0) REVERT: A 154 MET cc_start: 0.7655 (mmm) cc_final: 0.7216 (mmm) REVERT: A 166 LYS cc_start: 0.7575 (mtmm) cc_final: 0.7107 (mttp) REVERT: A 187 SER cc_start: 0.8260 (m) cc_final: 0.7784 (p) REVERT: A 209 ILE cc_start: 0.8392 (mm) cc_final: 0.7897 (mt) REVERT: A 211 ASP cc_start: 0.7890 (m-30) cc_final: 0.7601 (m-30) REVERT: A 215 ARG cc_start: 0.7324 (mtt180) cc_final: 0.7021 (mtt180) REVERT: A 226 ASN cc_start: 0.7348 (m110) cc_final: 0.7107 (m110) REVERT: A 237 SER cc_start: 0.8535 (m) cc_final: 0.8215 (t) REVERT: A 254 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 302 MET cc_start: 0.7965 (mmm) cc_final: 0.7566 (mmm) REVERT: A 309 HIS cc_start: 0.6716 (m-70) cc_final: 0.6339 (m-70) REVERT: A 424 ASP cc_start: 0.7591 (m-30) cc_final: 0.7296 (m-30) REVERT: B 53 GLU cc_start: 0.7048 (tp30) cc_final: 0.6724 (tp30) REVERT: B 73 MET cc_start: 0.7577 (mmm) cc_final: 0.7340 (mmm) REVERT: B 86 ARG cc_start: 0.7741 (mtt180) cc_final: 0.6731 (mmp-170) REVERT: B 99 ASN cc_start: 0.8092 (m-40) cc_final: 0.7793 (m-40) REVERT: B 108 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6131 (tm-30) REVERT: B 194 GLU cc_start: 0.6680 (tp30) cc_final: 0.6233 (tp30) REVERT: B 195 ASN cc_start: 0.7813 (m-40) cc_final: 0.7573 (m-40) REVERT: B 197 ASP cc_start: 0.7439 (m-30) cc_final: 0.7127 (m-30) REVERT: B 209 ASP cc_start: 0.7768 (t70) cc_final: 0.7338 (t0) REVERT: B 237 THR cc_start: 0.8207 (p) cc_final: 0.7816 (t) REVERT: B 241 ARG cc_start: 0.8830 (mtp180) cc_final: 0.8588 (mtm-85) REVERT: B 297 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7449 (mtmm) REVERT: B 318 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7779 (mtp-110) REVERT: B 380 ARG cc_start: 0.7103 (ptp-170) cc_final: 0.6813 (ptp-170) REVERT: B 391 ARG cc_start: 0.6754 (tpp80) cc_final: 0.6391 (mpt180) REVERT: B 418 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 421 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7551 (mt-10) REVERT: E 108 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 175 VAL cc_start: 0.7979 (m) cc_final: 0.7587 (t) REVERT: E 197 ASP cc_start: 0.7740 (m-30) cc_final: 0.7478 (m-30) REVERT: E 199 THR cc_start: 0.8039 (m) cc_final: 0.7741 (p) REVERT: E 209 ASP cc_start: 0.7877 (t0) cc_final: 0.5536 (t70) REVERT: E 213 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6504 (mtm180) REVERT: E 225 LEU cc_start: 0.8356 (mp) cc_final: 0.8103 (mp) REVERT: E 251 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7448 (tpp80) REVERT: E 257 MET cc_start: 0.6827 (mpp) cc_final: 0.6145 (mpp) REVERT: E 262 ARG cc_start: 0.6959 (mtp180) cc_final: 0.6719 (mtp-110) REVERT: E 279 GLN cc_start: 0.7666 (pt0) cc_final: 0.7274 (pt0) REVERT: E 324 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6590 (tmtt) REVERT: E 366 THR cc_start: 0.8372 (m) cc_final: 0.8143 (t) REVERT: E 391 ARG cc_start: 0.5294 (ptt180) cc_final: 0.3404 (ptt-90) REVERT: E 399 THR cc_start: 0.7830 (m) cc_final: 0.6820 (t) REVERT: E 405 GLU cc_start: 0.7326 (tt0) cc_final: 0.6797 (tt0) REVERT: F 3 GLU cc_start: 0.6575 (mp0) cc_final: 0.5987 (mp0) REVERT: F 24 TYR cc_start: 0.7964 (m-10) cc_final: 0.7681 (m-10) REVERT: F 50 ASN cc_start: 0.7940 (t0) cc_final: 0.6964 (t0) REVERT: F 69 ASP cc_start: 0.7861 (t0) cc_final: 0.7426 (t0) REVERT: F 70 LEU cc_start: 0.7867 (mm) cc_final: 0.7449 (mt) REVERT: F 77 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6763 (tm-30) REVERT: F 78 VAL cc_start: 0.8026 (t) cc_final: 0.7580 (t) REVERT: F 123 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6775 (tpp-160) REVERT: F 155 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6510 (mm-30) REVERT: F 161 TYR cc_start: 0.8177 (m-80) cc_final: 0.7833 (m-10) REVERT: F 248 LEU cc_start: 0.8062 (mp) cc_final: 0.7802 (mt) REVERT: F 301 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6589 (mp10) REVERT: F 306 ASP cc_start: 0.7704 (t0) cc_final: 0.7338 (t0) REVERT: F 326 LYS cc_start: 0.5228 (mttt) cc_final: 0.5005 (mttp) REVERT: F 342 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7759 (mm110) REVERT: F 352 LYS cc_start: 0.7989 (tptt) cc_final: 0.7066 (tppt) REVERT: F 367 ASP cc_start: 0.7352 (t0) cc_final: 0.7133 (t0) REVERT: F 417 GLU cc_start: 0.6602 (tt0) cc_final: 0.6345 (tt0) REVERT: F 432 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.5942 (t80) REVERT: F 434 GLU cc_start: 0.7944 (tt0) cc_final: 0.7579 (tt0) outliers start: 67 outliers final: 47 residues processed: 543 average time/residue: 0.3079 time to fit residues: 229.9601 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 : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU 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 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 8 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 SER 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 288 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS 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 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL 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 407 GLU 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 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 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 5 optimal weight: 0.3980 chunk 149 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 152 optimal weight: 0.0000 chunk 99 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 102 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS E 100 ASN F 88 HIS F 258 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.128096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114289 restraints weight = 19860.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.118419 restraints weight = 8729.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.121076 restraints weight = 4624.008| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4099 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= 0.126 Angle : 0.580 10.017 19237 Z= 0.296 Chirality : 0.044 0.162 2106 Planarity : 0.004 0.050 2502 Dihedral : 9.638 167.599 1994 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.84 % Allowed : 25.24 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1738 helix: 1.12 (0.19), residues: 783 sheet: -0.95 (0.30), residues: 270 loop : -0.80 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 346 HIS 0.005 0.001 HIS F 88 PHE 0.017 0.001 PHE B 367 TYR 0.012 0.001 TYR A 103 ARG 0.009 0.000 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 658) hydrogen bonds : angle 4.23833 ( 1911) covalent geometry : bond 0.00282 (14163) covalent geometry : angle 0.57963 (19237) *********************** 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 578 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 521 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7757 (m-80) cc_final: 0.7463 (m-80) REVERT: A 67 PHE cc_start: 0.8211 (m-80) cc_final: 0.7828 (m-80) REVERT: A 118 VAL cc_start: 0.8282 (p) cc_final: 0.8058 (m) REVERT: A 120 ASP cc_start: 0.7225 (m-30) cc_final: 0.6699 (t0) REVERT: A 154 MET cc_start: 0.7645 (mmm) cc_final: 0.7281 (mmm) REVERT: A 166 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7116 (mttp) REVERT: A 187 SER cc_start: 0.8182 (m) cc_final: 0.7794 (p) REVERT: A 209 ILE cc_start: 0.8373 (mm) cc_final: 0.7874 (mt) REVERT: A 211 ASP cc_start: 0.7785 (m-30) cc_final: 0.7493 (m-30) REVERT: A 215 ARG cc_start: 0.7258 (mtt180) cc_final: 0.6967 (mtt180) REVERT: A 226 ASN cc_start: 0.7226 (m110) cc_final: 0.6994 (m110) REVERT: A 229 ARG cc_start: 0.7736 (mpt-90) cc_final: 0.7478 (mmt90) REVERT: A 237 SER cc_start: 0.8506 (m) cc_final: 0.8196 (t) REVERT: A 254 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6736 (mt-10) REVERT: A 284 GLU cc_start: 0.7481 (tt0) cc_final: 0.7044 (tm-30) REVERT: A 290 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 297 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 302 MET cc_start: 0.7851 (mmm) cc_final: 0.7498 (mmm) REVERT: A 309 HIS cc_start: 0.6712 (m-70) cc_final: 0.6319 (m-70) REVERT: A 349 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8084 (p) REVERT: B 53 GLU cc_start: 0.7045 (tp30) cc_final: 0.6718 (tp30) REVERT: B 73 MET cc_start: 0.7564 (mmm) cc_final: 0.7349 (mmm) REVERT: B 86 ARG cc_start: 0.7730 (mtt180) cc_final: 0.6751 (mmp80) REVERT: B 99 ASN cc_start: 0.8010 (m-40) cc_final: 0.7675 (m-40) REVERT: B 100 ASN cc_start: 0.6977 (t0) cc_final: 0.6727 (t0) REVERT: B 194 GLU cc_start: 0.6689 (tp30) cc_final: 0.6239 (tp30) REVERT: B 195 ASN cc_start: 0.7836 (m-40) cc_final: 0.7598 (m-40) REVERT: B 197 ASP cc_start: 0.7356 (m-30) cc_final: 0.6975 (m-30) REVERT: B 209 ASP cc_start: 0.7752 (t70) cc_final: 0.7372 (t0) REVERT: B 237 THR cc_start: 0.8168 (p) cc_final: 0.7827 (t) REVERT: B 241 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8612 (mtm-85) REVERT: B 309 ARG cc_start: 0.7318 (mtt-85) cc_final: 0.6391 (mtt-85) REVERT: B 318 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7741 (mtp-110) REVERT: B 380 ARG cc_start: 0.7049 (ptp-170) cc_final: 0.6805 (ptp-170) REVERT: B 391 ARG cc_start: 0.6713 (tpp80) cc_final: 0.6255 (mpt180) REVERT: B 415 MET cc_start: 0.7977 (tpt) cc_final: 0.7684 (tpt) REVERT: B 418 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8195 (tp) REVERT: E 62 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7108 (mtt180) REVERT: E 108 GLU cc_start: 0.7704 (tm-30) cc_final: 0.6964 (tm-30) REVERT: E 175 VAL cc_start: 0.7920 (m) cc_final: 0.7555 (t) REVERT: E 199 THR cc_start: 0.7997 (m) cc_final: 0.7733 (p) REVERT: E 209 ASP cc_start: 0.7890 (t0) cc_final: 0.5553 (t70) REVERT: E 213 ARG cc_start: 0.7015 (mtm180) cc_final: 0.6500 (mtm180) REVERT: E 225 LEU cc_start: 0.8350 (mp) cc_final: 0.8117 (mp) REVERT: E 251 ARG cc_start: 0.7677 (tpp80) cc_final: 0.7467 (tpp80) REVERT: E 257 MET cc_start: 0.6779 (mpp) cc_final: 0.6117 (mpp) REVERT: E 279 GLN cc_start: 0.7630 (pt0) cc_final: 0.7239 (pt0) REVERT: E 324 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6393 (tmmt) REVERT: E 366 THR cc_start: 0.8323 (m) cc_final: 0.8114 (t) REVERT: E 391 ARG cc_start: 0.5266 (ptt180) cc_final: 0.3274 (ptt-90) REVERT: E 405 GLU cc_start: 0.6981 (tt0) cc_final: 0.6707 (tt0) REVERT: E 407 GLU cc_start: 0.6321 (pt0) cc_final: 0.4736 (pt0) REVERT: F 3 GLU cc_start: 0.6554 (mp0) cc_final: 0.5985 (mp0) REVERT: F 24 TYR cc_start: 0.7925 (m-10) cc_final: 0.7695 (m-10) REVERT: F 50 ASN cc_start: 0.7904 (t0) cc_final: 0.6907 (t0) REVERT: F 69 ASP cc_start: 0.7806 (t0) cc_final: 0.7424 (t0) REVERT: F 70 LEU cc_start: 0.7915 (mm) cc_final: 0.7489 (mt) REVERT: F 77 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6660 (tm-30) REVERT: F 78 VAL cc_start: 0.7949 (t) cc_final: 0.7112 (t) REVERT: F 97 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6677 (tm-30) REVERT: F 123 ARG cc_start: 0.7087 (tpp-160) cc_final: 0.6527 (tpp-160) REVERT: F 155 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6373 (mm-30) REVERT: F 239 THR cc_start: 0.8069 (m) cc_final: 0.7603 (t) REVERT: F 248 LEU cc_start: 0.7960 (mp) cc_final: 0.7738 (mt) REVERT: F 254 GLU cc_start: 0.1396 (OUTLIER) cc_final: -0.1709 (mt-10) REVERT: F 301 GLN cc_start: 0.6925 (mm-40) cc_final: 0.6581 (mp10) REVERT: F 306 ASP cc_start: 0.7685 (t0) cc_final: 0.7329 (t0) REVERT: F 326 LYS cc_start: 0.5201 (mttt) cc_final: 0.4964 (mttp) REVERT: F 352 LYS cc_start: 0.8037 (tptt) cc_final: 0.7087 (tppt) REVERT: F 404 PHE cc_start: 0.7826 (m-80) cc_final: 0.7608 (m-10) REVERT: F 432 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.5952 (t80) outliers start: 57 outliers final: 42 residues processed: 544 average time/residue: 0.3066 time to fit residues: 228.0759 Evaluate side-chains 547 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 500 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU 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 301 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 24 ILE 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 218 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET 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 179 VAL Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET 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 254 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 295 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 3 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 102 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 245 GLN F 88 HIS F 216 ASN F 342 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115103 restraints weight = 19844.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.119082 restraints weight = 8858.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.121653 restraints weight = 4739.208| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4238 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= 0.173 Angle : 0.625 10.482 19237 Z= 0.320 Chirality : 0.046 0.167 2106 Planarity : 0.004 0.047 2502 Dihedral : 9.766 167.695 1994 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.71 % Allowed : 24.63 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1738 helix: 1.08 (0.19), residues: 784 sheet: -0.87 (0.30), residues: 269 loop : -0.74 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 346 HIS 0.006 0.001 HIS F 88 PHE 0.022 0.002 PHE B 367 TYR 0.014 0.001 TYR A 432 ARG 0.007 0.000 ARG F 320 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 658) hydrogen bonds : angle 4.27668 ( 1911) covalent geometry : bond 0.00384 (14163) covalent geometry : angle 0.62541 (19237) *********************** 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 583 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 513 time to evaluate : 1.580 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: A 24 TYR cc_start: 0.7811 (m-80) cc_final: 0.7458 (m-80) REVERT: A 118 VAL cc_start: 0.8308 (p) cc_final: 0.8085 (m) REVERT: A 120 ASP cc_start: 0.7243 (m-30) cc_final: 0.6727 (t0) REVERT: A 154 MET cc_start: 0.7681 (mmm) cc_final: 0.7272 (mmm) REVERT: A 166 LYS cc_start: 0.7588 (mtmm) cc_final: 0.7161 (mttp) REVERT: A 187 SER cc_start: 0.8322 (m) cc_final: 0.7880 (p) REVERT: A 209 ILE cc_start: 0.8378 (mm) cc_final: 0.7881 (mt) REVERT: A 211 ASP cc_start: 0.7858 (m-30) cc_final: 0.7631 (m-30) REVERT: A 215 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6973 (mtt180) REVERT: A 226 ASN cc_start: 0.7353 (m110) cc_final: 0.7119 (m110) REVERT: A 237 SER cc_start: 0.8519 (m) cc_final: 0.8190 (t) REVERT: A 254 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6841 (mt-10) REVERT: A 284 GLU cc_start: 0.7413 (tt0) cc_final: 0.6999 (tm-30) REVERT: A 290 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 297 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 302 MET cc_start: 0.7927 (mmm) cc_final: 0.7512 (mmm) REVERT: A 309 HIS cc_start: 0.6755 (m-70) cc_final: 0.6354 (m-70) REVERT: A 349 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 414 GLU cc_start: 0.5947 (mp0) cc_final: 0.5553 (mp0) REVERT: A 434 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 53 GLU cc_start: 0.7094 (tp30) cc_final: 0.6751 (tp30) REVERT: B 86 ARG cc_start: 0.7758 (mtt180) cc_final: 0.6758 (mmp-170) REVERT: B 99 ASN cc_start: 0.8200 (m-40) cc_final: 0.7946 (m-40) REVERT: B 194 GLU cc_start: 0.6698 (tp30) cc_final: 0.6218 (tp30) REVERT: B 195 ASN cc_start: 0.7777 (m-40) cc_final: 0.7422 (m-40) REVERT: B 197 ASP cc_start: 0.7411 (m-30) cc_final: 0.7030 (m-30) REVERT: B 209 ASP cc_start: 0.7754 (t70) cc_final: 0.7409 (t0) REVERT: B 237 THR cc_start: 0.8218 (p) cc_final: 0.7799 (t) REVERT: B 241 ARG cc_start: 0.8853 (mtp180) cc_final: 0.8390 (mtp180) REVERT: B 309 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.6394 (mtt-85) REVERT: B 318 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: B 380 ARG cc_start: 0.7079 (ptp-170) cc_final: 0.6809 (ptp-170) REVERT: B 391 ARG cc_start: 0.6889 (tpp80) cc_final: 0.6395 (mpt180) REVERT: B 407 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: B 412 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 416 ASN cc_start: 0.7870 (t0) cc_final: 0.7652 (t0) REVERT: E 35 THR cc_start: 0.8689 (p) cc_final: 0.8483 (p) REVERT: E 62 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7049 (mtm-85) REVERT: E 67 ASP cc_start: 0.6815 (t0) cc_final: 0.6401 (t0) REVERT: E 108 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6947 (tm-30) REVERT: E 175 VAL cc_start: 0.7983 (m) cc_final: 0.7597 (t) REVERT: E 199 THR cc_start: 0.8065 (m) cc_final: 0.7850 (p) REVERT: E 225 LEU cc_start: 0.8365 (mp) cc_final: 0.8128 (mp) REVERT: E 251 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7487 (tpp80) REVERT: E 257 MET cc_start: 0.6872 (mpp) cc_final: 0.6034 (mpp) REVERT: E 279 GLN cc_start: 0.7613 (pt0) cc_final: 0.7219 (pt0) REVERT: E 359 ARG cc_start: 0.6495 (mmm160) cc_final: 0.6235 (mmm160) REVERT: E 366 THR cc_start: 0.8329 (m) cc_final: 0.8115 (t) REVERT: E 391 ARG cc_start: 0.5236 (ptt180) cc_final: 0.3476 (ptt90) REVERT: E 399 THR cc_start: 0.7849 (m) cc_final: 0.6778 (t) REVERT: E 403 MET cc_start: 0.6660 (mmm) cc_final: 0.6341 (tpt) REVERT: E 407 GLU cc_start: 0.6187 (pt0) cc_final: 0.5479 (pt0) REVERT: E 423 GLN cc_start: 0.8152 (tp40) cc_final: 0.7944 (tp40) REVERT: F 3 GLU cc_start: 0.6638 (mp0) cc_final: 0.6137 (mp0) REVERT: F 24 TYR cc_start: 0.7954 (m-10) cc_final: 0.7722 (m-10) REVERT: F 36 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: F 69 ASP cc_start: 0.7828 (t0) cc_final: 0.7477 (t0) REVERT: F 70 LEU cc_start: 0.7892 (mm) cc_final: 0.7476 (mt) REVERT: F 77 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6768 (tm-30) REVERT: F 78 VAL cc_start: 0.7932 (t) cc_final: 0.7380 (t) REVERT: F 123 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6782 (tpp-160) REVERT: F 154 MET cc_start: 0.7090 (mmm) cc_final: 0.6772 (mmm) REVERT: F 155 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6441 (mm-30) REVERT: F 161 TYR cc_start: 0.8126 (m-80) cc_final: 0.7829 (m-10) REVERT: F 239 THR cc_start: 0.8082 (m) cc_final: 0.7631 (t) REVERT: F 248 LEU cc_start: 0.7977 (mp) cc_final: 0.7754 (mt) REVERT: F 254 GLU cc_start: 0.1497 (OUTLIER) cc_final: -0.1510 (mt-10) REVERT: F 271 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7293 (p) REVERT: F 272 TYR cc_start: 0.8506 (t80) cc_final: 0.8282 (t80) REVERT: F 301 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6626 (mp10) REVERT: F 306 ASP cc_start: 0.7701 (t0) cc_final: 0.7358 (t0) REVERT: F 326 LYS cc_start: 0.5268 (mttt) cc_final: 0.5067 (mttp) REVERT: F 352 LYS cc_start: 0.7932 (tptt) cc_final: 0.7053 (tppt) REVERT: F 432 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.5994 (t80) outliers start: 70 outliers final: 54 residues processed: 539 average time/residue: 0.3048 time to fit residues: 224.7785 Evaluate side-chains 567 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 507 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 ASP 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 179 THR 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 301 GLN Chi-restraints excluded: chain A residue 349 THR 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 8 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 SER 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 288 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU 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 179 VAL Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET 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 223 THR Chi-restraints excluded: chain F residue 254 GLU 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 429 GLU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain F residue 433 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 43 GLN B 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 88 HIS ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.113569 restraints weight = 19818.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.117516 restraints weight = 8857.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.120076 restraints weight = 4748.631| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14163 Z= 0.208 Angle : 0.661 9.745 19237 Z= 0.339 Chirality : 0.047 0.181 2106 Planarity : 0.004 0.047 2502 Dihedral : 9.922 167.085 1994 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.44 % Allowed : 25.77 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1738 helix: 0.99 (0.19), residues: 777 sheet: -0.77 (0.30), residues: 275 loop : -0.74 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.031 0.002 PHE F 351 TYR 0.019 0.002 TYR A 432 ARG 0.007 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 658) hydrogen bonds : angle 4.38699 ( 1911) covalent geometry : bond 0.00459 (14163) covalent geometry : angle 0.66054 (19237) *********************** 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 592 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 526 time to evaluate : 1.398 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: 0.7826 (m-80) cc_final: 0.7454 (m-80) REVERT: A 118 VAL cc_start: 0.8336 (p) cc_final: 0.8110 (m) REVERT: A 120 ASP cc_start: 0.7243 (m-30) cc_final: 0.6734 (t0) REVERT: A 154 MET cc_start: 0.7705 (mmm) cc_final: 0.7151 (mmm) REVERT: A 166 LYS cc_start: 0.7587 (mtmm) cc_final: 0.7168 (mttp) REVERT: A 187 SER cc_start: 0.8342 (m) cc_final: 0.7887 (p) REVERT: A 209 ILE cc_start: 0.8372 (mm) cc_final: 0.7877 (mt) REVERT: A 211 ASP cc_start: 0.7862 (m-30) cc_final: 0.7642 (m-30) REVERT: A 215 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6916 (mtt180) REVERT: A 226 ASN cc_start: 0.7413 (m110) cc_final: 0.7181 (m110) REVERT: A 237 SER cc_start: 0.8621 (m) cc_final: 0.8305 (t) REVERT: A 254 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6814 (mt-10) REVERT: A 284 GLU cc_start: 0.7360 (tt0) cc_final: 0.6947 (tm-30) REVERT: A 290 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7034 (mt-10) REVERT: A 297 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 302 MET cc_start: 0.7953 (mmm) cc_final: 0.7533 (mmm) REVERT: A 309 HIS cc_start: 0.6826 (m-70) cc_final: 0.6355 (m-70) REVERT: A 349 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 414 GLU cc_start: 0.6053 (mp0) cc_final: 0.5613 (mp0) REVERT: A 434 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 53 GLU cc_start: 0.7120 (tp30) cc_final: 0.6754 (tp30) REVERT: B 73 MET cc_start: 0.7652 (mmm) cc_final: 0.7279 (mmm) REVERT: B 86 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6816 (mmp80) REVERT: B 99 ASN cc_start: 0.8214 (m-40) cc_final: 0.7956 (m-40) REVERT: B 194 GLU cc_start: 0.6708 (tp30) cc_final: 0.6212 (tp30) REVERT: B 195 ASN cc_start: 0.7784 (m-40) cc_final: 0.7417 (m-40) REVERT: B 197 ASP cc_start: 0.7480 (m-30) cc_final: 0.7052 (m-30) REVERT: B 209 ASP cc_start: 0.7753 (t70) cc_final: 0.7422 (t0) REVERT: B 241 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8382 (mtp180) REVERT: B 291 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7313 (mm-40) REVERT: B 295 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7190 (p0) REVERT: B 318 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7815 (mtp-110) REVERT: B 376 GLU cc_start: 0.7201 (mp0) cc_final: 0.6741 (mp0) REVERT: B 380 ARG cc_start: 0.7134 (ptp-170) cc_final: 0.6845 (ptp-170) REVERT: B 391 ARG cc_start: 0.6979 (tpp80) cc_final: 0.6363 (mpt180) REVERT: B 407 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: B 416 ASN cc_start: 0.7930 (t0) cc_final: 0.7712 (t0) REVERT: E 67 ASP cc_start: 0.6877 (t0) cc_final: 0.6434 (t0) REVERT: E 69 GLU cc_start: 0.7049 (tt0) cc_final: 0.6417 (mt-10) REVERT: E 108 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6969 (tm-30) REVERT: E 175 VAL cc_start: 0.7961 (m) cc_final: 0.7583 (t) REVERT: E 225 LEU cc_start: 0.8352 (mp) cc_final: 0.8110 (mp) REVERT: E 251 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7515 (tpp80) REVERT: E 257 MET cc_start: 0.6840 (mpp) cc_final: 0.6006 (mpp) REVERT: E 279 GLN cc_start: 0.7605 (pt0) cc_final: 0.7240 (pt0) REVERT: E 285 THR cc_start: 0.7985 (t) cc_final: 0.7649 (p) REVERT: E 359 ARG cc_start: 0.6493 (mmm160) cc_final: 0.6127 (mmm160) REVERT: E 366 THR cc_start: 0.8314 (m) cc_final: 0.8113 (t) REVERT: E 391 ARG cc_start: 0.5372 (ptt180) cc_final: 0.3356 (ptt-90) REVERT: E 399 THR cc_start: 0.8007 (m) cc_final: 0.6937 (t) REVERT: E 403 MET cc_start: 0.6720 (mmm) cc_final: 0.6414 (tpt) REVERT: E 405 GLU cc_start: 0.6864 (tt0) cc_final: 0.6270 (tt0) REVERT: E 421 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7044 (mt-10) REVERT: F 3 GLU cc_start: 0.6681 (mp0) cc_final: 0.6210 (mp0) REVERT: F 24 TYR cc_start: 0.7988 (m-10) cc_final: 0.7720 (m-10) REVERT: F 70 LEU cc_start: 0.7911 (mm) cc_final: 0.7550 (mt) REVERT: F 77 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6791 (tm-30) REVERT: F 78 VAL cc_start: 0.7977 (t) cc_final: 0.7469 (t) REVERT: F 123 ARG cc_start: 0.7115 (tpp-160) cc_final: 0.6600 (tpp-160) REVERT: F 154 MET cc_start: 0.7074 (mmm) cc_final: 0.6776 (mmm) REVERT: F 155 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6523 (mm-30) REVERT: F 239 THR cc_start: 0.8084 (m) cc_final: 0.7635 (t) REVERT: F 248 LEU cc_start: 0.8056 (mp) cc_final: 0.7827 (mt) REVERT: F 254 GLU cc_start: 0.1935 (OUTLIER) cc_final: -0.1133 (mt-10) REVERT: F 301 GLN cc_start: 0.7004 (mm-40) cc_final: 0.6637 (mp10) REVERT: F 306 ASP cc_start: 0.7746 (t0) cc_final: 0.7393 (t0) REVERT: F 340 SER cc_start: 0.7593 (p) cc_final: 0.7237 (t) REVERT: F 352 LYS cc_start: 0.7966 (tptt) cc_final: 0.6257 (mmtt) REVERT: F 422 ARG cc_start: 0.7470 (tpt170) cc_final: 0.7260 (tpt170) REVERT: F 432 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5819 (t80) outliers start: 66 outliers final: 53 residues processed: 555 average time/residue: 0.3145 time to fit residues: 239.9939 Evaluate side-chains 582 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 524 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 ASP 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 301 GLN Chi-restraints excluded: chain A residue 349 THR 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 8 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 SER 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 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 407 GLU 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 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 179 VAL Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET 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 254 GLU Chi-restraints excluded: chain F residue 271 THR 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 406 HIS 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 53 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 43 GLN B 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN E 99 ASN F 88 HIS ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.113310 restraints weight = 19894.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.117248 restraints weight = 8893.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.119819 restraints weight = 4772.523| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14163 Z= 0.220 Angle : 0.685 9.817 19237 Z= 0.352 Chirality : 0.048 0.182 2106 Planarity : 0.005 0.046 2502 Dihedral : 10.001 167.171 1994 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.31 % Allowed : 27.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1738 helix: 0.94 (0.19), residues: 775 sheet: -0.83 (0.31), residues: 269 loop : -0.75 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.031 0.002 PHE F 351 TYR 0.017 0.002 TYR A 432 ARG 0.008 0.001 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 658) hydrogen bonds : angle 4.43744 ( 1911) covalent geometry : bond 0.00486 (14163) covalent geometry : angle 0.68484 (19237) ********************** 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 585 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 521 time to evaluate : 1.518 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: A 24 TYR cc_start: 0.7830 (m-80) cc_final: 0.7451 (m-80) REVERT: A 80 THR cc_start: 0.8315 (m) cc_final: 0.7954 (p) REVERT: A 91 GLN cc_start: 0.8107 (pt0) cc_final: 0.7840 (pt0) REVERT: A 118 VAL cc_start: 0.8311 (p) cc_final: 0.8082 (m) REVERT: A 120 ASP cc_start: 0.7262 (m-30) cc_final: 0.6851 (t0) REVERT: A 141 PHE cc_start: 0.8269 (m-10) cc_final: 0.7918 (m-10) REVERT: A 154 MET cc_start: 0.7711 (mmm) cc_final: 0.7117 (mmm) REVERT: A 166 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7158 (mttp) REVERT: A 187 SER cc_start: 0.8342 (m) cc_final: 0.7845 (p) REVERT: A 209 ILE cc_start: 0.8356 (mm) cc_final: 0.7911 (mt) REVERT: A 215 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6924 (mtt180) REVERT: A 226 ASN cc_start: 0.7450 (m110) cc_final: 0.7232 (m110) REVERT: A 237 SER cc_start: 0.8616 (m) cc_final: 0.8313 (t) REVERT: A 254 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 284 GLU cc_start: 0.7344 (tt0) cc_final: 0.6947 (tm-30) REVERT: A 290 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6953 (mt-10) REVERT: A 297 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 302 MET cc_start: 0.8019 (mmm) cc_final: 0.7570 (mmm) REVERT: A 309 HIS cc_start: 0.6832 (m-70) cc_final: 0.6391 (m-70) REVERT: A 311 LYS cc_start: 0.8265 (mttm) cc_final: 0.7983 (mttp) REVERT: A 349 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 414 GLU cc_start: 0.6052 (mp0) cc_final: 0.5611 (mp0) REVERT: B 3 GLU cc_start: 0.7113 (pm20) cc_final: 0.6495 (pm20) REVERT: B 53 GLU cc_start: 0.7127 (tp30) cc_final: 0.6769 (tp30) REVERT: B 73 MET cc_start: 0.7616 (mmm) cc_final: 0.7178 (mmm) REVERT: B 86 ARG cc_start: 0.7814 (mtt180) cc_final: 0.6818 (mmp80) REVERT: B 99 ASN cc_start: 0.8250 (m-40) cc_final: 0.8033 (m-40) REVERT: B 194 GLU cc_start: 0.6700 (tp30) cc_final: 0.6214 (tp30) REVERT: B 195 ASN cc_start: 0.7864 (m-40) cc_final: 0.7563 (m-40) REVERT: B 197 ASP cc_start: 0.7504 (m-30) cc_final: 0.7086 (m-30) REVERT: B 209 ASP cc_start: 0.7740 (t70) cc_final: 0.7401 (t0) REVERT: B 237 THR cc_start: 0.8176 (p) cc_final: 0.7871 (t) REVERT: B 241 ARG cc_start: 0.8847 (mtp180) cc_final: 0.8639 (mtm-85) REVERT: B 318 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7804 (mtp-110) REVERT: B 324 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7320 (pttt) REVERT: B 376 GLU cc_start: 0.7211 (mp0) cc_final: 0.6778 (mp0) REVERT: B 380 ARG cc_start: 0.7195 (ptp-170) cc_final: 0.6848 (ptp-170) REVERT: B 391 ARG cc_start: 0.7035 (tpp80) cc_final: 0.6505 (mpt180) REVERT: B 407 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: E 3 GLU cc_start: 0.6949 (mp0) cc_final: 0.6275 (mp0) REVERT: E 67 ASP cc_start: 0.6887 (t0) cc_final: 0.6425 (t0) REVERT: E 69 GLU cc_start: 0.7097 (tt0) cc_final: 0.6421 (mt-10) REVERT: E 108 GLU cc_start: 0.7734 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 175 VAL cc_start: 0.7973 (m) cc_final: 0.7554 (t) REVERT: E 216 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8007 (mmtt) REVERT: E 225 LEU cc_start: 0.8349 (mp) cc_final: 0.8099 (mp) REVERT: E 251 ARG cc_start: 0.7734 (tpp80) cc_final: 0.7500 (tpp80) REVERT: E 257 MET cc_start: 0.6870 (mpp) cc_final: 0.6003 (mpp) REVERT: E 279 GLN cc_start: 0.7616 (pt0) cc_final: 0.7245 (pt0) REVERT: E 285 THR cc_start: 0.8033 (t) cc_final: 0.7693 (p) REVERT: E 300 MET cc_start: 0.8442 (mtp) cc_final: 0.8162 (mtm) REVERT: E 359 ARG cc_start: 0.6537 (mmm160) cc_final: 0.6191 (mmm160) REVERT: E 391 ARG cc_start: 0.5369 (ptt180) cc_final: 0.3207 (ptt-90) REVERT: E 399 THR cc_start: 0.8077 (m) cc_final: 0.7088 (t) REVERT: E 405 GLU cc_start: 0.6923 (tt0) cc_final: 0.6688 (tt0) REVERT: E 418 LEU cc_start: 0.8556 (tp) cc_final: 0.8327 (tp) REVERT: F 3 GLU cc_start: 0.6717 (mp0) cc_final: 0.6232 (mp0) REVERT: F 24 TYR cc_start: 0.7983 (m-10) cc_final: 0.7712 (m-10) REVERT: F 70 LEU cc_start: 0.7594 (mm) cc_final: 0.7320 (mt) REVERT: F 77 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6796 (tm-30) REVERT: F 78 VAL cc_start: 0.7994 (t) cc_final: 0.7514 (t) REVERT: F 119 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7939 (mt) REVERT: F 123 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6603 (tpp-160) REVERT: F 154 MET cc_start: 0.7077 (mmm) cc_final: 0.6733 (mmm) REVERT: F 155 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6534 (mm-30) REVERT: F 239 THR cc_start: 0.8080 (m) cc_final: 0.7621 (t) REVERT: F 248 LEU cc_start: 0.8054 (mp) cc_final: 0.7827 (mt) REVERT: F 254 GLU cc_start: 0.2002 (OUTLIER) cc_final: -0.1090 (mt-10) REVERT: F 271 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7299 (p) REVERT: F 301 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6914 (mp10) REVERT: F 306 ASP cc_start: 0.7790 (t0) cc_final: 0.7336 (t0) REVERT: F 326 LYS cc_start: 0.5428 (mttt) cc_final: 0.4739 (mttm) REVERT: F 352 LYS cc_start: 0.7932 (tptt) cc_final: 0.7061 (tppt) REVERT: F 417 GLU cc_start: 0.6638 (tt0) cc_final: 0.6414 (tt0) REVERT: F 432 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.5731 (t80) REVERT: F 434 GLU cc_start: 0.7967 (tt0) cc_final: 0.7725 (tt0) outliers start: 64 outliers final: 54 residues processed: 549 average time/residue: 0.3102 time to fit residues: 233.0833 Evaluate side-chains 571 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 510 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 ASP 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 349 THR 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 8 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 SER 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 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 407 GLU 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 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 179 VAL Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET 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 119 LEU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 271 THR 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 406 HIS 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 40 optimal weight: 0.6980 chunk 168 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 chunk 63 optimal weight: 0.5980 chunk 87 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 137 HIS B 291 GLN B 424 GLN E 99 ASN F 88 HIS F 216 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.129122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115439 restraints weight = 19980.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.119445 restraints weight = 8941.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.122067 restraints weight = 4795.408| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4530 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= 0.145 Angle : 0.641 9.939 19237 Z= 0.328 Chirality : 0.045 0.167 2106 Planarity : 0.004 0.047 2502 Dihedral : 9.810 168.556 1994 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.57 % Allowed : 27.73 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1738 helix: 1.09 (0.19), residues: 770 sheet: -0.91 (0.31), residues: 262 loop : -0.74 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.024 0.001 PHE F 351 TYR 0.013 0.001 TYR F 432 ARG 0.007 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 658) hydrogen bonds : angle 4.32645 ( 1911) covalent geometry : bond 0.00325 (14163) covalent geometry : angle 0.64136 (19237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.42 seconds wall clock time: 103 minutes 46.23 seconds (6226.23 seconds total)