Starting phenix.real_space_refine on Thu Jul 31 22:29:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t42_41018/07_2025/8t42_41018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t42_41018/07_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_41018/07_2025/8t42_41018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t42_41018/07_2025/8t42_41018.map" model { file = "/net/cci-nas-00/data/ceres_data/8t42_41018/07_2025/8t42_41018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t42_41018/07_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-5711/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: 12.01, per 1000 atoms: 0.87 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: 3.18 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: 1.41 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: 4.38 Time building geometry restraints manager: 3.82 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: 451.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.290 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 492.860 ------------------------------------------------------------------------------- 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 : 1.470 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: 0.7508 (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: 0.3249 time to fit residues: 249.8563 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 : 2.467 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117074 restraints weight = 19348.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.121188 restraints weight = 8695.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.123855 restraints weight = 4659.037| |-----------------------------------------------------------------------------| 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 : 1.486 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: 0.7797 (p0) cc_final: 0.7585 (p0) REVERT: A 67 PHE cc_start: 0.8266 (m-80) cc_final: 0.8056 (m-80) REVERT: A 91 GLN cc_start: 0.8115 (pt0) cc_final: 0.7838 (pt0) REVERT: A 154 MET cc_start: 0.7744 (mmm) cc_final: 0.7022 (mmm) REVERT: A 166 LYS cc_start: 0.7609 (mtmm) cc_final: 0.7376 (mttp) REVERT: A 168 GLU cc_start: 0.6143 (mp0) cc_final: 0.5925 (mp0) REVERT: A 176 GLN cc_start: 0.7212 (pm20) cc_final: 0.6749 (pm20) REVERT: A 179 THR cc_start: 0.8222 (p) cc_final: 0.7950 (t) REVERT: A 187 SER cc_start: 0.8252 (m) cc_final: 0.7790 (p) REVERT: A 215 ARG cc_start: 0.7266 (mtt180) cc_final: 0.7018 (mtt180) REVERT: A 226 ASN cc_start: 0.7342 (m110) cc_final: 0.7035 (m110) REVERT: A 237 SER cc_start: 0.8635 (m) cc_final: 0.8358 (t) REVERT: A 239 THR cc_start: 0.8013 (p) cc_final: 0.7653 (t) REVERT: A 254 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6656 (mt-10) REVERT: A 259 LEU cc_start: 0.7871 (tp) cc_final: 0.7585 (tt) REVERT: A 284 GLU cc_start: 0.7546 (tt0) cc_final: 0.7075 (tm-30) REVERT: A 290 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 304 LYS cc_start: 0.8157 (tppt) cc_final: 0.7894 (tppt) REVERT: A 309 HIS cc_start: 0.6683 (m-70) cc_final: 0.6324 (m-70) REVERT: A 311 LYS cc_start: 0.8221 (mttp) cc_final: 0.7972 (mttt) REVERT: A 370 LYS cc_start: 0.8293 (tptp) cc_final: 0.8072 (tptp) REVERT: A 376 CYS cc_start: 0.8114 (t) cc_final: 0.7864 (t) REVERT: A 401 LYS cc_start: 0.6326 (ptpp) cc_final: 0.6063 (ptpp) REVERT: A 402 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6962 (mmt-90) REVERT: A 405 VAL cc_start: 0.8236 (m) cc_final: 0.7969 (t) REVERT: A 424 ASP cc_start: 0.6515 (m-30) cc_final: 0.6278 (m-30) REVERT: B 73 MET cc_start: 0.7487 (mmm) cc_final: 0.6950 (mmm) REVERT: B 86 ARG cc_start: 0.7721 (mtt180) cc_final: 0.6833 (tpm170) REVERT: B 99 ASN cc_start: 0.7985 (m-40) cc_final: 0.7474 (m-40) REVERT: B 108 GLU cc_start: 0.6512 (tm-30) cc_final: 0.6254 (tm-30) REVERT: B 122 LYS cc_start: 0.7765 (tttt) cc_final: 0.7388 (tmtt) REVERT: B 209 ASP cc_start: 0.7721 (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: 0.8358 (t) cc_final: 0.8115 (p) REVERT: B 241 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8507 (mtm-85) REVERT: B 247 ASN cc_start: 0.7899 (m110) cc_final: 0.7600 (m-40) REVERT: B 279 GLN cc_start: 0.8050 (pm20) cc_final: 0.7576 (pp30) REVERT: B 298 ASN cc_start: 0.7011 (t0) cc_final: 0.6738 (t0) REVERT: B 318 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7361 (mtp-110) REVERT: B 375 GLN cc_start: 0.7870 (pt0) cc_final: 0.7656 (pt0) REVERT: B 415 MET cc_start: 0.8080 (mmm) cc_final: 0.7850 (tpt) REVERT: E 1 MET cc_start: 0.5498 (ptm) cc_final: 0.5255 (ptm) REVERT: E 3 GLU cc_start: 0.6879 (mp0) cc_final: 0.6368 (mp0) REVERT: E 4 ILE cc_start: 0.8689 (mm) cc_final: 0.8419 (mt) REVERT: E 19 LYS cc_start: 0.7580 (tptm) cc_final: 0.7349 (tptm) REVERT: E 41 ASP cc_start: 0.7424 (t0) cc_final: 0.7126 (t0) REVERT: E 53 GLU cc_start: 0.6759 (tp30) cc_final: 0.6540 (tp30) REVERT: E 69 GLU cc_start: 0.6864 (tt0) cc_final: 0.6551 (tt0) REVERT: E 108 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6786 (tm-30) REVERT: E 123 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7360 (mm-30) REVERT: E 137 HIS cc_start: 0.7643 (p90) cc_final: 0.7417 (p90) REVERT: E 154 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7509 (mmtm) REVERT: E 175 VAL cc_start: 0.8036 (m) cc_final: 0.7709 (t) REVERT: E 192 LEU cc_start: 0.8157 (tp) cc_final: 0.7935 (tp) REVERT: E 216 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8018 (mmtt) REVERT: E 225 LEU cc_start: 0.8380 (mp) cc_final: 0.8062 (mp) REVERT: E 279 GLN cc_start: 0.7773 (pt0) cc_final: 0.7542 (pt0) REVERT: E 285 THR cc_start: 0.7720 (t) cc_final: 0.7505 (t) REVERT: E 300 MET cc_start: 0.8489 (mtp) cc_final: 0.8245 (mtm) REVERT: E 368 ILE cc_start: 0.8451 (mp) cc_final: 0.8227 (mp) REVERT: E 385 PHE cc_start: 0.7904 (t80) cc_final: 0.7692 (t80) REVERT: E 391 ARG cc_start: 0.4485 (ptt180) cc_final: 0.3520 (ptt180) REVERT: E 392 LYS cc_start: 0.6948 (mmtp) cc_final: 0.6696 (mmtt) REVERT: E 413 SER cc_start: 0.8163 (m) cc_final: 0.7880 (p) REVERT: F 24 TYR cc_start: 0.8003 (m-10) cc_final: 0.7552 (m-10) REVERT: F 50 ASN cc_start: 0.8171 (t0) cc_final: 0.7850 (t0) REVERT: F 51 THR cc_start: 0.8386 (p) cc_final: 0.8167 (t) REVERT: F 70 LEU cc_start: 0.7834 (mm) cc_final: 0.7527 (mt) REVERT: F 102 ASN cc_start: 0.7166 (t0) cc_final: 0.6679 (t0) REVERT: F 123 ARG cc_start: 0.6946 (tpp-160) cc_final: 0.6506 (tpp-160) REVERT: F 154 MET cc_start: 0.7213 (mmm) cc_final: 0.6914 (mmm) REVERT: F 216 ASN cc_start: 0.8258 (m-40) cc_final: 0.7982 (m-40) REVERT: F 280 LYS cc_start: 0.5834 (tptt) cc_final: 0.4323 (tptt) REVERT: F 295 CYS cc_start: 0.7424 (m) cc_final: 0.7135 (m) REVERT: F 301 GLN cc_start: 0.6897 (mm-40) cc_final: 0.6542 (mp10) REVERT: F 304 LYS cc_start: 0.7797 (tppp) cc_final: 0.7386 (tppp) REVERT: F 306 ASP cc_start: 0.7712 (t0) cc_final: 0.7299 (t0) REVERT: F 376 CYS cc_start: 0.7667 (t) cc_final: 0.7416 (t) REVERT: F 380 ASN cc_start: 0.8006 (t0) cc_final: 0.7728 (t0) REVERT: F 391 LEU cc_start: 0.8070 (mm) cc_final: 0.7807 (tt) REVERT: F 404 PHE cc_start: 0.7939 (m-80) cc_final: 0.7695 (m-10) REVERT: F 425 MET cc_start: 0.7783 (tpp) cc_final: 0.7325 (tpt) outliers start: 58 outliers final: 36 residues processed: 561 average time/residue: 0.3227 time to fit residues: 248.8507 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 : 1.458 ------------------------------------------------------------------------------- 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: 0.0170 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN 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 329 ASN F 393 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.117931 restraints weight = 19479.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.122060 restraints weight = 8703.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.124749 restraints weight = 4650.244| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3108 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= 0.143 Angle : 0.595 8.911 19237 Z= 0.305 Chirality : 0.045 0.168 2106 Planarity : 0.004 0.070 2502 Dihedral : 9.856 165.446 1994 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.36 % Allowed : 18.37 % Favored : 78.26 % 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: -0.38 (0.20), residues: 1738 helix: 0.95 (0.18), residues: 778 sheet: -1.53 (0.28), residues: 286 loop : -0.99 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 407 HIS 0.004 0.001 HIS F 406 PHE 0.017 0.001 PHE B 133 TYR 0.014 0.001 TYR E 36 ARG 0.008 0.000 ARG F 422 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 658) hydrogen bonds : angle 4.59464 ( 1911) covalent geometry : bond 0.00316 (14163) covalent geometry : angle 0.59532 (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 584 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 534 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8305 (m-80) cc_final: 0.7875 (m-80) REVERT: A 123 ARG cc_start: 0.7111 (ttp80) cc_final: 0.6660 (ttp80) REVERT: A 154 MET cc_start: 0.7693 (mmm) cc_final: 0.7243 (mmm) REVERT: A 166 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7206 (mttp) REVERT: A 175 PRO cc_start: 0.8472 (Cg_endo) cc_final: 0.8257 (Cg_endo) REVERT: A 187 SER cc_start: 0.8188 (m) cc_final: 0.7773 (p) REVERT: A 209 ILE cc_start: 0.8322 (mm) cc_final: 0.7736 (mt) REVERT: A 215 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6994 (mtt180) REVERT: A 226 ASN cc_start: 0.7239 (m110) cc_final: 0.6958 (m110) REVERT: A 237 SER cc_start: 0.8530 (m) cc_final: 0.8254 (t) REVERT: A 254 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6655 (mt-10) REVERT: A 259 LEU cc_start: 0.7867 (tp) cc_final: 0.7601 (tt) REVERT: A 265 ILE cc_start: 0.7857 (mm) cc_final: 0.7644 (mm) REVERT: A 284 GLU cc_start: 0.7520 (tt0) cc_final: 0.7275 (tt0) REVERT: A 290 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 302 MET cc_start: 0.7897 (mmm) cc_final: 0.7484 (mmm) REVERT: A 304 LYS cc_start: 0.8123 (tppt) cc_final: 0.7902 (tppt) REVERT: A 309 HIS cc_start: 0.6682 (m-70) cc_final: 0.6310 (m-70) REVERT: A 402 ARG cc_start: 0.7066 (mpt180) cc_final: 0.6859 (mmt-90) REVERT: A 424 ASP cc_start: 0.7354 (m-30) cc_final: 0.6864 (m-30) REVERT: B 73 MET cc_start: 0.7466 (mmm) cc_final: 0.7148 (mmt) REVERT: B 86 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6773 (tpm170) REVERT: B 99 ASN cc_start: 0.7952 (m-40) cc_final: 0.7591 (m-40) REVERT: B 108 GLU cc_start: 0.6301 (tm-30) cc_final: 0.6045 (tm-30) REVERT: B 122 LYS cc_start: 0.7783 (tttt) cc_final: 0.7410 (tmtt) REVERT: B 194 GLU cc_start: 0.6707 (tp30) cc_final: 0.6497 (tp30) REVERT: B 209 ASP cc_start: 0.7686 (t70) cc_final: 0.7286 (t0) REVERT: B 213 ARG cc_start: 0.7316 (ptm160) cc_final: 0.7036 (ptm160) REVERT: B 237 THR cc_start: 0.8158 (p) cc_final: 0.7878 (t) REVERT: B 247 ASN cc_start: 0.7879 (m110) cc_final: 0.7463 (m-40) REVERT: B 280 GLN cc_start: 0.7506 (mt0) cc_final: 0.7213 (mt0) REVERT: B 298 ASN cc_start: 0.6949 (t0) cc_final: 0.6512 (t0) REVERT: B 309 ARG cc_start: 0.7280 (mtt-85) cc_final: 0.6449 (mtt-85) REVERT: B 318 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7413 (mtm-85) REVERT: B 415 MET cc_start: 0.8011 (mmm) cc_final: 0.7778 (tpt) REVERT: B 418 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8100 (tp) REVERT: E 3 GLU cc_start: 0.6889 (mp0) cc_final: 0.6301 (mp0) REVERT: E 4 ILE cc_start: 0.8618 (mm) cc_final: 0.8402 (mt) REVERT: E 41 ASP cc_start: 0.7417 (t0) cc_final: 0.7054 (t0) REVERT: E 108 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6914 (tm-30) REVERT: E 197 ASP cc_start: 0.7665 (m-30) cc_final: 0.7167 (m-30) REVERT: E 216 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8019 (mmtt) REVERT: E 251 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7187 (tpp80) REVERT: E 257 MET cc_start: 0.6894 (mpp) cc_final: 0.6324 (mpp) REVERT: E 265 PHE cc_start: 0.7983 (m-80) cc_final: 0.7775 (m-80) REVERT: E 279 GLN cc_start: 0.7740 (pt0) cc_final: 0.7457 (pt0) REVERT: E 385 PHE cc_start: 0.7882 (t80) cc_final: 0.7668 (t80) REVERT: E 391 ARG cc_start: 0.4843 (ptt180) cc_final: 0.3584 (ptt90) REVERT: E 392 LYS cc_start: 0.6853 (mmtp) cc_final: 0.6633 (mptt) REVERT: E 413 SER cc_start: 0.8140 (m) cc_final: 0.7911 (p) REVERT: F 3 GLU cc_start: 0.6589 (mp0) cc_final: 0.6046 (mp0) REVERT: F 24 TYR cc_start: 0.8013 (m-10) cc_final: 0.7678 (m-10) REVERT: F 50 ASN cc_start: 0.8165 (t0) cc_final: 0.7411 (t0) REVERT: F 70 LEU cc_start: 0.7850 (mm) cc_final: 0.7555 (mt) REVERT: F 77 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6712 (tm-30) REVERT: F 97 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6676 (tm-30) REVERT: F 102 ASN cc_start: 0.6984 (t0) cc_final: 0.6540 (t0) REVERT: F 123 ARG cc_start: 0.6983 (tpp-160) cc_final: 0.6397 (tpp-160) REVERT: F 248 LEU cc_start: 0.8020 (mp) cc_final: 0.7751 (mt) REVERT: F 280 LYS cc_start: 0.5768 (tptt) cc_final: 0.4284 (tptt) REVERT: F 295 CYS cc_start: 0.7376 (m) cc_final: 0.7126 (m) REVERT: F 306 ASP cc_start: 0.7714 (t0) cc_final: 0.7386 (t0) REVERT: F 352 LYS cc_start: 0.8027 (tptt) cc_final: 0.6287 (mmtt) REVERT: F 367 ASP cc_start: 0.7323 (t0) cc_final: 0.6948 (t0) REVERT: F 380 ASN cc_start: 0.8009 (t0) cc_final: 0.7708 (t0) REVERT: F 391 LEU cc_start: 0.8063 (mm) cc_final: 0.7812 (tt) REVERT: F 434 GLU cc_start: 0.8003 (tt0) cc_final: 0.7787 (tt0) outliers start: 50 outliers final: 33 residues processed: 550 average time/residue: 0.3272 time to fit residues: 246.8768 Evaluate side-chains 543 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 509 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU 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 135 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 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 179 VAL Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 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 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: 0.8980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 F 91 GLN F 101 ASN F 329 ASN F 342 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.127845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.114320 restraints weight = 19648.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118289 restraints weight = 8862.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.120870 restraints weight = 4772.233| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3681 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= 0.224 Angle : 0.642 8.905 19237 Z= 0.332 Chirality : 0.048 0.173 2106 Planarity : 0.005 0.060 2502 Dihedral : 9.973 164.800 1994 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.57 % Allowed : 21.27 % Favored : 75.17 % 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: -0.30 (0.20), residues: 1738 helix: 0.95 (0.19), residues: 773 sheet: -1.32 (0.28), residues: 294 loop : -0.91 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.002 PHE E 367 TYR 0.017 0.002 TYR F 312 ARG 0.004 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 658) hydrogen bonds : angle 4.55024 ( 1911) covalent geometry : bond 0.00492 (14163) covalent geometry : angle 0.64171 (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 582 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 529 time to evaluate : 1.598 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: 0.7858 (m-80) cc_final: 0.7508 (m-80) REVERT: A 120 ASP cc_start: 0.7173 (m-30) cc_final: 0.6787 (t0) REVERT: A 154 MET cc_start: 0.7678 (mmm) cc_final: 0.7157 (mmm) REVERT: A 166 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7135 (mttp) REVERT: A 179 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7942 (t) REVERT: A 187 SER cc_start: 0.8313 (m) cc_final: 0.7879 (p) REVERT: A 209 ILE cc_start: 0.8394 (mm) cc_final: 0.7860 (mt) REVERT: A 211 ASP cc_start: 0.7935 (m-30) cc_final: 0.7655 (m-30) REVERT: A 215 ARG cc_start: 0.7279 (mtt180) cc_final: 0.7013 (mtt180) REVERT: A 226 ASN cc_start: 0.7399 (m110) cc_final: 0.7167 (m110) REVERT: A 237 SER cc_start: 0.8596 (m) cc_final: 0.8260 (t) REVERT: A 254 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6727 (mt-10) REVERT: A 280 LYS cc_start: 0.8310 (ptpp) cc_final: 0.7950 (ptpp) REVERT: A 284 GLU cc_start: 0.7546 (tt0) cc_final: 0.7038 (tm-30) REVERT: A 290 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 302 MET cc_start: 0.7903 (mmm) cc_final: 0.7568 (mmm) REVERT: A 304 LYS cc_start: 0.8176 (tppt) cc_final: 0.7944 (tppt) REVERT: A 309 HIS cc_start: 0.6718 (m-70) cc_final: 0.6296 (m-70) REVERT: A 424 ASP cc_start: 0.7462 (m-30) cc_final: 0.7219 (m-30) REVERT: B 73 MET cc_start: 0.7541 (mmm) cc_final: 0.7222 (mmm) REVERT: B 86 ARG cc_start: 0.7807 (mtt180) cc_final: 0.6803 (tpm170) REVERT: B 99 ASN cc_start: 0.8081 (m-40) cc_final: 0.7692 (m-40) REVERT: B 108 GLU cc_start: 0.6557 (tm-30) cc_final: 0.6149 (tm-30) REVERT: B 194 GLU cc_start: 0.6724 (tp30) cc_final: 0.6492 (tp30) REVERT: B 209 ASP cc_start: 0.7694 (t70) cc_final: 0.7320 (t0) REVERT: B 213 ARG cc_start: 0.7291 (ptm160) cc_final: 0.6993 (ptm160) REVERT: B 247 ASN cc_start: 0.7929 (m110) cc_final: 0.7559 (m-40) REVERT: B 250 LEU cc_start: 0.7990 (tp) cc_final: 0.7695 (tp) REVERT: B 265 PHE cc_start: 0.8509 (m-80) cc_final: 0.8300 (m-80) REVERT: B 297 LYS cc_start: 0.7505 (mtmm) cc_final: 0.7094 (mtmm) REVERT: B 318 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7887 (mtm-85) REVERT: B 380 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6839 (ptp-170) REVERT: B 412 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 415 MET cc_start: 0.8082 (mmm) cc_final: 0.7611 (tpt) REVERT: E 3 GLU cc_start: 0.6996 (mp0) cc_final: 0.6355 (mp0) REVERT: E 41 ASP cc_start: 0.7456 (t0) cc_final: 0.7026 (t0) REVERT: E 86 ARG cc_start: 0.8065 (ttm170) cc_final: 0.6730 (tpm170) REVERT: E 108 GLU cc_start: 0.7618 (tm-30) cc_final: 0.6883 (tm-30) REVERT: E 197 ASP cc_start: 0.7706 (m-30) cc_final: 0.7277 (m-30) REVERT: E 199 THR cc_start: 0.8038 (m) cc_final: 0.7757 (p) REVERT: E 225 LEU cc_start: 0.8378 (mp) cc_final: 0.8132 (mp) REVERT: E 251 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7544 (tpp80) REVERT: E 257 MET cc_start: 0.6858 (mpp) cc_final: 0.6157 (mpp) REVERT: E 279 GLN cc_start: 0.7678 (pt0) cc_final: 0.7302 (pt0) REVERT: E 285 THR cc_start: 0.7743 (t) cc_final: 0.7369 (p) REVERT: E 300 MET cc_start: 0.8428 (mtp) cc_final: 0.8205 (mtm) REVERT: E 318 ARG cc_start: 0.8392 (mtm110) cc_final: 0.7899 (mtm180) REVERT: E 366 THR cc_start: 0.8360 (m) cc_final: 0.8152 (t) REVERT: E 391 ARG cc_start: 0.4906 (ptt180) cc_final: 0.4284 (ptt180) REVERT: E 392 LYS cc_start: 0.7312 (mmtp) cc_final: 0.7047 (mmtt) REVERT: E 399 THR cc_start: 0.7866 (m) cc_final: 0.6843 (t) REVERT: E 405 GLU cc_start: 0.7201 (tt0) cc_final: 0.6917 (tt0) REVERT: E 407 GLU cc_start: 0.6739 (pt0) cc_final: 0.6332 (pt0) REVERT: E 421 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6684 (mt-10) REVERT: F 3 GLU cc_start: 0.6591 (mp0) cc_final: 0.6106 (mp0) REVERT: F 24 TYR cc_start: 0.8012 (m-10) cc_final: 0.7643 (m-10) REVERT: F 50 ASN cc_start: 0.7977 (t0) cc_final: 0.7217 (t0) REVERT: F 69 ASP cc_start: 0.7935 (t0) cc_final: 0.7506 (t0) REVERT: F 70 LEU cc_start: 0.7869 (mm) cc_final: 0.7482 (mt) REVERT: F 77 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6799 (tm-30) REVERT: F 97 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6829 (tm-30) REVERT: F 102 ASN cc_start: 0.7121 (t0) cc_final: 0.6645 (t0) REVERT: F 123 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6610 (tpp-160) REVERT: F 161 TYR cc_start: 0.8195 (m-80) cc_final: 0.7628 (m-10) REVERT: F 164 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7854 (mmtp) REVERT: F 248 LEU cc_start: 0.8070 (mp) cc_final: 0.7783 (mt) REVERT: F 285 GLN cc_start: 0.7947 (mt0) cc_final: 0.7732 (mt0) REVERT: F 295 CYS cc_start: 0.7379 (m) cc_final: 0.7079 (m) REVERT: F 326 LYS cc_start: 0.5302 (mttt) cc_final: 0.5042 (mttp) REVERT: F 352 LYS cc_start: 0.8030 (tptt) cc_final: 0.6306 (mmtt) REVERT: F 367 ASP cc_start: 0.7331 (t0) cc_final: 0.7044 (t0) REVERT: F 380 ASN cc_start: 0.8125 (t0) cc_final: 0.7913 (t0) REVERT: F 398 MET cc_start: 0.7447 (tpp) cc_final: 0.7136 (mpp) REVERT: F 404 PHE cc_start: 0.7927 (m-80) cc_final: 0.7687 (m-10) REVERT: F 425 MET cc_start: 0.8258 (mmm) cc_final: 0.7578 (tpt) REVERT: F 432 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.5980 (t80) REVERT: F 434 GLU cc_start: 0.8078 (tt0) cc_final: 0.7575 (tt0) outliers start: 53 outliers final: 36 residues processed: 543 average time/residue: 0.3155 time to fit residues: 234.2293 Evaluate side-chains 557 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 519 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 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 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 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 179 VAL 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 51 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 54 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 143 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 A 176 GLN B 8 GLN B 43 GLN B 137 HIS B 329 GLN B 424 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS F 91 GLN F 342 GLN F 358 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114466 restraints weight = 19832.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.118444 restraints weight = 8954.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121044 restraints weight = 4821.707| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14163 Z= 0.188 Angle : 0.610 9.640 19237 Z= 0.315 Chirality : 0.046 0.174 2106 Planarity : 0.004 0.055 2502 Dihedral : 9.870 165.260 1994 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.24 % Allowed : 22.88 % Favored : 72.88 % 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: -0.15 (0.20), residues: 1738 helix: 1.07 (0.19), residues: 768 sheet: -1.19 (0.29), residues: 293 loop : -0.85 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 101 HIS 0.005 0.001 HIS F 88 PHE 0.017 0.001 PHE E 385 TYR 0.018 0.001 TYR A 103 ARG 0.005 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 658) hydrogen bonds : angle 4.43592 ( 1911) covalent geometry : bond 0.00412 (14163) covalent geometry : angle 0.61018 (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 592 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 529 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7826 (m-80) cc_final: 0.7371 (m-80) REVERT: A 67 PHE cc_start: 0.8302 (m-80) cc_final: 0.7921 (m-80) REVERT: A 120 ASP cc_start: 0.7265 (m-30) cc_final: 0.6843 (t0) REVERT: A 154 MET cc_start: 0.7676 (mmm) cc_final: 0.7188 (mmm) REVERT: A 166 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7095 (mttp) REVERT: A 179 THR cc_start: 0.8317 (p) cc_final: 0.7933 (t) REVERT: A 187 SER cc_start: 0.8296 (m) cc_final: 0.7870 (p) REVERT: A 209 ILE cc_start: 0.8391 (mm) cc_final: 0.7897 (mt) REVERT: A 211 ASP cc_start: 0.7898 (m-30) cc_final: 0.7627 (m-30) REVERT: A 215 ARG cc_start: 0.7289 (mtt180) cc_final: 0.7013 (mtt180) REVERT: A 226 ASN cc_start: 0.7367 (m110) cc_final: 0.7162 (m110) REVERT: A 237 SER cc_start: 0.8622 (m) cc_final: 0.8265 (t) REVERT: A 254 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6746 (mt-10) REVERT: A 284 GLU cc_start: 0.7538 (tt0) cc_final: 0.7254 (tt0) REVERT: A 290 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6935 (mt-10) REVERT: A 302 MET cc_start: 0.7917 (mmm) cc_final: 0.7554 (mmm) REVERT: A 304 LYS cc_start: 0.8116 (tppt) cc_final: 0.7915 (tppt) REVERT: A 309 HIS cc_start: 0.6699 (m-70) cc_final: 0.6309 (m-70) REVERT: A 424 ASP cc_start: 0.7570 (m-30) cc_final: 0.7274 (m-30) REVERT: B 53 GLU cc_start: 0.7023 (tp30) cc_final: 0.6730 (tp30) REVERT: B 73 MET cc_start: 0.7545 (mmm) cc_final: 0.7266 (mmm) REVERT: B 86 ARG cc_start: 0.7764 (mtt180) cc_final: 0.6743 (mmp80) REVERT: B 99 ASN cc_start: 0.8104 (m-40) cc_final: 0.7742 (m-40) REVERT: B 122 LYS cc_start: 0.7861 (tmtt) cc_final: 0.7551 (tmtt) REVERT: B 194 GLU cc_start: 0.6726 (tp30) cc_final: 0.6234 (tp30) REVERT: B 195 ASN cc_start: 0.7802 (m-40) cc_final: 0.7536 (m-40) REVERT: B 209 ASP cc_start: 0.7727 (t70) cc_final: 0.7380 (t0) REVERT: B 213 ARG cc_start: 0.7286 (ptm160) cc_final: 0.6805 (ptm160) REVERT: B 247 ASN cc_start: 0.7917 (m110) cc_final: 0.7534 (m-40) REVERT: B 279 GLN cc_start: 0.7827 (pm20) cc_final: 0.7236 (pp30) REVERT: B 280 GLN cc_start: 0.7519 (mt0) cc_final: 0.6998 (mt0) REVERT: B 297 LYS cc_start: 0.7527 (mtmm) cc_final: 0.7154 (mtmm) REVERT: B 318 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7788 (mtp-110) REVERT: B 380 ARG cc_start: 0.7125 (ptp-170) cc_final: 0.6800 (ptp-170) REVERT: B 391 ARG cc_start: 0.6669 (tpp80) cc_final: 0.6403 (mpt180) REVERT: B 418 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (tp) REVERT: E 3 GLU cc_start: 0.7033 (mp0) cc_final: 0.6282 (mp0) REVERT: E 67 ASP cc_start: 0.6646 (t0) cc_final: 0.6224 (t0) REVERT: E 108 GLU cc_start: 0.7629 (tm-30) cc_final: 0.6888 (tm-30) REVERT: E 197 ASP cc_start: 0.7750 (m-30) cc_final: 0.7453 (m-30) REVERT: E 199 THR cc_start: 0.8030 (m) cc_final: 0.7803 (p) REVERT: E 205 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6517 (tm-30) REVERT: E 257 MET cc_start: 0.6833 (mpp) cc_final: 0.6182 (mpp) REVERT: E 262 ARG cc_start: 0.7011 (mtp180) cc_final: 0.6742 (mtp-110) REVERT: E 279 GLN cc_start: 0.7670 (pt0) cc_final: 0.7297 (pt0) REVERT: E 285 THR cc_start: 0.7985 (t) cc_final: 0.7584 (p) REVERT: E 318 ARG cc_start: 0.8376 (mtm110) cc_final: 0.7871 (mtm110) REVERT: E 329 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6913 (mm-40) REVERT: E 366 THR cc_start: 0.8337 (m) cc_final: 0.8068 (t) REVERT: E 391 ARG cc_start: 0.5223 (ptt180) cc_final: 0.4708 (ptt180) REVERT: E 392 LYS cc_start: 0.7228 (mmtp) cc_final: 0.6956 (mmtt) REVERT: E 399 THR cc_start: 0.7888 (m) cc_final: 0.6876 (t) REVERT: F 3 GLU cc_start: 0.6619 (mp0) cc_final: 0.6081 (mp0) REVERT: F 24 TYR cc_start: 0.7968 (m-10) cc_final: 0.7678 (m-10) REVERT: F 50 ASN cc_start: 0.7990 (t0) cc_final: 0.7145 (t0) REVERT: F 69 ASP cc_start: 0.7892 (t0) cc_final: 0.7465 (t0) REVERT: F 70 LEU cc_start: 0.7864 (mm) cc_final: 0.7463 (mt) REVERT: F 77 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6792 (tm-30) REVERT: F 78 VAL cc_start: 0.8082 (t) cc_final: 0.7726 (t) REVERT: F 123 ARG cc_start: 0.7116 (tpp-160) cc_final: 0.6597 (tpp-160) REVERT: F 155 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6588 (mm-30) REVERT: F 164 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7865 (mmtp) REVERT: F 237 SER cc_start: 0.8544 (m) cc_final: 0.8268 (t) REVERT: F 248 LEU cc_start: 0.8023 (mp) cc_final: 0.7772 (mt) REVERT: F 254 GLU cc_start: 0.1740 (OUTLIER) cc_final: -0.1196 (mt-10) REVERT: F 326 LYS cc_start: 0.5302 (mttt) cc_final: 0.5065 (mttp) REVERT: F 352 LYS cc_start: 0.7972 (tptt) cc_final: 0.7057 (tppt) REVERT: F 367 ASP cc_start: 0.7377 (t0) cc_final: 0.7108 (t0) REVERT: F 380 ASN cc_start: 0.8128 (t0) cc_final: 0.7907 (t0) REVERT: F 425 MET cc_start: 0.8269 (mmm) cc_final: 0.7580 (tpt) REVERT: F 432 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5987 (t80) REVERT: F 434 GLU cc_start: 0.8074 (tt0) cc_final: 0.7795 (tt0) outliers start: 63 outliers final: 42 residues processed: 548 average time/residue: 0.3116 time to fit residues: 234.1663 Evaluate side-chains 554 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 509 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 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 405 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 112 LEU 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 336 LYS 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 276 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 131 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 256 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 298 ASN F 88 HIS F 91 GLN F 101 ASN F 285 GLN F 342 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113870 restraints weight = 19858.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.117862 restraints weight = 8770.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.120460 restraints weight = 4668.748| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14163 Z= 0.195 Angle : 0.622 9.744 19237 Z= 0.322 Chirality : 0.046 0.166 2106 Planarity : 0.005 0.063 2502 Dihedral : 9.882 166.265 1994 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.05 % Allowed : 23.76 % Favored : 71.20 % 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: -0.09 (0.20), residues: 1738 helix: 1.05 (0.19), residues: 771 sheet: -1.05 (0.30), residues: 280 loop : -0.81 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.004 0.001 HIS A 88 PHE 0.017 0.002 PHE B 367 TYR 0.016 0.001 TYR A 103 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 658) hydrogen bonds : angle 4.42187 ( 1911) covalent geometry : bond 0.00430 (14163) covalent geometry : angle 0.62185 (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 593 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 518 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7785 (m-80) cc_final: 0.7344 (m-80) REVERT: A 120 ASP cc_start: 0.7278 (m-30) cc_final: 0.6855 (t0) REVERT: A 145 THR cc_start: 0.7890 (m) cc_final: 0.7643 (p) REVERT: A 154 MET cc_start: 0.7686 (mmm) cc_final: 0.7155 (mmm) REVERT: A 166 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7112 (mttp) REVERT: A 179 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7938 (t) REVERT: A 187 SER cc_start: 0.8311 (m) cc_final: 0.7842 (p) REVERT: A 209 ILE cc_start: 0.8412 (mm) cc_final: 0.7915 (mt) REVERT: A 211 ASP cc_start: 0.7901 (m-30) cc_final: 0.7643 (m-30) REVERT: A 215 ARG cc_start: 0.7286 (mtt180) cc_final: 0.7033 (mtt180) REVERT: A 237 SER cc_start: 0.8614 (m) cc_final: 0.8271 (t) REVERT: A 254 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6743 (mt-10) REVERT: A 290 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7100 (mt-10) REVERT: A 302 MET cc_start: 0.7954 (mmm) cc_final: 0.7564 (mmm) REVERT: A 309 HIS cc_start: 0.6741 (m-70) cc_final: 0.6387 (m-70) REVERT: B 53 GLU cc_start: 0.7077 (tp30) cc_final: 0.6753 (tp30) REVERT: B 73 MET cc_start: 0.7538 (mmm) cc_final: 0.7285 (mmm) REVERT: B 86 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6869 (tpm170) REVERT: B 122 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7575 (tmtt) REVERT: B 194 GLU cc_start: 0.6702 (tp30) cc_final: 0.6237 (tp30) REVERT: B 195 ASN cc_start: 0.7806 (m-40) cc_final: 0.7577 (m-40) REVERT: B 197 ASP cc_start: 0.7455 (m-30) cc_final: 0.7138 (m-30) REVERT: B 209 ASP cc_start: 0.7737 (t70) cc_final: 0.7384 (t0) REVERT: B 213 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6858 (ptm160) REVERT: B 247 ASN cc_start: 0.7917 (m110) cc_final: 0.7545 (m-40) REVERT: B 297 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7223 (mtmm) REVERT: B 376 GLU cc_start: 0.7176 (mp0) cc_final: 0.6763 (mp0) REVERT: B 380 ARG cc_start: 0.7117 (ptp-170) cc_final: 0.6794 (ptp-170) REVERT: E 67 ASP cc_start: 0.6671 (t0) cc_final: 0.6226 (t0) REVERT: E 108 GLU cc_start: 0.7637 (tm-30) cc_final: 0.6890 (tm-30) REVERT: E 131 GLN cc_start: 0.7539 (tp40) cc_final: 0.7119 (tm-30) REVERT: E 197 ASP cc_start: 0.7789 (m-30) cc_final: 0.7507 (m-30) REVERT: E 199 THR cc_start: 0.8060 (m) cc_final: 0.7802 (p) REVERT: E 225 LEU cc_start: 0.8336 (mp) cc_final: 0.8120 (mp) REVERT: E 257 MET cc_start: 0.6889 (mpp) cc_final: 0.6191 (mpp) REVERT: E 262 ARG cc_start: 0.7018 (mtp180) cc_final: 0.6685 (mtp-110) REVERT: E 279 GLN cc_start: 0.7649 (pt0) cc_final: 0.7261 (pt0) REVERT: E 329 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6934 (mm-40) REVERT: E 366 THR cc_start: 0.8341 (m) cc_final: 0.8037 (t) REVERT: E 391 ARG cc_start: 0.5218 (ptt180) cc_final: 0.3726 (ptt90) REVERT: E 392 LYS cc_start: 0.7340 (mmtp) cc_final: 0.7082 (mmtt) REVERT: E 399 THR cc_start: 0.7878 (m) cc_final: 0.6830 (t) REVERT: E 407 GLU cc_start: 0.6572 (pt0) cc_final: 0.6198 (pp20) REVERT: F 3 GLU cc_start: 0.6640 (mp0) cc_final: 0.6078 (mp0) REVERT: F 24 TYR cc_start: 0.7946 (m-10) cc_final: 0.7563 (m-10) REVERT: F 50 ASN cc_start: 0.8005 (t0) cc_final: 0.7137 (t0) REVERT: F 69 ASP cc_start: 0.7887 (t0) cc_final: 0.7481 (t0) REVERT: F 70 LEU cc_start: 0.7885 (mm) cc_final: 0.7480 (mt) REVERT: F 77 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6806 (tm-30) REVERT: F 78 VAL cc_start: 0.8083 (t) cc_final: 0.7672 (t) REVERT: F 123 ARG cc_start: 0.7131 (tpp-160) cc_final: 0.6612 (tpp-160) REVERT: F 155 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6457 (mm-30) REVERT: F 237 SER cc_start: 0.8539 (m) cc_final: 0.8267 (t) REVERT: F 248 LEU cc_start: 0.8064 (mp) cc_final: 0.7812 (mt) REVERT: F 326 LYS cc_start: 0.5284 (mttt) cc_final: 0.5051 (mttp) REVERT: F 342 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7625 (mm-40) REVERT: F 352 LYS cc_start: 0.7986 (tptt) cc_final: 0.6273 (mmtt) REVERT: F 367 ASP cc_start: 0.7395 (t0) cc_final: 0.7158 (t0) REVERT: F 380 ASN cc_start: 0.8132 (t0) cc_final: 0.7910 (t0) REVERT: F 432 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6011 (t80) REVERT: F 434 GLU cc_start: 0.8056 (tt0) cc_final: 0.7733 (tt0) outliers start: 75 outliers final: 50 residues processed: 541 average time/residue: 0.3169 time to fit residues: 235.9223 Evaluate side-chains 570 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 518 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 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 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 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 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 338 SER 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 259 LEU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain F residue 433 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 5 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 122 optimal weight: 0.0010 chunk 3 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 99 optimal weight: 0.0030 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 99 ASN B 137 HIS E 99 ASN E 298 ASN F 88 HIS F 91 GLN F 285 GLN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.128985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115315 restraints weight = 19863.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.119356 restraints weight = 8846.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.121970 restraints weight = 4726.681| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14163 Z= 0.150 Angle : 0.603 9.762 19237 Z= 0.310 Chirality : 0.045 0.165 2106 Planarity : 0.004 0.050 2502 Dihedral : 9.767 167.140 1994 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.90 % Allowed : 25.44 % 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: 0.02 (0.20), residues: 1738 helix: 1.12 (0.19), residues: 772 sheet: -0.92 (0.30), residues: 270 loop : -0.76 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.005 0.001 HIS F 88 PHE 0.019 0.001 PHE F 351 TYR 0.013 0.001 TYR A 103 ARG 0.007 0.000 ARG F 214 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 658) hydrogen bonds : angle 4.34849 ( 1911) covalent geometry : bond 0.00333 (14163) covalent geometry : angle 0.60320 (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 581 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 523 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8239 (m-80) cc_final: 0.7876 (m-80) REVERT: A 118 VAL cc_start: 0.8304 (p) cc_final: 0.8073 (m) REVERT: A 120 ASP cc_start: 0.7232 (m-30) cc_final: 0.6705 (t0) REVERT: A 145 THR cc_start: 0.7857 (m) cc_final: 0.7634 (p) REVERT: A 154 MET cc_start: 0.7653 (mmm) cc_final: 0.7195 (mmm) REVERT: A 166 LYS cc_start: 0.7561 (mtmm) cc_final: 0.7120 (mttp) REVERT: A 179 THR cc_start: 0.8295 (p) cc_final: 0.7912 (t) REVERT: A 187 SER cc_start: 0.8227 (m) cc_final: 0.7813 (p) REVERT: A 209 ILE cc_start: 0.8381 (mm) cc_final: 0.7883 (mt) REVERT: A 211 ASP cc_start: 0.7871 (m-30) cc_final: 0.7607 (m-30) REVERT: A 215 ARG cc_start: 0.7308 (mtt180) cc_final: 0.7018 (mtt180) REVERT: A 237 SER cc_start: 0.8562 (m) cc_final: 0.8201 (t) REVERT: A 245 ASP cc_start: 0.7217 (m-30) cc_final: 0.6969 (m-30) REVERT: A 254 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 284 GLU cc_start: 0.7427 (tt0) cc_final: 0.7042 (tm-30) REVERT: A 290 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 297 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 302 MET cc_start: 0.7943 (mmm) cc_final: 0.7542 (mmm) REVERT: A 309 HIS cc_start: 0.6745 (m-70) cc_final: 0.6326 (m-70) REVERT: A 349 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 415 GLU cc_start: 0.6969 (tt0) cc_final: 0.6500 (tt0) REVERT: A 424 ASP cc_start: 0.7595 (m-30) cc_final: 0.7317 (m-30) REVERT: B 53 GLU cc_start: 0.7076 (tp30) cc_final: 0.6731 (tp30) REVERT: B 73 MET cc_start: 0.7566 (mmm) cc_final: 0.7339 (mmm) REVERT: B 86 ARG cc_start: 0.7750 (mtt180) cc_final: 0.6920 (tpm170) REVERT: B 194 GLU cc_start: 0.6729 (tp30) cc_final: 0.6248 (tp30) REVERT: B 195 ASN cc_start: 0.7838 (m-40) cc_final: 0.7573 (m-40) REVERT: B 197 ASP cc_start: 0.7409 (m-30) cc_final: 0.7080 (m-30) REVERT: B 209 ASP cc_start: 0.7766 (t70) cc_final: 0.7349 (t0) REVERT: B 213 ARG cc_start: 0.7322 (ptm160) cc_final: 0.7071 (ptm160) REVERT: B 216 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7896 (mmmm) REVERT: B 247 ASN cc_start: 0.7879 (m110) cc_final: 0.7535 (m-40) REVERT: B 297 LYS cc_start: 0.7623 (mtmm) cc_final: 0.7186 (mtmm) REVERT: B 318 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7713 (mtm-85) REVERT: B 329 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7336 (mp10) REVERT: B 380 ARG cc_start: 0.7117 (ptp-170) cc_final: 0.6810 (ptp-170) REVERT: E 67 ASP cc_start: 0.6707 (t0) cc_final: 0.6237 (t0) REVERT: E 69 GLU cc_start: 0.6986 (tt0) cc_final: 0.6414 (mt-10) REVERT: E 108 GLU cc_start: 0.7652 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 131 GLN cc_start: 0.7584 (tp40) cc_final: 0.7108 (tm-30) REVERT: E 199 THR cc_start: 0.8023 (m) cc_final: 0.7801 (p) REVERT: E 225 LEU cc_start: 0.8319 (mp) cc_final: 0.8096 (mp) REVERT: E 257 MET cc_start: 0.6814 (mpp) cc_final: 0.6118 (mpp) REVERT: E 279 GLN cc_start: 0.7604 (pt0) cc_final: 0.7224 (pt0) REVERT: E 329 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6831 (mm-40) REVERT: E 366 THR cc_start: 0.8315 (m) cc_final: 0.8033 (t) REVERT: E 391 ARG cc_start: 0.5196 (ptt180) cc_final: 0.4521 (ptt180) REVERT: E 399 THR cc_start: 0.7843 (m) cc_final: 0.6759 (t) REVERT: E 405 GLU cc_start: 0.7105 (tt0) cc_final: 0.6898 (tt0) REVERT: E 407 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6138 (pp20) REVERT: E 423 GLN cc_start: 0.8095 (tp40) cc_final: 0.7857 (tp40) REVERT: F 3 GLU cc_start: 0.6628 (mp0) cc_final: 0.6156 (mp0) REVERT: F 24 TYR cc_start: 0.7925 (m-10) cc_final: 0.7666 (m-10) REVERT: F 69 ASP cc_start: 0.7877 (t0) cc_final: 0.7421 (t0) REVERT: F 70 LEU cc_start: 0.7859 (mm) cc_final: 0.7428 (mt) REVERT: F 77 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6777 (tm-30) REVERT: F 78 VAL cc_start: 0.8024 (t) cc_final: 0.7541 (t) REVERT: F 97 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6625 (tm-30) REVERT: F 119 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7872 (mt) REVERT: F 123 ARG cc_start: 0.7110 (tpp-160) cc_final: 0.6624 (tpp-160) REVERT: F 155 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6447 (mm-30) REVERT: F 237 SER cc_start: 0.8442 (m) cc_final: 0.8199 (t) REVERT: F 248 LEU cc_start: 0.8035 (mp) cc_final: 0.7811 (mt) REVERT: F 254 GLU cc_start: 0.1621 (OUTLIER) cc_final: -0.1375 (mt-10) REVERT: F 326 LYS cc_start: 0.5229 (mttt) cc_final: 0.4981 (mttp) REVERT: F 342 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7876 (mm-40) REVERT: F 352 LYS cc_start: 0.7973 (tptt) cc_final: 0.7101 (tppt) REVERT: F 367 ASP cc_start: 0.7376 (t0) cc_final: 0.7160 (t0) REVERT: F 380 ASN cc_start: 0.8096 (t0) cc_final: 0.7880 (t0) REVERT: F 417 GLU cc_start: 0.6365 (tt0) cc_final: 0.6075 (tt0) REVERT: F 422 ARG cc_start: 0.7391 (tpt170) cc_final: 0.7085 (tpt170) REVERT: F 432 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5968 (t80) REVERT: F 434 GLU cc_start: 0.8040 (tt0) cc_final: 0.7341 (tt0) outliers start: 58 outliers final: 45 residues processed: 543 average time/residue: 0.3133 time to fit residues: 232.8154 Evaluate side-chains 564 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 514 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 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 432 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 GLN 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 409 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG 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 336 LYS 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 119 LEU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU 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: 1.9990 chunk 158 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 88 HIS F 91 GLN F 285 GLN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 482 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113199 restraints weight = 19913.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.117128 restraints weight = 8913.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.119674 restraints weight = 4768.372| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14163 Z= 0.222 Angle : 0.655 9.794 19237 Z= 0.338 Chirality : 0.047 0.182 2106 Planarity : 0.004 0.049 2502 Dihedral : 9.947 166.932 1994 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.11 % Allowed : 25.24 % Favored : 69.65 % 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: -0.08 (0.20), residues: 1738 helix: 0.94 (0.19), residues: 784 sheet: -0.93 (0.31), residues: 274 loop : -0.74 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.005 0.001 HIS F 88 PHE 0.021 0.002 PHE F 351 TYR 0.019 0.002 TYR A 432 ARG 0.007 0.001 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 658) hydrogen bonds : angle 4.46304 ( 1911) covalent geometry : bond 0.00486 (14163) covalent geometry : angle 0.65462 (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 596 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 520 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7811 (m-80) cc_final: 0.7470 (m-80) REVERT: A 80 THR cc_start: 0.8308 (m) cc_final: 0.7942 (p) REVERT: A 118 VAL cc_start: 0.8310 (p) cc_final: 0.8082 (m) REVERT: A 120 ASP cc_start: 0.7291 (m-30) cc_final: 0.6844 (t0) REVERT: A 145 THR cc_start: 0.7886 (m) cc_final: 0.7651 (p) REVERT: A 154 MET cc_start: 0.7704 (mmm) cc_final: 0.7121 (mmm) REVERT: A 166 LYS cc_start: 0.7556 (mtmm) cc_final: 0.7109 (mttp) REVERT: A 179 THR cc_start: 0.8375 (p) cc_final: 0.7987 (t) REVERT: A 187 SER cc_start: 0.8332 (m) cc_final: 0.7910 (p) REVERT: A 209 ILE cc_start: 0.8386 (mm) cc_final: 0.7866 (mt) REVERT: A 211 ASP cc_start: 0.7875 (m-30) cc_final: 0.7621 (m-30) REVERT: A 215 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7047 (mtt180) REVERT: A 237 SER cc_start: 0.8640 (m) cc_final: 0.8258 (t) REVERT: A 254 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 284 GLU cc_start: 0.7438 (tt0) cc_final: 0.7013 (tm-30) REVERT: A 290 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 297 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 302 MET cc_start: 0.7961 (mmm) cc_final: 0.7529 (mmm) REVERT: A 309 HIS cc_start: 0.6773 (m-70) cc_final: 0.6381 (m-70) REVERT: A 349 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8103 (p) REVERT: B 53 GLU cc_start: 0.7086 (tp30) cc_final: 0.6738 (tp30) REVERT: B 73 MET cc_start: 0.7573 (mmm) cc_final: 0.7348 (mmm) REVERT: B 86 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6929 (tpm170) REVERT: B 194 GLU cc_start: 0.6761 (tp30) cc_final: 0.6308 (tp30) REVERT: B 195 ASN cc_start: 0.7838 (m-40) cc_final: 0.7572 (m-40) REVERT: B 197 ASP cc_start: 0.7482 (m-30) cc_final: 0.7131 (m-30) REVERT: B 209 ASP cc_start: 0.7740 (t70) cc_final: 0.7389 (t0) REVERT: B 213 ARG cc_start: 0.7325 (ptm160) cc_final: 0.6881 (ptm160) REVERT: B 247 ASN cc_start: 0.7927 (m110) cc_final: 0.7614 (m-40) REVERT: B 265 PHE cc_start: 0.8476 (m-80) cc_final: 0.8257 (m-80) REVERT: B 297 LYS cc_start: 0.7590 (mtmm) cc_final: 0.7197 (mtmm) REVERT: B 318 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7445 (mtm-85) REVERT: B 376 GLU cc_start: 0.7231 (mp0) cc_final: 0.6766 (mp0) REVERT: B 380 ARG cc_start: 0.7148 (ptp-170) cc_final: 0.6832 (ptp-170) REVERT: B 407 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: E 67 ASP cc_start: 0.6865 (t0) cc_final: 0.6458 (t0) REVERT: E 108 GLU cc_start: 0.7714 (tm-30) cc_final: 0.6951 (tm-30) REVERT: E 199 THR cc_start: 0.8035 (m) cc_final: 0.7788 (p) REVERT: E 209 ASP cc_start: 0.7862 (t0) cc_final: 0.7619 (t0) REVERT: E 251 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7584 (tpp80) REVERT: E 257 MET cc_start: 0.6873 (mpp) cc_final: 0.6006 (mpp) REVERT: E 279 GLN cc_start: 0.7608 (pt0) cc_final: 0.7221 (pt0) REVERT: E 329 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6986 (mm-40) REVERT: E 366 THR cc_start: 0.8314 (m) cc_final: 0.8060 (t) REVERT: E 391 ARG cc_start: 0.5190 (ptt180) cc_final: 0.4465 (ptt180) REVERT: E 399 THR cc_start: 0.7961 (m) cc_final: 0.6922 (t) REVERT: E 403 MET cc_start: 0.6959 (tpt) cc_final: 0.5955 (tpt) REVERT: E 407 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6134 (pt0) REVERT: F 3 GLU cc_start: 0.6728 (mp0) cc_final: 0.6268 (mp0) REVERT: F 24 TYR cc_start: 0.7977 (m-10) cc_final: 0.7741 (m-10) REVERT: F 69 ASP cc_start: 0.7880 (t0) cc_final: 0.7476 (t0) REVERT: F 70 LEU cc_start: 0.7887 (mm) cc_final: 0.7480 (mt) REVERT: F 77 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6811 (tm-30) REVERT: F 78 VAL cc_start: 0.8070 (t) cc_final: 0.7588 (t) REVERT: F 90 GLU cc_start: 0.7691 (tp30) cc_final: 0.7172 (tp30) REVERT: F 123 ARG cc_start: 0.7195 (tpp-160) cc_final: 0.6651 (tpp-160) REVERT: F 154 MET cc_start: 0.7042 (mmm) cc_final: 0.6754 (tmm) REVERT: F 155 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6608 (mm-30) REVERT: F 237 SER cc_start: 0.8556 (m) cc_final: 0.8273 (t) REVERT: F 239 THR cc_start: 0.8086 (m) cc_final: 0.7639 (t) REVERT: F 248 LEU cc_start: 0.8063 (mp) cc_final: 0.7837 (mt) REVERT: F 254 GLU cc_start: 0.1995 (OUTLIER) cc_final: -0.1087 (mt-10) REVERT: F 271 THR cc_start: 0.7698 (t) cc_final: 0.7335 (p) REVERT: F 342 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7990 (mm-40) REVERT: F 352 LYS cc_start: 0.7946 (tptt) cc_final: 0.7039 (tppt) REVERT: F 367 ASP cc_start: 0.7440 (t0) cc_final: 0.7191 (t0) REVERT: F 380 ASN cc_start: 0.8099 (t0) cc_final: 0.7884 (t0) REVERT: F 413 MET cc_start: 0.6972 (tpp) cc_final: 0.6612 (tpp) REVERT: F 417 GLU cc_start: 0.6524 (tt0) cc_final: 0.6020 (tt0) REVERT: F 422 ARG cc_start: 0.7390 (tpt170) cc_final: 0.7120 (tpt170) REVERT: F 432 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.5987 (t80) REVERT: F 434 GLU cc_start: 0.8067 (tt0) cc_final: 0.7374 (tt0) outliers start: 76 outliers final: 55 residues processed: 548 average time/residue: 0.3485 time to fit residues: 262.0941 Evaluate side-chains 578 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 518 time to evaluate : 2.513 ------------------------------------------------------------------------------- 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 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 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain F residue 432 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 114 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN B 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN F 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113862 restraints weight = 19787.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117840 restraints weight = 8796.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.120433 restraints weight = 4707.912| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14163 Z= 0.185 Angle : 0.635 9.742 19237 Z= 0.328 Chirality : 0.047 0.172 2106 Planarity : 0.004 0.048 2502 Dihedral : 9.894 167.336 1994 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.78 % Allowed : 26.45 % Favored : 68.78 % 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: -0.04 (0.20), residues: 1738 helix: 0.99 (0.19), residues: 778 sheet: -0.90 (0.31), residues: 274 loop : -0.74 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS F 88 PHE 0.022 0.002 PHE B 367 TYR 0.016 0.001 TYR A 432 ARG 0.008 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 658) hydrogen bonds : angle 4.43974 ( 1911) covalent geometry : bond 0.00409 (14163) covalent geometry : angle 0.63510 (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 598 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 527 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7787 (m-80) cc_final: 0.7461 (m-80) REVERT: A 91 GLN cc_start: 0.8124 (pt0) cc_final: 0.7832 (pt0) REVERT: A 118 VAL cc_start: 0.8325 (p) cc_final: 0.8104 (m) REVERT: A 120 ASP cc_start: 0.7227 (m-30) cc_final: 0.6719 (t0) REVERT: A 141 PHE cc_start: 0.8233 (m-10) cc_final: 0.7858 (m-10) REVERT: A 154 MET cc_start: 0.7692 (mmm) cc_final: 0.7144 (mmm) REVERT: A 166 LYS cc_start: 0.7540 (mtmm) cc_final: 0.7087 (mttp) REVERT: A 179 THR cc_start: 0.8369 (p) cc_final: 0.7980 (t) REVERT: A 187 SER cc_start: 0.8355 (m) cc_final: 0.7877 (p) REVERT: A 209 ILE cc_start: 0.8369 (mm) cc_final: 0.7878 (mt) REVERT: A 211 ASP cc_start: 0.7764 (m-30) cc_final: 0.7541 (m-30) REVERT: A 215 ARG cc_start: 0.7311 (mtt180) cc_final: 0.7059 (mtt180) REVERT: A 237 SER cc_start: 0.8599 (m) cc_final: 0.8257 (t) REVERT: A 254 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6713 (mt-10) REVERT: A 284 GLU cc_start: 0.7412 (tt0) cc_final: 0.7009 (tm-30) REVERT: A 290 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6941 (mt-10) REVERT: A 297 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 302 MET cc_start: 0.7983 (mmm) cc_final: 0.7547 (mmm) REVERT: A 309 HIS cc_start: 0.6770 (m-70) cc_final: 0.6300 (m-70) REVERT: A 349 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8085 (p) REVERT: A 414 GLU cc_start: 0.5935 (mp0) cc_final: 0.5515 (mp0) REVERT: A 415 GLU cc_start: 0.6948 (tt0) cc_final: 0.6422 (tt0) REVERT: A 424 ASP cc_start: 0.7632 (m-30) cc_final: 0.7374 (m-30) REVERT: B 53 GLU cc_start: 0.7091 (tp30) cc_final: 0.6735 (tp30) REVERT: B 73 MET cc_start: 0.7572 (mmm) cc_final: 0.7370 (mmm) REVERT: B 86 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6940 (tpm170) REVERT: B 194 GLU cc_start: 0.6787 (tp30) cc_final: 0.6359 (tp30) REVERT: B 195 ASN cc_start: 0.7856 (m-40) cc_final: 0.7545 (m-40) REVERT: B 197 ASP cc_start: 0.7467 (m-30) cc_final: 0.7263 (m-30) REVERT: B 209 ASP cc_start: 0.7781 (t70) cc_final: 0.7407 (t0) REVERT: B 213 ARG cc_start: 0.7317 (ptm160) cc_final: 0.6874 (ptm160) REVERT: B 247 ASN cc_start: 0.7905 (m110) cc_final: 0.7597 (m-40) REVERT: B 265 PHE cc_start: 0.8435 (m-80) cc_final: 0.8234 (m-80) REVERT: B 297 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7220 (mtmm) REVERT: B 318 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7678 (mtp-110) REVERT: B 380 ARG cc_start: 0.7151 (ptp-170) cc_final: 0.6829 (ptp-170) REVERT: B 407 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: E 67 ASP cc_start: 0.6858 (t0) cc_final: 0.6431 (t0) REVERT: E 108 GLU cc_start: 0.7700 (tm-30) cc_final: 0.6953 (tm-30) REVERT: E 207 LEU cc_start: 0.8155 (mm) cc_final: 0.7913 (mt) REVERT: E 251 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7521 (tpp80) REVERT: E 257 MET cc_start: 0.6852 (mpp) cc_final: 0.6130 (mpp) REVERT: E 279 GLN cc_start: 0.7570 (pt0) cc_final: 0.7189 (pt0) REVERT: E 329 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6923 (mm-40) REVERT: E 366 THR cc_start: 0.8299 (m) cc_final: 0.8044 (t) REVERT: E 391 ARG cc_start: 0.5211 (ptt180) cc_final: 0.4533 (ptt180) REVERT: E 399 THR cc_start: 0.7946 (m) cc_final: 0.6906 (t) REVERT: E 403 MET cc_start: 0.6925 (tpt) cc_final: 0.6162 (tpt) REVERT: E 407 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.5993 (pt0) REVERT: F 3 GLU cc_start: 0.6700 (mp0) cc_final: 0.6248 (mp0) REVERT: F 24 TYR cc_start: 0.7963 (m-10) cc_final: 0.7699 (m-10) REVERT: F 69 ASP cc_start: 0.7854 (t0) cc_final: 0.7446 (t0) REVERT: F 70 LEU cc_start: 0.7882 (mm) cc_final: 0.7477 (mt) REVERT: F 77 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6805 (tm-30) REVERT: F 78 VAL cc_start: 0.8005 (t) cc_final: 0.7522 (t) REVERT: F 90 GLU cc_start: 0.7711 (tp30) cc_final: 0.7166 (tp30) REVERT: F 123 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6619 (tpp-160) REVERT: F 154 MET cc_start: 0.7018 (mmm) cc_final: 0.6700 (tmm) REVERT: F 155 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6708 (mm-30) REVERT: F 233 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7796 (mm110) REVERT: F 237 SER cc_start: 0.8509 (m) cc_final: 0.8260 (t) REVERT: F 248 LEU cc_start: 0.8072 (mp) cc_final: 0.7842 (mt) REVERT: F 254 GLU cc_start: 0.1857 (OUTLIER) cc_final: -0.1197 (mt-10) REVERT: F 301 GLN cc_start: 0.6398 (mt0) cc_final: 0.6163 (mt0) REVERT: F 342 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8028 (mm-40) REVERT: F 352 LYS cc_start: 0.7938 (tptt) cc_final: 0.7035 (tppt) REVERT: F 367 ASP cc_start: 0.7434 (t0) cc_final: 0.7218 (t0) REVERT: F 413 MET cc_start: 0.6977 (tpp) cc_final: 0.6494 (tpp) REVERT: F 417 GLU cc_start: 0.6565 (tt0) cc_final: 0.6013 (tt0) REVERT: F 422 ARG cc_start: 0.7355 (tpt170) cc_final: 0.7067 (tpt170) REVERT: F 432 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.5975 (t80) REVERT: F 434 GLU cc_start: 0.8058 (tt0) cc_final: 0.7697 (tt0) outliers start: 71 outliers final: 54 residues processed: 553 average time/residue: 0.3140 time to fit residues: 238.9526 Evaluate side-chains 578 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 519 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 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 295 ASP Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 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 62 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 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 119 LEU 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 376 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 53 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 163 optimal weight: 0.0170 chunk 123 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN A 285 GLN B 137 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 88 HIS F 285 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.114043 restraints weight = 19871.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.117991 restraints weight = 8842.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.120554 restraints weight = 4726.829| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4466 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= 0.190 Angle : 0.650 9.778 19237 Z= 0.335 Chirality : 0.047 0.181 2106 Planarity : 0.004 0.047 2502 Dihedral : 9.927 169.500 1994 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.51 % Allowed : 27.25 % Favored : 68.24 % 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: 1.01 (0.19), residues: 782 sheet: -0.89 (0.31), residues: 274 loop : -0.73 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS F 88 PHE 0.023 0.002 PHE B 367 TYR 0.016 0.001 TYR A 432 ARG 0.008 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 658) hydrogen bonds : angle 4.42987 ( 1911) covalent geometry : bond 0.00420 (14163) covalent geometry : angle 0.65032 (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 606 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 539 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7825 (m-80) cc_final: 0.7534 (m-80) REVERT: A 118 VAL cc_start: 0.8335 (p) cc_final: 0.8104 (m) REVERT: A 120 ASP cc_start: 0.7235 (m-30) cc_final: 0.6712 (t0) REVERT: A 154 MET cc_start: 0.7698 (mmm) cc_final: 0.7094 (mmm) REVERT: A 166 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7102 (mttp) REVERT: A 179 THR cc_start: 0.8370 (p) cc_final: 0.7989 (t) REVERT: A 187 SER cc_start: 0.8368 (m) cc_final: 0.7898 (p) REVERT: A 211 ASP cc_start: 0.7773 (m-30) cc_final: 0.7556 (m-30) REVERT: A 215 ARG cc_start: 0.7286 (mtt180) cc_final: 0.7031 (mtt180) REVERT: A 237 SER cc_start: 0.8630 (m) cc_final: 0.8266 (t) REVERT: A 254 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 284 GLU cc_start: 0.7389 (tt0) cc_final: 0.7019 (tm-30) REVERT: A 290 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 297 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 302 MET cc_start: 0.8077 (mmm) cc_final: 0.7505 (mmm) REVERT: A 309 HIS cc_start: 0.6837 (m-70) cc_final: 0.6534 (m-70) REVERT: A 349 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 414 GLU cc_start: 0.5958 (mp0) cc_final: 0.5511 (mp0) REVERT: A 415 GLU cc_start: 0.7005 (tt0) cc_final: 0.6530 (tt0) REVERT: A 424 ASP cc_start: 0.7647 (m-30) cc_final: 0.7376 (m-30) REVERT: B 53 GLU cc_start: 0.7094 (tp30) cc_final: 0.6728 (tp30) REVERT: B 86 ARG cc_start: 0.7787 (mtt180) cc_final: 0.6942 (tpm170) REVERT: B 194 GLU cc_start: 0.6840 (tp30) cc_final: 0.6334 (tp30) REVERT: B 195 ASN cc_start: 0.7815 (m-40) cc_final: 0.7559 (m-40) REVERT: B 197 ASP cc_start: 0.7485 (m-30) cc_final: 0.7148 (m-30) REVERT: B 209 ASP cc_start: 0.7779 (t70) cc_final: 0.7373 (t0) REVERT: B 213 ARG cc_start: 0.7325 (ptm160) cc_final: 0.7072 (ptm160) REVERT: B 247 ASN cc_start: 0.7905 (m110) cc_final: 0.7588 (m-40) REVERT: B 250 LEU cc_start: 0.7980 (tp) cc_final: 0.7743 (tp) REVERT: B 265 PHE cc_start: 0.8422 (m-80) cc_final: 0.8196 (m-80) REVERT: B 297 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7239 (mtmm) REVERT: B 318 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7654 (mtp-110) REVERT: B 333 VAL cc_start: 0.7593 (t) cc_final: 0.7356 (m) REVERT: B 380 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6839 (ptp-170) REVERT: B 407 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: B 414 ASN cc_start: 0.8058 (m-40) cc_final: 0.7828 (m-40) REVERT: E 67 ASP cc_start: 0.6902 (t0) cc_final: 0.6459 (t0) REVERT: E 108 GLU cc_start: 0.7731 (tm-30) cc_final: 0.6958 (tm-30) REVERT: E 207 LEU cc_start: 0.8124 (mm) cc_final: 0.7878 (mt) REVERT: E 251 ARG cc_start: 0.7858 (tpp80) cc_final: 0.7543 (tpp80) REVERT: E 257 MET cc_start: 0.6849 (mpp) cc_final: 0.6127 (mpp) REVERT: E 279 GLN cc_start: 0.7575 (pt0) cc_final: 0.7204 (pt0) REVERT: E 285 THR cc_start: 0.8092 (t) cc_final: 0.7737 (p) REVERT: E 318 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7845 (mtm110) REVERT: E 329 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6907 (mm-40) REVERT: E 366 THR cc_start: 0.8294 (m) cc_final: 0.8045 (t) REVERT: E 391 ARG cc_start: 0.5251 (ptt180) cc_final: 0.4572 (ptt180) REVERT: E 399 THR cc_start: 0.7986 (m) cc_final: 0.6917 (t) REVERT: E 403 MET cc_start: 0.6942 (tpt) cc_final: 0.6321 (tpt) REVERT: E 407 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5951 (pt0) REVERT: E 412 GLU cc_start: 0.7937 (tp30) cc_final: 0.7580 (tm-30) REVERT: F 3 GLU cc_start: 0.6747 (mp0) cc_final: 0.6291 (mp0) REVERT: F 24 TYR cc_start: 0.7984 (m-10) cc_final: 0.7714 (m-10) REVERT: F 69 ASP cc_start: 0.7857 (t0) cc_final: 0.7447 (t0) REVERT: F 70 LEU cc_start: 0.7915 (mm) cc_final: 0.7510 (mt) REVERT: F 77 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6789 (tm-30) REVERT: F 78 VAL cc_start: 0.7995 (t) cc_final: 0.7513 (t) REVERT: F 90 GLU cc_start: 0.7680 (tp30) cc_final: 0.7206 (tp30) REVERT: F 123 ARG cc_start: 0.7169 (tpp-160) cc_final: 0.6620 (tpp-160) REVERT: F 154 MET cc_start: 0.7008 (mmm) cc_final: 0.6533 (tmm) REVERT: F 155 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6725 (mm-30) REVERT: F 237 SER cc_start: 0.8533 (m) cc_final: 0.8260 (t) REVERT: F 248 LEU cc_start: 0.8058 (mp) cc_final: 0.7830 (mt) REVERT: F 254 GLU cc_start: 0.1830 (OUTLIER) cc_final: -0.1224 (mt-10) REVERT: F 271 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7362 (p) REVERT: F 342 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7933 (mm-40) REVERT: F 352 LYS cc_start: 0.7933 (tptt) cc_final: 0.7026 (tppt) REVERT: F 367 ASP cc_start: 0.7484 (t0) cc_final: 0.7232 (t0) REVERT: F 413 MET cc_start: 0.6976 (tpp) cc_final: 0.6458 (tpp) REVERT: F 417 GLU cc_start: 0.6625 (tt0) cc_final: 0.6036 (tt0) REVERT: F 422 ARG cc_start: 0.7346 (tpt170) cc_final: 0.7053 (tpt170) REVERT: F 432 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6038 (t80) REVERT: F 434 GLU cc_start: 0.8064 (tt0) cc_final: 0.7702 (tt0) outliers start: 67 outliers final: 57 residues processed: 565 average time/residue: 0.4045 time to fit residues: 316.8327 Evaluate side-chains 596 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 533 time to evaluate : 2.724 ------------------------------------------------------------------------------- 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 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 295 ASP Chi-restraints excluded: chain B residue 396 HIS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 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 62 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 GLU 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 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 376 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 40 optimal weight: 0.4980 chunk 168 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 137 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS F 285 GLN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115636 restraints weight = 19942.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.119607 restraints weight = 8922.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.122187 restraints weight = 4771.251| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14163 Z= 0.147 Angle : 0.629 9.837 19237 Z= 0.321 Chirality : 0.045 0.179 2106 Planarity : 0.004 0.048 2502 Dihedral : 9.788 171.220 1994 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.24 % Allowed : 27.99 % Favored : 67.77 % 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: 1.13 (0.19), residues: 777 sheet: -0.81 (0.31), residues: 260 loop : -0.75 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS F 88 PHE 0.023 0.001 PHE B 367 TYR 0.011 0.001 TYR A 103 ARG 0.007 0.000 ARG F 84 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 658) hydrogen bonds : angle 4.35103 ( 1911) covalent geometry : bond 0.00330 (14163) covalent geometry : angle 0.62886 (19237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7493.19 seconds wall clock time: 136 minutes 44.32 seconds (8204.32 seconds total)