Starting phenix.real_space_refine on Wed Mar 4 01:16:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x14_21988/03_2026/6x14_21988.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x14_21988/03_2026/6x14_21988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x14_21988/03_2026/6x14_21988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x14_21988/03_2026/6x14_21988.map" model { file = "/net/cci-nas-00/data/ceres_data/6x14_21988/03_2026/6x14_21988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x14_21988/03_2026/6x14_21988.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 6 5.49 5 S 54 5.16 5 C 6243 2.51 5 N 1500 2.21 5 O 1674 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9486 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3071 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 18, 'TRANS': 394} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'6OU': 2, '7O9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, C Time building chain proxies: 2.30, per 1000 atoms: 0.24 Number of scatterers: 9486 At special positions: 0 Unit cell: (114.838, 115.911, 70.8345, 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 54 16.00 P 6 15.00 F 9 9.00 O 1674 8.00 N 1500 7.00 C 6243 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: 0.73 Conformation dependent library (CDL) restraints added in 302.5 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 11 through 34 removed outlier: 3.746A pdb=" N ILE A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.673A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.800A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.720A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.633A pdb=" N ILE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.821A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.640A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.591A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 4.527A pdb=" N PHE A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 253 removed outlier: 4.193A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.671A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.649A pdb=" N ARG A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.507A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.573A pdb=" N LEU A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.605A pdb=" N GLY A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.929A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.300A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.882A pdb=" N ALA A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 11 through 34 removed outlier: 3.745A pdb=" N ILE B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.674A pdb=" N VAL B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.800A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.720A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 106 Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.633A pdb=" N ILE B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.821A pdb=" N LEU B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 170 removed outlier: 3.640A pdb=" N PHE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 220 removed outlier: 3.592A pdb=" N ASN B 199 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Proline residue: B 206 - end of helix removed outlier: 4.528A pdb=" N PHE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 253 removed outlier: 4.193A pdb=" N GLY B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.671A pdb=" N HIS B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.649A pdb=" N ARG B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.508A pdb=" N TYR B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.573A pdb=" N LEU B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 329 removed outlier: 3.605A pdb=" N GLY B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 322 " --> pdb=" O GLN B 318 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.929A pdb=" N VAL B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.299A pdb=" N LEU B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 416 removed outlier: 3.882A pdb=" N ALA B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 11 through 34 removed outlier: 3.746A pdb=" N ILE C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.673A pdb=" N VAL C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 removed outlier: 3.800A pdb=" N GLY C 47 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 73 removed outlier: 3.720A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 63 " --> pdb=" O MET C 59 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 106 Processing helix chain 'C' and resid 129 through 135 removed outlier: 3.633A pdb=" N ILE C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.822A pdb=" N LEU C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 170 removed outlier: 3.640A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 220 removed outlier: 3.591A pdb=" N ASN C 199 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Proline residue: C 206 - end of helix removed outlier: 4.528A pdb=" N PHE C 210 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 253 removed outlier: 4.192A pdb=" N GLY C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.671A pdb=" N HIS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 removed outlier: 3.649A pdb=" N ARG C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.507A pdb=" N TYR C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 removed outlier: 3.573A pdb=" N LEU C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 329 removed outlier: 3.604A pdb=" N GLY C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.929A pdb=" N VAL C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 removed outlier: 4.300A pdb=" N LEU C 363 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 416 removed outlier: 3.882A pdb=" N ALA C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1884 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: 1.33 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1455 1.31 - 1.43: 2360 1.43 - 1.55: 5686 1.55 - 1.68: 63 1.68 - 1.80: 102 Bond restraints: 9666 Sorted by residual: bond pdb=" N 7O9 A 501 " pdb=" C8 7O9 A 501 " ideal model delta sigma weight residual 1.354 1.450 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N 7O9 B 501 " pdb=" C8 7O9 B 501 " ideal model delta sigma weight residual 1.354 1.450 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N 7O9 C 501 " pdb=" C8 7O9 C 501 " ideal model delta sigma weight residual 1.354 1.449 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C16 6OU B 502 " pdb=" O18 6OU B 502 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C16 6OU C 502 " pdb=" O18 6OU C 502 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 9661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 12863 3.12 - 6.25: 235 6.25 - 9.37: 42 9.37 - 12.50: 9 12.50 - 15.62: 6 Bond angle restraints: 13155 Sorted by residual: angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 109.57 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU C 503 " pdb=" P23 6OU C 503 " pdb=" O26 6OU C 503 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU B 503 " pdb=" P23 6OU B 503 " pdb=" O26 6OU B 503 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU C 502 " pdb=" P23 6OU C 502 " pdb=" O26 6OU C 502 " ideal model delta sigma weight residual 93.95 109.41 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" O22 6OU B 502 " pdb=" P23 6OU B 502 " pdb=" O26 6OU B 502 " ideal model delta sigma weight residual 93.95 109.36 -15.41 3.00e+00 1.11e-01 2.64e+01 ... (remaining 13150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.79: 5323 25.79 - 51.59: 326 51.59 - 77.38: 51 77.38 - 103.17: 30 103.17 - 128.97: 6 Dihedral angle restraints: 5736 sinusoidal: 2214 harmonic: 3522 Sorted by residual: dihedral pdb=" C11 6OU C 502 " pdb=" C12 6OU C 502 " pdb=" C13 6OU C 502 " pdb=" C14 6OU C 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.68 128.97 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 6OU A 502 " pdb=" C12 6OU A 502 " pdb=" C13 6OU A 502 " pdb=" C14 6OU A 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.71 128.94 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 6OU B 502 " pdb=" C12 6OU B 502 " pdb=" C13 6OU B 502 " pdb=" C14 6OU B 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.75 128.90 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 5733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1144 0.050 - 0.101: 379 0.101 - 0.151: 81 0.151 - 0.201: 4 0.201 - 0.252: 9 Chirality restraints: 1617 Sorted by residual: chirality pdb=" C1 7O9 A 501 " pdb=" C 7O9 A 501 " pdb=" C2 7O9 A 501 " pdb=" N1 7O9 A 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 7O9 C 501 " pdb=" C 7O9 C 501 " pdb=" C2 7O9 C 501 " pdb=" N1 7O9 C 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 7O9 B 501 " pdb=" C 7O9 B 501 " pdb=" C2 7O9 B 501 " pdb=" N1 7O9 B 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1614 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 7O9 C 501 " -0.071 2.00e-02 2.50e+03 4.56e-02 2.60e+01 pdb=" C7 7O9 C 501 " 0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 C 501 " -0.013 2.00e-02 2.50e+03 pdb=" C9 7O9 C 501 " 0.042 2.00e-02 2.50e+03 pdb=" O5 7O9 C 501 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 7O9 A 501 " 0.071 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" C7 7O9 A 501 " -0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 A 501 " 0.013 2.00e-02 2.50e+03 pdb=" C9 7O9 A 501 " -0.042 2.00e-02 2.50e+03 pdb=" O5 7O9 A 501 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 7O9 B 501 " 0.071 2.00e-02 2.50e+03 4.54e-02 2.57e+01 pdb=" C7 7O9 B 501 " -0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C9 7O9 B 501 " -0.041 2.00e-02 2.50e+03 pdb=" O5 7O9 B 501 " 0.015 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2604 2.81 - 3.33: 8811 3.33 - 3.85: 15473 3.85 - 4.38: 17641 4.38 - 4.90: 30166 Nonbonded interactions: 74695 Sorted by model distance: nonbonded pdb=" OH TYR B 247 " pdb=" OD2 ASP B 312 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR C 247 " pdb=" OD2 ASP C 312 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.282 3.040 nonbonded pdb=" O THR C 271 " pdb=" OG1 THR C 275 " model vdw 2.348 3.040 nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 275 " model vdw 2.348 3.040 ... (remaining 74690 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.470 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.008 0.096 9666 Z= 0.365 Angle : 1.105 15.622 13155 Z= 0.516 Chirality : 0.052 0.252 1617 Planarity : 0.008 0.068 1608 Dihedral : 18.679 128.965 3504 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.16), residues: 1233 helix: -3.09 (0.11), residues: 993 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.018 0.002 TYR B 299 PHE 0.018 0.002 PHE C 323 HIS 0.002 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00763 ( 9666) covalent geometry : angle 1.10484 (13155) hydrogen bonds : bond 0.12255 ( 628) hydrogen bonds : angle 5.93202 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.306 Fit side-chains REVERT: A 42 TYR cc_start: 0.8027 (m-10) cc_final: 0.7798 (m-80) REVERT: A 195 TYR cc_start: 0.8904 (m-10) cc_final: 0.8569 (m-10) REVERT: A 241 LEU cc_start: 0.8820 (tt) cc_final: 0.8570 (tp) REVERT: A 263 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8531 (ptpp) REVERT: A 318 GLN cc_start: 0.8659 (mt0) cc_final: 0.8451 (mt0) REVERT: B 17 LEU cc_start: 0.8554 (tp) cc_final: 0.8211 (tt) REVERT: B 269 MET cc_start: 0.7687 (ttp) cc_final: 0.7413 (ttm) REVERT: B 318 GLN cc_start: 0.8718 (mt0) cc_final: 0.8433 (mt0) REVERT: C 263 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8418 (ptpp) REVERT: C 269 MET cc_start: 0.7825 (ttp) cc_final: 0.7325 (ttp) REVERT: C 318 GLN cc_start: 0.8465 (mt0) cc_final: 0.8109 (mt0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0685 time to fit residues: 22.6894 Evaluate side-chains 178 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 117 optimal weight: 3.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 337 GLN A 338 GLN B 318 GLN B 337 GLN C 40 HIS C 318 GLN C 337 GLN C 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.129626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.111508 restraints weight = 11926.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.114424 restraints weight = 7410.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.116601 restraints weight = 4901.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.117124 restraints weight = 3931.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.117187 restraints weight = 3425.361| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9666 Z= 0.108 Angle : 0.526 6.612 13155 Z= 0.273 Chirality : 0.037 0.175 1617 Planarity : 0.005 0.052 1608 Dihedral : 15.352 96.129 1533 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 13.93 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.22), residues: 1233 helix: -1.25 (0.15), residues: 993 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.025 0.001 TYR B 42 PHE 0.006 0.001 PHE B 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9666) covalent geometry : angle 0.52552 (13155) hydrogen bonds : bond 0.03746 ( 628) hydrogen bonds : angle 4.16204 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.325 Fit side-chains REVERT: A 42 TYR cc_start: 0.7969 (m-10) cc_final: 0.7673 (m-10) REVERT: A 148 ASN cc_start: 0.9111 (m-40) cc_final: 0.8855 (m110) REVERT: A 241 LEU cc_start: 0.8822 (tt) cc_final: 0.8416 (tp) REVERT: A 263 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8520 (ptpp) REVERT: B 18 ILE cc_start: 0.8548 (tp) cc_final: 0.8318 (tp) REVERT: C 220 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8284 (mm-40) REVERT: C 263 LYS cc_start: 0.8742 (ptpp) cc_final: 0.8385 (ptpp) REVERT: C 269 MET cc_start: 0.7560 (ttp) cc_final: 0.7281 (ttp) REVERT: C 318 GLN cc_start: 0.8444 (mt0) cc_final: 0.8026 (mt0) outliers start: 13 outliers final: 8 residues processed: 217 average time/residue: 0.0619 time to fit residues: 20.9231 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 368 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 0.0060 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.127670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.109361 restraints weight = 11942.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.112191 restraints weight = 7599.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.114017 restraints weight = 5209.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.114666 restraints weight = 4309.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.114899 restraints weight = 3669.973| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9666 Z= 0.112 Angle : 0.515 7.583 13155 Z= 0.265 Chirality : 0.038 0.145 1617 Planarity : 0.004 0.043 1608 Dihedral : 13.266 87.909 1533 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.17 % Allowed : 17.75 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1233 helix: -0.50 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.024 0.001 TYR C 299 PHE 0.006 0.001 PHE C 323 HIS 0.002 0.000 HIS C 368 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9666) covalent geometry : angle 0.51465 (13155) hydrogen bonds : bond 0.03759 ( 628) hydrogen bonds : angle 3.98534 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.313 Fit side-chains REVERT: A 126 GLN cc_start: 0.8988 (tp40) cc_final: 0.8661 (tp40) REVERT: A 148 ASN cc_start: 0.9074 (m-40) cc_final: 0.8807 (m110) REVERT: A 263 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8556 (ptpp) REVERT: B 18 ILE cc_start: 0.8577 (tp) cc_final: 0.8356 (tp) REVERT: B 286 MET cc_start: 0.7746 (mmm) cc_final: 0.7274 (mmt) REVERT: C 263 LYS cc_start: 0.8675 (ptpp) cc_final: 0.8382 (ptpp) REVERT: C 269 MET cc_start: 0.7612 (ttp) cc_final: 0.7107 (ttp) REVERT: C 318 GLN cc_start: 0.8307 (mt0) cc_final: 0.7927 (mt0) REVERT: C 399 MET cc_start: 0.8623 (tpp) cc_final: 0.8311 (tpt) outliers start: 21 outliers final: 16 residues processed: 212 average time/residue: 0.0668 time to fit residues: 22.0832 Evaluate side-chains 218 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN B 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.107214 restraints weight = 12052.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.110000 restraints weight = 7841.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.112120 restraints weight = 5379.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.112804 restraints weight = 4323.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.112920 restraints weight = 3656.334| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9666 Z= 0.123 Angle : 0.517 5.955 13155 Z= 0.267 Chirality : 0.038 0.131 1617 Planarity : 0.004 0.040 1608 Dihedral : 11.686 83.333 1533 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 20.12 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1233 helix: 0.04 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.025 0.001 TYR B 299 PHE 0.007 0.001 PHE A 323 HIS 0.002 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9666) covalent geometry : angle 0.51676 (13155) hydrogen bonds : bond 0.03858 ( 628) hydrogen bonds : angle 3.98934 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.318 Fit side-chains REVERT: A 126 GLN cc_start: 0.8990 (tp40) cc_final: 0.8583 (tp40) REVERT: A 148 ASN cc_start: 0.9011 (m-40) cc_final: 0.8743 (m110) REVERT: A 169 MET cc_start: 0.8255 (mtm) cc_final: 0.8050 (mtp) REVERT: A 263 LYS cc_start: 0.8755 (ptpp) cc_final: 0.8554 (ptpp) REVERT: B 18 ILE cc_start: 0.8576 (tp) cc_final: 0.8357 (tp) REVERT: B 286 MET cc_start: 0.7743 (mmm) cc_final: 0.7411 (mmt) REVERT: C 160 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8783 (tp) REVERT: C 263 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8332 (ptpp) REVERT: C 269 MET cc_start: 0.7703 (ttp) cc_final: 0.7067 (ttp) REVERT: C 318 GLN cc_start: 0.8390 (mt0) cc_final: 0.8050 (mt0) REVERT: C 399 MET cc_start: 0.8666 (tpp) cc_final: 0.8270 (tpt) outliers start: 25 outliers final: 16 residues processed: 213 average time/residue: 0.0644 time to fit residues: 21.4175 Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 chunk 35 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN B 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.130919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.112266 restraints weight = 11766.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.115313 restraints weight = 7629.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.117314 restraints weight = 5148.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.117841 restraints weight = 4166.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.118302 restraints weight = 3637.401| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9666 Z= 0.099 Angle : 0.496 7.585 13155 Z= 0.255 Chirality : 0.037 0.120 1617 Planarity : 0.004 0.038 1608 Dihedral : 10.412 82.668 1533 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.58 % Allowed : 20.54 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1233 helix: 0.43 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.36 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 397 TYR 0.025 0.001 TYR B 299 PHE 0.007 0.001 PHE B 323 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9666) covalent geometry : angle 0.49577 (13155) hydrogen bonds : bond 0.03290 ( 628) hydrogen bonds : angle 3.81279 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.322 Fit side-chains REVERT: A 126 GLN cc_start: 0.8959 (tp40) cc_final: 0.8551 (tp40) REVERT: A 148 ASN cc_start: 0.8987 (m-40) cc_final: 0.8713 (m110) REVERT: A 160 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8700 (tp) REVERT: A 169 MET cc_start: 0.8247 (mtm) cc_final: 0.7997 (mtp) REVERT: B 18 ILE cc_start: 0.8543 (tp) cc_final: 0.8319 (tp) REVERT: B 286 MET cc_start: 0.7688 (mmm) cc_final: 0.7401 (mmt) REVERT: C 263 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8293 (ptpp) REVERT: C 269 MET cc_start: 0.7531 (ttp) cc_final: 0.6980 (ttp) REVERT: C 318 GLN cc_start: 0.8202 (mt0) cc_final: 0.7792 (mt0) REVERT: C 399 MET cc_start: 0.8603 (tpp) cc_final: 0.8337 (tpt) outliers start: 25 outliers final: 15 residues processed: 205 average time/residue: 0.0616 time to fit residues: 19.9110 Evaluate side-chains 200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 116 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.109751 restraints weight = 11657.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.112588 restraints weight = 7221.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114593 restraints weight = 5155.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.115893 restraints weight = 4072.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.116911 restraints weight = 3446.390| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9666 Z= 0.117 Angle : 0.546 11.751 13155 Z= 0.271 Chirality : 0.039 0.258 1617 Planarity : 0.003 0.033 1608 Dihedral : 10.033 76.289 1533 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 22.08 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1233 helix: 0.57 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 397 TYR 0.026 0.001 TYR B 299 PHE 0.005 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9666) covalent geometry : angle 0.54609 (13155) hydrogen bonds : bond 0.03655 ( 628) hydrogen bonds : angle 3.86894 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.190 Fit side-chains REVERT: A 126 GLN cc_start: 0.8982 (tp40) cc_final: 0.8529 (tp40) REVERT: A 148 ASN cc_start: 0.8945 (m-40) cc_final: 0.8666 (m110) REVERT: A 160 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8662 (tp) REVERT: B 18 ILE cc_start: 0.8570 (tp) cc_final: 0.8337 (tp) REVERT: B 286 MET cc_start: 0.7810 (mmm) cc_final: 0.7527 (mmt) REVERT: C 18 ILE cc_start: 0.8375 (tp) cc_final: 0.8133 (tp) REVERT: C 42 TYR cc_start: 0.7724 (m-80) cc_final: 0.7184 (m-10) REVERT: C 160 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8707 (tp) REVERT: C 263 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8331 (ptpp) REVERT: C 269 MET cc_start: 0.7510 (ttp) cc_final: 0.6734 (ttp) REVERT: C 318 GLN cc_start: 0.8166 (mt0) cc_final: 0.7771 (mt0) REVERT: C 389 ILE cc_start: 0.8317 (tp) cc_final: 0.7983 (tp) REVERT: C 399 MET cc_start: 0.8774 (tpp) cc_final: 0.8186 (tpt) outliers start: 26 outliers final: 17 residues processed: 207 average time/residue: 0.0622 time to fit residues: 20.2156 Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.107481 restraints weight = 11737.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.110156 restraints weight = 7296.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.112200 restraints weight = 5261.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.113617 restraints weight = 4158.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.114583 restraints weight = 3488.588| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9666 Z= 0.133 Angle : 0.554 12.497 13155 Z= 0.278 Chirality : 0.039 0.196 1617 Planarity : 0.004 0.032 1608 Dihedral : 9.848 77.068 1533 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.41 % Allowed : 21.47 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1233 helix: 0.59 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.23 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.026 0.001 TYR B 299 PHE 0.008 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9666) covalent geometry : angle 0.55419 (13155) hydrogen bonds : bond 0.03928 ( 628) hydrogen bonds : angle 3.96015 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.237 Fit side-chains REVERT: A 148 ASN cc_start: 0.8956 (m-40) cc_final: 0.8648 (m110) REVERT: A 160 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 241 LEU cc_start: 0.8837 (tt) cc_final: 0.8427 (tp) REVERT: B 18 ILE cc_start: 0.8573 (tp) cc_final: 0.8343 (tp) REVERT: B 160 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8736 (tp) REVERT: C 18 ILE cc_start: 0.8548 (tp) cc_final: 0.8290 (tp) REVERT: C 42 TYR cc_start: 0.7758 (m-80) cc_final: 0.7293 (m-10) REVERT: C 160 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 263 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8388 (ptpp) REVERT: C 269 MET cc_start: 0.7706 (ttp) cc_final: 0.7282 (ttp) REVERT: C 318 GLN cc_start: 0.8251 (mt0) cc_final: 0.8018 (mt0) REVERT: C 389 ILE cc_start: 0.8409 (tp) cc_final: 0.8090 (tp) outliers start: 33 outliers final: 16 residues processed: 216 average time/residue: 0.0596 time to fit residues: 20.2847 Evaluate side-chains 214 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.0040 chunk 39 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.108964 restraints weight = 11571.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111784 restraints weight = 7223.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.113770 restraints weight = 5181.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.115150 restraints weight = 4092.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.116143 restraints weight = 3444.248| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9666 Z= 0.120 Angle : 0.551 12.442 13155 Z= 0.275 Chirality : 0.039 0.178 1617 Planarity : 0.003 0.033 1608 Dihedral : 9.583 76.040 1533 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.79 % Allowed : 22.29 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1233 helix: 0.78 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.94 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.025 0.001 TYR B 299 PHE 0.006 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9666) covalent geometry : angle 0.55053 (13155) hydrogen bonds : bond 0.03757 ( 628) hydrogen bonds : angle 3.90876 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.301 Fit side-chains REVERT: A 42 TYR cc_start: 0.7642 (m-10) cc_final: 0.7431 (m-10) REVERT: A 148 ASN cc_start: 0.8944 (m-40) cc_final: 0.8631 (m110) REVERT: A 160 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (tp) REVERT: B 18 ILE cc_start: 0.8529 (tp) cc_final: 0.8301 (tp) REVERT: B 160 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (tp) REVERT: B 286 MET cc_start: 0.7732 (mmm) cc_final: 0.7338 (mmt) REVERT: C 18 ILE cc_start: 0.8536 (tp) cc_final: 0.8284 (tp) REVERT: C 42 TYR cc_start: 0.7769 (m-80) cc_final: 0.7266 (m-10) REVERT: C 160 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8706 (tp) REVERT: C 263 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8411 (ptpp) REVERT: C 269 MET cc_start: 0.7704 (ttp) cc_final: 0.6993 (ttp) REVERT: C 389 ILE cc_start: 0.8353 (tp) cc_final: 0.8048 (tp) REVERT: C 399 MET cc_start: 0.8771 (tpp) cc_final: 0.8188 (tpt) outliers start: 27 outliers final: 21 residues processed: 210 average time/residue: 0.0602 time to fit residues: 20.0753 Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.0040 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN C 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.128702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.109218 restraints weight = 11640.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111966 restraints weight = 7241.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.114009 restraints weight = 5217.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.115440 restraints weight = 4115.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.116354 restraints weight = 3461.913| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9666 Z= 0.116 Angle : 0.555 12.284 13155 Z= 0.275 Chirality : 0.039 0.200 1617 Planarity : 0.003 0.034 1608 Dihedral : 9.329 74.197 1533 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.68 % Allowed : 22.91 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1233 helix: 0.86 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.026 0.002 TYR B 42 PHE 0.006 0.001 PHE C 323 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9666) covalent geometry : angle 0.55515 (13155) hydrogen bonds : bond 0.03686 ( 628) hydrogen bonds : angle 3.90364 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.325 Fit side-chains REVERT: A 42 TYR cc_start: 0.7755 (m-10) cc_final: 0.7545 (m-10) REVERT: A 148 ASN cc_start: 0.8939 (m-40) cc_final: 0.8633 (m110) REVERT: A 160 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8649 (tp) REVERT: B 18 ILE cc_start: 0.8501 (tp) cc_final: 0.8285 (tp) REVERT: B 160 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8681 (tp) REVERT: B 286 MET cc_start: 0.7646 (mmm) cc_final: 0.7335 (mmt) REVERT: B 340 THR cc_start: 0.8119 (m) cc_final: 0.7803 (m) REVERT: C 18 ILE cc_start: 0.8516 (tp) cc_final: 0.8265 (tp) REVERT: C 42 TYR cc_start: 0.7753 (m-80) cc_final: 0.7379 (m-10) REVERT: C 160 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8671 (tp) REVERT: C 263 LYS cc_start: 0.8633 (ptpp) cc_final: 0.8394 (ptpp) REVERT: C 269 MET cc_start: 0.7705 (ttp) cc_final: 0.7194 (ttp) REVERT: C 389 ILE cc_start: 0.8293 (tp) cc_final: 0.8022 (tp) REVERT: C 399 MET cc_start: 0.8800 (tpp) cc_final: 0.8549 (tpt) outliers start: 26 outliers final: 17 residues processed: 203 average time/residue: 0.0652 time to fit residues: 20.6645 Evaluate side-chains 205 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.108836 restraints weight = 11549.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.111703 restraints weight = 7181.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.113741 restraints weight = 5150.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.115172 restraints weight = 4057.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.116209 restraints weight = 3408.380| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9666 Z= 0.121 Angle : 0.551 12.400 13155 Z= 0.276 Chirality : 0.039 0.155 1617 Planarity : 0.003 0.034 1608 Dihedral : 9.219 73.300 1533 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.27 % Allowed : 24.05 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1233 helix: 0.88 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 397 TYR 0.027 0.002 TYR B 42 PHE 0.007 0.001 PHE C 323 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9666) covalent geometry : angle 0.55079 (13155) hydrogen bonds : bond 0.03776 ( 628) hydrogen bonds : angle 3.91821 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.329 Fit side-chains REVERT: A 148 ASN cc_start: 0.8905 (m-40) cc_final: 0.8584 (m110) REVERT: A 160 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8634 (tp) REVERT: A 241 LEU cc_start: 0.8795 (tt) cc_final: 0.8424 (tp) REVERT: B 18 ILE cc_start: 0.8495 (tp) cc_final: 0.8276 (tp) REVERT: B 160 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 286 MET cc_start: 0.7758 (mmm) cc_final: 0.7386 (mmt) REVERT: B 340 THR cc_start: 0.8109 (m) cc_final: 0.7787 (m) REVERT: C 42 TYR cc_start: 0.7765 (m-80) cc_final: 0.7439 (m-10) REVERT: C 160 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8645 (tp) REVERT: C 263 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8414 (ptpp) REVERT: C 269 MET cc_start: 0.7831 (ttp) cc_final: 0.7500 (ttp) outliers start: 22 outliers final: 19 residues processed: 188 average time/residue: 0.0678 time to fit residues: 19.8880 Evaluate side-chains 194 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 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 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.109775 restraints weight = 11542.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.112626 restraints weight = 7231.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.114693 restraints weight = 5191.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.116089 restraints weight = 4076.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.117031 restraints weight = 3437.762| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9666 Z= 0.120 Angle : 0.554 12.291 13155 Z= 0.276 Chirality : 0.039 0.188 1617 Planarity : 0.003 0.035 1608 Dihedral : 9.113 73.359 1533 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 23.32 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1233 helix: 0.94 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 397 TYR 0.025 0.002 TYR C 299 PHE 0.007 0.001 PHE C 323 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9666) covalent geometry : angle 0.55416 (13155) hydrogen bonds : bond 0.03740 ( 628) hydrogen bonds : angle 3.90438 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1296.82 seconds wall clock time: 23 minutes 8.56 seconds (1388.56 seconds total)