Starting phenix.real_space_refine on Fri Sep 11 14:18:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x14_21988/09_2026/6x14_21988.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x14_21988/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6x14_21988/09_2026/6x14_21988.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x14_21988/09_2026/6x14_21988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x14_21988/09_2026/6x14_21988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x14_21988/09_2026/6x14_21988.map" model { file = "/net/cci-nas-00/data/ceres_data/6x14_21988/09_2026/6x14_21988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x14_21988/09_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-2.2.1-6174/lib/python3.11/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: 2.26, 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: 0.72 Conformation dependent library (CDL) restraints added in 280.7 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: 0.16 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: 1.32 Time building geometry restraints manager: 0.81 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: 5299 25.79 - 51.59: 266 51.59 - 77.38: 45 77.38 - 103.17: 12 103.17 - 128.97: 3 Dihedral angle restraints: 5625 sinusoidal: 2103 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 5622 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: 0.03 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: 1.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 16.452 128.965 3393 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/Z covalent geometry : bond 0.00763 / 0.36 ( 9666) covalent geometry : angle 1.10484 / 0.52 (13155) hydrogen bonds : bond 0.12255 / 8.22 ( 628) hydrogen bonds : angle 5.93202 / 4.24 ( 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 : 0.215 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: 0.0704 time to fit residues: 23.3724 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 : 0.241 ------------------------------------------------------------------------------- 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... 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 = 0.3313 r_free = 0.3313 target = 0.128991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.110370 restraints weight = 11982.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.113211 restraints weight = 7272.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.115133 restraints weight = 5121.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.116542 restraints weight = 4028.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.117369 restraints weight = 3388.341| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9666 Z= 0.109 Angle : 0.527 6.333 13155 Z= 0.274 Chirality : 0.038 0.182 1617 Planarity : 0.005 0.052 1608 Dihedral : 12.237 92.865 1422 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.24 % Allowed : 13.93 % Favored : 84.83 % 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: -2.22 (0.22), residues: 1233 helix: -1.29 (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 0.028 0.001 TYR B 42 PHE 0.007 0.001 PHE B 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9666) covalent geometry : angle 0.52729 / 0.27 (13155) hydrogen bonds : bond 0.03835 / 2.60 ( 628) hydrogen bonds : angle 4.19025 / 2.97 ( 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 219 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.209 Fit side-chains REVERT: A 42 TYR cc_start: 0.7976 (m-10) cc_final: 0.7701 (m-10) REVERT: A 148 ASN cc_start: 0.9137 (m-40) cc_final: 0.8889 (m110) REVERT: A 195 TYR cc_start: 0.8795 (m-10) cc_final: 0.8588 (m-10) REVERT: A 241 LEU cc_start: 0.8851 (tt) cc_final: 0.8433 (tp) REVERT: A 263 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8493 (ptpp) REVERT: B 18 ILE cc_start: 0.8609 (tp) cc_final: 0.8375 (tp) REVERT: B 42 TYR cc_start: 0.8013 (m-80) cc_final: 0.7703 (m-10) REVERT: C 220 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8257 (mm-40) REVERT: C 263 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8346 (ptpp) REVERT: C 269 MET cc_start: 0.7554 (ttp) cc_final: 0.7280 (ttp) REVERT: C 318 GLN cc_start: 0.8408 (mt0) cc_final: 0.8030 (mt0) outliers start: 12 outliers final: 8 residues processed: 216 average time/residue: 0.0640 time to fit residues: 21.5437 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.2980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.121500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.103310 restraints weight = 12192.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.105782 restraints weight = 7723.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.108179 restraints weight = 5364.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.108607 restraints weight = 4244.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.108742 restraints weight = 3700.423| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9666 Z= 0.163 Angle : 0.580 11.592 13155 Z= 0.296 Chirality : 0.040 0.151 1617 Planarity : 0.004 0.043 1608 Dihedral : 11.164 89.655 1422 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.48 % Allowed : 18.78 % Favored : 78.74 % 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: -1.34 (0.23), residues: 1233 helix: -0.60 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.025 0.002 TYR C 299 PHE 0.012 0.001 PHE C 323 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 9666) covalent geometry : angle 0.57975 / 0.30 (13155) hydrogen bonds : bond 0.04537 / 3.08 ( 628) hydrogen bonds : angle 4.22932 / 2.99 ( 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 228 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.294 Fit side-chains REVERT: A 148 ASN cc_start: 0.9050 (m-40) cc_final: 0.8796 (m110) REVERT: A 241 LEU cc_start: 0.8896 (tt) cc_final: 0.8464 (tp) REVERT: A 263 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8593 (ptpp) REVERT: B 42 TYR cc_start: 0.7947 (m-80) cc_final: 0.7608 (m-10) REVERT: B 286 MET cc_start: 0.7786 (mmm) cc_final: 0.7397 (mmt) REVERT: C 160 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8768 (tp) REVERT: C 263 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8451 (ptpp) REVERT: C 269 MET cc_start: 0.7732 (ttp) cc_final: 0.7055 (ttp) REVERT: C 318 GLN cc_start: 0.8426 (mt0) cc_final: 0.8019 (mt0) REVERT: C 399 MET cc_start: 0.8770 (tpp) cc_final: 0.8317 (tpt) outliers start: 24 outliers final: 14 residues processed: 219 average time/residue: 0.0659 time to fit residues: 22.5361 Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 235 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 256 ILE 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 160 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 0.0570 chunk 13 optimal weight: 0.0970 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.128659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.110308 restraints weight = 11972.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.113159 restraints weight = 7550.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.115542 restraints weight = 5183.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.116138 restraints weight = 4117.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116356 restraints weight = 3446.458| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2240 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= 0.104 Angle : 0.508 11.584 13155 Z= 0.260 Chirality : 0.037 0.124 1617 Planarity : 0.004 0.044 1608 Dihedral : 10.254 85.783 1422 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 19.71 % Favored : 77.71 % 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: -0.52 (0.24), residues: 1233 helix: -0.04 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 397 TYR 0.024 0.001 TYR C 299 PHE 0.005 0.001 PHE B 323 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9666) covalent geometry : angle 0.50776 / 0.26 (13155) hydrogen bonds : bond 0.03448 / 2.36 ( 628) hydrogen bonds : angle 3.92413 / 2.78 ( 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 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 148 ASN cc_start: 0.8949 (m-40) cc_final: 0.8691 (m110) REVERT: A 263 LYS cc_start: 0.8773 (ptpp) cc_final: 0.8573 (ptpp) REVERT: B 286 MET cc_start: 0.7743 (mmm) cc_final: 0.7424 (mmt) REVERT: C 263 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8346 (ptpp) REVERT: C 269 MET cc_start: 0.7706 (ttp) cc_final: 0.7156 (ttp) REVERT: C 318 GLN cc_start: 0.8411 (mt0) cc_final: 0.7917 (mt0) REVERT: C 362 MET cc_start: 0.8290 (ttp) cc_final: 0.8067 (ttp) REVERT: C 399 MET cc_start: 0.8628 (tpp) cc_final: 0.8316 (tpt) outliers start: 25 outliers final: 19 residues processed: 206 average time/residue: 0.0636 time to fit residues: 20.4746 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 : 0.231 ------------------------------------------------------------------------------- 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 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 138 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR 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 308 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 368 HIS Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3277 r_free = 0.3277 target = 0.126733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.107494 restraints weight = 11839.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.110235 restraints weight = 7297.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.112295 restraints weight = 5232.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.113547 restraints weight = 4127.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.114577 restraints weight = 3502.444| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9666 Z= 0.123 Angle : 0.531 12.145 13155 Z= 0.269 Chirality : 0.038 0.141 1617 Planarity : 0.004 0.038 1608 Dihedral : 9.609 81.268 1422 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.79 % Allowed : 21.47 % Favored : 75.75 % 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: 0.29 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.36 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 397 TYR 0.025 0.001 TYR C 299 PHE 0.007 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9666) covalent geometry : angle 0.53063 / 0.27 (13155) hydrogen bonds : bond 0.03804 / 2.58 ( 628) hydrogen bonds : angle 3.95792 / 2.80 ( 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 224 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.390 Fit side-chains REVERT: A 126 GLN cc_start: 0.8982 (tp40) cc_final: 0.8533 (tp40) REVERT: A 148 ASN cc_start: 0.8995 (m-40) cc_final: 0.8720 (m110) REVERT: A 241 LEU cc_start: 0.8814 (tt) cc_final: 0.8415 (tp) REVERT: B 170 ASN cc_start: 0.8122 (p0) cc_final: 0.7776 (m-40) REVERT: B 286 MET cc_start: 0.7767 (mmm) cc_final: 0.7467 (mmt) REVERT: C 160 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8744 (tp) REVERT: C 263 LYS cc_start: 0.8644 (ptpp) cc_final: 0.8352 (ptpp) REVERT: C 269 MET cc_start: 0.7599 (ttp) cc_final: 0.6945 (ttp) REVERT: C 318 GLN cc_start: 0.8382 (mt0) cc_final: 0.7971 (mt0) REVERT: C 399 MET cc_start: 0.8661 (tpp) cc_final: 0.8267 (tpt) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 0.0695 time to fit residues: 22.9356 Evaluate side-chains 209 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 223 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 308 THR 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 223 HIS 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 160 ILE Chi-restraints excluded: chain C residue 309 ILE 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: 0.8980 chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3273 r_free = 0.3273 target = 0.126387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.107015 restraints weight = 11821.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.109824 restraints weight = 7308.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.111822 restraints weight = 5220.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.113074 restraints weight = 4122.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.114054 restraints weight = 3508.950| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9666 Z= 0.127 Angle : 0.538 12.526 13155 Z= 0.273 Chirality : 0.039 0.121 1617 Planarity : 0.004 0.036 1608 Dihedral : 9.394 80.708 1422 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.20 % Allowed : 21.47 % Favored : 75.34 % 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: 0.13 (0.24), residues: 1233 helix: 0.48 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.45 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.026 0.001 TYR C 299 PHE 0.008 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9666) covalent geometry : angle 0.53845 / 0.27 (13155) hydrogen bonds : bond 0.03878 / 2.64 ( 628) hydrogen bonds : angle 3.96012 / 2.80 ( 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 226 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.214 Fit side-chains REVERT: A 148 ASN cc_start: 0.8982 (m-40) cc_final: 0.8672 (m110) REVERT: A 241 LEU cc_start: 0.8807 (tt) cc_final: 0.8428 (tp) REVERT: A 387 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8112 (mp) REVERT: B 286 MET cc_start: 0.7910 (mmm) cc_final: 0.7605 (mmt) REVERT: C 160 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 263 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8394 (ptpp) REVERT: C 269 MET cc_start: 0.7742 (ttp) cc_final: 0.7041 (ttp) REVERT: C 389 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8110 (tp) REVERT: C 399 MET cc_start: 0.8699 (tpp) cc_final: 0.8246 (tpt) outliers start: 31 outliers final: 18 residues processed: 211 average time/residue: 0.0670 time to fit residues: 22.2479 Evaluate side-chains 211 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 223 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR 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 223 HIS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 389 ILE 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: 1.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3236 r_free = 0.3236 target = 0.123410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.104121 restraints weight = 11958.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.106845 restraints weight = 7371.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.108783 restraints weight = 5288.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.110165 restraints weight = 4182.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.111100 restraints weight = 3544.100| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9666 Z= 0.154 Angle : 0.577 13.005 13155 Z= 0.290 Chirality : 0.040 0.187 1617 Planarity : 0.004 0.036 1608 Dihedral : 9.268 77.972 1422 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.89 % Allowed : 21.67 % Favored : 75.44 % 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: 0.30 (0.25), residues: 1233 helix: 0.58 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -1.14 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.025 0.002 TYR C 299 PHE 0.011 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 9666) covalent geometry : angle 0.57691 / 0.29 (13155) hydrogen bonds : bond 0.04243 / 2.88 ( 628) hydrogen bonds : angle 4.06680 / 2.88 ( 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 225 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.353 Fit side-chains REVERT: A 42 TYR cc_start: 0.7784 (m-80) cc_final: 0.7581 (m-10) REVERT: A 148 ASN cc_start: 0.8975 (m-40) cc_final: 0.8671 (m110) REVERT: A 241 LEU cc_start: 0.8816 (tt) cc_final: 0.8426 (tp) REVERT: C 160 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8775 (tp) REVERT: C 263 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8448 (ptpp) REVERT: C 269 MET cc_start: 0.7808 (ttp) cc_final: 0.7071 (ttp) REVERT: C 389 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 399 MET cc_start: 0.8858 (tpp) cc_final: 0.8310 (tpt) outliers start: 28 outliers final: 19 residues processed: 214 average time/residue: 0.0673 time to fit residues: 22.7774 Evaluate side-chains 215 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 223 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 288 VAL 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 223 HIS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 389 ILE 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: 0.6980 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3269 r_free = 0.3269 target = 0.126310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.106908 restraints weight = 11716.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.109735 restraints weight = 7288.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.111674 restraints weight = 5247.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.113077 restraints weight = 4165.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.114026 restraints weight = 3523.607| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2618 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= 0.125 Angle : 0.551 12.504 13155 Z= 0.278 Chirality : 0.039 0.135 1617 Planarity : 0.004 0.036 1608 Dihedral : 9.033 78.646 1422 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.99 % Allowed : 22.70 % Favored : 74.30 % 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: 0.40 (0.25), residues: 1233 helix: 0.66 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.026 0.001 TYR C 299 PHE 0.007 0.001 PHE A 323 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 9666) covalent geometry : angle 0.55054 / 0.28 (13155) hydrogen bonds : bond 0.03866 / 2.63 ( 628) hydrogen bonds : angle 3.95704 / 2.80 ( 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 217 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.339 Fit side-chains REVERT: A 148 ASN cc_start: 0.8954 (m-40) cc_final: 0.8639 (m110) REVERT: A 241 LEU cc_start: 0.8804 (tt) cc_final: 0.8439 (tp) REVERT: B 170 ASN cc_start: 0.8066 (p0) cc_final: 0.7779 (m-40) REVERT: B 387 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8037 (mp) REVERT: C 160 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8739 (tp) REVERT: C 263 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8428 (ptpp) REVERT: C 269 MET cc_start: 0.7796 (ttp) cc_final: 0.7062 (ttp) REVERT: C 389 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8123 (tp) REVERT: C 399 MET cc_start: 0.8773 (tpp) cc_final: 0.8263 (tpt) outliers start: 29 outliers final: 18 residues processed: 207 average time/residue: 0.0691 time to fit residues: 22.5639 Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 223 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 138 VAL 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 B residue 387 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 389 ILE 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: 0.2980 chunk 122 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3318 r_free = 0.3318 target = 0.129930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.110593 restraints weight = 11654.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.113460 restraints weight = 7155.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.115499 restraints weight = 5083.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.116966 restraints weight = 3997.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.117997 restraints weight = 3359.348| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2804 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 : 0.535 11.949 13155 Z= 0.271 Chirality : 0.038 0.125 1617 Planarity : 0.004 0.035 1608 Dihedral : 8.659 79.540 1422 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.48 % Allowed : 23.74 % Favored : 73.79 % 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: 0.61 (0.25), residues: 1233 helix: 0.80 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 397 TYR 0.024 0.001 TYR C 299 PHE 0.005 0.001 PHE B 323 HIS 0.001 0.000 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9666) covalent geometry : angle 0.53505 / 0.27 (13155) hydrogen bonds : bond 0.03509 / 2.40 ( 628) hydrogen bonds : angle 3.85991 / 2.74 ( 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 207 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.346 Fit side-chains REVERT: A 148 ASN cc_start: 0.8907 (m-40) cc_final: 0.8602 (m110) REVERT: A 241 LEU cc_start: 0.8803 (tt) cc_final: 0.8442 (tp) REVERT: B 286 MET cc_start: 0.7728 (mmm) cc_final: 0.7358 (mmt) REVERT: B 387 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7981 (mp) REVERT: C 160 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8683 (tp) REVERT: C 263 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8412 (ptpp) REVERT: C 269 MET cc_start: 0.7621 (ttp) cc_final: 0.6919 (ttp) REVERT: C 389 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7921 (tp) REVERT: C 399 MET cc_start: 0.8649 (tpp) cc_final: 0.8217 (tpt) outliers start: 24 outliers final: 14 residues processed: 200 average time/residue: 0.0652 time to fit residues: 20.7903 Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 223 HIS Chi-restraints excluded: chain A residue 309 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 329 LEU Chi-restraints excluded: chain B residue 387 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 389 ILE 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 58 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3295 r_free = 0.3295 target = 0.127898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.108685 restraints weight = 11617.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.111523 restraints weight = 7171.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113557 restraints weight = 5111.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.114806 restraints weight = 4019.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.115844 restraints weight = 3416.783| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2832 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= 0.124 Angle : 0.559 12.356 13155 Z= 0.281 Chirality : 0.039 0.180 1617 Planarity : 0.004 0.035 1608 Dihedral : 8.581 77.798 1422 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.27 % Allowed : 23.43 % Favored : 74.30 % 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: 0.77 (0.25), residues: 1233 helix: 0.91 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -1.05 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 105 TYR 0.025 0.001 TYR C 299 PHE 0.007 0.001 PHE A 323 HIS 0.002 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9666) covalent geometry : angle 0.55894 / 0.28 (13155) hydrogen bonds : bond 0.03863 / 2.62 ( 628) hydrogen bonds : angle 3.94041 / 2.80 ( 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 199 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.327 Fit side-chains REVERT: A 148 ASN cc_start: 0.8920 (m-40) cc_final: 0.8607 (m110) REVERT: B 286 MET cc_start: 0.7752 (mmm) cc_final: 0.7353 (mmt) REVERT: B 340 THR cc_start: 0.8088 (m) cc_final: 0.7777 (m) REVERT: C 160 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8707 (tp) REVERT: C 269 MET cc_start: 0.7656 (ttp) cc_final: 0.6930 (ttp) REVERT: C 389 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (tp) REVERT: C 399 MET cc_start: 0.8729 (tpp) cc_final: 0.8204 (tpt) outliers start: 22 outliers final: 15 residues processed: 192 average time/residue: 0.0677 time to fit residues: 20.5537 Evaluate side-chains 193 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 223 HIS Chi-restraints excluded: chain A residue 309 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 329 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 389 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: 0.7980 chunk 66 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3285 r_free = 0.3285 target = 0.127043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.108112 restraints weight = 11643.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.111067 restraints weight = 7471.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.112768 restraints weight = 5070.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.113453 restraints weight = 4314.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.113661 restraints weight = 3687.088| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2860 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= 0.126 Angle : 0.565 12.403 13155 Z= 0.284 Chirality : 0.039 0.144 1617 Planarity : 0.004 0.035 1608 Dihedral : 8.536 77.794 1422 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.06 % Allowed : 23.84 % Favored : 74.10 % 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: 0.82 (0.25), residues: 1233 helix: 0.95 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -1.04 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 397 TYR 0.026 0.001 TYR B 299 PHE 0.008 0.001 PHE A 323 HIS 0.002 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9666) covalent geometry : angle 0.56519 / 0.28 (13155) hydrogen bonds : bond 0.03880 / 2.64 ( 628) hydrogen bonds : angle 3.94184 / 2.79 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.78 seconds wall clock time: 24 minutes 53.62 seconds (1493.62 seconds total)