Starting phenix.real_space_refine on Sun Jul 27 22:53:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x14_21988/07_2025/6x14_21988.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x14_21988/07_2025/6x14_21988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x14_21988/07_2025/6x14_21988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x14_21988/07_2025/6x14_21988.map" model { file = "/net/cci-nas-00/data/ceres_data/6x14_21988/07_2025/6x14_21988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x14_21988/07_2025/6x14_21988.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B Time building chain proxies: 6.40, per 1000 atoms: 0.67 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 2.71 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1455 1.31 - 1.43: 2360 1.43 - 1.55: 5686 1.55 - 1.68: 63 1.68 - 1.80: 102 Bond restraints: 9666 Sorted by residual: bond pdb=" N 7O9 A 501 " pdb=" C8 7O9 A 501 " ideal model delta sigma weight residual 1.354 1.450 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N 7O9 B 501 " pdb=" C8 7O9 B 501 " ideal model delta sigma weight residual 1.354 1.450 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N 7O9 C 501 " pdb=" C8 7O9 C 501 " ideal model delta sigma weight residual 1.354 1.449 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C16 6OU B 502 " pdb=" O18 6OU B 502 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C16 6OU C 502 " pdb=" O18 6OU C 502 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 9661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 12863 3.12 - 6.25: 235 6.25 - 9.37: 42 9.37 - 12.50: 9 12.50 - 15.62: 6 Bond angle restraints: 13155 Sorted by residual: angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 109.57 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU C 503 " pdb=" P23 6OU C 503 " pdb=" O26 6OU C 503 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU B 503 " pdb=" P23 6OU B 503 " pdb=" O26 6OU B 503 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU C 502 " pdb=" P23 6OU C 502 " pdb=" O26 6OU C 502 " ideal model delta sigma weight residual 93.95 109.41 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" O22 6OU B 502 " pdb=" P23 6OU B 502 " pdb=" O26 6OU B 502 " ideal model delta sigma weight residual 93.95 109.36 -15.41 3.00e+00 1.11e-01 2.64e+01 ... (remaining 13150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.79: 5323 25.79 - 51.59: 326 51.59 - 77.38: 51 77.38 - 103.17: 30 103.17 - 128.97: 6 Dihedral angle restraints: 5736 sinusoidal: 2214 harmonic: 3522 Sorted by residual: dihedral pdb=" C11 6OU C 502 " pdb=" C12 6OU C 502 " pdb=" C13 6OU C 502 " pdb=" C14 6OU C 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.68 128.97 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 6OU A 502 " pdb=" C12 6OU A 502 " pdb=" C13 6OU A 502 " pdb=" C14 6OU A 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.71 128.94 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 6OU B 502 " pdb=" C12 6OU B 502 " pdb=" C13 6OU B 502 " pdb=" C14 6OU B 502 " ideal model delta sinusoidal sigma weight residual 179.65 50.75 128.90 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 5733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1144 0.050 - 0.101: 379 0.101 - 0.151: 81 0.151 - 0.201: 4 0.201 - 0.252: 9 Chirality restraints: 1617 Sorted by residual: chirality pdb=" C1 7O9 A 501 " pdb=" C 7O9 A 501 " pdb=" C2 7O9 A 501 " pdb=" N1 7O9 A 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 7O9 C 501 " pdb=" C 7O9 C 501 " pdb=" C2 7O9 C 501 " pdb=" N1 7O9 C 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 7O9 B 501 " pdb=" C 7O9 B 501 " pdb=" C2 7O9 B 501 " pdb=" N1 7O9 B 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1614 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 7O9 C 501 " -0.071 2.00e-02 2.50e+03 4.56e-02 2.60e+01 pdb=" C7 7O9 C 501 " 0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 C 501 " -0.013 2.00e-02 2.50e+03 pdb=" C9 7O9 C 501 " 0.042 2.00e-02 2.50e+03 pdb=" O5 7O9 C 501 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 7O9 A 501 " 0.071 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" C7 7O9 A 501 " -0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 A 501 " 0.013 2.00e-02 2.50e+03 pdb=" C9 7O9 A 501 " -0.042 2.00e-02 2.50e+03 pdb=" O5 7O9 A 501 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 7O9 B 501 " 0.071 2.00e-02 2.50e+03 4.54e-02 2.57e+01 pdb=" C7 7O9 B 501 " -0.057 2.00e-02 2.50e+03 pdb=" C8 7O9 B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C9 7O9 B 501 " -0.041 2.00e-02 2.50e+03 pdb=" O5 7O9 B 501 " 0.015 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2604 2.81 - 3.33: 8811 3.33 - 3.85: 15473 3.85 - 4.38: 17641 4.38 - 4.90: 30166 Nonbonded interactions: 74695 Sorted by model distance: nonbonded pdb=" OH TYR B 247 " pdb=" OD2 ASP B 312 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR C 247 " pdb=" OD2 ASP C 312 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.282 3.040 nonbonded pdb=" O THR C 271 " pdb=" OG1 THR C 275 " model vdw 2.348 3.040 nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 275 " model vdw 2.348 3.040 ... (remaining 74690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.370 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.860 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 9666 Z= 0.365 Angle : 1.105 15.622 13155 Z= 0.516 Chirality : 0.052 0.252 1617 Planarity : 0.008 0.068 1608 Dihedral : 18.679 128.965 3504 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS B 132 PHE 0.018 0.002 PHE C 323 TYR 0.018 0.002 TYR B 299 ARG 0.003 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.12255 ( 628) hydrogen bonds : angle 5.93202 ( 1884) covalent geometry : bond 0.00763 ( 9666) covalent geometry : angle 1.10484 (13155) *********************** 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 : 0.909 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: 0.8568 (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: 0.1707 time to fit residues: 55.3663 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 : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 0.0010 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 337 GLN A 338 GLN B 318 GLN B 337 GLN C 40 HIS C 318 GLN C 337 GLN C 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.128385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.110284 restraints weight = 11897.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.112916 restraints weight = 7371.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.115148 restraints weight = 5062.647| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9666 Z= 0.115 Angle : 0.529 6.250 13155 Z= 0.275 Chirality : 0.038 0.176 1617 Planarity : 0.005 0.051 1608 Dihedral : 15.219 93.099 1533 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 14.24 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1233 helix: -1.23 (0.15), residues: 993 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.006 0.001 PHE C 323 TYR 0.026 0.001 TYR B 42 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 628) hydrogen bonds : angle 4.16628 ( 1884) covalent geometry : bond 0.00243 ( 9666) covalent geometry : angle 0.52907 (13155) *********************** 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 221 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.937 Fit side-chains REVERT: A 42 TYR cc_start: 0.7993 (m-10) cc_final: 0.7792 (m-80) REVERT: A 148 ASN cc_start: 0.9130 (m-40) cc_final: 0.8863 (m110) REVERT: A 241 LEU cc_start: 0.8864 (tt) cc_final: 0.8442 (tp) REVERT: A 263 LYS cc_start: 0.8816 (ptpp) cc_final: 0.8534 (ptpp) REVERT: B 42 TYR cc_start: 0.8016 (m-80) cc_final: 0.7722 (m-10) REVERT: C 220 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8267 (mm-40) REVERT: C 263 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8393 (ptpp) REVERT: C 269 MET cc_start: 0.7599 (ttp) cc_final: 0.7298 (ttp) REVERT: C 318 GLN cc_start: 0.8394 (mt0) cc_final: 0.8014 (mt0) outliers start: 13 outliers final: 8 residues processed: 218 average time/residue: 0.1586 time to fit residues: 52.4759 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 : 0.944 ------------------------------------------------------------------------------- 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 22 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.125760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.107525 restraints weight = 12047.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.110080 restraints weight = 7721.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.112497 restraints weight = 5304.528| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2015 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= 0.122 Angle : 0.539 10.654 13155 Z= 0.275 Chirality : 0.039 0.185 1617 Planarity : 0.004 0.043 1608 Dihedral : 13.081 89.717 1533 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.17 % Allowed : 18.27 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.23), residues: 1233 helix: -0.46 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 368 PHE 0.007 0.001 PHE C 323 TYR 0.025 0.001 TYR C 299 ARG 0.001 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 628) hydrogen bonds : angle 4.05904 ( 1884) covalent geometry : bond 0.00278 ( 9666) covalent geometry : angle 0.53859 (13155) *********************** 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 224 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.024 Fit side-chains REVERT: A 148 ASN cc_start: 0.9009 (m-40) cc_final: 0.8753 (m110) REVERT: A 169 MET cc_start: 0.8275 (mtm) cc_final: 0.8065 (mtp) REVERT: A 241 LEU cc_start: 0.8853 (tt) cc_final: 0.8430 (tp) REVERT: A 263 LYS cc_start: 0.8822 (ptpp) cc_final: 0.8560 (ptpp) REVERT: B 42 TYR cc_start: 0.7900 (m-80) cc_final: 0.7678 (m-80) REVERT: B 286 MET cc_start: 0.7750 (mmm) cc_final: 0.7385 (mmt) REVERT: C 263 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8385 (ptpp) REVERT: C 269 MET cc_start: 0.7664 (ttp) cc_final: 0.6867 (ttp) REVERT: C 318 GLN cc_start: 0.8366 (mt0) cc_final: 0.7978 (mt0) REVERT: C 399 MET cc_start: 0.8821 (tpp) cc_final: 0.8122 (tpt) outliers start: 21 outliers final: 15 residues processed: 214 average time/residue: 0.1762 time to fit residues: 57.3808 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.127358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.108934 restraints weight = 11785.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.111672 restraints weight = 7653.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.113355 restraints weight = 5283.364| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2293 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= 0.115 Angle : 0.522 11.697 13155 Z= 0.267 Chirality : 0.038 0.189 1617 Planarity : 0.004 0.040 1608 Dihedral : 11.428 82.689 1533 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.48 % Allowed : 20.02 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1233 helix: 0.06 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.005 0.001 PHE A 323 TYR 0.025 0.001 TYR B 299 ARG 0.001 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 628) hydrogen bonds : angle 3.96705 ( 1884) covalent geometry : bond 0.00259 ( 9666) covalent geometry : angle 0.52231 (13155) *********************** 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 226 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.997 Fit side-chains REVERT: A 148 ASN cc_start: 0.8995 (m-40) cc_final: 0.8730 (m110) REVERT: A 169 MET cc_start: 0.8299 (mtm) cc_final: 0.8066 (mtp) REVERT: A 263 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8554 (ptpp) REVERT: B 286 MET cc_start: 0.7735 (mmm) cc_final: 0.7427 (mmt) REVERT: B 318 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: B 362 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7927 (ttp) REVERT: C 18 ILE cc_start: 0.8473 (tp) cc_final: 0.8220 (tp) REVERT: C 160 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8683 (tp) REVERT: C 263 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8379 (ptpp) REVERT: C 269 MET cc_start: 0.7718 (ttp) cc_final: 0.6889 (ttp) REVERT: C 318 GLN cc_start: 0.8401 (mt0) cc_final: 0.7928 (mt0) REVERT: C 389 ILE cc_start: 0.8221 (tp) cc_final: 0.7954 (tp) REVERT: C 399 MET cc_start: 0.8769 (tpp) cc_final: 0.8140 (tpt) outliers start: 24 outliers final: 15 residues processed: 215 average time/residue: 0.1622 time to fit residues: 53.3843 Evaluate side-chains 220 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 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 B residue 362 MET Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN B 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.130619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.111451 restraints weight = 11582.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.114184 restraints weight = 7174.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.116280 restraints weight = 5133.283| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2506 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= 0.103 Angle : 0.514 11.895 13155 Z= 0.260 Chirality : 0.037 0.120 1617 Planarity : 0.004 0.036 1608 Dihedral : 10.483 81.570 1533 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.68 % Allowed : 21.67 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1233 helix: 0.42 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.005 0.001 PHE B 323 TYR 0.024 0.001 TYR C 299 ARG 0.001 0.000 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 628) hydrogen bonds : angle 3.84939 ( 1884) covalent geometry : bond 0.00219 ( 9666) covalent geometry : angle 0.51419 (13155) *********************** 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 216 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.023 Fit side-chains REVERT: A 148 ASN cc_start: 0.8964 (m-40) cc_final: 0.8668 (m110) REVERT: A 160 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8709 (tp) REVERT: A 169 MET cc_start: 0.8264 (mtm) cc_final: 0.8026 (mtp) REVERT: B 286 MET cc_start: 0.7718 (mmm) cc_final: 0.7454 (mmt) REVERT: C 160 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8695 (tp) REVERT: C 263 LYS cc_start: 0.8628 (ptpp) cc_final: 0.8311 (ptpp) REVERT: C 269 MET cc_start: 0.7689 (ttp) cc_final: 0.7086 (ttp) REVERT: C 318 GLN cc_start: 0.8338 (mt0) cc_final: 0.7950 (mt0) REVERT: C 399 MET cc_start: 0.8837 (tpp) cc_final: 0.8401 (tpt) outliers start: 26 outliers final: 15 residues processed: 203 average time/residue: 0.1583 time to fit residues: 49.1017 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 : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 6 LYS 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 160 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.129749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.110535 restraints weight = 11623.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.113371 restraints weight = 7240.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.115261 restraints weight = 5160.187| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2635 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 : 0.516 12.160 13155 Z= 0.262 Chirality : 0.038 0.116 1617 Planarity : 0.003 0.034 1608 Dihedral : 10.022 80.650 1533 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.79 % Allowed : 22.29 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1233 helix: 0.59 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.005 0.001 PHE A 323 TYR 0.025 0.001 TYR B 299 ARG 0.001 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 628) hydrogen bonds : angle 3.82802 ( 1884) covalent geometry : bond 0.00238 ( 9666) covalent geometry : angle 0.51637 (13155) *********************** 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 214 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.931 Fit side-chains REVERT: A 148 ASN cc_start: 0.8939 (m-40) cc_final: 0.8650 (m110) REVERT: A 160 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8673 (tp) REVERT: B 286 MET cc_start: 0.7708 (mmm) cc_final: 0.7442 (mmt) REVERT: C 160 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (tp) REVERT: C 263 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8343 (ptpp) REVERT: C 269 MET cc_start: 0.7666 (ttp) cc_final: 0.6962 (ttp) REVERT: C 318 GLN cc_start: 0.8315 (mt0) cc_final: 0.8010 (mt0) REVERT: C 399 MET cc_start: 0.8742 (tpp) cc_final: 0.8163 (tpt) outliers start: 27 outliers final: 16 residues processed: 201 average time/residue: 0.1551 time to fit residues: 47.8059 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 309 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 99 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 107 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.129791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.110501 restraints weight = 11639.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.113276 restraints weight = 7227.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.115348 restraints weight = 5180.009| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9666 Z= 0.108 Angle : 0.522 12.462 13155 Z= 0.263 Chirality : 0.038 0.154 1617 Planarity : 0.003 0.034 1608 Dihedral : 9.619 80.193 1533 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.30 % Allowed : 22.29 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1233 helix: 0.69 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.005 0.001 PHE A 323 TYR 0.025 0.001 TYR B 299 ARG 0.001 0.000 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 628) hydrogen bonds : angle 3.81367 ( 1884) covalent geometry : bond 0.00241 ( 9666) covalent geometry : angle 0.52191 (13155) *********************** 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 214 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.947 Fit side-chains REVERT: A 148 ASN cc_start: 0.8930 (m-40) cc_final: 0.8639 (m110) REVERT: A 160 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 387 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 160 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8691 (tp) REVERT: B 286 MET cc_start: 0.7794 (mmm) cc_final: 0.7546 (mmt) REVERT: C 160 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8706 (tp) REVERT: C 263 LYS cc_start: 0.8630 (ptpp) cc_final: 0.8375 (ptpp) REVERT: C 269 MET cc_start: 0.7642 (ttp) cc_final: 0.6928 (ttp) REVERT: C 318 GLN cc_start: 0.8313 (mt0) cc_final: 0.8029 (mt0) REVERT: C 399 MET cc_start: 0.8796 (tpp) cc_final: 0.8189 (tpt) outliers start: 32 outliers final: 20 residues processed: 201 average time/residue: 0.1537 time to fit residues: 47.8374 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 362 MET 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 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 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 115 optimal weight: 0.0970 chunk 47 optimal weight: 0.0010 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.131014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.111952 restraints weight = 11640.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.114899 restraints weight = 7549.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.117398 restraints weight = 5070.575| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.002 0.031 9666 Z= 0.106 Angle : 0.525 12.372 13155 Z= 0.264 Chirality : 0.038 0.196 1617 Planarity : 0.003 0.033 1608 Dihedral : 9.323 80.573 1533 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.68 % Allowed : 23.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1233 helix: 0.81 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 32 PHE 0.005 0.001 PHE A 301 TYR 0.024 0.001 TYR C 299 ARG 0.001 0.000 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 628) hydrogen bonds : angle 3.80116 ( 1884) covalent geometry : bond 0.00234 ( 9666) covalent geometry : angle 0.52505 (13155) *********************** 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 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.992 Fit side-chains REVERT: A 148 ASN cc_start: 0.8931 (m-40) cc_final: 0.8636 (m110) REVERT: A 160 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (tp) REVERT: A 387 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 160 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8553 (tp) REVERT: B 286 MET cc_start: 0.7775 (mmm) cc_final: 0.7530 (mmt) REVERT: C 42 TYR cc_start: 0.7752 (m-80) cc_final: 0.7331 (m-10) REVERT: C 160 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8644 (tp) REVERT: C 263 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8385 (ptpp) REVERT: C 269 MET cc_start: 0.7635 (ttp) cc_final: 0.7002 (ttp) REVERT: C 318 GLN cc_start: 0.8305 (mt0) cc_final: 0.8022 (mt0) REVERT: C 399 MET cc_start: 0.8868 (tpp) cc_final: 0.8399 (tpt) outliers start: 26 outliers final: 19 residues processed: 200 average time/residue: 0.2043 time to fit residues: 63.1894 Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain 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 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 392 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 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 105 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.130674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.111341 restraints weight = 11563.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.114217 restraints weight = 7172.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.116258 restraints weight = 5120.240| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2945 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= 0.114 Angle : 0.539 12.708 13155 Z= 0.270 Chirality : 0.039 0.198 1617 Planarity : 0.003 0.033 1608 Dihedral : 9.150 74.015 1533 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.10 % Allowed : 23.32 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1233 helix: 0.93 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 32 PHE 0.005 0.001 PHE A 301 TYR 0.025 0.001 TYR C 299 ARG 0.001 0.000 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 628) hydrogen bonds : angle 3.83548 ( 1884) covalent geometry : bond 0.00257 ( 9666) covalent geometry : angle 0.53918 (13155) *********************** 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 211 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.045 Fit side-chains REVERT: A 148 ASN cc_start: 0.8944 (m-40) cc_final: 0.8654 (m110) REVERT: A 160 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 387 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 160 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8684 (tp) REVERT: B 286 MET cc_start: 0.7843 (mmm) cc_final: 0.7581 (mmt) REVERT: B 387 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7984 (mp) REVERT: C 160 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8689 (tp) REVERT: C 263 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8396 (ptpp) REVERT: C 269 MET cc_start: 0.7668 (ttp) cc_final: 0.7038 (ttp) REVERT: C 318 GLN cc_start: 0.8224 (mt0) cc_final: 0.7975 (mt0) REVERT: C 399 MET cc_start: 0.8835 (tpp) cc_final: 0.8432 (tpt) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.1720 time to fit residues: 52.1729 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 309 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 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.109174 restraints weight = 11769.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.111839 restraints weight = 7638.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.114172 restraints weight = 5331.343| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9666 Z= 0.133 Angle : 0.558 12.867 13155 Z= 0.281 Chirality : 0.039 0.177 1617 Planarity : 0.003 0.033 1608 Dihedral : 9.217 73.378 1533 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.48 % Allowed : 24.05 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1233 helix: 0.92 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.98 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.007 0.001 PHE C 323 TYR 0.025 0.001 TYR C 299 ARG 0.001 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 628) hydrogen bonds : angle 3.92909 ( 1884) covalent geometry : bond 0.00313 ( 9666) covalent geometry : angle 0.55802 (13155) ********************** 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: 24 poor density : 175 time to evaluate : 1.181 Fit side-chains REVERT: A 148 ASN cc_start: 0.8967 (m-40) cc_final: 0.8651 (m110) REVERT: A 160 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8708 (tp) REVERT: A 387 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 160 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8631 (tp) REVERT: B 340 THR cc_start: 0.8105 (m) cc_final: 0.7825 (m) REVERT: B 387 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8045 (mp) REVERT: C 18 ILE cc_start: 0.8545 (tp) cc_final: 0.8290 (tp) REVERT: C 160 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 263 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8464 (ptpp) REVERT: C 269 MET cc_start: 0.7747 (ttp) cc_final: 0.7090 (ttp) REVERT: C 389 ILE cc_start: 0.8413 (tp) cc_final: 0.8125 (tp) REVERT: C 399 MET cc_start: 0.8897 (tpp) cc_final: 0.8439 (tpt) outliers start: 24 outliers final: 15 residues processed: 191 average time/residue: 0.1729 time to fit residues: 50.7621 Evaluate side-chains 193 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 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 349 SER Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.129958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.110759 restraints weight = 11580.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.113446 restraints weight = 7290.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.115524 restraints weight = 5275.634| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9666 Z= 0.116 Angle : 0.539 12.526 13155 Z= 0.272 Chirality : 0.039 0.160 1617 Planarity : 0.003 0.033 1608 Dihedral : 9.025 73.577 1533 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.48 % Allowed : 23.63 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1233 helix: 1.01 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -0.92 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 368 PHE 0.007 0.001 PHE C 323 TYR 0.025 0.001 TYR C 299 ARG 0.001 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 628) hydrogen bonds : angle 3.86248 ( 1884) covalent geometry : bond 0.00264 ( 9666) covalent geometry : angle 0.53941 (13155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.84 seconds wall clock time: 56 minutes 3.10 seconds (3363.10 seconds total)