Starting phenix.real_space_refine on Thu Sep 18 08:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ema_19815/09_2025/9ema_19815_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ema_19815/09_2025/9ema_19815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ema_19815/09_2025/9ema_19815_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ema_19815/09_2025/9ema_19815_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ema_19815/09_2025/9ema_19815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ema_19815/09_2025/9ema_19815.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 18 5.49 5 Mg 4 5.21 5 S 78 5.16 5 Cl 3 4.86 5 C 9735 2.51 5 N 2724 2.21 5 O 2997 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15562 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2508 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 2 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2508 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 2 Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2508 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 2 Chain: "D" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2576 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 1 Chain: "E" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2576 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 1 Chain: "F" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2576 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'A1H5V': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'A1H5V': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'A1H5V': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.19, per 1000 atoms: 0.27 Number of scatterers: 15562 At special positions: 0 Unit cell: (129.337, 127.689, 75.7896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 3 17.00 S 78 16.00 P 18 15.00 Mg 4 11.99 F 3 9.00 O 2997 8.00 N 2724 7.00 C 9735 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: 1.39 Conformation dependent library (CDL) restraints added in 829.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 24 sheets defined 54.6% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.731A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.503A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.069A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.632A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.774A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.667A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.669A pdb=" N LYS B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.579A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 272 through 289 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.714A pdb=" N HIS B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.717A pdb=" N ARG B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.570A pdb=" N ILE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.547A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.534A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.565A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.613A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.512A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.540A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.569A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.637A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.834A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 removed outlier: 3.776A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.503A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 445 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 126 removed outlier: 3.512A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 253 removed outlier: 4.029A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 removed outlier: 4.212A pdb=" N PHE E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.640A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.869A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 353 removed outlier: 3.779A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.650A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 445 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.536A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.186A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.600A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.800A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 379 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.720A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.521A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.320A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 239 Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.617A pdb=" N CYS B 336 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.301A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.509A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.535A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY E 77 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR E 359 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA E 76 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC2, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.298A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 240 through 243 Processing sheet with id=AC6, first strand: chain 'F' and resid 333 through 334 797 hydrogen bonds defined for protein. 2307 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: 2.81 Time building geometry restraints manager: 1.85 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: 2634 1.31 - 1.44: 3665 1.44 - 1.56: 9277 1.56 - 1.69: 48 1.69 - 1.82: 141 Bond restraints: 15765 Sorted by residual: bond pdb=" C04 A1H5V B 501 " pdb=" C05 A1H5V B 501 " ideal model delta sigma weight residual 1.371 1.555 -0.184 2.00e-02 2.50e+03 8.51e+01 bond pdb=" C04 A1H5V C 502 " pdb=" C05 A1H5V C 502 " ideal model delta sigma weight residual 1.371 1.554 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C04 A1H5V A 502 " pdb=" C05 A1H5V A 502 " ideal model delta sigma weight residual 1.371 1.553 -0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" C05 A1H5V C 502 " pdb=" C28 A1H5V C 502 " ideal model delta sigma weight residual 1.433 1.563 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C05 A1H5V B 501 " pdb=" C28 A1H5V B 501 " ideal model delta sigma weight residual 1.433 1.561 -0.128 2.00e-02 2.50e+03 4.09e+01 ... (remaining 15760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 20919 3.50 - 7.00: 352 7.00 - 10.51: 17 10.51 - 14.01: 3 14.01 - 17.51: 3 Bond angle restraints: 21294 Sorted by residual: angle pdb=" N LEU E 395 " pdb=" CA LEU E 395 " pdb=" C LEU E 395 " ideal model delta sigma weight residual 112.38 104.89 7.49 1.22e+00 6.72e-01 3.77e+01 angle pdb=" N GLY A 349 " pdb=" CA GLY A 349 " pdb=" C GLY A 349 " ideal model delta sigma weight residual 115.30 106.79 8.51 1.39e+00 5.18e-01 3.74e+01 angle pdb=" C04 A1H5V C 502 " pdb=" N30 A1H5V C 502 " pdb=" C31 A1H5V C 502 " ideal model delta sigma weight residual 131.03 113.52 17.51 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C04 A1H5V B 501 " pdb=" N30 A1H5V B 501 " pdb=" C31 A1H5V B 501 " ideal model delta sigma weight residual 131.03 114.92 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" C04 A1H5V A 502 " pdb=" N30 A1H5V A 502 " pdb=" C31 A1H5V A 502 " ideal model delta sigma weight residual 131.03 115.02 16.01 3.00e+00 1.11e-01 2.85e+01 ... (remaining 21289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 9494 35.09 - 70.18: 367 70.18 - 105.27: 36 105.27 - 140.37: 0 140.37 - 175.46: 6 Dihedral angle restraints: 9903 sinusoidal: 4248 harmonic: 5655 Sorted by residual: dihedral pdb=" C09 A1H5V C 502 " pdb=" C07 A1H5V C 502 " pdb=" C08 A1H5V C 502 " pdb=" O27 A1H5V C 502 " ideal model delta sinusoidal sigma weight residual -83.32 92.14 -175.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 A1H5V C 502 " pdb=" C05 A1H5V C 502 " pdb=" N06 A1H5V C 502 " pdb=" C28 A1H5V C 502 " ideal model delta sinusoidal sigma weight residual 278.01 103.84 174.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 A1H5V C 502 " pdb=" C18 A1H5V C 502 " pdb=" O17 A1H5V C 502 " pdb=" C19 A1H5V C 502 " ideal model delta sinusoidal sigma weight residual 75.45 -93.19 168.64 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1979 0.060 - 0.121: 362 0.121 - 0.181: 112 0.181 - 0.241: 12 0.241 - 0.301: 13 Chirality restraints: 2478 Sorted by residual: chirality pdb=" C3' ATP F 802 " pdb=" C2' ATP F 802 " pdb=" C4' ATP F 802 " pdb=" O3' ATP F 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' ATP D 801 " pdb=" C2' ATP D 801 " pdb=" C4' ATP D 801 " pdb=" O3' ATP D 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ATP E 801 " pdb=" C2' ATP E 801 " pdb=" C4' ATP E 801 " pdb=" O3' ATP E 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2475 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 419 " -0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE B 419 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE B 419 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN B 420 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 25 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" C GLY C 25 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY C 25 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 26 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 388 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C THR E 388 " 0.048 2.00e-02 2.50e+03 pdb=" O THR E 388 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL E 389 " -0.016 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 82 2.58 - 3.16: 12262 3.16 - 3.74: 25738 3.74 - 4.32: 36503 4.32 - 4.90: 58703 Nonbonded interactions: 133288 Sorted by model distance: nonbonded pdb=" O3G ATP A 501 " pdb="MG MG F 801 " model vdw 1.999 2.170 nonbonded pdb=" O1A ATP A 501 " pdb="MG MG F 801 " model vdw 2.006 2.170 nonbonded pdb=" O2B ATP F 802 " pdb="MG MG F 803 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 803 " model vdw 2.037 2.170 nonbonded pdb=" O2B ATP E 801 " pdb="MG MG E 802 " model vdw 2.101 2.170 ... (remaining 133283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 16 through 451) selection = (chain 'E' and resid 16 through 451) selection = (chain 'F' and resid 16 through 451) } 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 individual isotropic 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 0.184 15765 Z= 0.386 Angle : 1.072 17.512 21294 Z= 0.565 Chirality : 0.056 0.301 2478 Planarity : 0.007 0.099 2694 Dihedral : 18.259 175.457 6249 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % Rotamer: Outliers : 0.42 % Allowed : 12.20 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 1944 helix: -0.01 (0.14), residues: 1041 sheet: -0.78 (0.29), residues: 252 loop : 0.22 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 123 TYR 0.029 0.002 TYR D 442 PHE 0.019 0.002 PHE E 257 TRP 0.004 0.001 TRP D 283 HIS 0.005 0.001 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.00832 (15765) covalent geometry : angle 1.07249 (21294) hydrogen bonds : bond 0.16109 ( 797) hydrogen bonds : angle 5.86005 ( 2307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 311 time to evaluate : 0.649 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 314 average time/residue: 0.6944 time to fit residues: 238.4599 Evaluate side-chains 159 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 449 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.092137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078303 restraints weight = 28512.364| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.30 r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15765 Z= 0.143 Angle : 0.576 9.364 21294 Z= 0.300 Chirality : 0.043 0.217 2478 Planarity : 0.005 0.044 2694 Dihedral : 13.278 178.546 2474 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.54 % Allowed : 15.04 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.18), residues: 1944 helix: 1.04 (0.15), residues: 1050 sheet: -0.17 (0.30), residues: 264 loop : 0.62 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.010 0.001 TYR E 387 PHE 0.016 0.001 PHE F 257 TRP 0.008 0.001 TRP F 283 HIS 0.006 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00317 (15765) covalent geometry : angle 0.57631 (21294) hydrogen bonds : bond 0.03422 ( 797) hydrogen bonds : angle 4.02415 ( 2307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.677 Fit side-chains REVERT: A 96 MET cc_start: 0.8484 (ttt) cc_final: 0.8234 (ttt) REVERT: A 123 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8112 (ttt90) REVERT: A 342 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7554 (pm20) REVERT: A 388 GLU cc_start: 0.8212 (pm20) cc_final: 0.7844 (tp30) REVERT: B 455 MET cc_start: 0.8588 (mmt) cc_final: 0.8359 (mmm) REVERT: C 410 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8030 (mm) REVERT: D 46 MET cc_start: 0.8802 (mmm) cc_final: 0.8590 (mmt) REVERT: E 112 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: E 282 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: E 442 TYR cc_start: 0.7815 (m-80) cc_final: 0.7382 (m-10) REVERT: F 131 ILE cc_start: 0.8580 (pp) cc_final: 0.8098 (mp) REVERT: F 132 LYS cc_start: 0.8098 (mttm) cc_final: 0.7649 (mtmm) outliers start: 42 outliers final: 10 residues processed: 217 average time/residue: 0.6553 time to fit residues: 156.5284 Evaluate side-chains 164 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 189 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.076040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061247 restraints weight = 27645.231| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.31 r_work: 0.2686 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15765 Z= 0.142 Angle : 0.522 7.974 21294 Z= 0.273 Chirality : 0.042 0.157 2478 Planarity : 0.004 0.044 2694 Dihedral : 13.749 176.573 2472 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.75 % Allowed : 15.88 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.19), residues: 1944 helix: 1.49 (0.16), residues: 1050 sheet: -0.03 (0.28), residues: 276 loop : 0.72 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 249 TYR 0.008 0.001 TYR B 366 PHE 0.008 0.001 PHE D 257 TRP 0.005 0.001 TRP F 283 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00322 (15765) covalent geometry : angle 0.52194 (21294) hydrogen bonds : bond 0.04304 ( 797) hydrogen bonds : angle 4.02247 ( 2307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.537 Fit side-chains REVERT: B 264 MET cc_start: 0.8300 (mtp) cc_final: 0.8029 (mtt) REVERT: B 367 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8435 (p) REVERT: B 435 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: B 455 MET cc_start: 0.8741 (mmt) cc_final: 0.8538 (mmm) REVERT: C 236 GLN cc_start: 0.7634 (tp40) cc_final: 0.7308 (tt0) REVERT: C 451 GLN cc_start: 0.8138 (pt0) cc_final: 0.7916 (pp30) REVERT: C 455 MET cc_start: 0.8651 (mmt) cc_final: 0.8434 (mmm) REVERT: E 112 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: E 240 HIS cc_start: 0.7592 (m-70) cc_final: 0.7356 (m-70) REVERT: E 364 GLU cc_start: 0.8745 (tt0) cc_final: 0.8540 (tm-30) REVERT: E 442 TYR cc_start: 0.8253 (m-80) cc_final: 0.7727 (m-10) REVERT: F 132 LYS cc_start: 0.8334 (mttm) cc_final: 0.7937 (mtmm) REVERT: F 282 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: F 387 TYR cc_start: 0.8911 (m-80) cc_final: 0.8689 (m-80) outliers start: 29 outliers final: 6 residues processed: 183 average time/residue: 0.6947 time to fit residues: 139.3214 Evaluate side-chains 146 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 129 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 = 0.3073 r_free = 0.3073 target = 0.073513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.058965 restraints weight = 27736.365| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.25 r_work: 0.2633 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15765 Z= 0.155 Angle : 0.494 7.855 21294 Z= 0.262 Chirality : 0.042 0.165 2478 Planarity : 0.004 0.050 2694 Dihedral : 13.815 178.275 2472 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.51 % Allowed : 14.92 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.19), residues: 1944 helix: 1.65 (0.16), residues: 1053 sheet: 0.14 (0.28), residues: 276 loop : 0.66 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 249 TYR 0.010 0.001 TYR D 446 PHE 0.011 0.001 PHE F 257 TRP 0.002 0.000 TRP F 283 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00367 (15765) covalent geometry : angle 0.49416 (21294) hydrogen bonds : bond 0.03658 ( 797) hydrogen bonds : angle 3.91728 ( 2307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.656 Fit side-chains REVERT: B 367 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 455 MET cc_start: 0.8809 (mmt) cc_final: 0.8602 (mmm) REVERT: C 376 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8434 (tmtt) REVERT: C 451 GLN cc_start: 0.8386 (pt0) cc_final: 0.8116 (pp30) REVERT: E 279 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8350 (tppt) REVERT: E 364 GLU cc_start: 0.8843 (tt0) cc_final: 0.8627 (tm-30) REVERT: E 442 TYR cc_start: 0.8397 (m-80) cc_final: 0.7911 (m-10) REVERT: F 131 ILE cc_start: 0.8739 (pp) cc_final: 0.8204 (mp) REVERT: F 132 LYS cc_start: 0.8213 (mttm) cc_final: 0.7862 (mtmm) REVERT: F 365 LYS cc_start: 0.8861 (mppt) cc_final: 0.8657 (mtpp) REVERT: F 414 ARG cc_start: 0.8306 (mtm110) cc_final: 0.8045 (mtt-85) outliers start: 25 outliers final: 8 residues processed: 162 average time/residue: 0.7391 time to fit residues: 130.4842 Evaluate side-chains 145 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 170 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.074856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060332 restraints weight = 27549.436| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.27 r_work: 0.2668 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15765 Z= 0.101 Angle : 0.443 8.240 21294 Z= 0.235 Chirality : 0.040 0.185 2478 Planarity : 0.004 0.043 2694 Dihedral : 13.384 176.346 2472 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.27 % Allowed : 15.34 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 1944 helix: 1.79 (0.16), residues: 1053 sheet: 0.29 (0.29), residues: 276 loop : 0.80 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 249 TYR 0.011 0.001 TYR D 446 PHE 0.007 0.001 PHE D 257 TRP 0.003 0.000 TRP F 283 HIS 0.002 0.000 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00230 (15765) covalent geometry : angle 0.44280 (21294) hydrogen bonds : bond 0.03113 ( 797) hydrogen bonds : angle 3.72756 ( 2307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.573 Fit side-chains REVERT: B 367 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 455 MET cc_start: 0.8800 (mmt) cc_final: 0.8593 (mmm) REVERT: C 376 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8402 (tmtt) REVERT: C 451 GLN cc_start: 0.8280 (pt0) cc_final: 0.7826 (pp30) REVERT: E 279 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8351 (tppt) REVERT: E 364 GLU cc_start: 0.8825 (tt0) cc_final: 0.8591 (tm-30) REVERT: E 442 TYR cc_start: 0.8389 (m-80) cc_final: 0.7915 (m-10) REVERT: F 132 LYS cc_start: 0.8238 (mttm) cc_final: 0.7921 (mtmm) REVERT: F 365 LYS cc_start: 0.8830 (mppt) cc_final: 0.8578 (mtpp) REVERT: F 414 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7989 (mtt-85) outliers start: 21 outliers final: 5 residues processed: 155 average time/residue: 0.7171 time to fit residues: 121.5253 Evaluate side-chains 141 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3024 r_free = 0.3024 target = 0.071281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.056542 restraints weight = 27860.583| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.29 r_work: 0.2563 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15765 Z= 0.199 Angle : 0.513 8.740 21294 Z= 0.269 Chirality : 0.043 0.181 2478 Planarity : 0.004 0.054 2694 Dihedral : 14.139 179.634 2472 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.15 % Allowed : 15.58 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.19), residues: 1944 helix: 1.56 (0.16), residues: 1074 sheet: 0.37 (0.29), residues: 276 loop : 0.54 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 249 TYR 0.012 0.001 TYR D 362 PHE 0.013 0.001 PHE E 257 TRP 0.002 0.000 TRP D 283 HIS 0.004 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00475 (15765) covalent geometry : angle 0.51259 (21294) hydrogen bonds : bond 0.04158 ( 797) hydrogen bonds : angle 4.00935 ( 2307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.677 Fit side-chains REVERT: A 125 LYS cc_start: 0.6581 (tptt) cc_final: 0.6280 (tptt) REVERT: B 263 LEU cc_start: 0.7887 (pp) cc_final: 0.7630 (mp) REVERT: B 455 MET cc_start: 0.8787 (mmt) cc_final: 0.8536 (mmm) REVERT: C 346 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8770 (t) REVERT: C 451 GLN cc_start: 0.8541 (pt0) cc_final: 0.8026 (pp30) REVERT: C 455 MET cc_start: 0.8681 (mmm) cc_final: 0.8336 (mmt) REVERT: E 279 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8377 (tppt) REVERT: E 364 GLU cc_start: 0.8906 (tt0) cc_final: 0.8705 (tm-30) REVERT: E 437 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8743 (p) REVERT: E 442 TYR cc_start: 0.8413 (m-80) cc_final: 0.7923 (m-10) REVERT: F 132 LYS cc_start: 0.8234 (mttm) cc_final: 0.7964 (mtmm) REVERT: F 270 SER cc_start: 0.9291 (m) cc_final: 0.8949 (p) REVERT: F 414 ARG cc_start: 0.8271 (mtm110) cc_final: 0.7994 (mtt-85) REVERT: F 446 TYR cc_start: 0.7818 (m-80) cc_final: 0.7355 (m-10) outliers start: 19 outliers final: 6 residues processed: 151 average time/residue: 0.7361 time to fit residues: 121.7778 Evaluate side-chains 137 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 437 SER Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 165 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.073439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.058835 restraints weight = 27641.864| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.28 r_work: 0.2617 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15765 Z= 0.106 Angle : 0.452 8.303 21294 Z= 0.240 Chirality : 0.040 0.161 2478 Planarity : 0.004 0.047 2694 Dihedral : 13.558 177.801 2472 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.72 % Allowed : 15.70 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.19), residues: 1944 helix: 1.67 (0.16), residues: 1077 sheet: 0.47 (0.29), residues: 276 loop : 0.62 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 249 TYR 0.012 0.001 TYR D 446 PHE 0.006 0.001 PHE D 311 TRP 0.002 0.000 TRP F 283 HIS 0.002 0.000 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.00242 (15765) covalent geometry : angle 0.45152 (21294) hydrogen bonds : bond 0.03226 ( 797) hydrogen bonds : angle 3.77102 ( 2307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.653 Fit side-chains REVERT: A 125 LYS cc_start: 0.6576 (tptt) cc_final: 0.6150 (tptp) REVERT: B 263 LEU cc_start: 0.7827 (pp) cc_final: 0.7503 (mp) REVERT: B 455 MET cc_start: 0.8770 (mmt) cc_final: 0.8522 (mmm) REVERT: C 451 GLN cc_start: 0.8428 (pt0) cc_final: 0.7946 (pp30) REVERT: C 455 MET cc_start: 0.8625 (mmm) cc_final: 0.8305 (mmt) REVERT: E 279 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8387 (tppt) REVERT: E 364 GLU cc_start: 0.8844 (tt0) cc_final: 0.8640 (tm-30) REVERT: E 442 TYR cc_start: 0.8411 (m-80) cc_final: 0.7943 (m-10) REVERT: F 132 LYS cc_start: 0.8231 (mttm) cc_final: 0.7963 (mtmm) REVERT: F 414 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8008 (mtt-85) REVERT: F 446 TYR cc_start: 0.7799 (m-80) cc_final: 0.7293 (m-10) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.7195 time to fit residues: 115.1785 Evaluate side-chains 140 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 24 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.074092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.059489 restraints weight = 27776.844| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.29 r_work: 0.2631 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15765 Z= 0.103 Angle : 0.438 7.714 21294 Z= 0.232 Chirality : 0.040 0.187 2478 Planarity : 0.004 0.046 2694 Dihedral : 13.253 177.329 2472 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.79 % Allowed : 15.64 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.19), residues: 1944 helix: 1.88 (0.16), residues: 1053 sheet: 0.56 (0.29), residues: 276 loop : 0.83 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 249 TYR 0.013 0.001 TYR D 446 PHE 0.011 0.001 PHE F 257 TRP 0.002 0.000 TRP F 283 HIS 0.002 0.000 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.00237 (15765) covalent geometry : angle 0.43772 (21294) hydrogen bonds : bond 0.03071 ( 797) hydrogen bonds : angle 3.67786 ( 2307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.670 Fit side-chains REVERT: A 125 LYS cc_start: 0.6477 (tptt) cc_final: 0.6058 (tptp) REVERT: B 263 LEU cc_start: 0.7794 (pp) cc_final: 0.7454 (mp) REVERT: B 455 MET cc_start: 0.8744 (mmt) cc_final: 0.8502 (mmm) REVERT: C 451 GLN cc_start: 0.8428 (pt0) cc_final: 0.7947 (pp30) REVERT: C 455 MET cc_start: 0.8606 (mmm) cc_final: 0.8291 (mmt) REVERT: E 279 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8348 (tppt) REVERT: E 364 GLU cc_start: 0.8827 (tt0) cc_final: 0.8617 (tm-30) REVERT: E 442 TYR cc_start: 0.8413 (m-80) cc_final: 0.7938 (m-10) REVERT: F 132 LYS cc_start: 0.8259 (mttm) cc_final: 0.7998 (mtmm) REVERT: F 414 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7990 (mtt-85) REVERT: F 446 TYR cc_start: 0.7831 (m-80) cc_final: 0.7342 (m-10) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 0.7416 time to fit residues: 116.0673 Evaluate side-chains 138 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 193 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 45 optimal weight: 0.0030 chunk 152 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.074998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.060410 restraints weight = 27831.091| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.30 r_work: 0.2653 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15765 Z= 0.093 Angle : 0.434 7.720 21294 Z= 0.229 Chirality : 0.040 0.175 2478 Planarity : 0.004 0.047 2694 Dihedral : 12.884 177.696 2472 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.60 % Allowed : 15.82 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.19), residues: 1944 helix: 1.92 (0.16), residues: 1053 sheet: 0.62 (0.29), residues: 276 loop : 0.88 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 414 TYR 0.013 0.001 TYR D 446 PHE 0.008 0.001 PHE D 257 TRP 0.002 0.000 TRP D 283 HIS 0.002 0.000 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.00211 (15765) covalent geometry : angle 0.43386 (21294) hydrogen bonds : bond 0.02853 ( 797) hydrogen bonds : angle 3.59714 ( 2307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.666 Fit side-chains REVERT: A 125 LYS cc_start: 0.6415 (tptt) cc_final: 0.6023 (tptp) REVERT: B 263 LEU cc_start: 0.7775 (pp) cc_final: 0.7402 (mp) REVERT: B 455 MET cc_start: 0.8675 (mmt) cc_final: 0.8440 (mmm) REVERT: C 451 GLN cc_start: 0.8404 (pt0) cc_final: 0.7932 (pp30) REVERT: E 279 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8372 (tppt) REVERT: E 364 GLU cc_start: 0.8813 (tt0) cc_final: 0.8573 (tm-30) REVERT: E 442 TYR cc_start: 0.8416 (m-80) cc_final: 0.7964 (m-10) REVERT: F 132 LYS cc_start: 0.8297 (mttm) cc_final: 0.8043 (mtmm) REVERT: F 414 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7989 (mtt-85) REVERT: F 446 TYR cc_start: 0.7898 (m-80) cc_final: 0.7404 (m-10) outliers start: 10 outliers final: 8 residues processed: 145 average time/residue: 0.7283 time to fit residues: 115.6031 Evaluate side-chains 141 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 173 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3058 r_free = 0.3058 target = 0.072999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.058293 restraints weight = 27775.519| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.30 r_work: 0.2603 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15765 Z= 0.135 Angle : 0.468 7.897 21294 Z= 0.246 Chirality : 0.041 0.179 2478 Planarity : 0.004 0.050 2694 Dihedral : 13.281 175.547 2472 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.42 % Allowed : 16.12 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.19), residues: 1944 helix: 1.75 (0.16), residues: 1077 sheet: 0.60 (0.29), residues: 276 loop : 0.69 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 414 TYR 0.013 0.001 TYR D 446 PHE 0.014 0.001 PHE F 257 TRP 0.002 0.000 TRP F 283 HIS 0.003 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00319 (15765) covalent geometry : angle 0.46835 (21294) hydrogen bonds : bond 0.03438 ( 797) hydrogen bonds : angle 3.74217 ( 2307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.695 Fit side-chains REVERT: A 125 LYS cc_start: 0.6443 (tptt) cc_final: 0.5949 (tptp) REVERT: B 263 LEU cc_start: 0.7783 (pp) cc_final: 0.7418 (mp) REVERT: B 455 MET cc_start: 0.8758 (mmt) cc_final: 0.8517 (mmm) REVERT: C 451 GLN cc_start: 0.8474 (pt0) cc_final: 0.7975 (pp30) REVERT: E 279 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8406 (tppt) REVERT: E 364 GLU cc_start: 0.8851 (tt0) cc_final: 0.8629 (tm-30) REVERT: E 442 TYR cc_start: 0.8423 (m-80) cc_final: 0.7973 (m-10) REVERT: F 132 LYS cc_start: 0.8285 (mttm) cc_final: 0.8048 (mtmm) REVERT: F 414 ARG cc_start: 0.8290 (mtm110) cc_final: 0.8015 (mtt-85) REVERT: F 441 GLN cc_start: 0.8447 (tt0) cc_final: 0.8011 (pt0) REVERT: F 442 TYR cc_start: 0.8325 (m-80) cc_final: 0.8042 (m-80) REVERT: F 446 TYR cc_start: 0.7932 (m-80) cc_final: 0.7457 (m-10) outliers start: 7 outliers final: 7 residues processed: 138 average time/residue: 0.7331 time to fit residues: 110.8869 Evaluate side-chains 135 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 167 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3050 r_free = 0.3050 target = 0.072572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057841 restraints weight = 27818.972| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.30 r_work: 0.2592 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15765 Z= 0.147 Angle : 0.476 7.821 21294 Z= 0.250 Chirality : 0.042 0.174 2478 Planarity : 0.004 0.051 2694 Dihedral : 13.416 176.619 2472 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.48 % Allowed : 16.12 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.19), residues: 1944 helix: 1.70 (0.16), residues: 1077 sheet: 0.62 (0.29), residues: 276 loop : 0.69 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 414 TYR 0.013 0.001 TYR D 446 PHE 0.009 0.001 PHE D 257 TRP 0.001 0.000 TRP F 283 HIS 0.003 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00350 (15765) covalent geometry : angle 0.47649 (21294) hydrogen bonds : bond 0.03556 ( 797) hydrogen bonds : angle 3.80765 ( 2307) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5653.64 seconds wall clock time: 96 minutes 44.46 seconds (5804.46 seconds total)