Starting phenix.real_space_refine on Sat May 17 08:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ema_19815/05_2025/9ema_19815_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ema_19815/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ema_19815/05_2025/9ema_19815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ema_19815/05_2025/9ema_19815.map" model { file = "/net/cci-nas-00/data/ceres_data/9ema_19815/05_2025/9ema_19815_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ema_19815/05_2025/9ema_19815_neut.cif" } resolution = 2.4 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= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.71, per 1000 atoms: 0.62 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: 4.05 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.86 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: 5.65 Time building geometry restraints manager: 4.61 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: 1.940 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.450 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:14.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.790 ------------------------------------------------------------------------------- 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 (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: -0.24 (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 TRP 0.004 0.001 TRP D 283 HIS 0.005 0.001 HIS E 245 PHE 0.019 0.002 PHE E 257 TYR 0.029 0.002 TYR D 442 ARG 0.019 0.001 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.16109 ( 797) hydrogen bonds : angle 5.86005 ( 2307) covalent geometry : bond 0.00832 (15765) covalent geometry : angle 1.07249 (21294) *********************** 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 : 1.953 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 314 average time/residue: 1.3342 time to fit residues: 459.7851 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 : 1.689 ------------------------------------------------------------------------------- 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 164 optimal weight: 0.0980 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.096506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083008 restraints weight = 28676.285| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.29 r_work: 0.3128 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15765 Z= 0.131 Angle : 0.558 9.112 21294 Z= 0.290 Chirality : 0.043 0.238 2478 Planarity : 0.004 0.041 2694 Dihedral : 13.212 179.927 2474 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.36 % Allowed : 15.10 % Favored : 82.55 % 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: 0.99 (0.18), residues: 1944 helix: 1.06 (0.15), residues: 1050 sheet: -0.18 (0.30), residues: 264 loop : 0.62 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 283 HIS 0.005 0.001 HIS C 393 PHE 0.017 0.001 PHE F 257 TYR 0.010 0.001 TYR E 387 ARG 0.006 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 797) hydrogen bonds : angle 4.00136 ( 2307) covalent geometry : bond 0.00290 (15765) covalent geometry : angle 0.55750 (21294) *********************** 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 232 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 2.011 Fit side-chains REVERT: A 96 MET cc_start: 0.8392 (ttt) cc_final: 0.8134 (ttt) REVERT: A 123 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8045 (ttt90) REVERT: A 342 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7589 (pm20) REVERT: A 388 GLU cc_start: 0.8176 (pm20) cc_final: 0.7803 (tp30) REVERT: B 455 MET cc_start: 0.8567 (mmt) cc_final: 0.8332 (mmm) REVERT: C 125 LYS cc_start: 0.7459 (pttm) cc_final: 0.6987 (ptpp) REVERT: D 46 MET cc_start: 0.8571 (mmm) cc_final: 0.8283 (mmp) REVERT: E 112 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: E 282 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: E 442 TYR cc_start: 0.7759 (m-80) cc_final: 0.7339 (m-10) REVERT: F 132 LYS cc_start: 0.8049 (mttm) cc_final: 0.7675 (mtmm) outliers start: 39 outliers final: 8 residues processed: 223 average time/residue: 1.2740 time to fit residues: 313.9785 Evaluate side-chains 163 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 D residue 16 VAL 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 54 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3129 r_free = 0.3129 target = 0.076539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.061768 restraints weight = 27470.856| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.30 r_work: 0.2698 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15765 Z= 0.140 Angle : 0.535 8.016 21294 Z= 0.279 Chirality : 0.042 0.161 2478 Planarity : 0.004 0.048 2694 Dihedral : 13.785 176.644 2472 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.57 % Allowed : 16.24 % Favored : 82.19 % 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: 1.41 (0.18), residues: 1944 helix: 1.51 (0.16), residues: 1047 sheet: -0.07 (0.28), residues: 276 loop : 0.66 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 283 HIS 0.005 0.001 HIS E 27 PHE 0.008 0.001 PHE F 311 TYR 0.009 0.001 TYR C 405 ARG 0.008 0.001 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 797) hydrogen bonds : angle 4.06192 ( 2307) covalent geometry : bond 0.00316 (15765) covalent geometry : angle 0.53512 (21294) *********************** 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 187 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.930 Fit side-chains REVERT: B 264 MET cc_start: 0.8266 (mtp) cc_final: 0.8000 (mtt) REVERT: B 420 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8060 (m110) REVERT: B 435 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: B 455 MET cc_start: 0.8775 (mmt) cc_final: 0.8571 (mmm) REVERT: C 236 GLN cc_start: 0.7598 (tp40) cc_final: 0.7261 (tt0) REVERT: E 112 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: E 442 TYR cc_start: 0.8221 (m-80) cc_final: 0.7730 (m-10) REVERT: F 132 LYS cc_start: 0.8254 (mttm) cc_final: 0.7942 (mtmm) REVERT: F 285 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8568 (mm-30) outliers start: 26 outliers final: 5 residues processed: 179 average time/residue: 1.4068 time to fit residues: 276.4308 Evaluate side-chains 143 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 GLU 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 276 ILE Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 40 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3052 r_free = 0.3052 target = 0.072545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.057976 restraints weight = 27738.392| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.27 r_work: 0.2607 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15765 Z= 0.190 Angle : 0.527 7.978 21294 Z= 0.277 Chirality : 0.044 0.173 2478 Planarity : 0.004 0.052 2694 Dihedral : 14.082 178.952 2472 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.51 % Allowed : 15.28 % Favored : 83.21 % 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: 1.37 (0.19), residues: 1944 helix: 1.44 (0.16), residues: 1074 sheet: 0.14 (0.28), residues: 276 loop : 0.52 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 283 HIS 0.004 0.001 HIS B 348 PHE 0.010 0.001 PHE F 257 TYR 0.010 0.001 TYR D 446 ARG 0.008 0.001 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 797) hydrogen bonds : angle 4.03708 ( 2307) covalent geometry : bond 0.00456 (15765) covalent geometry : angle 0.52671 (21294) *********************** 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 164 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 2.177 Fit side-chains REVERT: B 260 MET cc_start: 0.5162 (tpp) cc_final: 0.4928 (tpp) REVERT: B 263 LEU cc_start: 0.7894 (pp) cc_final: 0.7624 (mp) REVERT: B 435 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: B 455 MET cc_start: 0.8791 (mmt) cc_final: 0.8571 (mmm) REVERT: C 236 GLN cc_start: 0.7728 (tp40) cc_final: 0.7499 (tt0) REVERT: C 371 MET cc_start: 0.9156 (mtp) cc_final: 0.8925 (mtt) REVERT: E 279 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8273 (tppt) REVERT: E 442 TYR cc_start: 0.8425 (m-80) cc_final: 0.7929 (m-10) REVERT: F 131 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8135 (mp) REVERT: F 132 LYS cc_start: 0.8220 (mttm) cc_final: 0.7897 (mtmm) REVERT: F 365 LYS cc_start: 0.8798 (mppt) cc_final: 0.8595 (mtpp) REVERT: F 414 ARG cc_start: 0.8305 (mtm110) cc_final: 0.8050 (mtt-85) REVERT: F 441 GLN cc_start: 0.8563 (tt0) cc_final: 0.8148 (pt0) REVERT: F 446 TYR cc_start: 0.7721 (m-80) cc_final: 0.7265 (m-10) outliers start: 25 outliers final: 8 residues processed: 157 average time/residue: 1.5467 time to fit residues: 267.2470 Evaluate side-chains 141 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 435 GLU 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 E residue 348 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 95 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.073250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.058579 restraints weight = 27889.841| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.30 r_work: 0.2604 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.6847 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= 0.128 Angle : 0.464 7.160 21294 Z= 0.246 Chirality : 0.041 0.184 2478 Planarity : 0.004 0.048 2694 Dihedral : 13.730 178.572 2472 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.91 % Allowed : 15.58 % Favored : 83.51 % 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: 1.55 (0.19), residues: 1944 helix: 1.57 (0.16), residues: 1077 sheet: 0.29 (0.29), residues: 276 loop : 0.59 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 283 HIS 0.002 0.001 HIS A 241 PHE 0.006 0.001 PHE F 311 TYR 0.011 0.001 TYR D 446 ARG 0.009 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 797) hydrogen bonds : angle 3.84434 ( 2307) covalent geometry : bond 0.00298 (15765) covalent geometry : angle 0.46383 (21294) *********************** 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 151 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.769 Fit side-chains REVERT: B 455 MET cc_start: 0.8775 (mmt) cc_final: 0.8548 (mmm) REVERT: C 371 MET cc_start: 0.9127 (mtp) cc_final: 0.8902 (mtt) REVERT: E 279 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8253 (tppt) REVERT: E 442 TYR cc_start: 0.8427 (m-80) cc_final: 0.7919 (m-10) REVERT: F 131 ILE cc_start: 0.8657 (pp) cc_final: 0.8135 (mp) REVERT: F 132 LYS cc_start: 0.8194 (mttm) cc_final: 0.7906 (mtmm) REVERT: F 365 LYS cc_start: 0.8826 (mppt) cc_final: 0.8623 (mtpp) REVERT: F 414 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8017 (mtt-85) REVERT: F 441 GLN cc_start: 0.8527 (tt0) cc_final: 0.8185 (pt0) REVERT: F 442 TYR cc_start: 0.8327 (m-80) cc_final: 0.8076 (m-80) REVERT: F 446 TYR cc_start: 0.7730 (m-80) cc_final: 0.7252 (m-10) outliers start: 15 outliers final: 5 residues processed: 147 average time/residue: 1.4079 time to fit residues: 227.5738 Evaluate side-chains 135 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 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 121 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3031 r_free = 0.3031 target = 0.071801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.057157 restraints weight = 27928.120| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.29 r_work: 0.2571 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15765 Z= 0.173 Angle : 0.493 8.247 21294 Z= 0.260 Chirality : 0.043 0.179 2478 Planarity : 0.004 0.053 2694 Dihedral : 14.021 179.346 2472 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.27 % Allowed : 15.40 % Favored : 83.33 % 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: 1.54 (0.19), residues: 1944 helix: 1.57 (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 TRP 0.001 0.000 TRP D 283 HIS 0.004 0.001 HIS B 348 PHE 0.010 0.001 PHE E 257 TYR 0.011 0.001 TYR D 446 ARG 0.009 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 797) hydrogen bonds : angle 3.95117 ( 2307) covalent geometry : bond 0.00412 (15765) covalent geometry : angle 0.49314 (21294) *********************** 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: 21 poor density : 133 time to evaluate : 1.886 Fit side-chains REVERT: A 125 LYS cc_start: 0.6442 (tptt) cc_final: 0.6074 (tptt) REVERT: B 455 MET cc_start: 0.8809 (mmt) cc_final: 0.8556 (mmm) REVERT: C 371 MET cc_start: 0.9157 (mtp) cc_final: 0.8941 (mtt) REVERT: E 279 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8316 (tppt) REVERT: E 442 TYR cc_start: 0.8431 (m-80) cc_final: 0.7903 (m-10) REVERT: F 131 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8239 (mt) REVERT: F 132 LYS cc_start: 0.8192 (mttm) cc_final: 0.7921 (mtmm) REVERT: F 414 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8014 (mtt-85) REVERT: F 441 GLN cc_start: 0.8530 (tt0) cc_final: 0.8209 (pt0) REVERT: F 442 TYR cc_start: 0.8324 (m-80) cc_final: 0.8099 (m-80) REVERT: F 446 TYR cc_start: 0.7892 (m-80) cc_final: 0.7431 (m-10) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 1.4551 time to fit residues: 239.1668 Evaluate side-chains 137 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 47 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3037 r_free = 0.3037 target = 0.072224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.057541 restraints weight = 27952.066| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.30 r_work: 0.2582 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.7006 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= 0.148 Angle : 0.477 9.095 21294 Z= 0.252 Chirality : 0.042 0.167 2478 Planarity : 0.004 0.051 2694 Dihedral : 13.884 179.696 2472 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.33 % 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: 1.59 (0.19), residues: 1944 helix: 1.60 (0.16), residues: 1077 sheet: 0.40 (0.29), residues: 276 loop : 0.57 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 283 HIS 0.003 0.001 HIS B 348 PHE 0.007 0.001 PHE D 311 TYR 0.012 0.001 TYR D 446 ARG 0.011 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 797) hydrogen bonds : angle 3.87041 ( 2307) covalent geometry : bond 0.00351 (15765) covalent geometry : angle 0.47675 (21294) *********************** 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 146 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.996 Fit side-chains REVERT: A 125 LYS cc_start: 0.6406 (tptt) cc_final: 0.5970 (tptp) REVERT: B 263 LEU cc_start: 0.7820 (pp) cc_final: 0.7524 (mp) REVERT: B 455 MET cc_start: 0.8777 (mmt) cc_final: 0.8515 (mmm) REVERT: C 371 MET cc_start: 0.9138 (mtp) cc_final: 0.8907 (mtt) REVERT: E 279 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8360 (tppt) REVERT: E 442 TYR cc_start: 0.8449 (m-80) cc_final: 0.7960 (m-10) REVERT: F 131 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8283 (mt) REVERT: F 132 LYS cc_start: 0.8139 (mttm) cc_final: 0.7908 (mtmm) REVERT: F 414 ARG cc_start: 0.8287 (mtm110) cc_final: 0.8025 (mtt-85) REVERT: F 441 GLN cc_start: 0.8538 (tt0) cc_final: 0.8231 (pt0) REVERT: F 446 TYR cc_start: 0.7847 (m-80) cc_final: 0.7377 (m-10) outliers start: 14 outliers final: 6 residues processed: 143 average time/residue: 1.4384 time to fit residues: 226.0945 Evaluate side-chains 136 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR 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 E residue 348 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 77 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 141 optimal weight: 0.0070 chunk 110 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.074550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.059950 restraints weight = 27646.013| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.29 r_work: 0.2640 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.7080 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= 0.094 Angle : 0.436 8.240 21294 Z= 0.232 Chirality : 0.040 0.165 2478 Planarity : 0.004 0.045 2694 Dihedral : 13.142 179.928 2472 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.91 % Allowed : 15.76 % Favored : 83.33 % 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: 1.91 (0.19), residues: 1944 helix: 1.86 (0.16), residues: 1053 sheet: 0.46 (0.29), residues: 276 loop : 0.79 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 283 HIS 0.002 0.000 HIS E 245 PHE 0.009 0.001 PHE E 257 TYR 0.012 0.001 TYR D 446 ARG 0.007 0.000 ARG E 414 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 797) hydrogen bonds : angle 3.63994 ( 2307) covalent geometry : bond 0.00212 (15765) covalent geometry : angle 0.43561 (21294) *********************** 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 151 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.974 Fit side-chains REVERT: A 125 LYS cc_start: 0.6374 (tptt) cc_final: 0.5934 (tptp) REVERT: A 342 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: B 263 LEU cc_start: 0.7756 (pp) cc_final: 0.7394 (mp) REVERT: B 455 MET cc_start: 0.8754 (mmt) cc_final: 0.8515 (mmm) REVERT: C 371 MET cc_start: 0.9051 (mtp) cc_final: 0.8837 (mtt) REVERT: E 279 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8345 (tppt) REVERT: E 320 MET cc_start: 0.9227 (mmp) cc_final: 0.9024 (tpt) REVERT: E 442 TYR cc_start: 0.8431 (m-80) cc_final: 0.7927 (m-10) REVERT: F 132 LYS cc_start: 0.8081 (mttm) cc_final: 0.7863 (mtmm) REVERT: F 414 ARG cc_start: 0.8274 (mtm110) cc_final: 0.8002 (mtt-85) REVERT: F 441 GLN cc_start: 0.8491 (tt0) cc_final: 0.8151 (pt0) REVERT: F 446 TYR cc_start: 0.7826 (m-80) cc_final: 0.7316 (m-10) outliers start: 15 outliers final: 7 residues processed: 147 average time/residue: 1.3768 time to fit residues: 223.4876 Evaluate side-chains 139 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU 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 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 = 0.072825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.058150 restraints weight = 27775.125| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.29 r_work: 0.2598 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15765 Z= 0.134 Angle : 0.466 7.901 21294 Z= 0.245 Chirality : 0.041 0.195 2478 Planarity : 0.004 0.049 2694 Dihedral : 13.437 177.694 2472 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.72 % Allowed : 16.24 % Favored : 83.03 % 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: 1.73 (0.19), residues: 1944 helix: 1.71 (0.16), residues: 1077 sheet: 0.47 (0.29), residues: 276 loop : 0.62 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 283 HIS 0.002 0.001 HIS B 348 PHE 0.012 0.001 PHE F 257 TYR 0.013 0.001 TYR D 446 ARG 0.007 0.000 ARG E 414 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 797) hydrogen bonds : angle 3.77042 ( 2307) covalent geometry : bond 0.00315 (15765) covalent geometry : angle 0.46576 (21294) *********************** 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 142 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.797 Fit side-chains REVERT: A 125 LYS cc_start: 0.6371 (tptt) cc_final: 0.5858 (tptp) REVERT: A 342 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: B 263 LEU cc_start: 0.7760 (pp) cc_final: 0.7401 (mp) REVERT: B 455 MET cc_start: 0.8753 (mmt) cc_final: 0.8500 (mmm) REVERT: C 371 MET cc_start: 0.9125 (mtp) cc_final: 0.8909 (mtt) REVERT: E 279 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8352 (tppt) REVERT: E 442 TYR cc_start: 0.8438 (m-80) cc_final: 0.7957 (m-10) REVERT: F 131 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8815 (mt) REVERT: F 270 SER cc_start: 0.9320 (m) cc_final: 0.8971 (p) REVERT: F 414 ARG cc_start: 0.8300 (mtm110) cc_final: 0.8027 (mtt-85) REVERT: F 441 GLN cc_start: 0.8450 (tt0) cc_final: 0.8107 (pt0) REVERT: F 446 TYR cc_start: 0.7886 (m-80) cc_final: 0.7411 (m-10) outliers start: 12 outliers final: 9 residues processed: 139 average time/residue: 1.3721 time to fit residues: 210.1601 Evaluate side-chains 138 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU 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 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 61 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 161 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 = 0.3074 r_free = 0.3074 target = 0.074011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.059363 restraints weight = 28010.550| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.31 r_work: 0.2623 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15765 Z= 0.105 Angle : 0.450 7.879 21294 Z= 0.238 Chirality : 0.041 0.186 2478 Planarity : 0.004 0.049 2694 Dihedral : 13.118 178.635 2472 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.48 % Allowed : 16.79 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.19), residues: 1944 helix: 1.74 (0.16), residues: 1074 sheet: 0.48 (0.29), residues: 276 loop : 0.68 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 283 HIS 0.002 0.000 HIS D 27 PHE 0.012 0.001 PHE E 257 TYR 0.014 0.001 TYR D 446 ARG 0.009 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 797) hydrogen bonds : angle 3.68132 ( 2307) covalent geometry : bond 0.00240 (15765) covalent geometry : angle 0.45042 (21294) ********************** 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 135 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.841 Fit side-chains REVERT: A 125 LYS cc_start: 0.6323 (tptt) cc_final: 0.5797 (tptp) REVERT: B 263 LEU cc_start: 0.7762 (pp) cc_final: 0.7396 (mp) REVERT: C 371 MET cc_start: 0.9095 (mtp) cc_final: 0.8872 (mtt) REVERT: E 279 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8338 (tppt) REVERT: E 442 TYR cc_start: 0.8451 (m-80) cc_final: 0.7980 (m-10) REVERT: F 414 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8020 (mtt-85) REVERT: F 446 TYR cc_start: 0.7844 (m-80) cc_final: 0.7361 (m-10) outliers start: 8 outliers final: 9 residues processed: 133 average time/residue: 1.3605 time to fit residues: 199.7727 Evaluate side-chains 134 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 159 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 168 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.3790 ------------------------------------------------------------------------------- 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 = 0.073154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.058471 restraints weight = 27922.008| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.30 r_work: 0.2603 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.7086 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= 0.128 Angle : 0.463 7.785 21294 Z= 0.243 Chirality : 0.041 0.182 2478 Planarity : 0.004 0.053 2694 Dihedral : 13.233 177.078 2472 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.66 % Allowed : 16.67 % Favored : 82.67 % 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: 1.76 (0.19), residues: 1944 helix: 1.72 (0.16), residues: 1077 sheet: 0.49 (0.29), residues: 276 loop : 0.66 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 283 HIS 0.002 0.001 HIS B 348 PHE 0.017 0.001 PHE F 257 TYR 0.013 0.001 TYR D 446 ARG 0.009 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 797) hydrogen bonds : angle 3.74464 ( 2307) covalent geometry : bond 0.00300 (15765) covalent geometry : angle 0.46263 (21294) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 10520.29 seconds wall clock time: 181 minutes 22.85 seconds (10882.85 seconds total)