Starting phenix.real_space_refine on Thu Jul 2 07:44:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avx_15686/07_2026/8avx_15686.map" } resolution = 3.5 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= 0.014 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4715 2.51 5 N 1327 2.21 5 O 1363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7427 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3668 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 443} Chain breaks: 3 Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3673 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 444} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.26 Number of scatterers: 7427 At special positions: 0 Unit cell: (81.8615, 95.6487, 121.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1363 8.00 N 1327 7.00 C 4715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 355.6 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 41.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.440A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.524A pdb=" N PHE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.578A pdb=" N LEU A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 3.749A pdb=" N MET A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 342 removed outlier: 3.644A pdb=" N ARG A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.766A pdb=" N THR A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 352' Processing helix chain 'A' and resid 358 through 364 removed outlier: 4.164A pdb=" N LEU A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.511A pdb=" N ALA A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.950A pdb=" N LEU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 removed outlier: 3.901A pdb=" N THR A 471 " --> pdb=" O HIS A 467 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.625A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 503 through 521 removed outlier: 3.738A pdb=" N SER A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.418A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.522A pdb=" N PHE B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.581A pdb=" N LEU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.751A pdb=" N MET B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 342 removed outlier: 3.675A pdb=" N ARG B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.766A pdb=" N THR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 358 through 364 removed outlier: 4.171A pdb=" N LEU B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.512A pdb=" N ALA B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.948A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 474 removed outlier: 3.894A pdb=" N THR B 471 " --> pdb=" O HIS B 467 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.624A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 503 through 521 removed outlier: 3.716A pdb=" N SER B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.774A pdb=" N VAL A 51 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 45 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 55 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 41 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 103 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.689A pdb=" N THR A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 288 " --> pdb=" O MET A 174 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 277 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 286 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 275 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 288 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 273 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 380 removed outlier: 4.585A pdb=" N GLU A 436 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 424 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.775A pdb=" N VAL B 51 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 45 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 55 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 41 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 103 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.689A pdb=" N THR B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 288 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 277 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 286 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 275 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 288 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 273 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 380 removed outlier: 4.568A pdb=" N GLU B 436 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 424 " --> pdb=" O ARG B 442 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 906 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: 0.86 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1481 1.33 - 1.45: 1744 1.45 - 1.57: 4349 1.57 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7610 Sorted by residual: bond pdb=" C2B BLA B1000 " pdb=" C3B BLA B1000 " ideal model delta sigma weight residual 1.357 1.432 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C2B BLA A1000 " pdb=" C3B BLA A1000 " ideal model delta sigma weight residual 1.357 1.429 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1D BLA A1000 " pdb=" CHD BLA A1000 " ideal model delta sigma weight residual 1.440 1.373 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C2C BLA A1000 " pdb=" C3C BLA A1000 " ideal model delta sigma weight residual 1.351 1.415 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1D BLA B1000 " pdb=" CHD BLA B1000 " ideal model delta sigma weight residual 1.440 1.377 0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8600 1.83 - 3.65: 1643 3.65 - 5.48: 156 5.48 - 7.30: 8 7.30 - 9.13: 3 Bond angle restraints: 10410 Sorted by residual: angle pdb=" C PHE B 203 " pdb=" CA PHE B 203 " pdb=" CB PHE B 203 " ideal model delta sigma weight residual 108.87 115.23 -6.36 1.55e+00 4.16e-01 1.68e+01 angle pdb=" C PHE A 203 " pdb=" CA PHE A 203 " pdb=" CB PHE A 203 " ideal model delta sigma weight residual 108.87 115.05 -6.18 1.55e+00 4.16e-01 1.59e+01 angle pdb=" CB ARG A 375 " pdb=" CG ARG A 375 " pdb=" CD ARG A 375 " ideal model delta sigma weight residual 111.30 120.43 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" C PRO B 384 " pdb=" N ALA B 385 " pdb=" CA ALA B 385 " ideal model delta sigma weight residual 120.09 124.82 -4.73 1.25e+00 6.40e-01 1.43e+01 angle pdb=" C PRO A 384 " pdb=" N ALA A 385 " pdb=" CA ALA A 385 " ideal model delta sigma weight residual 120.09 124.79 -4.70 1.25e+00 6.40e-01 1.41e+01 ... (remaining 10405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3883 17.27 - 34.54: 440 34.54 - 51.80: 120 51.80 - 69.07: 71 69.07 - 86.34: 6 Dihedral angle restraints: 4520 sinusoidal: 1776 harmonic: 2744 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CG ARG B 514 " pdb=" CD ARG B 514 " pdb=" NE ARG B 514 " pdb=" CZ ARG B 514 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 627 0.050 - 0.100: 285 0.100 - 0.151: 190 0.151 - 0.201: 54 0.201 - 0.251: 17 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 449 " pdb=" CA VAL A 449 " pdb=" CG1 VAL A 449 " pdb=" CG2 VAL A 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1170 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1000 " -0.001 2.00e-02 2.50e+03 2.84e-01 2.01e+03 pdb=" C1D BLA B1000 " 0.520 2.00e-02 2.50e+03 pdb=" C2C BLA B1000 " -0.007 2.00e-02 2.50e+03 pdb=" C3C BLA B1000 " -0.040 2.00e-02 2.50e+03 pdb=" C4C BLA B1000 " -0.264 2.00e-02 2.50e+03 pdb=" CAC BLA B1000 " 0.147 2.00e-02 2.50e+03 pdb=" CHD BLA B1000 " -0.254 2.00e-02 2.50e+03 pdb=" CMC BLA B1000 " 0.055 2.00e-02 2.50e+03 pdb=" NC BLA B1000 " -0.503 2.00e-02 2.50e+03 pdb=" OC BLA B1000 " 0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1000 " -0.384 2.00e-02 2.50e+03 2.82e-01 1.98e+03 pdb=" OB BLA B1000 " 0.184 2.00e-02 2.50e+03 pdb=" C1B BLA B1000 " -0.180 2.00e-02 2.50e+03 pdb=" C2B BLA B1000 " -0.174 2.00e-02 2.50e+03 pdb=" C3B BLA B1000 " 0.071 2.00e-02 2.50e+03 pdb=" C4A BLA B1000 " 0.543 2.00e-02 2.50e+03 pdb=" C4B BLA B1000 " -0.019 2.00e-02 2.50e+03 pdb=" CAB BLA B1000 " 0.348 2.00e-02 2.50e+03 pdb=" CHB BLA B1000 " -0.032 2.00e-02 2.50e+03 pdb=" CMB BLA B1000 " -0.357 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1000 " -0.034 2.00e-02 2.50e+03 2.78e-01 1.93e+03 pdb=" C1D BLA A1000 " 0.551 2.00e-02 2.50e+03 pdb=" C2C BLA A1000 " 0.033 2.00e-02 2.50e+03 pdb=" C3C BLA A1000 " -0.075 2.00e-02 2.50e+03 pdb=" C4C BLA A1000 " -0.247 2.00e-02 2.50e+03 pdb=" CAC BLA A1000 " 0.008 2.00e-02 2.50e+03 pdb=" CHD BLA A1000 " -0.175 2.00e-02 2.50e+03 pdb=" CMC BLA A1000 " 0.210 2.00e-02 2.50e+03 pdb=" NC BLA A1000 " -0.515 2.00e-02 2.50e+03 pdb=" OC BLA A1000 " 0.243 2.00e-02 2.50e+03 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1574 2.83 - 3.35: 6100 3.35 - 3.87: 11931 3.87 - 4.38: 13281 4.38 - 4.90: 23340 Nonbonded interactions: 56226 Sorted by model distance: nonbonded pdb=" O ALA A 107 " pdb=" N GLY A 109 " model vdw 2.316 3.120 nonbonded pdb=" O LEU B 516 " pdb=" OG SER B 519 " model vdw 2.584 3.040 nonbonded pdb=" O LEU A 516 " pdb=" OG SER A 519 " model vdw 2.585 3.040 nonbonded pdb=" O GLY A 39 " pdb=" ND2 ASN A 57 " model vdw 2.600 3.120 nonbonded pdb=" O GLY B 39 " pdb=" ND2 ASN B 57 " model vdw 2.601 3.120 ... (remaining 56221 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' and (resid 22 through 107 or resid 109 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.770 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 0.075 7610 Z= 0.512 Angle : 1.384 9.131 10410 Z= 0.921 Chirality : 0.079 0.251 1173 Planarity : 0.015 0.284 1364 Dihedral : 17.787 86.341 2746 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.54 % Favored : 95.25 % Rotamer: Outliers : 4.23 % Allowed : 11.64 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.22), residues: 947 helix: -3.67 (0.16), residues: 369 sheet: -1.34 (0.36), residues: 180 loop : -2.13 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 100 TYR 0.030 0.003 TYR B 307 PHE 0.011 0.002 PHE B 170 TRP 0.017 0.002 TRP A 451 HIS 0.006 0.002 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.51 ( 7610) covalent geometry : angle 1.38375 / 0.92 (10410) hydrogen bonds : bond 0.27770 / 19.16 ( 322) hydrogen bonds : angle 9.75593 / 6.77 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6840 (mtp180) cc_final: 0.5249 (tpt170) REVERT: A 363 MET cc_start: 0.6975 (mmp) cc_final: 0.6549 (tpp) REVERT: A 466 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.1648 (mmp80) REVERT: B 227 THR cc_start: 0.7630 (p) cc_final: 0.7189 (p) REVERT: B 381 GLU cc_start: 0.7836 (pm20) cc_final: 0.7243 (pp20) REVERT: B 493 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7326 (t0) outliers start: 32 outliers final: 4 residues processed: 174 average time/residue: 0.0794 time to fit residues: 17.8747 Evaluate side-chains 95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 493 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 110 HIS A 239 ASN A 513 ASN B 334 HIS B 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.193137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.167799 restraints weight = 13181.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.171947 restraints weight = 7444.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.174694 restraints weight = 4991.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.176413 restraints weight = 3772.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.177508 restraints weight = 3124.896| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7610 Z= 0.117 Angle : 0.625 8.428 10410 Z= 0.296 Chirality : 0.041 0.130 1173 Planarity : 0.004 0.031 1364 Dihedral : 7.217 76.802 1071 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.84 % Allowed : 16.27 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.25), residues: 947 helix: -2.05 (0.23), residues: 372 sheet: -0.79 (0.36), residues: 193 loop : -1.43 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.013 0.002 TYR A 479 PHE 0.019 0.002 PHE B 126 TRP 0.011 0.001 TRP A 284 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7610) covalent geometry : angle 0.62547 / 0.30 (10410) hydrogen bonds : bond 0.03668 / 2.44 ( 322) hydrogen bonds : angle 5.58155 / 3.93 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6744 (mtp180) cc_final: 0.5710 (tpt170) REVERT: A 466 ARG cc_start: 0.4939 (OUTLIER) cc_final: 0.1764 (mmt180) REVERT: B 45 ASP cc_start: 0.5234 (t70) cc_final: 0.4897 (m-30) REVERT: B 227 THR cc_start: 0.7054 (p) cc_final: 0.6836 (p) REVERT: B 493 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7294 (t0) outliers start: 29 outliers final: 7 residues processed: 128 average time/residue: 0.0782 time to fit residues: 13.2320 Evaluate side-chains 89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 493 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 0.1980 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 HIS A 262 GLN A 266 ASN B 57 ASN B 290 HIS B 329 GLN B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.181957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157110 restraints weight = 13758.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.160564 restraints weight = 8312.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.162908 restraints weight = 5877.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.164414 restraints weight = 4611.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.165496 restraints weight = 3910.081| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7610 Z= 0.220 Angle : 0.753 9.275 10410 Z= 0.365 Chirality : 0.046 0.158 1173 Planarity : 0.006 0.038 1364 Dihedral : 7.270 56.693 1066 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.63 % Allowed : 19.18 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.25), residues: 947 helix: -1.75 (0.24), residues: 372 sheet: -0.61 (0.37), residues: 189 loop : -1.29 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.022 0.003 TYR B 295 PHE 0.019 0.002 PHE B 327 TRP 0.023 0.003 TRP A 105 HIS 0.010 0.002 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 ( 7610) covalent geometry : angle 0.75326 / 0.36 (10410) hydrogen bonds : bond 0.04892 / 3.29 ( 322) hydrogen bonds : angle 5.83302 / 4.09 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6900 (mtp180) cc_final: 0.5815 (tpt170) REVERT: A 238 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 307 TYR cc_start: 0.7286 (m-10) cc_final: 0.6994 (m-80) REVERT: A 363 MET cc_start: 0.6099 (tpp) cc_final: 0.5891 (tpp) REVERT: A 466 ARG cc_start: 0.5264 (OUTLIER) cc_final: 0.1667 (mmt180) REVERT: B 45 ASP cc_start: 0.5453 (t70) cc_final: 0.5065 (m-30) REVERT: B 177 LYS cc_start: 0.7983 (tptt) cc_final: 0.7614 (tptt) REVERT: B 286 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6045 (tp) REVERT: B 355 PRO cc_start: 0.6554 (Cg_exo) cc_final: 0.6249 (Cg_endo) REVERT: B 432 GLU cc_start: 0.6638 (tp30) cc_final: 0.6298 (pt0) REVERT: B 441 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6347 (tp) REVERT: B 493 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7190 (t0) REVERT: B 504 GLU cc_start: 0.7790 (tp30) cc_final: 0.7341 (tp30) outliers start: 35 outliers final: 20 residues processed: 115 average time/residue: 0.0648 time to fit residues: 10.4707 Evaluate side-chains 92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.184417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.159825 restraints weight = 13677.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.163522 restraints weight = 8043.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165925 restraints weight = 5560.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.167581 restraints weight = 4313.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.168628 restraints weight = 3601.610| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7610 Z= 0.121 Angle : 0.629 9.018 10410 Z= 0.291 Chirality : 0.041 0.137 1173 Planarity : 0.005 0.037 1364 Dihedral : 6.438 58.518 1066 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.97 % Allowed : 20.50 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.26), residues: 947 helix: -1.04 (0.26), residues: 377 sheet: -0.62 (0.36), residues: 191 loop : -0.92 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.011 0.001 TYR B 295 PHE 0.021 0.002 PHE B 327 TRP 0.020 0.001 TRP A 284 HIS 0.012 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7610) covalent geometry : angle 0.62869 / 0.29 (10410) hydrogen bonds : bond 0.03445 / 2.33 ( 322) hydrogen bonds : angle 5.04608 / 3.58 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6781 (mtp180) cc_final: 0.5866 (tpt170) REVERT: A 27 GLU cc_start: 0.6999 (tp30) cc_final: 0.6798 (tp30) REVERT: A 199 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 466 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.1886 (mmt180) REVERT: B 45 ASP cc_start: 0.5217 (t70) cc_final: 0.4932 (m-30) REVERT: B 355 PRO cc_start: 0.6452 (Cg_exo) cc_final: 0.6182 (Cg_endo) REVERT: B 504 GLU cc_start: 0.7764 (tp30) cc_final: 0.7477 (tp30) outliers start: 30 outliers final: 17 residues processed: 105 average time/residue: 0.0753 time to fit residues: 10.6301 Evaluate side-chains 86 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 0.0070 chunk 84 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 484 HIS B 57 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.185592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.162661 restraints weight = 13398.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.164806 restraints weight = 8573.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.166183 restraints weight = 6233.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.167843 restraints weight = 5143.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.167825 restraints weight = 4963.994| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7610 Z= 0.109 Angle : 0.596 9.191 10410 Z= 0.277 Chirality : 0.041 0.220 1173 Planarity : 0.005 0.037 1364 Dihedral : 6.073 57.441 1064 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.04 % Allowed : 22.49 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.27), residues: 947 helix: -0.61 (0.28), residues: 370 sheet: -0.49 (0.36), residues: 191 loop : -0.80 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.015 0.002 TYR A 263 PHE 0.023 0.001 PHE B 327 TRP 0.029 0.001 TRP A 284 HIS 0.011 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7610) covalent geometry : angle 0.59600 / 0.28 (10410) hydrogen bonds : bond 0.03209 / 2.21 ( 322) hydrogen bonds : angle 4.71909 / 3.35 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.208 Fit side-chains REVERT: A 26 ARG cc_start: 0.6910 (mtp180) cc_final: 0.5845 (tpt170) REVERT: A 199 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 45 ASP cc_start: 0.5124 (t70) cc_final: 0.4754 (m-30) REVERT: B 105 TRP cc_start: 0.6201 (m-10) cc_final: 0.5948 (m-10) REVERT: B 355 PRO cc_start: 0.6392 (Cg_exo) cc_final: 0.6143 (Cg_endo) REVERT: B 504 GLU cc_start: 0.7709 (tp30) cc_final: 0.7386 (tp30) outliers start: 23 outliers final: 15 residues processed: 89 average time/residue: 0.0794 time to fit residues: 9.7406 Evaluate side-chains 80 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.184814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.162842 restraints weight = 13531.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.163805 restraints weight = 9101.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.165571 restraints weight = 6852.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.166578 restraints weight = 5451.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.166706 restraints weight = 5070.710| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7610 Z= 0.109 Angle : 0.586 9.271 10410 Z= 0.272 Chirality : 0.041 0.166 1173 Planarity : 0.005 0.037 1364 Dihedral : 5.826 53.696 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.17 % Allowed : 22.75 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.27), residues: 947 helix: -0.36 (0.27), residues: 374 sheet: -0.20 (0.37), residues: 186 loop : -0.81 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.024 0.002 TYR A 307 PHE 0.019 0.002 PHE B 327 TRP 0.022 0.001 TRP A 284 HIS 0.007 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7610) covalent geometry : angle 0.58598 / 0.27 (10410) hydrogen bonds : bond 0.03142 / 2.17 ( 322) hydrogen bonds : angle 4.60484 / 3.27 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6998 (mtp180) cc_final: 0.5874 (tpt170) REVERT: A 199 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7529 (tt) REVERT: B 105 TRP cc_start: 0.6139 (m-10) cc_final: 0.5925 (m-10) REVERT: B 355 PRO cc_start: 0.6346 (Cg_exo) cc_final: 0.6109 (Cg_endo) outliers start: 24 outliers final: 20 residues processed: 92 average time/residue: 0.0807 time to fit residues: 10.0690 Evaluate side-chains 85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.184155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.161575 restraints weight = 13550.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.164242 restraints weight = 9358.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.165464 restraints weight = 6011.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.165678 restraints weight = 5326.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165948 restraints weight = 4889.412| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7610 Z= 0.114 Angle : 0.591 9.622 10410 Z= 0.275 Chirality : 0.041 0.166 1173 Planarity : 0.005 0.037 1364 Dihedral : 5.847 49.768 1064 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.17 % Allowed : 23.68 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.27), residues: 947 helix: -0.25 (0.28), residues: 376 sheet: -0.23 (0.37), residues: 186 loop : -0.80 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.025 0.002 TYR A 263 PHE 0.017 0.001 PHE B 327 TRP 0.023 0.001 TRP A 284 HIS 0.005 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 7610) covalent geometry : angle 0.59102 / 0.27 (10410) hydrogen bonds : bond 0.03181 / 2.16 ( 322) hydrogen bonds : angle 4.61490 / 3.27 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.268 Fit side-chains REVERT: A 26 ARG cc_start: 0.7070 (mtp180) cc_final: 0.5946 (tpt170) REVERT: A 199 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7546 (tt) outliers start: 24 outliers final: 18 residues processed: 89 average time/residue: 0.0742 time to fit residues: 9.1089 Evaluate side-chains 78 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159356 restraints weight = 13716.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.160910 restraints weight = 9136.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162850 restraints weight = 6689.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.163751 restraints weight = 5068.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.164012 restraints weight = 4995.663| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7610 Z= 0.149 Angle : 0.652 9.465 10410 Z= 0.306 Chirality : 0.043 0.179 1173 Planarity : 0.005 0.040 1364 Dihedral : 6.196 55.042 1064 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.23 % Allowed : 23.28 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 947 helix: -0.33 (0.27), residues: 376 sheet: -0.19 (0.37), residues: 187 loop : -0.87 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.028 0.002 TYR A 263 PHE 0.016 0.002 PHE B 327 TRP 0.021 0.002 TRP A 284 HIS 0.006 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7610) covalent geometry : angle 0.65225 / 0.31 (10410) hydrogen bonds : bond 0.03695 / 2.49 ( 322) hydrogen bonds : angle 4.87141 / 3.44 ( 906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.239 Fit side-chains REVERT: A 26 ARG cc_start: 0.7041 (mtp180) cc_final: 0.6059 (tpt170) REVERT: A 199 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7647 (tt) outliers start: 32 outliers final: 26 residues processed: 90 average time/residue: 0.0832 time to fit residues: 10.2294 Evaluate side-chains 87 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 6 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.0050 chunk 5 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 overall best weight: 0.1172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.187620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.164693 restraints weight = 13330.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168162 restraints weight = 8128.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.170378 restraints weight = 5724.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.171585 restraints weight = 4475.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.172780 restraints weight = 3822.530| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7610 Z= 0.092 Angle : 0.577 10.389 10410 Z= 0.267 Chirality : 0.040 0.161 1173 Planarity : 0.005 0.040 1364 Dihedral : 5.498 51.783 1064 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.98 % Allowed : 25.26 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.28), residues: 947 helix: 0.10 (0.28), residues: 368 sheet: -0.24 (0.38), residues: 190 loop : -0.56 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 70 TYR 0.030 0.002 TYR A 263 PHE 0.016 0.001 PHE B 327 TRP 0.045 0.001 TRP A 284 HIS 0.004 0.001 HIS B 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 7610) covalent geometry : angle 0.57704 / 0.27 (10410) hydrogen bonds : bond 0.02637 / 1.76 ( 322) hydrogen bonds : angle 4.38337 / 3.14 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6164 (tpt170) REVERT: A 199 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7496 (tt) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 0.0772 time to fit residues: 8.7988 Evaluate side-chains 74 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.185486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162223 restraints weight = 13566.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165529 restraints weight = 8304.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.167743 restraints weight = 5870.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.168957 restraints weight = 4601.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.170142 restraints weight = 3941.552| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7610 Z= 0.102 Angle : 0.592 9.967 10410 Z= 0.275 Chirality : 0.040 0.141 1173 Planarity : 0.005 0.041 1364 Dihedral : 5.509 49.114 1064 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.98 % Allowed : 25.53 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 947 helix: 0.17 (0.28), residues: 377 sheet: -0.16 (0.38), residues: 180 loop : -0.51 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.023 0.002 TYR A 307 PHE 0.045 0.002 PHE A 327 TRP 0.037 0.001 TRP A 284 HIS 0.008 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 7610) covalent geometry : angle 0.59163 / 0.27 (10410) hydrogen bonds : bond 0.02871 / 1.93 ( 322) hydrogen bonds : angle 4.38767 / 3.13 ( 906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6161 (tpt170) REVERT: A 199 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7516 (tt) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.0844 time to fit residues: 8.7514 Evaluate side-chains 72 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.158604 restraints weight = 13465.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.161317 restraints weight = 8028.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.162184 restraints weight = 5655.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.164352 restraints weight = 4874.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.164285 restraints weight = 4649.161| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 0.034 7610 Z= 0.139 Angle : 0.652 9.760 10410 Z= 0.305 Chirality : 0.042 0.140 1173 Planarity : 0.005 0.040 1364 Dihedral : 5.991 52.525 1064 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.51 % Allowed : 25.79 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.28), residues: 947 helix: 0.07 (0.28), residues: 372 sheet: -0.12 (0.38), residues: 186 loop : -0.68 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.015 0.002 TYR A 307 PHE 0.048 0.002 PHE A 327 TRP 0.036 0.002 TRP A 284 HIS 0.014 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7610) covalent geometry : angle 0.65239 / 0.31 (10410) hydrogen bonds : bond 0.03586 / 2.44 ( 322) hydrogen bonds : angle 4.67954 / 3.31 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.12 seconds wall clock time: 22 minutes 53.03 seconds (1373.03 seconds total)