Starting phenix.real_space_refine on Sun Aug 9 04:12:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxn_71975/08_2026/9pxn_71975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxn_71975/08_2026/9pxn_71975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pxn_71975/08_2026/9pxn_71975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxn_71975/08_2026/9pxn_71975.map" model { file = "/net/cci-nas-00/data/ceres_data/9pxn_71975/08_2026/9pxn_71975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxn_71975/08_2026/9pxn_71975.cif" } resolution = 2.5 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= 0.002 sd= 0.056 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 C 10196 2.51 5 N 2600 2.21 5 O 2756 1.98 5 H 15772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31460 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 7865 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Chain: "A" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 7865 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Chain: "C" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 7865 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Chain: "D" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 7865 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Time building chain proxies: 5.01, per 1000 atoms: 0.16 Number of scatterers: 31460 At special positions: 0 Unit cell: (124.777, 124.777, 122.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 O 2756 8.00 N 2600 7.00 C 10196 6.00 H 15772 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 917.6 milliseconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 12 sheets defined 71.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 96 through 103 removed outlier: 3.583A pdb=" N SER B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 131 removed outlier: 3.805A pdb=" N GLY B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 167 Proline residue: B 161 - end of helix removed outlier: 3.576A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 194 Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 252 through 265 Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 270 through 287 removed outlier: 3.789A pdb=" N ARG B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 Proline residue: B 320 - end of helix removed outlier: 3.688A pdb=" N GLN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.843A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.801A pdb=" N ARG B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 472 removed outlier: 5.710A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.874A pdb=" N LYS B 546 " --> pdb=" O CYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 4.247A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.537A pdb=" N ARG B 580 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG B 581 " --> pdb=" O MET B 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 577 through 581' Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.806A pdb=" N GLY A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 167 Proline residue: A 161 - end of helix removed outlier: 3.577A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 287 removed outlier: 3.789A pdb=" N ARG A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Proline residue: A 320 - end of helix removed outlier: 3.688A pdb=" N GLN A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.843A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.801A pdb=" N ARG A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 472 removed outlier: 5.710A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.874A pdb=" N LYS A 546 " --> pdb=" O CYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 4.247A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 removed outlier: 3.537A pdb=" N ARG A 580 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 581 " --> pdb=" O MET A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 581' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 131 removed outlier: 3.806A pdb=" N GLY C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 167 Proline residue: C 161 - end of helix removed outlier: 3.576A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 194 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 252 through 265 Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 270 through 287 removed outlier: 3.789A pdb=" N ARG C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 Proline residue: C 320 - end of helix removed outlier: 3.688A pdb=" N GLN C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.843A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.801A pdb=" N ARG C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 472 removed outlier: 5.710A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.874A pdb=" N LYS C 546 " --> pdb=" O CYS C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 4.246A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 581 removed outlier: 3.537A pdb=" N ARG C 580 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 581 " --> pdb=" O MET C 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 577 through 581' Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 131 removed outlier: 3.807A pdb=" N GLY D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 167 Proline residue: D 161 - end of helix removed outlier: 3.576A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 252 through 265 Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 270 through 287 removed outlier: 3.789A pdb=" N ARG D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 Proline residue: D 320 - end of helix removed outlier: 3.688A pdb=" N GLN D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.843A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.801A pdb=" N ARG D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 472 removed outlier: 5.709A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.875A pdb=" N LYS D 546 " --> pdb=" O CYS D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 4.246A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 581 removed outlier: 3.537A pdb=" N ARG D 580 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 581 " --> pdb=" O MET D 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 577 through 581' Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.576A pdb=" N THR B 198 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.936A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 564 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR B 513 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.527A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.576A pdb=" N THR A 198 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.936A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 564 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A 513 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.526A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 198 through 199 removed outlier: 3.576A pdb=" N THR C 198 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.934A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU C 564 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR C 513 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.525A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.576A pdb=" N THR D 198 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.934A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU D 564 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR D 513 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.526A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2976 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: 6.98 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15740 1.03 - 1.23: 32 1.23 - 1.42: 6844 1.42 - 1.62: 8984 1.62 - 1.81: 240 Bond restraints: 31840 Sorted by residual: bond pdb=" CB ILE A 160 " pdb=" CG2 ILE A 160 " ideal model delta sigma weight residual 1.521 1.573 -0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CB ILE C 160 " pdb=" CG2 ILE C 160 " ideal model delta sigma weight residual 1.521 1.572 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB ILE D 160 " pdb=" CG2 ILE D 160 " ideal model delta sigma weight residual 1.521 1.572 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB ILE B 160 " pdb=" CG2 ILE B 160 " ideal model delta sigma weight residual 1.521 1.571 -0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" CB PHE A 132 " pdb=" CG PHE A 132 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.30e-02 1.89e+03 1.27e+00 ... (remaining 31835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 52381 1.11 - 2.22: 4584 2.22 - 3.34: 355 3.34 - 4.45: 96 4.45 - 5.56: 36 Bond angle restraints: 57452 Sorted by residual: angle pdb=" CA MET D 356 " pdb=" CB MET D 356 " pdb=" CG MET D 356 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.24e+00 angle pdb=" CA MET C 356 " pdb=" CB MET C 356 " pdb=" CG MET C 356 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.24e+00 angle pdb=" CA MET A 356 " pdb=" CB MET A 356 " pdb=" CG MET A 356 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.24e+00 angle pdb=" CA MET B 356 " pdb=" CB MET B 356 " pdb=" CG MET B 356 " ideal model delta sigma weight residual 114.10 118.20 -4.10 2.00e+00 2.50e-01 4.20e+00 angle pdb=" CA TYR D 411 " pdb=" CB TYR D 411 " pdb=" CG TYR D 411 " ideal model delta sigma weight residual 113.90 110.59 3.31 1.80e+00 3.09e-01 3.38e+00 ... (remaining 57447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 13695 17.15 - 34.31: 924 34.31 - 51.46: 160 51.46 - 68.61: 137 68.61 - 85.77: 44 Dihedral angle restraints: 14960 sinusoidal: 8004 harmonic: 6956 Sorted by residual: dihedral pdb=" CA ASN C 465 " pdb=" C ASN C 465 " pdb=" N CYS C 466 " pdb=" CA CYS C 466 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASN D 465 " pdb=" C ASN D 465 " pdb=" N CYS D 466 " pdb=" CA CYS D 466 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASN A 465 " pdb=" C ASN A 465 " pdb=" N CYS A 466 " pdb=" CA CYS A 466 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 14957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1447 0.028 - 0.057: 586 0.057 - 0.085: 239 0.085 - 0.114: 60 0.114 - 0.142: 60 Chirality restraints: 2392 Sorted by residual: chirality pdb=" CA ILE B 503 " pdb=" N ILE B 503 " pdb=" C ILE B 503 " pdb=" CB ILE B 503 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE C 503 " pdb=" N ILE C 503 " pdb=" C ILE C 503 " pdb=" CB ILE C 503 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE D 503 " pdb=" N ILE D 503 " pdb=" C ILE D 503 " pdb=" CB ILE D 503 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 2389 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 278 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ILE B 278 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE B 278 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 279 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 278 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ILE C 278 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE C 278 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS C 279 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 278 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ILE D 278 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE D 278 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS D 279 " -0.013 2.00e-02 2.50e+03 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.53: 23192 2.53 - 3.04: 72179 3.04 - 3.56: 75810 3.56 - 4.08: 100426 4.08 - 4.60: 150550 Nonbonded interactions: 422157 Sorted by model distance: nonbonded pdb=" H VAL A 519 " pdb=" HG1 THR A 557 " model vdw 2.008 2.100 nonbonded pdb=" H VAL D 519 " pdb=" HG1 THR D 557 " model vdw 2.008 2.100 nonbonded pdb=" H VAL C 519 " pdb=" HG1 THR C 557 " model vdw 2.009 2.100 nonbonded pdb=" H VAL B 519 " pdb=" HG1 THR B 557 " model vdw 2.009 2.100 nonbonded pdb=" HB3 SER B 378 " pdb=" HG SER B 378 " model vdw 2.015 1.816 ... (remaining 422152 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.210 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 28.480 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.004 0.052 16068 Z= 0.183 Angle : 0.587 5.560 21712 Z= 0.322 Chirality : 0.041 0.142 2392 Planarity : 0.005 0.043 2712 Dihedral : 10.895 80.287 5932 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 1900 helix: 1.78 (0.14), residues: 1248 sheet: 0.70 (0.47), residues: 88 loop : -0.57 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.014 0.002 TYR C 411 PHE 0.010 0.001 PHE B 178 TRP 0.010 0.001 TRP B 373 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (16068) covalent geometry : angle 0.58676 / 0.32 (21712) hydrogen bonds : bond 0.15605 / 10.00 ( 1016) hydrogen bonds : angle 5.34251 / 3.97 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8557 (mtp) cc_final: 0.8282 (mtp) REVERT: B 433 ASP cc_start: 0.8306 (m-30) cc_final: 0.8057 (m-30) REVERT: B 467 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7410 (ttt-90) REVERT: A 305 MET cc_start: 0.8549 (mtp) cc_final: 0.8279 (mtp) REVERT: A 433 ASP cc_start: 0.8296 (m-30) cc_final: 0.8045 (m-30) REVERT: A 467 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7409 (ttt-90) REVERT: C 305 MET cc_start: 0.8552 (mtp) cc_final: 0.8277 (mtp) REVERT: C 433 ASP cc_start: 0.8297 (m-30) cc_final: 0.8046 (m-30) REVERT: C 467 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7408 (ttt-90) REVERT: D 305 MET cc_start: 0.8555 (mtp) cc_final: 0.8279 (mtp) REVERT: D 433 ASP cc_start: 0.8296 (m-30) cc_final: 0.8046 (m-30) REVERT: D 467 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7407 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 1.3927 time to fit residues: 572.7178 Evaluate side-chains 256 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN A 156 ASN C 156 ASN D 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.170786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123405 restraints weight = 44705.942| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.04 r_work: 0.3593 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16068 Z= 0.196 Angle : 0.573 6.101 21712 Z= 0.314 Chirality : 0.041 0.127 2392 Planarity : 0.005 0.057 2712 Dihedral : 4.267 18.768 2104 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.31 % Allowed : 11.34 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 1900 helix: 1.81 (0.14), residues: 1276 sheet: 0.76 (0.45), residues: 88 loop : -0.80 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 554 TYR 0.018 0.002 TYR D 411 PHE 0.014 0.002 PHE A 483 TRP 0.011 0.001 TRP A 373 HIS 0.005 0.002 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (16068) covalent geometry : angle 0.57341 / 0.31 (21712) hydrogen bonds : bond 0.08214 / 5.30 ( 1016) hydrogen bonds : angle 4.34662 / 3.21 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7503 (m-30) cc_final: 0.7256 (m-30) REVERT: B 255 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5090 (ttt180) REVERT: B 305 MET cc_start: 0.8437 (mtp) cc_final: 0.8215 (mtp) REVERT: B 433 ASP cc_start: 0.7981 (m-30) cc_final: 0.7765 (m-30) REVERT: B 446 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: B 575 GLU cc_start: 0.5395 (mp0) cc_final: 0.4958 (mp0) REVERT: A 183 ASP cc_start: 0.7516 (m-30) cc_final: 0.7273 (m-30) REVERT: A 255 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5093 (ttt180) REVERT: A 433 ASP cc_start: 0.7953 (m-30) cc_final: 0.7746 (m-30) REVERT: A 446 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: A 575 GLU cc_start: 0.5345 (mp0) cc_final: 0.4911 (mp0) REVERT: C 183 ASP cc_start: 0.7516 (m-30) cc_final: 0.7272 (m-30) REVERT: C 255 ARG cc_start: 0.5826 (OUTLIER) cc_final: 0.5087 (ttt180) REVERT: C 433 ASP cc_start: 0.7953 (m-30) cc_final: 0.7748 (m-30) REVERT: C 446 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: C 575 GLU cc_start: 0.5392 (mp0) cc_final: 0.4957 (mp0) REVERT: D 183 ASP cc_start: 0.7518 (m-30) cc_final: 0.7277 (m-30) REVERT: D 255 ARG cc_start: 0.5826 (OUTLIER) cc_final: 0.5087 (ttt180) REVERT: D 305 MET cc_start: 0.8431 (mtp) cc_final: 0.8229 (mtp) REVERT: D 433 ASP cc_start: 0.7942 (m-30) cc_final: 0.7736 (m-30) REVERT: D 446 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: D 575 GLU cc_start: 0.5392 (mp0) cc_final: 0.4957 (mp0) outliers start: 40 outliers final: 9 residues processed: 266 average time/residue: 1.3797 time to fit residues: 404.6755 Evaluate side-chains 249 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN B 398 GLN A 156 ASN A 398 GLN C 156 ASN C 398 GLN D 156 ASN D 398 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125628 restraints weight = 44558.288| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.04 r_work: 0.3625 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16068 Z= 0.132 Angle : 0.480 5.596 21712 Z= 0.263 Chirality : 0.038 0.133 2392 Planarity : 0.004 0.044 2712 Dihedral : 4.069 18.215 2104 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.50 % Allowed : 12.44 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 1900 helix: 2.12 (0.14), residues: 1256 sheet: 0.98 (0.47), residues: 88 loop : -0.64 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 554 TYR 0.015 0.002 TYR D 411 PHE 0.012 0.001 PHE A 483 TRP 0.010 0.001 TRP D 373 HIS 0.003 0.001 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16068) covalent geometry : angle 0.47953 / 0.26 (21712) hydrogen bonds : bond 0.06748 / 4.36 ( 1016) hydrogen bonds : angle 4.12674 / 3.04 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5489 (ptm) REVERT: B 183 ASP cc_start: 0.7549 (m-30) cc_final: 0.7315 (m-30) REVERT: B 200 ASN cc_start: 0.8208 (m-40) cc_final: 0.7618 (m110) REVERT: B 575 GLU cc_start: 0.5531 (mp0) cc_final: 0.5001 (mp0) REVERT: A 183 ASP cc_start: 0.7587 (m-30) cc_final: 0.7361 (m-30) REVERT: A 200 ASN cc_start: 0.8221 (m-40) cc_final: 0.7636 (m110) REVERT: A 575 GLU cc_start: 0.5509 (mp0) cc_final: 0.4981 (mp0) REVERT: C 183 ASP cc_start: 0.7585 (m-30) cc_final: 0.7351 (m-30) REVERT: C 200 ASN cc_start: 0.8212 (m-40) cc_final: 0.7624 (m110) REVERT: C 575 GLU cc_start: 0.5500 (mp0) cc_final: 0.4976 (mp0) REVERT: D 183 ASP cc_start: 0.7567 (m-30) cc_final: 0.7335 (m-30) REVERT: D 200 ASN cc_start: 0.8193 (m-40) cc_final: 0.7590 (m110) REVERT: D 305 MET cc_start: 0.8497 (mtp) cc_final: 0.8294 (mtp) REVERT: D 575 GLU cc_start: 0.5528 (mp0) cc_final: 0.5003 (mp0) outliers start: 26 outliers final: 7 residues processed: 259 average time/residue: 1.2743 time to fit residues: 365.7684 Evaluate side-chains 244 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 115 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123295 restraints weight = 44291.779| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.03 r_work: 0.3591 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16068 Z= 0.160 Angle : 0.510 5.911 21712 Z= 0.280 Chirality : 0.039 0.130 2392 Planarity : 0.004 0.046 2712 Dihedral : 4.132 18.158 2104 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.79 % Allowed : 12.44 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 1900 helix: 1.99 (0.14), residues: 1276 sheet: 1.05 (0.48), residues: 88 loop : -0.84 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 405 TYR 0.018 0.002 TYR D 411 PHE 0.013 0.001 PHE A 483 TRP 0.009 0.001 TRP D 373 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16068) covalent geometry : angle 0.50997 / 0.28 (21712) hydrogen bonds : bond 0.07352 / 4.76 ( 1016) hydrogen bonds : angle 4.12756 / 3.04 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.848 Fit side-chains REVERT: B 169 GLU cc_start: 0.6406 (mt-10) cc_final: 0.5389 (mm-30) REVERT: B 183 ASP cc_start: 0.7570 (m-30) cc_final: 0.7361 (m-30) REVERT: B 200 ASN cc_start: 0.8203 (m-40) cc_final: 0.7615 (m110) REVERT: B 433 ASP cc_start: 0.8063 (m-30) cc_final: 0.7806 (m-30) REVERT: B 446 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 575 GLU cc_start: 0.5612 (mp0) cc_final: 0.4990 (mp0) REVERT: A 169 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5409 (mm-30) REVERT: A 183 ASP cc_start: 0.7606 (m-30) cc_final: 0.7398 (m-30) REVERT: A 200 ASN cc_start: 0.8190 (m-40) cc_final: 0.7619 (m110) REVERT: A 433 ASP cc_start: 0.8067 (m-30) cc_final: 0.7804 (m-30) REVERT: A 446 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: A 575 GLU cc_start: 0.5579 (mp0) cc_final: 0.4934 (mp0) REVERT: C 169 GLU cc_start: 0.6396 (mt-10) cc_final: 0.5429 (mm-30) REVERT: C 183 ASP cc_start: 0.7605 (m-30) cc_final: 0.7374 (m-30) REVERT: C 200 ASN cc_start: 0.8177 (m-40) cc_final: 0.7603 (m110) REVERT: C 433 ASP cc_start: 0.8070 (m-30) cc_final: 0.7807 (m-30) REVERT: C 446 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: C 575 GLU cc_start: 0.5614 (mp0) cc_final: 0.4986 (mp0) REVERT: D 169 GLU cc_start: 0.6424 (mt-10) cc_final: 0.5437 (mm-30) REVERT: D 183 ASP cc_start: 0.7578 (m-30) cc_final: 0.7344 (m-30) REVERT: D 200 ASN cc_start: 0.8165 (m-40) cc_final: 0.7579 (m110) REVERT: D 433 ASP cc_start: 0.8065 (m-30) cc_final: 0.7796 (m-30) REVERT: D 446 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: D 575 GLU cc_start: 0.5610 (mp0) cc_final: 0.4990 (mp0) outliers start: 31 outliers final: 8 residues processed: 262 average time/residue: 1.2927 time to fit residues: 374.0803 Evaluate side-chains 247 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 235 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.172506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125964 restraints weight = 44758.838| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.03 r_work: 0.3627 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16068 Z= 0.118 Angle : 0.465 6.177 21712 Z= 0.254 Chirality : 0.037 0.132 2392 Planarity : 0.004 0.044 2712 Dihedral : 3.955 17.590 2104 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 12.67 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.19), residues: 1900 helix: 2.25 (0.14), residues: 1256 sheet: 1.18 (0.48), residues: 88 loop : -0.64 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 554 TYR 0.015 0.001 TYR B 411 PHE 0.012 0.001 PHE A 483 TRP 0.009 0.001 TRP C 373 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (16068) covalent geometry : angle 0.46487 / 0.25 (21712) hydrogen bonds : bond 0.06123 / 3.96 ( 1016) hydrogen bonds : angle 3.99797 / 2.94 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.5634 (ptm) REVERT: B 169 GLU cc_start: 0.6395 (mt-10) cc_final: 0.5451 (mm-30) REVERT: B 183 ASP cc_start: 0.7625 (m-30) cc_final: 0.7396 (m-30) REVERT: B 255 ARG cc_start: 0.6029 (tmt170) cc_final: 0.5772 (ptm-80) REVERT: B 446 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: B 575 GLU cc_start: 0.5614 (mp0) cc_final: 0.4834 (mp0) REVERT: A 169 GLU cc_start: 0.6383 (mt-10) cc_final: 0.5436 (mm-30) REVERT: A 183 ASP cc_start: 0.7633 (m-30) cc_final: 0.7405 (m-30) REVERT: A 255 ARG cc_start: 0.6036 (tmt170) cc_final: 0.5782 (ptm-80) REVERT: A 446 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 575 GLU cc_start: 0.5578 (mp0) cc_final: 0.4842 (mp0) REVERT: C 169 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5459 (mm-30) REVERT: C 183 ASP cc_start: 0.7648 (m-30) cc_final: 0.7420 (m-30) REVERT: C 255 ARG cc_start: 0.6014 (tmt170) cc_final: 0.5757 (ptm-80) REVERT: C 446 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: C 575 GLU cc_start: 0.5603 (mp0) cc_final: 0.4867 (mp0) REVERT: D 169 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5465 (mm-30) REVERT: D 183 ASP cc_start: 0.7640 (m-30) cc_final: 0.7413 (m-30) REVERT: D 255 ARG cc_start: 0.6016 (tmt170) cc_final: 0.5759 (ptm-80) REVERT: D 446 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: D 575 GLU cc_start: 0.5598 (mp0) cc_final: 0.4863 (mp0) outliers start: 36 outliers final: 7 residues processed: 269 average time/residue: 1.3792 time to fit residues: 411.0806 Evaluate side-chains 261 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 163 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.171871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125159 restraints weight = 44277.002| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.02 r_work: 0.3608 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16068 Z= 0.127 Angle : 0.473 6.123 21712 Z= 0.258 Chirality : 0.038 0.131 2392 Planarity : 0.004 0.043 2712 Dihedral : 3.946 17.814 2104 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.26 % Allowed : 13.37 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 1900 helix: 2.29 (0.14), residues: 1256 sheet: 1.16 (0.48), residues: 88 loop : -0.58 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 554 TYR 0.016 0.002 TYR C 411 PHE 0.013 0.001 PHE B 483 TRP 0.009 0.001 TRP B 373 HIS 0.004 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (16068) covalent geometry : angle 0.47331 / 0.26 (21712) hydrogen bonds : bond 0.06335 / 4.10 ( 1016) hydrogen bonds : angle 3.96926 / 2.92 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 169 GLU cc_start: 0.6336 (mt-10) cc_final: 0.5280 (mm-30) REVERT: B 183 ASP cc_start: 0.7530 (m-30) cc_final: 0.7292 (m-30) REVERT: B 200 ASN cc_start: 0.8195 (m-40) cc_final: 0.7698 (m110) REVERT: B 446 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: B 575 GLU cc_start: 0.5429 (mp0) cc_final: 0.4778 (mp0) REVERT: A 169 GLU cc_start: 0.6284 (mt-10) cc_final: 0.5253 (mm-30) REVERT: A 183 ASP cc_start: 0.7536 (m-30) cc_final: 0.7298 (m-30) REVERT: A 200 ASN cc_start: 0.8205 (m-40) cc_final: 0.7708 (m110) REVERT: A 446 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: A 575 GLU cc_start: 0.5391 (mp0) cc_final: 0.4744 (mp0) REVERT: C 169 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5279 (mm-30) REVERT: C 183 ASP cc_start: 0.7545 (m-30) cc_final: 0.7305 (m-30) REVERT: C 200 ASN cc_start: 0.8190 (m-40) cc_final: 0.7691 (m110) REVERT: C 446 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: C 575 GLU cc_start: 0.5416 (mp0) cc_final: 0.4770 (mp0) REVERT: D 169 GLU cc_start: 0.6303 (mt-10) cc_final: 0.5279 (mm-30) REVERT: D 183 ASP cc_start: 0.7538 (m-30) cc_final: 0.7300 (m-30) REVERT: D 200 ASN cc_start: 0.8185 (m-40) cc_final: 0.7682 (m110) REVERT: D 446 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: D 575 GLU cc_start: 0.5425 (mp0) cc_final: 0.4779 (mp0) outliers start: 39 outliers final: 14 residues processed: 263 average time/residue: 1.2938 time to fit residues: 377.2263 Evaluate side-chains 257 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123892 restraints weight = 44631.748| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.03 r_work: 0.3596 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16068 Z= 0.139 Angle : 0.490 6.214 21712 Z= 0.266 Chirality : 0.038 0.129 2392 Planarity : 0.004 0.043 2712 Dihedral : 3.959 17.736 2104 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.45 % Allowed : 14.87 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1900 helix: 2.27 (0.14), residues: 1256 sheet: 1.22 (0.49), residues: 88 loop : -0.61 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.016 0.002 TYR A 411 PHE 0.014 0.001 PHE C 483 TRP 0.010 0.001 TRP A 373 HIS 0.004 0.001 HIS D 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16068) covalent geometry : angle 0.49032 / 0.27 (21712) hydrogen bonds : bond 0.06652 / 4.30 ( 1016) hydrogen bonds : angle 3.98159 / 2.93 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5272 (mm-30) REVERT: B 183 ASP cc_start: 0.7511 (m-30) cc_final: 0.7282 (m-30) REVERT: B 446 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 575 GLU cc_start: 0.5450 (mp0) cc_final: 0.4822 (mp0) REVERT: A 169 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5263 (mm-30) REVERT: A 183 ASP cc_start: 0.7540 (m-30) cc_final: 0.7315 (m-30) REVERT: A 433 ASP cc_start: 0.7936 (m-30) cc_final: 0.7653 (m-30) REVERT: A 446 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 575 GLU cc_start: 0.5438 (mp0) cc_final: 0.4811 (mp0) REVERT: C 169 GLU cc_start: 0.6270 (mt-10) cc_final: 0.5291 (mm-30) REVERT: C 183 ASP cc_start: 0.7536 (m-30) cc_final: 0.7312 (m-30) REVERT: C 446 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: C 575 GLU cc_start: 0.5450 (mp0) cc_final: 0.4826 (mp0) REVERT: D 169 GLU cc_start: 0.6271 (mt-10) cc_final: 0.5280 (mm-30) REVERT: D 183 ASP cc_start: 0.7535 (m-30) cc_final: 0.7310 (m-30) REVERT: D 446 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: D 575 GLU cc_start: 0.5448 (mp0) cc_final: 0.4825 (mp0) outliers start: 25 outliers final: 10 residues processed: 244 average time/residue: 1.3289 time to fit residues: 359.7250 Evaluate side-chains 246 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 232 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.169885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123059 restraints weight = 44539.096| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.02 r_work: 0.3595 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16068 Z= 0.150 Angle : 0.502 6.287 21712 Z= 0.273 Chirality : 0.038 0.129 2392 Planarity : 0.004 0.044 2712 Dihedral : 4.032 18.529 2104 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.39 % Allowed : 15.10 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.99 (0.19), residues: 1900 helix: 2.15 (0.14), residues: 1276 sheet: 1.21 (0.49), residues: 88 loop : -0.74 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 258 TYR 0.017 0.002 TYR C 411 PHE 0.015 0.001 PHE C 483 TRP 0.009 0.001 TRP B 373 HIS 0.004 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16068) covalent geometry : angle 0.50241 / 0.27 (21712) hydrogen bonds : bond 0.06971 / 4.51 ( 1016) hydrogen bonds : angle 4.00364 / 2.94 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 GLU cc_start: 0.6398 (mt-10) cc_final: 0.5462 (mm-30) REVERT: B 433 ASP cc_start: 0.8100 (m-30) cc_final: 0.7826 (m-30) REVERT: B 446 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: B 575 GLU cc_start: 0.5613 (mp0) cc_final: 0.4963 (mp0) REVERT: A 169 GLU cc_start: 0.6386 (mt-10) cc_final: 0.5455 (mm-30) REVERT: A 433 ASP cc_start: 0.8102 (m-30) cc_final: 0.7826 (m-30) REVERT: A 446 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: A 575 GLU cc_start: 0.5600 (mp0) cc_final: 0.4950 (mp0) REVERT: C 169 GLU cc_start: 0.6380 (mt-10) cc_final: 0.5463 (mm-30) REVERT: C 433 ASP cc_start: 0.8112 (m-30) cc_final: 0.7836 (m-30) REVERT: C 446 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: C 575 GLU cc_start: 0.5603 (mp0) cc_final: 0.4954 (mp0) REVERT: D 169 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5459 (mm-30) REVERT: D 433 ASP cc_start: 0.8108 (m-30) cc_final: 0.7830 (m-30) REVERT: D 446 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: D 575 GLU cc_start: 0.5596 (mp0) cc_final: 0.4952 (mp0) outliers start: 24 outliers final: 12 residues processed: 247 average time/residue: 1.3717 time to fit residues: 375.5096 Evaluate side-chains 247 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 182 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124291 restraints weight = 44632.877| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.02 r_work: 0.3610 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16068 Z= 0.129 Angle : 0.486 6.342 21712 Z= 0.264 Chirality : 0.038 0.130 2392 Planarity : 0.004 0.044 2712 Dihedral : 3.950 17.841 2104 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.45 % Allowed : 15.22 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.10 (0.19), residues: 1900 helix: 2.25 (0.14), residues: 1256 sheet: 1.19 (0.49), residues: 88 loop : -0.60 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.017 0.002 TYR B 411 PHE 0.015 0.001 PHE C 236 TRP 0.009 0.001 TRP B 373 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16068) covalent geometry : angle 0.48602 / 0.26 (21712) hydrogen bonds : bond 0.06416 / 4.15 ( 1016) hydrogen bonds : angle 3.96361 / 2.91 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 GLU cc_start: 0.6343 (mt-10) cc_final: 0.5435 (mm-30) REVERT: B 446 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 575 GLU cc_start: 0.5603 (mp0) cc_final: 0.4939 (mp0) REVERT: A 169 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5417 (mm-30) REVERT: A 433 ASP cc_start: 0.8094 (m-30) cc_final: 0.7819 (m-30) REVERT: A 446 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: A 575 GLU cc_start: 0.5589 (mp0) cc_final: 0.4928 (mp0) REVERT: C 169 GLU cc_start: 0.6322 (mt-10) cc_final: 0.5426 (mm-30) REVERT: C 446 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: C 575 GLU cc_start: 0.5594 (mp0) cc_final: 0.4936 (mp0) REVERT: D 169 GLU cc_start: 0.6332 (mt-10) cc_final: 0.5428 (mm-30) REVERT: D 446 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: D 575 GLU cc_start: 0.5594 (mp0) cc_final: 0.4938 (mp0) outliers start: 25 outliers final: 12 residues processed: 245 average time/residue: 1.2764 time to fit residues: 346.5392 Evaluate side-chains 246 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 87 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126892 restraints weight = 44933.981| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.02 r_work: 0.3629 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16068 Z= 0.109 Angle : 0.460 6.107 21712 Z= 0.250 Chirality : 0.037 0.130 2392 Planarity : 0.004 0.044 2712 Dihedral : 3.837 17.791 2104 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.98 % Allowed : 15.57 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.19), residues: 1900 helix: 2.39 (0.14), residues: 1256 sheet: 1.23 (0.48), residues: 88 loop : -0.53 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 549 TYR 0.014 0.001 TYR B 411 PHE 0.015 0.001 PHE C 483 TRP 0.009 0.001 TRP D 373 HIS 0.004 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (16068) covalent geometry : angle 0.46049 / 0.25 (21712) hydrogen bonds : bond 0.05512 / 3.58 ( 1016) hydrogen bonds : angle 3.86866 / 2.84 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5387 (ptm) REVERT: B 169 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5244 (mm-30) REVERT: B 200 ASN cc_start: 0.8221 (m-40) cc_final: 0.7729 (m110) REVERT: B 446 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 575 GLU cc_start: 0.5442 (mp0) cc_final: 0.4648 (mp0) REVERT: A 101 MET cc_start: 0.6414 (OUTLIER) cc_final: 0.5443 (ptm) REVERT: A 169 GLU cc_start: 0.6270 (mt-10) cc_final: 0.5239 (mm-30) REVERT: A 200 ASN cc_start: 0.8236 (m-40) cc_final: 0.7757 (m110) REVERT: A 446 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: A 575 GLU cc_start: 0.5408 (mp0) cc_final: 0.4625 (mp0) REVERT: C 101 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5455 (ptm) REVERT: C 169 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5230 (mm-30) REVERT: C 200 ASN cc_start: 0.8208 (m-40) cc_final: 0.7686 (m110) REVERT: C 446 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: C 575 GLU cc_start: 0.5412 (mp0) cc_final: 0.4628 (mp0) REVERT: D 101 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5461 (ptm) REVERT: D 169 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5242 (mm-30) REVERT: D 200 ASN cc_start: 0.8209 (m-40) cc_final: 0.7684 (m110) REVERT: D 446 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: D 575 GLU cc_start: 0.5431 (mp0) cc_final: 0.4655 (mp0) outliers start: 17 outliers final: 5 residues processed: 250 average time/residue: 1.1820 time to fit residues: 330.0326 Evaluate side-chains 245 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 446 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 186 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126750 restraints weight = 44902.814| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.03 r_work: 0.3628 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16068 Z= 0.112 Angle : 0.462 6.126 21712 Z= 0.251 Chirality : 0.037 0.129 2392 Planarity : 0.004 0.044 2712 Dihedral : 3.792 17.636 2104 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.27 % Allowed : 15.74 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1900 helix: 2.39 (0.14), residues: 1256 sheet: 1.11 (0.48), residues: 88 loop : -0.51 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 549 TYR 0.015 0.001 TYR B 411 PHE 0.014 0.001 PHE B 236 TRP 0.008 0.001 TRP B 373 HIS 0.004 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (16068) covalent geometry : angle 0.46225 / 0.25 (21712) hydrogen bonds : bond 0.05543 / 3.59 ( 1016) hydrogen bonds : angle 3.84166 / 2.82 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11597.93 seconds wall clock time: 196 minutes 15.26 seconds (11775.26 seconds total)