Starting phenix.real_space_refine on Tue Nov 18 19:58:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lft_23306/11_2025/7lft_23306_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lft_23306/11_2025/7lft_23306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lft_23306/11_2025/7lft_23306_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lft_23306/11_2025/7lft_23306_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lft_23306/11_2025/7lft_23306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lft_23306/11_2025/7lft_23306.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 8 5.49 5 S 76 5.16 5 C 10280 2.51 5 N 2380 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15479 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {' K': 3, 'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-1': 4, 'CPL:plan-2': 4, 'CPL:plan-3': 6, 'CPL:plan-4': 6} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.46, per 1000 atoms: 0.22 Number of scatterers: 15479 At special positions: 0 Unit cell: (95.372, 95.372, 119.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 76 16.00 P 8 15.00 O 2732 8.00 N 2380 7.00 C 10280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 682.5 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 68.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 Proline residue: A 175 - end of helix removed outlier: 5.210A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.750A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.820A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 4.073A pdb=" N LYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.642A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.866A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 458 through 477 removed outlier: 6.118A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.515A pdb=" N ASP A 482 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A 483 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 605 Processing helix chain 'B' and resid 162 through 189 Proline residue: B 175 - end of helix removed outlier: 5.210A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.750A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.821A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.072A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.641A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.866A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 404 through 424 Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 458 through 477 removed outlier: 6.118A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.515A pdb=" N ASP B 482 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS B 483 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 588 through 605 Processing helix chain 'C' and resid 162 through 189 Proline residue: C 175 - end of helix removed outlier: 5.210A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.750A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.821A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.073A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.640A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.866A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 477 removed outlier: 6.118A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 4.516A pdb=" N ASP C 482 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS C 483 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'D' and resid 162 through 189 Proline residue: D 175 - end of helix removed outlier: 5.210A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.750A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 254 removed outlier: 3.821A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.072A pdb=" N LYS D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.642A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 290 removed outlier: 3.866A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 458 through 477 removed outlier: 6.118A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 removed outlier: 4.515A pdb=" N ASP D 482 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS D 483 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.486A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.486A pdb=" N ILE B 565 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.486A pdb=" N ILE C 565 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 498 Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.486A pdb=" N ILE D 565 " --> pdb=" O ILE D 506 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2376 1.27 - 1.41: 3932 1.41 - 1.54: 9096 1.54 - 1.67: 280 1.67 - 1.80: 128 Bond restraints: 15812 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" O VAL D 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL A 370 " pdb=" O VAL A 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL B 370 " pdb=" O VAL B 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL C 370 " pdb=" O VAL C 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.98e+01 bond pdb=" C31 CPL D 706 " pdb=" O2 CPL D 706 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 15807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 21112 4.58 - 9.16: 172 9.16 - 13.74: 32 13.74 - 18.32: 8 18.32 - 22.90: 4 Bond angle restraints: 21328 Sorted by residual: angle pdb=" O3P CPL A 707 " pdb=" P CPL A 707 " pdb=" O4P CPL A 707 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL D 706 " pdb=" P CPL D 706 " pdb=" O4P CPL D 706 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL C 706 " pdb=" P CPL C 706 " pdb=" O4P CPL C 706 " ideal model delta sigma weight residual 93.29 116.17 -22.88 3.00e+00 1.11e-01 5.82e+01 angle pdb=" O3P CPL B 706 " pdb=" P CPL B 706 " pdb=" O4P CPL B 706 " ideal model delta sigma weight residual 93.29 116.12 -22.83 3.00e+00 1.11e-01 5.79e+01 angle pdb=" N VAL A 370 " pdb=" CA VAL A 370 " pdb=" C VAL A 370 " ideal model delta sigma weight residual 111.56 106.32 5.24 8.60e-01 1.35e+00 3.71e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 9396 27.56 - 55.12: 460 55.12 - 82.68: 44 82.68 - 110.24: 8 110.24 - 137.79: 8 Dihedral angle restraints: 9916 sinusoidal: 4592 harmonic: 5324 Sorted by residual: dihedral pdb=" C3 CPL B 706 " pdb=" C1 CPL B 706 " pdb=" C2 CPL B 706 " pdb=" O3P CPL B 706 " ideal model delta sinusoidal sigma weight residual 72.09 -150.12 -137.79 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3 CPL C 706 " pdb=" C1 CPL C 706 " pdb=" C2 CPL C 706 " pdb=" O3P CPL C 706 " ideal model delta sinusoidal sigma weight residual 72.09 -150.14 -137.77 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3 CPL A 707 " pdb=" C1 CPL A 707 " pdb=" C2 CPL A 707 " pdb=" O3P CPL A 707 " ideal model delta sinusoidal sigma weight residual 72.09 -150.14 -137.77 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 9913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2238 0.094 - 0.188: 93 0.188 - 0.282: 29 0.282 - 0.377: 0 0.377 - 0.471: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" C10 CLR A 702 " pdb=" C1 CLR A 702 " pdb=" C5 CLR A 702 " pdb=" C9 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C10 CLR C 701 " pdb=" C1 CLR C 701 " pdb=" C5 CLR C 701 " pdb=" C9 CLR C 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C10 CLR D 701 " pdb=" C1 CLR D 701 " pdb=" C5 CLR D 701 " pdb=" C9 CLR D 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2365 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 501 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO D 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 501 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 502 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 501 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.020 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.49: 69 2.49 - 3.16: 13167 3.16 - 3.82: 32456 3.82 - 4.48: 45964 4.48 - 5.14: 71633 Nonbonded interactions: 163289 Sorted by model distance: nonbonded pdb=" K K A 710 " pdb=" K K A 711 " model vdw 1.832 2.660 nonbonded pdb=" OG SER A 567 " pdb=" OG SER A 571 " model vdw 2.187 3.040 nonbonded pdb=" OG SER D 567 " pdb=" OG SER D 571 " model vdw 2.188 3.040 nonbonded pdb=" OG SER C 567 " pdb=" OG SER C 571 " model vdw 2.188 3.040 nonbonded pdb=" OG SER B 567 " pdb=" OG SER B 571 " model vdw 2.188 3.040 ... (remaining 163284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 708) selection = chain 'B' 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.009 0.102 15812 Z= 0.459 Angle : 1.096 22.901 21328 Z= 0.478 Chirality : 0.057 0.471 2368 Planarity : 0.004 0.036 2552 Dihedral : 16.077 137.795 6500 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.25 % Allowed : 1.97 % Favored : 97.78 % 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: -0.82 (0.18), residues: 1792 helix: -0.10 (0.14), residues: 1176 sheet: -2.84 (1.00), residues: 20 loop : -1.13 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 287 TYR 0.022 0.002 TYR A 349 PHE 0.014 0.002 PHE D 298 TRP 0.021 0.002 TRP C 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00912 (15812) covalent geometry : angle 1.09636 (21328) hydrogen bonds : bond 0.11430 ( 952) hydrogen bonds : angle 4.89472 ( 2736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.627 Fit side-chains REVERT: A 399 MET cc_start: 0.8352 (ttm) cc_final: 0.8068 (ttp) REVERT: A 403 MET cc_start: 0.8494 (mtp) cc_final: 0.8182 (mtp) REVERT: A 409 GLU cc_start: 0.7688 (tt0) cc_final: 0.7415 (tt0) REVERT: A 551 ASN cc_start: 0.6890 (m-40) cc_final: 0.6672 (m-40) REVERT: A 572 ASP cc_start: 0.6943 (t0) cc_final: 0.6734 (t0) REVERT: A 594 MET cc_start: 0.7125 (ttp) cc_final: 0.6524 (tmt) REVERT: A 597 GLU cc_start: 0.6597 (tm-30) cc_final: 0.6263 (tm-30) REVERT: B 399 MET cc_start: 0.8350 (ttm) cc_final: 0.8067 (ttp) REVERT: B 403 MET cc_start: 0.8494 (mtp) cc_final: 0.8182 (mtp) REVERT: B 409 GLU cc_start: 0.7687 (tt0) cc_final: 0.7415 (tt0) REVERT: B 551 ASN cc_start: 0.6871 (m-40) cc_final: 0.6650 (m-40) REVERT: B 572 ASP cc_start: 0.6943 (t0) cc_final: 0.6733 (t0) REVERT: B 594 MET cc_start: 0.7131 (ttp) cc_final: 0.6534 (tmt) REVERT: B 597 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6262 (tm-30) REVERT: C 399 MET cc_start: 0.8349 (ttm) cc_final: 0.8061 (ttp) REVERT: C 403 MET cc_start: 0.8509 (mtp) cc_final: 0.8203 (mtp) REVERT: C 409 GLU cc_start: 0.7688 (tt0) cc_final: 0.7415 (tt0) REVERT: C 551 ASN cc_start: 0.6855 (m-40) cc_final: 0.6642 (m-40) REVERT: C 572 ASP cc_start: 0.6926 (t0) cc_final: 0.6697 (t0) REVERT: C 594 MET cc_start: 0.7131 (ttp) cc_final: 0.6542 (tmt) REVERT: C 597 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6227 (tm-30) REVERT: D 399 MET cc_start: 0.8350 (ttm) cc_final: 0.8066 (ttp) REVERT: D 403 MET cc_start: 0.8507 (mtp) cc_final: 0.8202 (mtp) REVERT: D 409 GLU cc_start: 0.7693 (tt0) cc_final: 0.7419 (tt0) REVERT: D 551 ASN cc_start: 0.6849 (m-40) cc_final: 0.6634 (m-40) REVERT: D 572 ASP cc_start: 0.6930 (t0) cc_final: 0.6700 (t0) REVERT: D 594 MET cc_start: 0.7134 (ttp) cc_final: 0.6550 (tmt) REVERT: D 597 GLU cc_start: 0.6532 (tm-30) cc_final: 0.6230 (tm-30) outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.6922 time to fit residues: 174.5765 Evaluate side-chains 173 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 470 HIS A 534 GLN A 559 ASN B 226 GLN B 470 HIS B 534 GLN B 559 ASN C 226 GLN C 470 HIS C 534 GLN C 559 ASN D 226 GLN D 470 HIS D 534 GLN D 559 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107666 restraints weight = 17825.421| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.11 r_work: 0.3115 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15812 Z= 0.105 Angle : 0.463 8.280 21328 Z= 0.244 Chirality : 0.039 0.144 2368 Planarity : 0.003 0.031 2552 Dihedral : 13.179 82.604 2920 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.17 % Allowed : 7.57 % Favored : 91.26 % 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: 0.93 (0.19), residues: 1792 helix: 1.35 (0.15), residues: 1184 sheet: -2.44 (0.97), residues: 20 loop : -0.71 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 514 TYR 0.012 0.001 TYR A 349 PHE 0.009 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00232 (15812) covalent geometry : angle 0.46348 (21328) hydrogen bonds : bond 0.03353 ( 952) hydrogen bonds : angle 3.67475 ( 2736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.497 Fit side-chains REVERT: A 198 GLU cc_start: 0.7504 (pm20) cc_final: 0.7202 (mm-30) REVERT: A 205 TYR cc_start: 0.6875 (m-80) cc_final: 0.6436 (t80) REVERT: A 399 MET cc_start: 0.8695 (ttm) cc_final: 0.8438 (ttp) REVERT: A 409 GLU cc_start: 0.8505 (tt0) cc_final: 0.8159 (tt0) REVERT: A 428 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7619 (mptp) REVERT: A 551 ASN cc_start: 0.7081 (m-40) cc_final: 0.6498 (m110) REVERT: A 572 ASP cc_start: 0.7364 (t0) cc_final: 0.7150 (t0) REVERT: A 597 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6581 (tm-30) REVERT: A 600 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6509 (ptmm) REVERT: B 198 GLU cc_start: 0.7502 (pm20) cc_final: 0.7202 (mm-30) REVERT: B 205 TYR cc_start: 0.6895 (m-80) cc_final: 0.6449 (t80) REVERT: B 399 MET cc_start: 0.8707 (ttm) cc_final: 0.8449 (ttp) REVERT: B 409 GLU cc_start: 0.8514 (tt0) cc_final: 0.8157 (tt0) REVERT: B 428 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7619 (mptp) REVERT: B 551 ASN cc_start: 0.7077 (m-40) cc_final: 0.6564 (m110) REVERT: B 572 ASP cc_start: 0.7372 (t0) cc_final: 0.7158 (t0) REVERT: B 597 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6553 (tm-30) REVERT: B 600 LYS cc_start: 0.7124 (ttpt) cc_final: 0.6500 (ptmm) REVERT: C 198 GLU cc_start: 0.7501 (pm20) cc_final: 0.7206 (mm-30) REVERT: C 205 TYR cc_start: 0.6907 (m-80) cc_final: 0.6463 (t80) REVERT: C 226 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7491 (mp-120) REVERT: C 399 MET cc_start: 0.8710 (ttm) cc_final: 0.8451 (ttp) REVERT: C 409 GLU cc_start: 0.8519 (tt0) cc_final: 0.8157 (tt0) REVERT: C 428 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7615 (mptp) REVERT: C 551 ASN cc_start: 0.7058 (m-40) cc_final: 0.6596 (m110) REVERT: C 597 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 600 LYS cc_start: 0.7104 (ttpt) cc_final: 0.6539 (ptmm) REVERT: D 198 GLU cc_start: 0.7497 (pm20) cc_final: 0.7203 (mm-30) REVERT: D 205 TYR cc_start: 0.6896 (m-80) cc_final: 0.6455 (t80) REVERT: D 399 MET cc_start: 0.8706 (ttm) cc_final: 0.8448 (ttp) REVERT: D 409 GLU cc_start: 0.8508 (tt0) cc_final: 0.8147 (tt0) REVERT: D 428 LYS cc_start: 0.8067 (mmmm) cc_final: 0.7645 (mptp) REVERT: D 551 ASN cc_start: 0.7056 (m-40) cc_final: 0.6587 (m110) REVERT: D 572 ASP cc_start: 0.7368 (t0) cc_final: 0.7136 (t0) REVERT: D 597 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6561 (tm-30) REVERT: D 600 LYS cc_start: 0.7100 (ttpt) cc_final: 0.6539 (ptmm) outliers start: 19 outliers final: 0 residues processed: 227 average time/residue: 0.6412 time to fit residues: 158.8590 Evaluate side-chains 172 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 170 optimal weight: 0.2980 chunk 135 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 498 GLN B 226 GLN B 286 GLN B 498 GLN C 226 GLN C 286 GLN C 498 GLN D 226 GLN D 286 GLN D 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106567 restraints weight = 18031.582| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.14 r_work: 0.3065 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15812 Z= 0.134 Angle : 0.475 6.115 21328 Z= 0.254 Chirality : 0.040 0.144 2368 Planarity : 0.003 0.030 2552 Dihedral : 11.962 81.083 2920 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 8.56 % Favored : 89.96 % 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: 1.34 (0.20), residues: 1792 helix: 1.65 (0.15), residues: 1208 sheet: -2.18 (1.01), residues: 20 loop : -0.61 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.020 0.002 TYR B 349 PHE 0.013 0.002 PHE D 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00307 (15812) covalent geometry : angle 0.47501 (21328) hydrogen bonds : bond 0.03669 ( 952) hydrogen bonds : angle 3.71117 ( 2736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.611 Fit side-chains REVERT: A 205 TYR cc_start: 0.7016 (m-80) cc_final: 0.6422 (t80) REVERT: A 226 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7538 (mp-120) REVERT: A 399 MET cc_start: 0.8773 (ttm) cc_final: 0.8508 (ttp) REVERT: A 409 GLU cc_start: 0.8625 (tt0) cc_final: 0.8274 (tt0) REVERT: A 428 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7590 (mptp) REVERT: A 551 ASN cc_start: 0.6987 (m-40) cc_final: 0.6424 (m110) REVERT: A 572 ASP cc_start: 0.7503 (t0) cc_final: 0.7260 (t0) REVERT: A 597 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6707 (tp30) REVERT: A 600 LYS cc_start: 0.7131 (ttpt) cc_final: 0.6574 (ptmm) REVERT: B 205 TYR cc_start: 0.7019 (m-80) cc_final: 0.6422 (t80) REVERT: B 226 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7535 (mp-120) REVERT: B 399 MET cc_start: 0.8787 (ttm) cc_final: 0.8523 (ttp) REVERT: B 409 GLU cc_start: 0.8621 (tt0) cc_final: 0.8269 (tt0) REVERT: B 428 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7617 (mptp) REVERT: B 551 ASN cc_start: 0.7099 (m-40) cc_final: 0.6581 (m110) REVERT: B 572 ASP cc_start: 0.7523 (t0) cc_final: 0.7262 (t0) REVERT: B 597 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6630 (tm-30) REVERT: B 600 LYS cc_start: 0.7130 (ttpt) cc_final: 0.6579 (ptmm) REVERT: C 205 TYR cc_start: 0.7001 (m-80) cc_final: 0.6450 (t80) REVERT: C 399 MET cc_start: 0.8777 (ttm) cc_final: 0.8512 (ttp) REVERT: C 409 GLU cc_start: 0.8618 (tt0) cc_final: 0.8261 (tt0) REVERT: C 428 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7614 (mptp) REVERT: C 551 ASN cc_start: 0.7068 (m-40) cc_final: 0.6565 (m110) REVERT: C 572 ASP cc_start: 0.7557 (t0) cc_final: 0.7342 (t0) REVERT: C 597 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6655 (tp30) REVERT: C 600 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6603 (ptmm) REVERT: D 205 TYR cc_start: 0.7001 (m-80) cc_final: 0.6446 (t80) REVERT: D 226 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7517 (mp-120) REVERT: D 399 MET cc_start: 0.8773 (ttm) cc_final: 0.8506 (ttp) REVERT: D 409 GLU cc_start: 0.8617 (tt0) cc_final: 0.8259 (tt0) REVERT: D 428 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7616 (mptp) REVERT: D 551 ASN cc_start: 0.7058 (m-40) cc_final: 0.6558 (m110) REVERT: D 572 ASP cc_start: 0.7453 (t0) cc_final: 0.7186 (t0) REVERT: D 597 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6655 (tp30) REVERT: D 600 LYS cc_start: 0.7050 (ttpt) cc_final: 0.6601 (ptmm) outliers start: 24 outliers final: 0 residues processed: 199 average time/residue: 0.7593 time to fit residues: 163.4950 Evaluate side-chains 173 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain D residue 226 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105639 restraints weight = 17820.182| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.09 r_work: 0.3090 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15812 Z= 0.123 Angle : 0.460 5.252 21328 Z= 0.246 Chirality : 0.040 0.147 2368 Planarity : 0.003 0.030 2552 Dihedral : 11.490 78.273 2920 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.17 % Allowed : 10.41 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.20), residues: 1792 helix: 1.86 (0.15), residues: 1208 sheet: -1.95 (1.03), residues: 20 loop : -0.49 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.017 0.001 TYR C 349 PHE 0.013 0.001 PHE D 298 TRP 0.017 0.002 TRP D 168 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00279 (15812) covalent geometry : angle 0.46014 (21328) hydrogen bonds : bond 0.03454 ( 952) hydrogen bonds : angle 3.63984 ( 2736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.550 Fit side-chains REVERT: A 205 TYR cc_start: 0.6889 (m-10) cc_final: 0.6439 (t80) REVERT: A 399 MET cc_start: 0.8715 (ttm) cc_final: 0.8478 (ttp) REVERT: A 409 GLU cc_start: 0.8604 (tt0) cc_final: 0.8261 (tt0) REVERT: A 428 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7550 (mptp) REVERT: A 431 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: A 551 ASN cc_start: 0.7094 (m-40) cc_final: 0.6509 (m110) REVERT: A 572 ASP cc_start: 0.7479 (t0) cc_final: 0.7187 (t0) REVERT: A 597 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6686 (tp30) REVERT: A 600 LYS cc_start: 0.7201 (ttpt) cc_final: 0.6642 (ptmm) REVERT: B 205 TYR cc_start: 0.6886 (m-10) cc_final: 0.6436 (t80) REVERT: B 399 MET cc_start: 0.8721 (ttm) cc_final: 0.8486 (ttp) REVERT: B 409 GLU cc_start: 0.8603 (tt0) cc_final: 0.8261 (tt0) REVERT: B 428 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7559 (mptp) REVERT: B 551 ASN cc_start: 0.7111 (m-40) cc_final: 0.6582 (m110) REVERT: B 572 ASP cc_start: 0.7467 (t0) cc_final: 0.7179 (t0) REVERT: B 597 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6682 (tp30) REVERT: B 600 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6634 (ptmm) REVERT: C 205 TYR cc_start: 0.6860 (m-10) cc_final: 0.6417 (t80) REVERT: C 399 MET cc_start: 0.8726 (ttm) cc_final: 0.8491 (ttp) REVERT: C 409 GLU cc_start: 0.8596 (tt0) cc_final: 0.8252 (tt0) REVERT: C 428 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7552 (mptp) REVERT: C 572 ASP cc_start: 0.7506 (t0) cc_final: 0.7190 (t0) REVERT: C 597 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6687 (tp30) REVERT: C 600 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6656 (ptmm) REVERT: D 205 TYR cc_start: 0.6855 (m-10) cc_final: 0.6417 (t80) REVERT: D 399 MET cc_start: 0.8726 (ttm) cc_final: 0.8491 (ttp) REVERT: D 409 GLU cc_start: 0.8605 (tt0) cc_final: 0.8257 (tt0) REVERT: D 428 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7551 (mptp) REVERT: D 431 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: D 572 ASP cc_start: 0.7441 (t0) cc_final: 0.7160 (t0) REVERT: D 597 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6687 (tp30) REVERT: D 600 LYS cc_start: 0.7137 (ttpt) cc_final: 0.6655 (ptmm) outliers start: 19 outliers final: 5 residues processed: 193 average time/residue: 0.7376 time to fit residues: 154.2429 Evaluate side-chains 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 431 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 0.0370 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.0370 chunk 56 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109274 restraints weight = 18233.490| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.13 r_work: 0.3138 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15812 Z= 0.090 Angle : 0.424 6.254 21328 Z= 0.225 Chirality : 0.038 0.142 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.313 73.237 2920 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.79 % Allowed : 11.08 % Favored : 87.13 % 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: 1.81 (0.20), residues: 1792 helix: 2.04 (0.15), residues: 1216 sheet: -1.69 (1.01), residues: 20 loop : -0.55 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 514 TYR 0.010 0.001 TYR C 349 PHE 0.012 0.001 PHE B 298 TRP 0.016 0.001 TRP D 168 HIS 0.001 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00198 (15812) covalent geometry : angle 0.42383 (21328) hydrogen bonds : bond 0.02964 ( 952) hydrogen bonds : angle 3.37814 ( 2736) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.378 Fit side-chains REVERT: A 174 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8368 (mp) REVERT: A 199 TYR cc_start: 0.8315 (m-80) cc_final: 0.7731 (m-80) REVERT: A 226 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7551 (mp-120) REVERT: A 399 MET cc_start: 0.8620 (ttm) cc_final: 0.8334 (ttp) REVERT: A 409 GLU cc_start: 0.8549 (tt0) cc_final: 0.8204 (tt0) REVERT: A 428 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7519 (mptp) REVERT: A 431 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: A 551 ASN cc_start: 0.7124 (m-40) cc_final: 0.6544 (m110) REVERT: A 572 ASP cc_start: 0.7446 (t0) cc_final: 0.7189 (t0) REVERT: A 597 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6628 (tp30) REVERT: A 600 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6717 (ptmt) REVERT: B 174 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8376 (mp) REVERT: B 199 TYR cc_start: 0.8318 (m-80) cc_final: 0.7727 (m-80) REVERT: B 226 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7546 (mp-120) REVERT: B 399 MET cc_start: 0.8614 (ttm) cc_final: 0.8327 (ttp) REVERT: B 409 GLU cc_start: 0.8538 (tt0) cc_final: 0.8193 (tt0) REVERT: B 428 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7459 (mptp) REVERT: B 431 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 572 ASP cc_start: 0.7451 (t0) cc_final: 0.7182 (t0) REVERT: B 597 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6629 (tp30) REVERT: B 600 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6707 (ptmt) REVERT: C 174 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 199 TYR cc_start: 0.8321 (m-80) cc_final: 0.7726 (m-80) REVERT: C 399 MET cc_start: 0.8625 (ttm) cc_final: 0.8339 (ttp) REVERT: C 409 GLU cc_start: 0.8541 (tt0) cc_final: 0.8195 (tt0) REVERT: C 428 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7464 (mptp) REVERT: C 431 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: C 490 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: C 572 ASP cc_start: 0.7464 (t0) cc_final: 0.7224 (t0) REVERT: C 597 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6629 (tp30) REVERT: C 600 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6741 (ptmt) REVERT: D 174 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8414 (mp) REVERT: D 199 TYR cc_start: 0.8317 (m-80) cc_final: 0.7724 (m-80) REVERT: D 226 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7534 (mp-120) REVERT: D 399 MET cc_start: 0.8628 (ttm) cc_final: 0.8343 (ttp) REVERT: D 409 GLU cc_start: 0.8551 (tt0) cc_final: 0.8203 (tt0) REVERT: D 428 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7501 (mptp) REVERT: D 431 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: D 490 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: D 572 ASP cc_start: 0.7413 (t0) cc_final: 0.7176 (t0) REVERT: D 597 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6633 (tp30) REVERT: D 600 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6740 (ptmt) outliers start: 29 outliers final: 5 residues processed: 211 average time/residue: 0.7146 time to fit residues: 163.4082 Evaluate side-chains 176 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 0.0570 chunk 133 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 8 optimal weight: 0.0170 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 498 GLN A 534 GLN B 226 GLN B 286 GLN B 498 GLN B 534 GLN C 226 GLN C 286 GLN C 498 GLN C 534 GLN D 226 GLN D 286 GLN D 498 GLN D 534 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110053 restraints weight = 17840.082| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.06 r_work: 0.3145 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15812 Z= 0.090 Angle : 0.421 6.874 21328 Z= 0.223 Chirality : 0.038 0.144 2368 Planarity : 0.003 0.029 2552 Dihedral : 9.980 73.358 2920 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.29 % Allowed : 12.07 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.94 (0.20), residues: 1792 helix: 2.11 (0.15), residues: 1212 sheet: -1.78 (0.71), residues: 40 loop : -0.33 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 514 TYR 0.012 0.001 TYR A 349 PHE 0.012 0.001 PHE A 298 TRP 0.016 0.001 TRP B 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00196 (15812) covalent geometry : angle 0.42089 (21328) hydrogen bonds : bond 0.02961 ( 952) hydrogen bonds : angle 3.35624 ( 2736) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.527 Fit side-chains REVERT: A 174 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 199 TYR cc_start: 0.8274 (m-80) cc_final: 0.7664 (m-80) REVERT: A 226 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7421 (mp-120) REVERT: A 399 MET cc_start: 0.8596 (ttm) cc_final: 0.8308 (ttp) REVERT: A 409 GLU cc_start: 0.8520 (tt0) cc_final: 0.8184 (tt0) REVERT: A 428 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7475 (mptp) REVERT: A 431 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: A 551 ASN cc_start: 0.7008 (m-40) cc_final: 0.6418 (m110) REVERT: A 597 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6636 (tp30) REVERT: A 600 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6809 (ptmt) REVERT: B 174 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8333 (mp) REVERT: B 199 TYR cc_start: 0.8272 (m-80) cc_final: 0.7654 (m-80) REVERT: B 226 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7434 (mp-120) REVERT: B 399 MET cc_start: 0.8602 (ttm) cc_final: 0.8316 (ttp) REVERT: B 409 GLU cc_start: 0.8513 (tt0) cc_final: 0.8177 (tt0) REVERT: B 428 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7547 (mptp) REVERT: B 431 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: B 572 ASP cc_start: 0.7428 (t0) cc_final: 0.7226 (t0) REVERT: B 597 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6657 (tp30) REVERT: B 600 LYS cc_start: 0.7219 (ttpt) cc_final: 0.6799 (ptmt) REVERT: C 174 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 198 GLU cc_start: 0.7328 (pm20) cc_final: 0.7053 (mm-30) REVERT: C 199 TYR cc_start: 0.8274 (m-80) cc_final: 0.7651 (m-80) REVERT: C 226 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7545 (mp-120) REVERT: C 399 MET cc_start: 0.8605 (ttm) cc_final: 0.8317 (ttp) REVERT: C 409 GLU cc_start: 0.8499 (tt0) cc_final: 0.8165 (tt0) REVERT: C 428 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7538 (mptp) REVERT: C 431 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: C 572 ASP cc_start: 0.7450 (t0) cc_final: 0.7197 (t0) REVERT: C 597 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6658 (tp30) REVERT: C 600 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6820 (ptmt) REVERT: D 174 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8341 (mp) REVERT: D 199 TYR cc_start: 0.8275 (m-80) cc_final: 0.7658 (m-80) REVERT: D 226 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7405 (mp-120) REVERT: D 399 MET cc_start: 0.8602 (ttm) cc_final: 0.8312 (ttp) REVERT: D 409 GLU cc_start: 0.8517 (tt0) cc_final: 0.8179 (tt0) REVERT: D 428 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7484 (mptp) REVERT: D 431 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: D 572 ASP cc_start: 0.7398 (t0) cc_final: 0.7165 (t0) REVERT: D 597 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6654 (tp30) REVERT: D 600 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6811 (ptmt) outliers start: 21 outliers final: 9 residues processed: 189 average time/residue: 0.6537 time to fit residues: 135.7399 Evaluate side-chains 186 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN B 534 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108696 restraints weight = 17809.462| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.08 r_work: 0.3130 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15812 Z= 0.099 Angle : 0.432 7.167 21328 Z= 0.229 Chirality : 0.039 0.144 2368 Planarity : 0.003 0.029 2552 Dihedral : 9.878 73.585 2920 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.54 % Allowed : 11.95 % Favored : 86.51 % 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: 2.00 (0.20), residues: 1792 helix: 2.13 (0.15), residues: 1212 sheet: -1.42 (0.79), residues: 40 loop : -0.27 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.014 0.001 TYR A 349 PHE 0.012 0.001 PHE A 298 TRP 0.016 0.001 TRP D 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00221 (15812) covalent geometry : angle 0.43235 (21328) hydrogen bonds : bond 0.03092 ( 952) hydrogen bonds : angle 3.38891 ( 2736) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.484 Fit side-chains REVERT: A 174 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 198 GLU cc_start: 0.7354 (pm20) cc_final: 0.7061 (mm-30) REVERT: A 199 TYR cc_start: 0.8284 (m-80) cc_final: 0.7716 (m-80) REVERT: A 226 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7512 (mp-120) REVERT: A 399 MET cc_start: 0.8637 (ttm) cc_final: 0.8353 (ttp) REVERT: A 409 GLU cc_start: 0.8532 (tt0) cc_final: 0.8202 (tt0) REVERT: A 428 LYS cc_start: 0.8021 (mmmm) cc_final: 0.7475 (mptp) REVERT: A 431 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: A 551 ASN cc_start: 0.7080 (m-40) cc_final: 0.6491 (m110) REVERT: A 594 MET cc_start: 0.7641 (ttp) cc_final: 0.7101 (tmt) REVERT: A 597 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6640 (tp30) REVERT: A 600 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6803 (ptmt) REVERT: B 174 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 198 GLU cc_start: 0.7361 (pm20) cc_final: 0.7057 (mm-30) REVERT: B 199 TYR cc_start: 0.8276 (m-80) cc_final: 0.7707 (m-80) REVERT: B 226 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7505 (mp-120) REVERT: B 232 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6900 (mm-30) REVERT: B 399 MET cc_start: 0.8644 (ttm) cc_final: 0.8363 (ttp) REVERT: B 409 GLU cc_start: 0.8521 (tt0) cc_final: 0.8191 (tt0) REVERT: B 428 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7539 (mptp) REVERT: B 431 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: B 572 ASP cc_start: 0.7462 (t0) cc_final: 0.7179 (t0) REVERT: B 594 MET cc_start: 0.7605 (ttp) cc_final: 0.7335 (tmt) REVERT: B 597 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6759 (tp30) REVERT: B 600 LYS cc_start: 0.7214 (ttpt) cc_final: 0.6927 (mtpt) REVERT: C 174 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 198 GLU cc_start: 0.7343 (pm20) cc_final: 0.7054 (mm-30) REVERT: C 199 TYR cc_start: 0.8286 (m-80) cc_final: 0.7712 (m-80) REVERT: C 226 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7231 (mp-120) REVERT: C 399 MET cc_start: 0.8645 (ttm) cc_final: 0.8360 (ttp) REVERT: C 409 GLU cc_start: 0.8522 (tt0) cc_final: 0.8192 (tt0) REVERT: C 428 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7537 (mptp) REVERT: C 431 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: C 572 ASP cc_start: 0.7478 (t0) cc_final: 0.7194 (t0) REVERT: C 594 MET cc_start: 0.7618 (ttp) cc_final: 0.7374 (tmt) REVERT: C 597 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6652 (tp30) REVERT: C 600 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6814 (ptmt) REVERT: D 174 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8323 (mp) REVERT: D 198 GLU cc_start: 0.7346 (pm20) cc_final: 0.7061 (mm-30) REVERT: D 199 TYR cc_start: 0.8281 (m-80) cc_final: 0.7707 (m-80) REVERT: D 226 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7493 (mp-120) REVERT: D 399 MET cc_start: 0.8641 (ttm) cc_final: 0.8359 (ttp) REVERT: D 409 GLU cc_start: 0.8530 (tt0) cc_final: 0.8196 (tt0) REVERT: D 428 LYS cc_start: 0.8035 (mmmm) cc_final: 0.7482 (mptp) REVERT: D 431 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: D 572 ASP cc_start: 0.7444 (t0) cc_final: 0.7166 (t0) REVERT: D 594 MET cc_start: 0.7570 (ttp) cc_final: 0.7324 (tmt) REVERT: D 597 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6631 (tp30) REVERT: D 600 LYS cc_start: 0.7173 (ttpt) cc_final: 0.6811 (ptmt) outliers start: 25 outliers final: 8 residues processed: 190 average time/residue: 0.6862 time to fit residues: 142.1929 Evaluate side-chains 187 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107159 restraints weight = 17830.966| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.09 r_work: 0.3109 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15812 Z= 0.113 Angle : 0.448 7.697 21328 Z= 0.237 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.028 2552 Dihedral : 9.951 74.017 2920 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.97 % Allowed : 11.58 % Favored : 86.45 % 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: 2.26 (0.20), residues: 1792 helix: 2.29 (0.15), residues: 1180 sheet: -1.07 (1.14), residues: 20 loop : 0.02 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.017 0.001 TYR B 349 PHE 0.013 0.001 PHE D 298 TRP 0.016 0.001 TRP D 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00255 (15812) covalent geometry : angle 0.44824 (21328) hydrogen bonds : bond 0.03241 ( 952) hydrogen bonds : angle 3.46547 ( 2736) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.599 Fit side-chains REVERT: A 174 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 198 GLU cc_start: 0.7407 (pm20) cc_final: 0.7060 (mm-30) REVERT: A 226 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7318 (mp-120) REVERT: A 399 MET cc_start: 0.8678 (ttm) cc_final: 0.8401 (ttp) REVERT: A 409 GLU cc_start: 0.8543 (tt0) cc_final: 0.8211 (tt0) REVERT: A 428 LYS cc_start: 0.8026 (mmmm) cc_final: 0.7479 (mptp) REVERT: A 431 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: A 551 ASN cc_start: 0.7088 (m-40) cc_final: 0.6483 (m110) REVERT: A 594 MET cc_start: 0.7615 (ttp) cc_final: 0.7391 (tmt) REVERT: A 597 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6635 (tp30) REVERT: A 600 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6693 (ptmm) REVERT: B 174 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8328 (mp) REVERT: B 198 GLU cc_start: 0.7395 (pm20) cc_final: 0.7055 (mm-30) REVERT: B 226 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7308 (mp-120) REVERT: B 399 MET cc_start: 0.8684 (ttm) cc_final: 0.8406 (ttp) REVERT: B 409 GLU cc_start: 0.8526 (tt0) cc_final: 0.8195 (tt0) REVERT: B 428 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7521 (mptp) REVERT: B 431 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: B 572 ASP cc_start: 0.7494 (t0) cc_final: 0.7199 (t0) REVERT: B 594 MET cc_start: 0.7612 (ttp) cc_final: 0.7396 (tmt) REVERT: B 597 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6593 (tp30) REVERT: B 600 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6637 (ptmm) REVERT: C 174 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8325 (mp) REVERT: C 198 GLU cc_start: 0.7378 (pm20) cc_final: 0.7059 (mm-30) REVERT: C 399 MET cc_start: 0.8681 (ttm) cc_final: 0.8403 (ttp) REVERT: C 409 GLU cc_start: 0.8537 (tt0) cc_final: 0.8205 (tt0) REVERT: C 428 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7542 (mptp) REVERT: C 431 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: C 572 ASP cc_start: 0.7470 (t0) cc_final: 0.7154 (t0) REVERT: C 594 MET cc_start: 0.7635 (ttp) cc_final: 0.7393 (tmt) REVERT: C 597 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6634 (tp30) REVERT: C 600 LYS cc_start: 0.7183 (ttpt) cc_final: 0.6792 (ptmt) REVERT: D 174 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8325 (mp) REVERT: D 198 GLU cc_start: 0.7389 (pm20) cc_final: 0.7059 (mm-30) REVERT: D 226 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7299 (mp-120) REVERT: D 399 MET cc_start: 0.8684 (ttm) cc_final: 0.8406 (ttp) REVERT: D 409 GLU cc_start: 0.8546 (tt0) cc_final: 0.8210 (tt0) REVERT: D 428 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7471 (mptp) REVERT: D 431 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: D 572 ASP cc_start: 0.7458 (t0) cc_final: 0.7154 (t0) REVERT: D 594 MET cc_start: 0.7589 (ttp) cc_final: 0.7345 (tmt) REVERT: D 597 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6627 (tp30) REVERT: D 600 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6827 (ptmt) outliers start: 32 outliers final: 14 residues processed: 190 average time/residue: 0.6773 time to fit residues: 140.3353 Evaluate side-chains 188 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 586 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 0.0570 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106481 restraints weight = 17739.494| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.13 r_work: 0.3080 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15812 Z= 0.114 Angle : 0.456 8.361 21328 Z= 0.240 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.028 2552 Dihedral : 9.960 73.892 2920 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.97 % Allowed : 11.64 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1792 helix: 2.25 (0.15), residues: 1180 sheet: -1.12 (1.13), residues: 20 loop : 0.00 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.017 0.001 TYR D 349 PHE 0.013 0.001 PHE B 298 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00258 (15812) covalent geometry : angle 0.45587 (21328) hydrogen bonds : bond 0.03274 ( 952) hydrogen bonds : angle 3.49658 ( 2736) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.640 Fit side-chains REVERT: A 174 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 198 GLU cc_start: 0.7448 (pm20) cc_final: 0.7055 (mm-30) REVERT: A 226 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7442 (mp-120) REVERT: A 399 MET cc_start: 0.8699 (ttm) cc_final: 0.8412 (ttp) REVERT: A 409 GLU cc_start: 0.8578 (tt0) cc_final: 0.8241 (tt0) REVERT: A 428 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7485 (mptp) REVERT: A 431 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: A 490 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: A 551 ASN cc_start: 0.7109 (m-40) cc_final: 0.6488 (m110) REVERT: A 594 MET cc_start: 0.7662 (ttp) cc_final: 0.7371 (tmt) REVERT: A 597 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6771 (tp30) REVERT: A 600 LYS cc_start: 0.7152 (ttpt) cc_final: 0.6895 (mtpt) REVERT: B 174 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 198 GLU cc_start: 0.7427 (pm20) cc_final: 0.7051 (mm-30) REVERT: B 226 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7497 (mp-120) REVERT: B 232 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6830 (mm-30) REVERT: B 399 MET cc_start: 0.8704 (ttm) cc_final: 0.8426 (ttp) REVERT: B 409 GLU cc_start: 0.8564 (tt0) cc_final: 0.8228 (tt0) REVERT: B 428 LYS cc_start: 0.8005 (mmmm) cc_final: 0.7526 (mptp) REVERT: B 431 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: B 572 ASP cc_start: 0.7535 (t0) cc_final: 0.7225 (t0) REVERT: B 594 MET cc_start: 0.7650 (ttp) cc_final: 0.7347 (tmt) REVERT: B 597 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6773 (tp30) REVERT: B 600 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6931 (mtpt) REVERT: C 174 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 198 GLU cc_start: 0.7412 (pm20) cc_final: 0.7050 (mm-30) REVERT: C 226 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7423 (mp-120) REVERT: C 232 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6885 (mm-30) REVERT: C 399 MET cc_start: 0.8706 (ttm) cc_final: 0.8420 (ttp) REVERT: C 409 GLU cc_start: 0.8582 (tt0) cc_final: 0.8244 (tt0) REVERT: C 428 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7543 (mptp) REVERT: C 431 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: C 572 ASP cc_start: 0.7493 (t0) cc_final: 0.7196 (t0) REVERT: C 594 MET cc_start: 0.7640 (ttp) cc_final: 0.7341 (tmt) REVERT: C 597 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6786 (tp30) REVERT: C 600 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6959 (mtpt) REVERT: D 174 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8357 (mp) REVERT: D 198 GLU cc_start: 0.7422 (pm20) cc_final: 0.7053 (mm-30) REVERT: D 226 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7441 (mp-120) REVERT: D 399 MET cc_start: 0.8706 (ttm) cc_final: 0.8419 (ttp) REVERT: D 409 GLU cc_start: 0.8568 (tt0) cc_final: 0.8228 (tt0) REVERT: D 428 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7504 (mptp) REVERT: D 431 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: D 572 ASP cc_start: 0.7505 (t0) cc_final: 0.7212 (t0) REVERT: D 594 MET cc_start: 0.7585 (ttp) cc_final: 0.7286 (tmt) REVERT: D 597 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6781 (tp30) REVERT: D 600 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6943 (mtpt) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 0.6913 time to fit residues: 142.2751 Evaluate side-chains 191 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 586 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107442 restraints weight = 17819.406| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.08 r_work: 0.3098 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15812 Z= 0.108 Angle : 0.455 9.312 21328 Z= 0.239 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.029 2552 Dihedral : 9.854 73.372 2920 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.16 % Allowed : 11.27 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.26 (0.20), residues: 1792 helix: 2.27 (0.15), residues: 1180 sheet: -1.10 (1.13), residues: 20 loop : 0.04 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.016 0.001 TYR C 349 PHE 0.013 0.001 PHE C 298 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00243 (15812) covalent geometry : angle 0.45504 (21328) hydrogen bonds : bond 0.03242 ( 952) hydrogen bonds : angle 3.47978 ( 2736) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.655 Fit side-chains REVERT: A 174 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 198 GLU cc_start: 0.7409 (pm20) cc_final: 0.7052 (mm-30) REVERT: A 226 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7186 (mp-120) REVERT: A 399 MET cc_start: 0.8670 (ttm) cc_final: 0.8387 (ttp) REVERT: A 409 GLU cc_start: 0.8538 (tt0) cc_final: 0.8199 (tt0) REVERT: A 428 LYS cc_start: 0.8026 (mmmm) cc_final: 0.7470 (mptp) REVERT: A 431 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: A 490 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: A 551 ASN cc_start: 0.7090 (m-40) cc_final: 0.6466 (m110) REVERT: A 594 MET cc_start: 0.7624 (ttp) cc_final: 0.7326 (tmt) REVERT: A 597 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6776 (tp30) REVERT: A 600 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6933 (mtpt) REVERT: B 174 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 198 GLU cc_start: 0.7389 (pm20) cc_final: 0.7045 (mm-30) REVERT: B 226 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7191 (mp-120) REVERT: B 232 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6807 (mm-30) REVERT: B 399 MET cc_start: 0.8684 (ttm) cc_final: 0.8394 (ttp) REVERT: B 409 GLU cc_start: 0.8528 (tt0) cc_final: 0.8185 (tt0) REVERT: B 428 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7515 (mptp) REVERT: B 431 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: B 572 ASP cc_start: 0.7511 (t0) cc_final: 0.7155 (t0) REVERT: B 594 MET cc_start: 0.7620 (ttp) cc_final: 0.7311 (tmt) REVERT: B 597 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6767 (tp30) REVERT: B 600 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6895 (mtpt) REVERT: C 174 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8342 (mp) REVERT: C 198 GLU cc_start: 0.7384 (pm20) cc_final: 0.7052 (mm-30) REVERT: C 226 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7332 (mp-120) REVERT: C 232 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6834 (mm-30) REVERT: C 399 MET cc_start: 0.8671 (ttm) cc_final: 0.8388 (ttp) REVERT: C 409 GLU cc_start: 0.8542 (tt0) cc_final: 0.8201 (tt0) REVERT: C 428 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7543 (mptp) REVERT: C 431 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: C 572 ASP cc_start: 0.7457 (t0) cc_final: 0.7132 (t0) REVERT: C 594 MET cc_start: 0.7614 (ttp) cc_final: 0.7289 (tmt) REVERT: C 597 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6767 (tp30) REVERT: D 174 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8345 (mp) REVERT: D 198 GLU cc_start: 0.7389 (pm20) cc_final: 0.7043 (mm-30) REVERT: D 226 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7164 (mp-120) REVERT: D 399 MET cc_start: 0.8683 (ttm) cc_final: 0.8398 (ttp) REVERT: D 409 GLU cc_start: 0.8535 (tt0) cc_final: 0.8186 (tt0) REVERT: D 428 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7494 (mptp) REVERT: D 431 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: D 572 ASP cc_start: 0.7469 (t0) cc_final: 0.7155 (t0) REVERT: D 594 MET cc_start: 0.7556 (ttp) cc_final: 0.7229 (tmt) REVERT: D 597 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6767 (tp30) REVERT: D 600 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6952 (mtpt) outliers start: 35 outliers final: 18 residues processed: 190 average time/residue: 0.6709 time to fit residues: 139.3175 Evaluate side-chains 192 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 586 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 329 ASN B 226 GLN B 286 GLN B 329 ASN C 226 GLN C 286 GLN C 329 ASN D 226 GLN D 286 GLN D 329 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104741 restraints weight = 17620.039| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.13 r_work: 0.3067 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15812 Z= 0.145 Angle : 0.494 9.633 21328 Z= 0.259 Chirality : 0.040 0.146 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.371 75.189 2920 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.34 % Allowed : 11.27 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.20), residues: 1792 helix: 2.28 (0.15), residues: 1172 sheet: -1.34 (1.11), residues: 20 loop : 0.20 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.020 0.002 TYR D 349 PHE 0.015 0.002 PHE C 298 TRP 0.016 0.002 TRP A 168 HIS 0.003 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00335 (15812) covalent geometry : angle 0.49435 (21328) hydrogen bonds : bond 0.03568 ( 952) hydrogen bonds : angle 3.63730 ( 2736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5501.41 seconds wall clock time: 94 minutes 38.66 seconds (5678.66 seconds total)