Starting phenix.real_space_refine on Fri Jul 3 23:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lft_23306/07_2026/7lft_23306_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lft_23306/07_2026/7lft_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_23306/07_2026/7lft_23306_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lft_23306/07_2026/7lft_23306_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lft_23306/07_2026/7lft_23306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lft_23306/07_2026/7lft_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15479 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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, 179 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 3 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: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: "D" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 179 Unusual residues: {'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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} Time building chain proxies: 3.74, per 1000 atoms: 0.24 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: 1.62 Conformation dependent library (CDL) restraints added in 791.4 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: 0.45 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: 2.76 Time building geometry restraints manager: 2.10 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 4.140 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: 2.260 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.210 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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/Z covalent geometry : bond 0.00912 / 0.46 (15812) covalent geometry : angle 1.09636 / 0.48 (21328) hydrogen bonds : bond 0.11430 / 7.48 ( 952) hydrogen bonds : angle 4.89472 / 3.48 ( 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 : 0.635 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: 0.8349 (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: 0.8506 (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: 0.7437 time to fit residues: 188.3755 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 : 0.596 ------------------------------------------------------------------------------- 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: 3.9990 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... 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 = 0.3559 r_free = 0.3559 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107339 restraints weight = 17705.176| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.10 r_work: 0.3103 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1673 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= 0.105 Angle : 0.462 8.132 21328 Z= 0.244 Chirality : 0.039 0.143 2368 Planarity : 0.003 0.031 2552 Dihedral : 13.253 82.647 2920 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.77 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: 0.90 (0.19), residues: 1792 helix: 1.33 (0.15), residues: 1184 sheet: -2.48 (0.97), residues: 20 loop : -0.73 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 514 TYR 0.013 0.001 TYR A 349 PHE 0.009 0.001 PHE A 298 TRP 0.018 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (15812) covalent geometry : angle 0.46233 / 0.24 (21328) hydrogen bonds : bond 0.03422 / 2.21 ( 952) hydrogen bonds : angle 3.71463 / 2.67 ( 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 234 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.728 Fit side-chains REVERT: A 198 GLU cc_start: 0.7490 (pm20) cc_final: 0.7187 (mm-30) REVERT: A 205 TYR cc_start: 0.6931 (m-80) cc_final: 0.6472 (t80) REVERT: A 399 MET cc_start: 0.8694 (ttm) cc_final: 0.8426 (ttp) REVERT: A 403 MET cc_start: 0.8849 (mtp) cc_final: 0.8579 (mtp) REVERT: A 409 GLU cc_start: 0.8504 (tt0) cc_final: 0.8142 (tt0) REVERT: A 428 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7610 (mptp) REVERT: A 551 ASN cc_start: 0.7074 (m-40) cc_final: 0.6490 (m110) REVERT: A 572 ASP cc_start: 0.7412 (t0) cc_final: 0.7208 (t0) REVERT: A 597 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6581 (tm-30) REVERT: A 600 LYS cc_start: 0.7106 (ttpt) cc_final: 0.6554 (ptmm) REVERT: B 198 GLU cc_start: 0.7514 (pm20) cc_final: 0.7206 (mm-30) REVERT: B 205 TYR cc_start: 0.6924 (m-80) cc_final: 0.6471 (t80) REVERT: B 399 MET cc_start: 0.8702 (ttm) cc_final: 0.8439 (ttp) REVERT: B 409 GLU cc_start: 0.8514 (tt0) cc_final: 0.8145 (tt0) REVERT: B 428 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7606 (mptp) REVERT: B 551 ASN cc_start: 0.7070 (m-40) cc_final: 0.6480 (m110) REVERT: B 572 ASP cc_start: 0.7427 (t0) cc_final: 0.7221 (t0) REVERT: B 597 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6567 (tm-30) REVERT: B 600 LYS cc_start: 0.7114 (ttpt) cc_final: 0.6502 (ptmm) REVERT: C 198 GLU cc_start: 0.7521 (pm20) cc_final: 0.7216 (mm-30) REVERT: C 205 TYR cc_start: 0.6952 (m-80) cc_final: 0.6468 (t80) REVERT: C 226 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7514 (mp-120) REVERT: C 399 MET cc_start: 0.8706 (ttm) cc_final: 0.8443 (ttp) REVERT: C 409 GLU cc_start: 0.8520 (tt0) cc_final: 0.8162 (tt0) REVERT: C 428 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7607 (mptp) REVERT: C 551 ASN cc_start: 0.7053 (m-40) cc_final: 0.6587 (m110) REVERT: C 572 ASP cc_start: 0.7411 (t0) cc_final: 0.7201 (t0) REVERT: C 597 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6559 (tm-30) REVERT: C 600 LYS cc_start: 0.7061 (ttpt) cc_final: 0.6503 (ptmm) REVERT: D 198 GLU cc_start: 0.7513 (pm20) cc_final: 0.7208 (mm-30) REVERT: D 205 TYR cc_start: 0.6944 (m-80) cc_final: 0.6464 (t80) REVERT: D 399 MET cc_start: 0.8702 (ttm) cc_final: 0.8439 (ttp) REVERT: D 409 GLU cc_start: 0.8504 (tt0) cc_final: 0.8148 (tt0) REVERT: D 428 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7589 (mmtm) REVERT: D 551 ASN cc_start: 0.7066 (m-40) cc_final: 0.6594 (m110) REVERT: D 572 ASP cc_start: 0.7411 (t0) cc_final: 0.7199 (t0) REVERT: D 597 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6558 (tm-30) REVERT: D 600 LYS cc_start: 0.7066 (ttpt) cc_final: 0.6511 (ptmm) outliers start: 19 outliers final: 0 residues processed: 226 average time/residue: 0.6826 time to fit residues: 169.2798 Evaluate side-chains 171 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 2.9990 chunk 170 optimal weight: 0.4980 chunk 135 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 0.0270 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 286 GLN A 498 GLN B 226 GLN B 286 GLN B 498 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 498 GLN D 226 GLN D 286 GLN D 498 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105469 restraints weight = 17825.263| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.12 r_work: 0.3086 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1827 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= 0.124 Angle : 0.466 6.448 21328 Z= 0.248 Chirality : 0.039 0.144 2368 Planarity : 0.003 0.030 2552 Dihedral : 11.910 81.128 2920 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.11 % Allowed : 8.87 % Favored : 90.02 % 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: 1.35 (0.20), residues: 1792 helix: 1.65 (0.15), residues: 1208 sheet: -2.11 (1.01), residues: 20 loop : -0.62 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 514 TYR 0.018 0.001 TYR D 349 PHE 0.013 0.001 PHE C 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15812) covalent geometry : angle 0.46551 / 0.25 (21328) hydrogen bonds : bond 0.03551 / 2.30 ( 952) hydrogen bonds : angle 3.66864 / 2.64 ( 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 204 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.591 Fit side-chains REVERT: A 198 GLU cc_start: 0.7510 (pm20) cc_final: 0.7194 (mm-30) REVERT: A 205 TYR cc_start: 0.6935 (m-80) cc_final: 0.6456 (t80) REVERT: A 226 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7543 (mp-120) REVERT: A 399 MET cc_start: 0.8726 (ttm) cc_final: 0.8464 (ttp) REVERT: A 409 GLU cc_start: 0.8590 (tt0) cc_final: 0.8247 (tt0) REVERT: A 428 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7601 (mptp) REVERT: A 551 ASN cc_start: 0.7025 (m-40) cc_final: 0.6480 (m110) REVERT: A 572 ASP cc_start: 0.7486 (t0) cc_final: 0.7242 (t0) REVERT: A 597 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6719 (tp30) REVERT: A 600 LYS cc_start: 0.7156 (ttpt) cc_final: 0.6602 (ptmm) REVERT: B 198 GLU cc_start: 0.7500 (pm20) cc_final: 0.7189 (mm-30) REVERT: B 205 TYR cc_start: 0.6937 (m-80) cc_final: 0.6455 (t80) REVERT: B 226 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7552 (mp-120) REVERT: B 399 MET cc_start: 0.8732 (ttm) cc_final: 0.8480 (ttp) REVERT: B 409 GLU cc_start: 0.8605 (tt0) cc_final: 0.8260 (tt0) REVERT: B 428 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7594 (mptp) REVERT: B 551 ASN cc_start: 0.7040 (m-40) cc_final: 0.6493 (m110) REVERT: B 572 ASP cc_start: 0.7464 (t0) cc_final: 0.7228 (t0) REVERT: B 597 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6722 (tp30) REVERT: B 600 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6590 (ptmm) REVERT: C 198 GLU cc_start: 0.7501 (pm20) cc_final: 0.7195 (mm-30) REVERT: C 205 TYR cc_start: 0.6949 (m-80) cc_final: 0.6453 (t80) REVERT: C 399 MET cc_start: 0.8728 (ttm) cc_final: 0.8476 (ttp) REVERT: C 409 GLU cc_start: 0.8595 (tt0) cc_final: 0.8249 (tt0) REVERT: C 428 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7607 (mptp) REVERT: C 551 ASN cc_start: 0.7046 (m-40) cc_final: 0.6557 (m110) REVERT: C 572 ASP cc_start: 0.7481 (t0) cc_final: 0.7227 (t0) REVERT: C 597 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6703 (tp30) REVERT: C 600 LYS cc_start: 0.7069 (ttpt) cc_final: 0.6630 (ptmm) REVERT: D 198 GLU cc_start: 0.7503 (pm20) cc_final: 0.7189 (mm-30) REVERT: D 205 TYR cc_start: 0.6943 (m-80) cc_final: 0.6454 (t80) REVERT: D 226 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7544 (mp-120) REVERT: D 399 MET cc_start: 0.8729 (ttm) cc_final: 0.8476 (ttp) REVERT: D 409 GLU cc_start: 0.8591 (tt0) cc_final: 0.8244 (tt0) REVERT: D 428 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7614 (mptp) REVERT: D 551 ASN cc_start: 0.7049 (m-40) cc_final: 0.6559 (m110) REVERT: D 572 ASP cc_start: 0.7407 (t0) cc_final: 0.7156 (t0) REVERT: D 597 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6708 (tp30) REVERT: D 600 LYS cc_start: 0.7066 (ttpt) cc_final: 0.6625 (ptmm) outliers start: 18 outliers final: 0 residues processed: 194 average time/residue: 0.7881 time to fit residues: 165.8875 Evaluate side-chains 175 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 10.0000 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3558 r_free = 0.3558 target = 0.131210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107630 restraints weight = 17699.113| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.08 r_work: 0.3123 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2103 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= 0.103 Angle : 0.438 5.277 21328 Z= 0.233 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.029 2552 Dihedral : 11.196 78.035 2920 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.29 % Allowed : 10.22 % Favored : 88.49 % 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: 1.80 (0.20), residues: 1792 helix: 2.03 (0.15), residues: 1184 sheet: -1.87 (1.03), residues: 20 loop : -0.42 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.014 0.001 TYR D 349 PHE 0.012 0.001 PHE D 298 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (15812) covalent geometry : angle 0.43809 / 0.23 (21328) hydrogen bonds : bond 0.03252 / 2.11 ( 952) hydrogen bonds : angle 3.54312 / 2.55 ( 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 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.657 Fit side-chains REVERT: A 198 GLU cc_start: 0.7439 (pm20) cc_final: 0.7106 (mm-30) REVERT: A 205 TYR cc_start: 0.6713 (m-10) cc_final: 0.6436 (t80) REVERT: A 399 MET cc_start: 0.8646 (ttm) cc_final: 0.8388 (ttp) REVERT: A 409 GLU cc_start: 0.8561 (tt0) cc_final: 0.8220 (tt0) REVERT: A 428 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7547 (mptp) REVERT: A 431 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: A 551 ASN cc_start: 0.7036 (m-40) cc_final: 0.6493 (m110) REVERT: A 572 ASP cc_start: 0.7447 (t0) cc_final: 0.7179 (t0) REVERT: A 597 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6649 (tp30) REVERT: A 600 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6630 (ptmm) REVERT: B 198 GLU cc_start: 0.7432 (pm20) cc_final: 0.7104 (mm-30) REVERT: B 205 TYR cc_start: 0.6726 (m-10) cc_final: 0.6438 (t80) REVERT: B 399 MET cc_start: 0.8656 (ttm) cc_final: 0.8383 (ttp) REVERT: B 409 GLU cc_start: 0.8561 (tt0) cc_final: 0.8213 (tt0) REVERT: B 428 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7542 (mptp) REVERT: B 431 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: B 551 ASN cc_start: 0.7043 (m-40) cc_final: 0.6498 (m110) REVERT: B 572 ASP cc_start: 0.7446 (t0) cc_final: 0.7173 (t0) REVERT: B 597 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6657 (tp30) REVERT: B 600 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6628 (ptmm) REVERT: C 198 GLU cc_start: 0.7417 (pm20) cc_final: 0.7101 (mm-30) REVERT: C 205 TYR cc_start: 0.6736 (m-10) cc_final: 0.6445 (t80) REVERT: C 226 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7260 (mp-120) REVERT: C 399 MET cc_start: 0.8662 (ttm) cc_final: 0.8389 (ttp) REVERT: C 409 GLU cc_start: 0.8561 (tt0) cc_final: 0.8219 (tt0) REVERT: C 428 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7524 (mptp) REVERT: C 431 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: C 572 ASP cc_start: 0.7441 (t0) cc_final: 0.7154 (t0) REVERT: C 597 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6663 (tp30) REVERT: C 600 LYS cc_start: 0.7167 (ttpt) cc_final: 0.6667 (ptmm) REVERT: D 198 GLU cc_start: 0.7439 (pm20) cc_final: 0.7099 (mm-30) REVERT: D 205 TYR cc_start: 0.6744 (m-10) cc_final: 0.6449 (t80) REVERT: D 399 MET cc_start: 0.8671 (ttm) cc_final: 0.8399 (ttp) REVERT: D 409 GLU cc_start: 0.8562 (tt0) cc_final: 0.8212 (tt0) REVERT: D 428 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7538 (mptp) REVERT: D 431 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: D 572 ASP cc_start: 0.7410 (t0) cc_final: 0.7127 (t0) REVERT: D 597 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6666 (tp30) REVERT: D 600 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6642 (ptmm) outliers start: 21 outliers final: 5 residues processed: 202 average time/residue: 0.7675 time to fit residues: 168.7054 Evaluate side-chains 175 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 381 ASP Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 381 ASP 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: 2.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 0.0030 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 0.0050 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 534 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110095 restraints weight = 17753.970| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.08 r_work: 0.3161 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15812 Z= 0.091 Angle : 0.423 6.183 21328 Z= 0.224 Chirality : 0.038 0.142 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.384 74.538 2920 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.54 % Allowed : 12.07 % 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: 1.83 (0.20), residues: 1792 helix: 2.04 (0.15), residues: 1216 sheet: -1.51 (1.04), residues: 20 loop : -0.53 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 514 TYR 0.011 0.001 TYR C 349 PHE 0.012 0.001 PHE D 298 TRP 0.016 0.001 TRP A 168 HIS 0.001 0.001 HIS B 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (15812) covalent geometry : angle 0.42289 / 0.22 (21328) hydrogen bonds : bond 0.02981 / 1.94 ( 952) hydrogen bonds : angle 3.38668 / 2.43 ( 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 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.630 Fit side-chains REVERT: A 174 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 198 GLU cc_start: 0.7276 (pm20) cc_final: 0.6981 (mm-30) REVERT: A 226 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7512 (mp-120) REVERT: A 399 MET cc_start: 0.8605 (ttm) cc_final: 0.8339 (ttp) REVERT: A 409 GLU cc_start: 0.8536 (tt0) cc_final: 0.8192 (tt0) REVERT: A 428 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7518 (mptp) REVERT: A 431 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: A 551 ASN cc_start: 0.7166 (m-40) cc_final: 0.6604 (m110) REVERT: A 572 ASP cc_start: 0.7453 (t0) cc_final: 0.7242 (t0) REVERT: A 597 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6635 (tp30) REVERT: A 600 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6634 (ptmm) REVERT: B 174 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 198 GLU cc_start: 0.7267 (pm20) cc_final: 0.6980 (mm-30) REVERT: B 226 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7510 (mp-120) REVERT: B 399 MET cc_start: 0.8631 (ttm) cc_final: 0.8335 (ttp) REVERT: B 409 GLU cc_start: 0.8508 (tt0) cc_final: 0.8168 (tt0) REVERT: B 428 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7523 (mptp) REVERT: B 431 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: B 551 ASN cc_start: 0.7157 (m-40) cc_final: 0.6590 (m110) REVERT: B 597 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6620 (tp30) REVERT: B 600 LYS cc_start: 0.7183 (ttpt) cc_final: 0.6620 (ptmm) REVERT: C 174 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 198 GLU cc_start: 0.7257 (pm20) cc_final: 0.6969 (mm-30) REVERT: C 399 MET cc_start: 0.8636 (ttm) cc_final: 0.8340 (ttp) REVERT: C 409 GLU cc_start: 0.8516 (tt0) cc_final: 0.8174 (tt0) REVERT: C 428 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7517 (mptp) REVERT: C 431 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 572 ASP cc_start: 0.7436 (t0) cc_final: 0.7229 (t0) REVERT: C 597 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6659 (tp30) REVERT: C 600 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6694 (ptmm) REVERT: D 174 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8343 (mp) REVERT: D 198 GLU cc_start: 0.7275 (pm20) cc_final: 0.6970 (mm-30) REVERT: D 226 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7517 (mp-120) REVERT: D 399 MET cc_start: 0.8632 (ttm) cc_final: 0.8336 (ttp) REVERT: D 409 GLU cc_start: 0.8532 (tt0) cc_final: 0.8184 (tt0) REVERT: D 428 LYS cc_start: 0.8089 (mmmm) cc_final: 0.7532 (mptp) REVERT: D 431 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: D 572 ASP cc_start: 0.7408 (t0) cc_final: 0.7160 (t0) REVERT: D 597 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6668 (tp30) REVERT: D 600 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6689 (ptmm) outliers start: 25 outliers final: 6 residues processed: 205 average time/residue: 0.7380 time to fit residues: 165.0296 Evaluate side-chains 186 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 539 SER 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 111 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 286 GLN A 534 GLN B 226 GLN B 286 GLN B 534 GLN C 226 GLN C 286 GLN C 534 GLN D 226 GLN D 286 GLN D 498 GLN D 534 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105356 restraints weight = 17729.475| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.11 r_work: 0.3087 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2380 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= 0.122 Angle : 0.455 6.466 21328 Z= 0.243 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.546 76.319 2920 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.97 % Allowed : 11.51 % 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: 2.05 (0.20), residues: 1792 helix: 2.15 (0.15), residues: 1208 sheet: -1.53 (1.07), residues: 20 loop : -0.25 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 514 TYR 0.018 0.001 TYR B 349 PHE 0.014 0.001 PHE D 298 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (15812) covalent geometry : angle 0.45519 / 0.24 (21328) hydrogen bonds : bond 0.03374 / 2.19 ( 952) hydrogen bonds : angle 3.54461 / 2.54 ( 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 198 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.655 Fit side-chains REVERT: A 174 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 198 GLU cc_start: 0.7390 (pm20) cc_final: 0.6978 (mm-30) REVERT: A 226 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7529 (mp-120) REVERT: A 399 MET cc_start: 0.8743 (ttm) cc_final: 0.8459 (ttp) REVERT: A 409 GLU cc_start: 0.8591 (tt0) cc_final: 0.8248 (tt0) REVERT: A 428 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7517 (mptp) REVERT: A 431 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: A 490 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: A 551 ASN cc_start: 0.7056 (m-40) cc_final: 0.6453 (m110) REVERT: A 572 ASP cc_start: 0.7545 (t0) cc_final: 0.7242 (t0) REVERT: A 594 MET cc_start: 0.7646 (ttp) cc_final: 0.7128 (tmt) REVERT: A 597 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6675 (tp30) REVERT: A 600 LYS cc_start: 0.7178 (ttpt) cc_final: 0.6652 (ptmm) REVERT: B 174 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 198 GLU cc_start: 0.7385 (pm20) cc_final: 0.6977 (mm-30) REVERT: B 226 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7548 (mp-120) REVERT: B 399 MET cc_start: 0.8734 (ttm) cc_final: 0.8452 (ttp) REVERT: B 409 GLU cc_start: 0.8582 (tt0) cc_final: 0.8238 (tt0) REVERT: B 428 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7510 (mptp) REVERT: B 431 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: B 490 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: B 551 ASN cc_start: 0.7048 (m-40) cc_final: 0.6444 (m110) REVERT: B 597 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6670 (tp30) REVERT: B 600 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6645 (ptmm) REVERT: C 174 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8341 (mp) REVERT: C 198 GLU cc_start: 0.7374 (pm20) cc_final: 0.6976 (mm-30) REVERT: C 226 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7474 (mp-120) REVERT: C 399 MET cc_start: 0.8726 (ttm) cc_final: 0.8459 (ttp) REVERT: C 409 GLU cc_start: 0.8596 (tt0) cc_final: 0.8250 (tt0) REVERT: C 428 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7511 (mptp) REVERT: C 431 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: C 490 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: C 572 ASP cc_start: 0.7545 (t0) cc_final: 0.7229 (t0) REVERT: C 597 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6680 (tp30) REVERT: C 600 LYS cc_start: 0.7175 (ttpt) cc_final: 0.6698 (ptmm) REVERT: D 174 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8344 (mp) REVERT: D 198 GLU cc_start: 0.7371 (pm20) cc_final: 0.6972 (mm-30) REVERT: D 226 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7539 (mp-120) REVERT: D 399 MET cc_start: 0.8733 (ttm) cc_final: 0.8453 (ttp) REVERT: D 409 GLU cc_start: 0.8586 (tt0) cc_final: 0.8241 (tt0) REVERT: D 428 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7528 (mptp) REVERT: D 431 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: D 490 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: D 572 ASP cc_start: 0.7513 (t0) cc_final: 0.7187 (t0) REVERT: D 594 MET cc_start: 0.7620 (ttp) cc_final: 0.7154 (tmt) REVERT: D 597 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6683 (tp30) REVERT: D 600 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6693 (ptmm) outliers start: 32 outliers final: 8 residues processed: 190 average time/residue: 0.7363 time to fit residues: 152.5685 Evaluate side-chains 183 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 490 GLU 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 490 GLU Chi-restraints excluded: chain B residue 539 SER 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 431 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 539 SER 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 Chi-restraints excluded: chain D residue 539 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3559 r_free = 0.3559 target = 0.131307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107662 restraints weight = 17608.954| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.08 r_work: 0.3116 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2500 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= 0.102 Angle : 0.438 7.128 21328 Z= 0.232 Chirality : 0.039 0.146 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.175 74.087 2920 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.85 % Allowed : 11.27 % Favored : 86.88 % 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: 2.23 (0.20), residues: 1792 helix: 2.30 (0.15), residues: 1180 sheet: -1.30 (1.09), residues: 20 loop : -0.08 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 514 TYR 0.015 0.001 TYR B 349 PHE 0.013 0.001 PHE B 298 TRP 0.017 0.001 TRP B 168 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (15812) covalent geometry : angle 0.43798 / 0.23 (21328) hydrogen bonds : bond 0.03184 / 2.07 ( 952) hydrogen bonds : angle 3.47916 / 2.49 ( 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 193 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.647 Fit side-chains REVERT: A 174 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 198 GLU cc_start: 0.7361 (pm20) cc_final: 0.7026 (mm-30) REVERT: A 226 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7576 (mp-120) REVERT: A 399 MET cc_start: 0.8644 (ttm) cc_final: 0.8375 (ttp) REVERT: A 409 GLU cc_start: 0.8549 (tt0) cc_final: 0.8210 (tt0) REVERT: A 428 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7514 (mptp) REVERT: A 431 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: A 551 ASN cc_start: 0.7103 (m-40) cc_final: 0.6497 (m110) REVERT: A 572 ASP cc_start: 0.7479 (t0) cc_final: 0.7171 (t0) REVERT: A 594 MET cc_start: 0.7651 (ttp) cc_final: 0.7146 (tmt) REVERT: A 597 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6656 (tp30) REVERT: A 600 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6669 (ptmm) REVERT: B 174 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 198 GLU cc_start: 0.7339 (pm20) cc_final: 0.7022 (mm-30) REVERT: B 226 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7594 (mp-120) REVERT: B 232 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6894 (mm-30) REVERT: B 399 MET cc_start: 0.8665 (ttm) cc_final: 0.8378 (ttp) REVERT: B 409 GLU cc_start: 0.8546 (tt0) cc_final: 0.8210 (tt0) REVERT: B 428 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7501 (mptp) REVERT: B 431 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: B 551 ASN cc_start: 0.7102 (m-40) cc_final: 0.6489 (m110) REVERT: B 594 MET cc_start: 0.7660 (ttp) cc_final: 0.7191 (tmt) REVERT: B 597 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6654 (tp30) REVERT: B 600 LYS cc_start: 0.7183 (ttpt) cc_final: 0.6662 (ptmm) REVERT: C 174 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 198 GLU cc_start: 0.7336 (pm20) cc_final: 0.7023 (mm-30) REVERT: C 226 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7295 (mp-120) REVERT: C 399 MET cc_start: 0.8648 (ttm) cc_final: 0.8373 (ttp) REVERT: C 409 GLU cc_start: 0.8554 (tt0) cc_final: 0.8217 (tt0) REVERT: C 428 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7487 (mptp) REVERT: C 431 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: C 572 ASP cc_start: 0.7498 (t0) cc_final: 0.7188 (t0) REVERT: C 594 MET cc_start: 0.7660 (ttp) cc_final: 0.7174 (tmt) REVERT: C 597 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6676 (tp30) REVERT: C 600 LYS cc_start: 0.7183 (ttpt) cc_final: 0.6712 (ptmm) REVERT: D 174 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8355 (mp) REVERT: D 198 GLU cc_start: 0.7317 (pm20) cc_final: 0.7020 (mm-30) REVERT: D 226 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7600 (mp-120) REVERT: D 232 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6888 (mm-30) REVERT: D 399 MET cc_start: 0.8673 (ttm) cc_final: 0.8389 (ttp) REVERT: D 409 GLU cc_start: 0.8558 (tt0) cc_final: 0.8219 (tt0) REVERT: D 428 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7524 (mptp) REVERT: D 431 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: D 572 ASP cc_start: 0.7445 (t0) cc_final: 0.7157 (t0) REVERT: D 594 MET cc_start: 0.7657 (ttp) cc_final: 0.7349 (tmt) REVERT: D 597 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6661 (tp30) REVERT: D 600 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6702 (ptmm) outliers start: 30 outliers final: 12 residues processed: 189 average time/residue: 0.7269 time to fit residues: 149.8884 Evaluate side-chains 183 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 539 SER 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 539 SER 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 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 539 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3533 r_free = 0.3533 target = 0.129271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105367 restraints weight = 17677.147| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.09 r_work: 0.3079 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2366 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= 0.136 Angle : 0.471 7.460 21328 Z= 0.250 Chirality : 0.040 0.146 2368 Planarity : 0.003 0.028 2552 Dihedral : 10.505 75.381 2920 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.52 % Allowed : 10.41 % Favored : 87.07 % 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: 2.33 (0.20), residues: 1792 helix: 2.33 (0.15), residues: 1172 sheet: -1.32 (1.12), residues: 20 loop : 0.10 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 514 TYR 0.020 0.001 TYR D 349 PHE 0.015 0.002 PHE D 298 TRP 0.016 0.001 TRP D 168 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15812) covalent geometry : angle 0.47129 / 0.25 (21328) hydrogen bonds : bond 0.03482 / 2.26 ( 952) hydrogen bonds : angle 3.61759 / 2.59 ( 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 199 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.665 Fit side-chains REVERT: A 174 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 226 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7486 (mp-120) REVERT: A 399 MET cc_start: 0.8753 (ttm) cc_final: 0.8470 (ttp) REVERT: A 409 GLU cc_start: 0.8590 (tt0) cc_final: 0.8249 (tt0) REVERT: A 428 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7514 (mptp) REVERT: A 431 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: A 490 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: A 551 ASN cc_start: 0.7025 (m-40) cc_final: 0.6412 (m110) REVERT: A 594 MET cc_start: 0.7667 (ttp) cc_final: 0.7359 (tmt) REVERT: A 597 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6639 (tp30) REVERT: A 600 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6650 (ptmm) REVERT: B 174 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8353 (mp) REVERT: B 226 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7488 (mp-120) REVERT: B 399 MET cc_start: 0.8752 (ttm) cc_final: 0.8487 (ttp) REVERT: B 409 GLU cc_start: 0.8580 (tt0) cc_final: 0.8239 (tt0) REVERT: B 428 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7511 (mptp) REVERT: B 431 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 490 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: B 551 ASN cc_start: 0.7037 (m-40) cc_final: 0.6420 (m110) REVERT: B 594 MET cc_start: 0.7661 (ttp) cc_final: 0.7115 (tmt) REVERT: B 597 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6633 (tp30) REVERT: B 600 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6650 (ptmm) REVERT: C 174 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 399 MET cc_start: 0.8748 (ttm) cc_final: 0.8470 (ttp) REVERT: C 409 GLU cc_start: 0.8588 (tt0) cc_final: 0.8248 (tt0) REVERT: C 428 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7514 (mptp) REVERT: C 431 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: C 490 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: C 572 ASP cc_start: 0.7519 (t0) cc_final: 0.7232 (t0) REVERT: C 594 MET cc_start: 0.7664 (ttp) cc_final: 0.7344 (tmt) REVERT: C 597 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6639 (tp30) REVERT: C 600 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6704 (ptmm) REVERT: D 174 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8352 (mp) REVERT: D 226 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7474 (mp-120) REVERT: D 399 MET cc_start: 0.8762 (ttm) cc_final: 0.8497 (ttp) REVERT: D 409 GLU cc_start: 0.8587 (tt0) cc_final: 0.8245 (tt0) REVERT: D 428 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7521 (mptp) REVERT: D 431 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: D 490 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7677 (tp30) REVERT: D 572 ASP cc_start: 0.7497 (t0) cc_final: 0.7200 (t0) REVERT: D 594 MET cc_start: 0.7641 (ttp) cc_final: 0.7324 (tmt) REVERT: D 597 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6636 (tp30) REVERT: D 600 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6697 (ptmm) outliers start: 41 outliers final: 16 residues processed: 191 average time/residue: 0.7218 time to fit residues: 150.5637 Evaluate side-chains 188 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 431 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 490 GLU 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 350 VAL Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 490 GLU 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 490 GLU 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: 0.9980 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3531 r_free = 0.3531 target = 0.129130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104993 restraints weight = 17897.401| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.13 r_work: 0.3077 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2425 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= 0.122 Angle : 0.471 7.969 21328 Z= 0.249 Chirality : 0.039 0.146 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.346 74.337 2920 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.46 % Allowed : 10.34 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.29 (0.20), residues: 1792 helix: 2.31 (0.15), residues: 1172 sheet: -1.42 (1.09), residues: 20 loop : 0.09 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.018 0.001 TYR D 349 PHE 0.014 0.001 PHE A 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS D 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15812) covalent geometry : angle 0.47080 / 0.25 (21328) hydrogen bonds : bond 0.03387 / 2.20 ( 952) hydrogen bonds : angle 3.59418 / 2.58 ( 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 198 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.657 Fit side-chains REVERT: A 174 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 198 GLU cc_start: 0.7425 (pm20) cc_final: 0.6837 (pm20) REVERT: A 226 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7543 (mp-120) REVERT: A 399 MET cc_start: 0.8759 (ttm) cc_final: 0.8478 (ttp) REVERT: A 409 GLU cc_start: 0.8619 (tt0) cc_final: 0.8268 (tt0) REVERT: A 428 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7514 (mptp) REVERT: A 431 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: A 490 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: A 551 ASN cc_start: 0.7082 (m-40) cc_final: 0.6444 (m110) REVERT: A 594 MET cc_start: 0.7708 (ttp) cc_final: 0.7324 (tmt) REVERT: A 597 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6662 (tp30) REVERT: A 600 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6661 (ptmm) REVERT: B 174 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 198 GLU cc_start: 0.7426 (pm20) cc_final: 0.6836 (pm20) REVERT: B 226 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7524 (mp-120) REVERT: B 399 MET cc_start: 0.8749 (ttm) cc_final: 0.8480 (ttp) REVERT: B 409 GLU cc_start: 0.8612 (tt0) cc_final: 0.8260 (tt0) REVERT: B 428 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7505 (mptp) REVERT: B 431 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: B 490 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: B 551 ASN cc_start: 0.7118 (m-40) cc_final: 0.6488 (m110) REVERT: B 594 MET cc_start: 0.7705 (ttp) cc_final: 0.7304 (tmt) REVERT: B 597 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6661 (tp30) REVERT: B 600 LYS cc_start: 0.7192 (ttpt) cc_final: 0.6681 (ptmm) REVERT: C 174 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 198 GLU cc_start: 0.7421 (pm20) cc_final: 0.6830 (pm20) REVERT: C 226 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7447 (mp-120) REVERT: C 399 MET cc_start: 0.8757 (ttm) cc_final: 0.8491 (ttp) REVERT: C 409 GLU cc_start: 0.8612 (tt0) cc_final: 0.8264 (tt0) REVERT: C 428 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7510 (mptp) REVERT: C 431 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: C 490 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: C 572 ASP cc_start: 0.7526 (t0) cc_final: 0.7206 (t0) REVERT: C 594 MET cc_start: 0.7642 (ttp) cc_final: 0.7422 (tmt) REVERT: C 597 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6673 (tp30) REVERT: C 600 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6721 (ptmm) REVERT: D 174 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8360 (mp) REVERT: D 198 GLU cc_start: 0.7404 (pm20) cc_final: 0.6812 (pm20) REVERT: D 226 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7533 (mp-120) REVERT: D 399 MET cc_start: 0.8761 (ttm) cc_final: 0.8492 (ttp) REVERT: D 409 GLU cc_start: 0.8607 (tt0) cc_final: 0.8257 (tt0) REVERT: D 428 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7517 (mptp) REVERT: D 431 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: D 490 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: D 572 ASP cc_start: 0.7517 (t0) cc_final: 0.7181 (t0) REVERT: D 594 MET cc_start: 0.7651 (ttp) cc_final: 0.7422 (tmt) REVERT: D 597 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6668 (tp30) REVERT: D 600 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6710 (ptmm) outliers start: 40 outliers final: 20 residues processed: 190 average time/residue: 0.7339 time to fit residues: 152.3900 Evaluate side-chains 194 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 490 GLU 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 490 GLU 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 490 GLU 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: 0.7980 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3542 r_free = 0.3542 target = 0.130126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106359 restraints weight = 17638.364| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.07 r_work: 0.3087 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2441 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= 0.120 Angle : 0.471 8.868 21328 Z= 0.248 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.259 74.062 2920 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.46 % Allowed : 10.34 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.35 (0.20), residues: 1792 helix: 2.34 (0.15), residues: 1172 sheet: -1.36 (1.10), residues: 20 loop : 0.13 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.017 0.001 TYR D 349 PHE 0.014 0.001 PHE C 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15812) covalent geometry : angle 0.47079 / 0.25 (21328) hydrogen bonds : bond 0.03376 / 2.19 ( 952) hydrogen bonds : angle 3.58304 / 2.57 ( 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 198 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.643 Fit side-chains REVERT: A 174 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 198 GLU cc_start: 0.7396 (pm20) cc_final: 0.6792 (pm20) REVERT: A 226 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7235 (mp-120) REVERT: A 399 MET cc_start: 0.8725 (ttm) cc_final: 0.8443 (ttp) REVERT: A 409 GLU cc_start: 0.8578 (tt0) cc_final: 0.8234 (tt0) REVERT: A 428 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7505 (mptp) REVERT: A 431 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: A 490 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: A 551 ASN cc_start: 0.7121 (m-40) cc_final: 0.6490 (m110) REVERT: A 594 MET cc_start: 0.7643 (ttp) cc_final: 0.7237 (tmt) REVERT: A 597 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6656 (tp30) REVERT: A 600 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6653 (ptmm) REVERT: B 174 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 198 GLU cc_start: 0.7392 (pm20) cc_final: 0.6790 (pm20) REVERT: B 226 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7232 (mp-120) REVERT: B 399 MET cc_start: 0.8714 (ttm) cc_final: 0.8446 (ttp) REVERT: B 409 GLU cc_start: 0.8577 (tt0) cc_final: 0.8231 (tt0) REVERT: B 428 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7502 (mptp) REVERT: B 431 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: B 490 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: B 551 ASN cc_start: 0.7064 (m-40) cc_final: 0.6425 (m110) REVERT: B 594 MET cc_start: 0.7616 (ttp) cc_final: 0.7220 (tmt) REVERT: B 597 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6765 (tp30) REVERT: B 600 LYS cc_start: 0.7160 (ttpt) cc_final: 0.6886 (mtpt) REVERT: C 174 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 198 GLU cc_start: 0.7378 (pm20) cc_final: 0.6771 (pm20) REVERT: C 226 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7321 (mp-120) REVERT: C 399 MET cc_start: 0.8715 (ttm) cc_final: 0.8451 (ttp) REVERT: C 409 GLU cc_start: 0.8574 (tt0) cc_final: 0.8231 (tt0) REVERT: C 428 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7504 (mptp) REVERT: C 431 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: C 490 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: C 572 ASP cc_start: 0.7497 (t0) cc_final: 0.7193 (t0) REVERT: C 594 MET cc_start: 0.7620 (ttp) cc_final: 0.7325 (tmt) REVERT: C 597 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6654 (tp30) REVERT: C 600 LYS cc_start: 0.7151 (ttpt) cc_final: 0.6653 (ptmm) REVERT: D 174 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8354 (mp) REVERT: D 198 GLU cc_start: 0.7373 (pm20) cc_final: 0.6769 (pm20) REVERT: D 226 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7230 (mp-120) REVERT: D 399 MET cc_start: 0.8728 (ttm) cc_final: 0.8461 (ttp) REVERT: D 409 GLU cc_start: 0.8566 (tt0) cc_final: 0.8222 (tt0) REVERT: D 428 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7513 (mptp) REVERT: D 431 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: D 490 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: D 572 ASP cc_start: 0.7494 (t0) cc_final: 0.7147 (t0) REVERT: D 594 MET cc_start: 0.7586 (ttp) cc_final: 0.7286 (tmt) REVERT: D 597 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6657 (tp30) REVERT: D 600 LYS cc_start: 0.7160 (ttpt) cc_final: 0.6676 (ptmm) outliers start: 40 outliers final: 20 residues processed: 190 average time/residue: 0.7315 time to fit residues: 151.7544 Evaluate side-chains 193 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 490 GLU 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 490 GLU 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 490 GLU 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 54 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 170 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3513 r_free = 0.3513 target = 0.127774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103892 restraints weight = 17922.301| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.12 r_work: 0.3036 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15812 Z= 0.158 Angle : 0.509 9.187 21328 Z= 0.267 Chirality : 0.041 0.147 2368 Planarity : 0.003 0.029 2552 Dihedral : 10.761 75.667 2920 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.46 % Allowed : 10.41 % 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: 2.21 (0.20), residues: 1792 helix: 2.22 (0.15), residues: 1172 sheet: -1.61 (1.07), residues: 20 loop : 0.11 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.022 0.002 TYR B 349 PHE 0.016 0.002 PHE A 298 TRP 0.017 0.002 TRP A 168 HIS 0.003 0.002 HIS D 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15812) covalent geometry : angle 0.50915 / 0.27 (21328) hydrogen bonds : bond 0.03694 / 2.40 ( 952) hydrogen bonds : angle 3.71907 / 2.67 ( 2736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5546.43 seconds wall clock time: 95 minutes 47.44 seconds (5747.44 seconds total)