Starting phenix.real_space_refine on Wed Mar 4 22:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lft_23306/03_2026/7lft_23306_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lft_23306/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lft_23306/03_2026/7lft_23306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lft_23306/03_2026/7lft_23306.map" model { file = "/net/cci-nas-00/data/ceres_data/7lft_23306/03_2026/7lft_23306_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lft_23306/03_2026/7lft_23306_trim.cif" } 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-5986/lib/python3.9/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, 182 Unusual residues: {' K': 3, 'CLR': 2, 'CPL': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-1': 4, 'CPL:plan-2': 4, 'CPL:plan-3': 6, 'CPL:plan-4': 6} Unresolved non-hydrogen planarities: 74 Chain: "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: 3.68, 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: 1.42 Conformation dependent library (CDL) restraints added in 692.9 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: 0.53 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: 2.73 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2376 1.27 - 1.41: 3932 1.41 - 1.54: 9096 1.54 - 1.67: 280 1.67 - 1.80: 128 Bond restraints: 15812 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" O VAL D 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL A 370 " pdb=" O VAL A 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL B 370 " pdb=" O VAL B 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.99e+01 bond pdb=" C VAL C 370 " pdb=" O VAL C 370 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.15e-02 7.56e+03 2.98e+01 bond pdb=" C31 CPL D 706 " pdb=" O2 CPL D 706 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 15807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 21112 4.58 - 9.16: 172 9.16 - 13.74: 32 13.74 - 18.32: 8 18.32 - 22.90: 4 Bond angle restraints: 21328 Sorted by residual: angle pdb=" O3P CPL A 707 " pdb=" P CPL A 707 " pdb=" O4P CPL A 707 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL D 706 " pdb=" P CPL D 706 " pdb=" O4P CPL D 706 " ideal model delta sigma weight residual 93.29 116.19 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O3P CPL C 706 " pdb=" P CPL C 706 " pdb=" O4P CPL C 706 " ideal model delta sigma weight residual 93.29 116.17 -22.88 3.00e+00 1.11e-01 5.82e+01 angle pdb=" O3P CPL B 706 " pdb=" P CPL B 706 " pdb=" O4P CPL B 706 " ideal model delta sigma weight residual 93.29 116.12 -22.83 3.00e+00 1.11e-01 5.79e+01 angle pdb=" N VAL A 370 " pdb=" CA VAL A 370 " pdb=" C VAL A 370 " ideal model delta sigma weight residual 111.56 106.32 5.24 8.60e-01 1.35e+00 3.71e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 9396 27.56 - 55.12: 460 55.12 - 82.68: 44 82.68 - 110.24: 8 110.24 - 137.79: 8 Dihedral angle restraints: 9916 sinusoidal: 4592 harmonic: 5324 Sorted by residual: dihedral pdb=" C3 CPL B 706 " pdb=" C1 CPL B 706 " pdb=" C2 CPL B 706 " pdb=" O3P CPL B 706 " ideal model delta sinusoidal sigma weight residual 72.09 -150.12 -137.79 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3 CPL C 706 " pdb=" C1 CPL C 706 " pdb=" C2 CPL C 706 " pdb=" O3P CPL C 706 " ideal model delta sinusoidal sigma weight residual 72.09 -150.14 -137.77 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3 CPL A 707 " pdb=" C1 CPL A 707 " pdb=" C2 CPL A 707 " pdb=" O3P CPL A 707 " ideal model delta sinusoidal sigma weight residual 72.09 -150.14 -137.77 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 9913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2238 0.094 - 0.188: 93 0.188 - 0.282: 29 0.282 - 0.377: 0 0.377 - 0.471: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" C10 CLR A 702 " pdb=" C1 CLR A 702 " pdb=" C5 CLR A 702 " pdb=" C9 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C10 CLR C 701 " pdb=" C1 CLR C 701 " pdb=" C5 CLR C 701 " pdb=" C9 CLR C 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C10 CLR D 701 " pdb=" C1 CLR D 701 " pdb=" C5 CLR D 701 " pdb=" C9 CLR D 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2365 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 501 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO D 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 501 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 502 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 501 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 502 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.020 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.49: 69 2.49 - 3.16: 13167 3.16 - 3.82: 32456 3.82 - 4.48: 45964 4.48 - 5.14: 71633 Nonbonded interactions: 163289 Sorted by model distance: nonbonded pdb=" K K A 710 " pdb=" K K A 711 " model vdw 1.832 2.660 nonbonded pdb=" OG SER A 567 " pdb=" OG SER A 571 " model vdw 2.187 3.040 nonbonded pdb=" OG SER D 567 " pdb=" OG SER D 571 " model vdw 2.188 3.040 nonbonded pdb=" OG SER C 567 " pdb=" OG SER C 571 " model vdw 2.188 3.040 nonbonded pdb=" OG SER B 567 " pdb=" OG SER B 571 " model vdw 2.188 3.040 ... (remaining 163284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 708) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 15812 Z= 0.459 Angle : 1.096 22.901 21328 Z= 0.478 Chirality : 0.057 0.471 2368 Planarity : 0.004 0.036 2552 Dihedral : 16.077 137.795 6500 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.25 % Allowed : 1.97 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 1792 helix: -0.10 (0.14), residues: 1176 sheet: -2.84 (1.00), residues: 20 loop : -1.13 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 287 TYR 0.022 0.002 TYR A 349 PHE 0.014 0.002 PHE D 298 TRP 0.021 0.002 TRP C 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00912 (15812) covalent geometry : angle 1.09636 (21328) hydrogen bonds : bond 0.11430 ( 952) hydrogen bonds : angle 4.89472 ( 2736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.395 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: 0.6602 time to fit residues: 166.3784 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 : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 470 HIS A 534 GLN A 559 ASN B 226 GLN B 470 HIS B 534 GLN B 559 ASN C 226 GLN C 470 HIS C 534 GLN C 559 ASN D 226 GLN D 470 HIS D 534 GLN D 559 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107666 restraints weight = 17825.421| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.11 r_work: 0.3115 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15812 Z= 0.105 Angle : 0.463 8.280 21328 Z= 0.244 Chirality : 0.039 0.144 2368 Planarity : 0.003 0.031 2552 Dihedral : 13.179 82.604 2920 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.17 % Allowed : 7.57 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1792 helix: 1.35 (0.15), residues: 1184 sheet: -2.44 (0.97), residues: 20 loop : -0.71 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 514 TYR 0.012 0.001 TYR A 349 PHE 0.009 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00232 (15812) covalent geometry : angle 0.46348 (21328) hydrogen bonds : bond 0.03353 ( 952) hydrogen bonds : angle 3.67475 ( 2736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.571 Fit side-chains REVERT: A 198 GLU cc_start: 0.7504 (pm20) cc_final: 0.7202 (mm-30) REVERT: A 205 TYR cc_start: 0.6875 (m-80) cc_final: 0.6436 (t80) REVERT: A 399 MET cc_start: 0.8695 (ttm) cc_final: 0.8438 (ttp) REVERT: A 409 GLU cc_start: 0.8505 (tt0) cc_final: 0.8159 (tt0) REVERT: A 428 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7619 (mptp) REVERT: A 551 ASN cc_start: 0.7081 (m-40) cc_final: 0.6498 (m110) REVERT: A 572 ASP cc_start: 0.7364 (t0) cc_final: 0.7150 (t0) REVERT: A 597 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6581 (tm-30) REVERT: A 600 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6509 (ptmm) REVERT: B 198 GLU cc_start: 0.7501 (pm20) cc_final: 0.7202 (mm-30) REVERT: B 205 TYR cc_start: 0.6895 (m-80) cc_final: 0.6449 (t80) REVERT: B 399 MET cc_start: 0.8707 (ttm) cc_final: 0.8449 (ttp) REVERT: B 409 GLU cc_start: 0.8515 (tt0) cc_final: 0.8157 (tt0) REVERT: B 428 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7619 (mptp) REVERT: B 551 ASN cc_start: 0.7077 (m-40) cc_final: 0.6564 (m110) REVERT: B 572 ASP cc_start: 0.7372 (t0) cc_final: 0.7158 (t0) REVERT: B 597 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6553 (tm-30) REVERT: B 600 LYS cc_start: 0.7124 (ttpt) cc_final: 0.6500 (ptmm) REVERT: C 198 GLU cc_start: 0.7501 (pm20) cc_final: 0.7206 (mm-30) REVERT: C 205 TYR cc_start: 0.6907 (m-80) cc_final: 0.6463 (t80) REVERT: C 226 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7491 (mp-120) REVERT: C 399 MET cc_start: 0.8710 (ttm) cc_final: 0.8451 (ttp) REVERT: C 409 GLU cc_start: 0.8519 (tt0) cc_final: 0.8157 (tt0) REVERT: C 428 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7615 (mptp) REVERT: C 551 ASN cc_start: 0.7058 (m-40) cc_final: 0.6596 (m110) REVERT: C 597 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 600 LYS cc_start: 0.7104 (ttpt) cc_final: 0.6539 (ptmm) REVERT: D 198 GLU cc_start: 0.7497 (pm20) cc_final: 0.7203 (mm-30) REVERT: D 205 TYR cc_start: 0.6897 (m-80) cc_final: 0.6455 (t80) REVERT: D 399 MET cc_start: 0.8706 (ttm) cc_final: 0.8448 (ttp) REVERT: D 409 GLU cc_start: 0.8508 (tt0) cc_final: 0.8147 (tt0) REVERT: D 428 LYS cc_start: 0.8067 (mmmm) cc_final: 0.7645 (mptp) REVERT: D 551 ASN cc_start: 0.7056 (m-40) cc_final: 0.6587 (m110) REVERT: D 572 ASP cc_start: 0.7368 (t0) cc_final: 0.7136 (t0) REVERT: D 597 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6561 (tm-30) REVERT: D 600 LYS cc_start: 0.7100 (ttpt) cc_final: 0.6539 (ptmm) outliers start: 19 outliers final: 0 residues processed: 227 average time/residue: 0.6317 time to fit residues: 156.8290 Evaluate side-chains 172 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 170 optimal weight: 0.2980 chunk 135 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 498 GLN B 226 GLN B 286 GLN B 498 GLN C 226 GLN C 286 GLN C 498 GLN D 226 GLN D 286 GLN D 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106567 restraints weight = 18031.584| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.14 r_work: 0.3063 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15812 Z= 0.134 Angle : 0.475 6.115 21328 Z= 0.254 Chirality : 0.040 0.144 2368 Planarity : 0.003 0.030 2552 Dihedral : 11.962 81.083 2920 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 8.56 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1792 helix: 1.65 (0.15), residues: 1208 sheet: -2.18 (1.01), residues: 20 loop : -0.61 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.020 0.002 TYR B 349 PHE 0.013 0.002 PHE D 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00307 (15812) covalent geometry : angle 0.47501 (21328) hydrogen bonds : bond 0.03669 ( 952) hydrogen bonds : angle 3.71117 ( 2736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.598 Fit side-chains REVERT: A 205 TYR cc_start: 0.7012 (m-80) cc_final: 0.6426 (t80) REVERT: A 226 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7549 (mp-120) REVERT: A 399 MET cc_start: 0.8773 (ttm) cc_final: 0.8509 (ttp) REVERT: A 409 GLU cc_start: 0.8634 (tt0) cc_final: 0.8281 (tt0) REVERT: A 428 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7589 (mptp) REVERT: A 551 ASN cc_start: 0.6999 (m-40) cc_final: 0.6443 (m110) REVERT: A 572 ASP cc_start: 0.7496 (t0) cc_final: 0.7257 (t0) REVERT: A 597 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6724 (tp30) REVERT: A 600 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6605 (ptmm) REVERT: B 205 TYR cc_start: 0.7017 (m-80) cc_final: 0.6426 (t80) REVERT: B 226 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7544 (mp-120) REVERT: B 399 MET cc_start: 0.8784 (ttm) cc_final: 0.8521 (ttp) REVERT: B 409 GLU cc_start: 0.8628 (tt0) cc_final: 0.8276 (tt0) REVERT: B 428 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7620 (mptp) REVERT: B 551 ASN cc_start: 0.7109 (m-40) cc_final: 0.6598 (m110) REVERT: B 572 ASP cc_start: 0.7517 (t0) cc_final: 0.7260 (t0) REVERT: B 597 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 600 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6609 (ptmm) REVERT: C 205 TYR cc_start: 0.6999 (m-80) cc_final: 0.6454 (t80) REVERT: C 399 MET cc_start: 0.8774 (ttm) cc_final: 0.8510 (ttp) REVERT: C 409 GLU cc_start: 0.8625 (tt0) cc_final: 0.8268 (tt0) REVERT: C 428 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7614 (mptp) REVERT: C 551 ASN cc_start: 0.7078 (m-40) cc_final: 0.6583 (m110) REVERT: C 572 ASP cc_start: 0.7557 (t0) cc_final: 0.7343 (t0) REVERT: C 597 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6670 (tp30) REVERT: C 600 LYS cc_start: 0.7118 (ttpt) cc_final: 0.6633 (ptmm) REVERT: D 205 TYR cc_start: 0.6998 (m-80) cc_final: 0.6452 (t80) REVERT: D 226 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7525 (mp-120) REVERT: D 399 MET cc_start: 0.8770 (ttm) cc_final: 0.8505 (ttp) REVERT: D 409 GLU cc_start: 0.8624 (tt0) cc_final: 0.8266 (tt0) REVERT: D 428 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7614 (mptp) REVERT: D 551 ASN cc_start: 0.7069 (m-40) cc_final: 0.6576 (m110) REVERT: D 572 ASP cc_start: 0.7448 (t0) cc_final: 0.7185 (t0) REVERT: D 597 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6670 (tp30) REVERT: D 600 LYS cc_start: 0.7077 (ttpt) cc_final: 0.6633 (ptmm) outliers start: 24 outliers final: 0 residues processed: 199 average time/residue: 0.7281 time to fit residues: 157.0040 Evaluate side-chains 173 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 20.0000 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104569 restraints weight = 17824.519| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.12 r_work: 0.3073 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1877 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= 0.135 Angle : 0.472 5.306 21328 Z= 0.253 Chirality : 0.040 0.147 2368 Planarity : 0.003 0.030 2552 Dihedral : 11.681 78.889 2920 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 1.59 (0.20), residues: 1792 helix: 1.83 (0.14), residues: 1208 sheet: -2.00 (1.04), residues: 20 loop : -0.49 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.019 0.002 TYR A 349 PHE 0.014 0.001 PHE D 298 TRP 0.017 0.002 TRP D 168 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00308 (15812) covalent geometry : angle 0.47180 (21328) hydrogen bonds : bond 0.03569 ( 952) hydrogen bonds : angle 3.69361 ( 2736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.453 Fit side-chains REVERT: A 205 TYR cc_start: 0.6963 (m-10) cc_final: 0.6436 (t80) REVERT: A 399 MET cc_start: 0.8761 (ttm) cc_final: 0.8527 (ttp) REVERT: A 409 GLU cc_start: 0.8636 (tt0) cc_final: 0.8294 (tt0) REVERT: A 428 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7521 (mptp) REVERT: A 431 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: A 551 ASN cc_start: 0.7106 (m-40) cc_final: 0.6518 (m110) REVERT: A 572 ASP cc_start: 0.7491 (t0) cc_final: 0.7216 (t0) REVERT: A 597 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6684 (tp30) REVERT: A 600 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6633 (ptmm) REVERT: B 205 TYR cc_start: 0.6956 (m-10) cc_final: 0.6465 (t80) REVERT: B 399 MET cc_start: 0.8766 (ttm) cc_final: 0.8533 (ttp) REVERT: B 409 GLU cc_start: 0.8631 (tt0) cc_final: 0.8288 (tt0) REVERT: B 428 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7552 (mptp) REVERT: B 431 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: B 551 ASN cc_start: 0.7133 (m-40) cc_final: 0.6586 (m110) REVERT: B 597 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6683 (tp30) REVERT: B 600 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6624 (ptmm) REVERT: C 205 TYR cc_start: 0.7007 (m-10) cc_final: 0.6490 (t80) REVERT: C 399 MET cc_start: 0.8773 (ttm) cc_final: 0.8540 (ttp) REVERT: C 409 GLU cc_start: 0.8626 (tt0) cc_final: 0.8283 (tt0) REVERT: C 428 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7548 (mptp) REVERT: C 431 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: C 572 ASP cc_start: 0.7544 (t0) cc_final: 0.7268 (t0) REVERT: C 597 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6669 (tp30) REVERT: C 600 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6652 (ptmm) REVERT: D 205 TYR cc_start: 0.7002 (m-10) cc_final: 0.6489 (t80) REVERT: D 399 MET cc_start: 0.8776 (ttm) cc_final: 0.8543 (ttp) REVERT: D 409 GLU cc_start: 0.8635 (tt0) cc_final: 0.8289 (tt0) REVERT: D 428 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7518 (mptp) REVERT: D 431 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: D 572 ASP cc_start: 0.7464 (t0) cc_final: 0.7169 (t0) REVERT: D 597 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6680 (tp30) REVERT: D 600 LYS cc_start: 0.7127 (ttpt) cc_final: 0.6647 (ptmm) outliers start: 21 outliers final: 5 residues processed: 193 average time/residue: 0.7040 time to fit residues: 147.2814 Evaluate side-chains 181 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 431 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106429 restraints weight = 17888.311| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.08 r_work: 0.3098 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2109 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= 0.112 Angle : 0.450 5.354 21328 Z= 0.241 Chirality : 0.039 0.144 2368 Planarity : 0.003 0.030 2552 Dihedral : 10.973 75.618 2920 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.16 % Allowed : 10.47 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.15), residues: 1208 sheet: -1.90 (1.01), residues: 20 loop : -0.39 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.016 0.001 TYR C 349 PHE 0.013 0.001 PHE D 298 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00255 (15812) covalent geometry : angle 0.45046 (21328) hydrogen bonds : bond 0.03316 ( 952) hydrogen bonds : angle 3.56899 ( 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 222 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.652 Fit side-chains REVERT: A 174 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 205 TYR cc_start: 0.6770 (m-10) cc_final: 0.6428 (t80) REVERT: A 226 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7512 (mp-120) REVERT: A 399 MET cc_start: 0.8707 (ttm) cc_final: 0.8472 (ttp) REVERT: A 409 GLU cc_start: 0.8573 (tt0) cc_final: 0.8236 (tt0) REVERT: A 428 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7536 (mptp) REVERT: A 431 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: A 490 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: A 551 ASN cc_start: 0.7117 (m-40) cc_final: 0.6512 (m110) REVERT: A 572 ASP cc_start: 0.7488 (t0) cc_final: 0.7202 (t0) REVERT: A 597 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6698 (tp30) REVERT: A 600 LYS cc_start: 0.7161 (ttpt) cc_final: 0.6594 (ptmm) REVERT: B 174 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8374 (mp) REVERT: B 205 TYR cc_start: 0.6773 (m-10) cc_final: 0.6426 (t80) REVERT: B 226 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7521 (mp-120) REVERT: B 399 MET cc_start: 0.8698 (ttm) cc_final: 0.8462 (ttp) REVERT: B 409 GLU cc_start: 0.8567 (tt0) cc_final: 0.8231 (tt0) REVERT: B 428 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7567 (mptp) REVERT: B 490 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: B 572 ASP cc_start: 0.7516 (t0) cc_final: 0.7240 (t0) REVERT: B 597 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6693 (tp30) REVERT: B 600 LYS cc_start: 0.7147 (ttpt) cc_final: 0.6577 (ptmm) REVERT: C 174 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 205 TYR cc_start: 0.6792 (m-10) cc_final: 0.6433 (t80) REVERT: C 399 MET cc_start: 0.8706 (ttm) cc_final: 0.8469 (ttp) REVERT: C 409 GLU cc_start: 0.8566 (tt0) cc_final: 0.8226 (tt0) REVERT: C 428 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7563 (mptp) REVERT: C 490 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: C 572 ASP cc_start: 0.7441 (t0) cc_final: 0.7146 (t0) REVERT: C 597 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6698 (tp30) REVERT: C 600 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6649 (ptmm) REVERT: D 174 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8381 (mp) REVERT: D 205 TYR cc_start: 0.6797 (m-10) cc_final: 0.6443 (t80) REVERT: D 226 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7503 (mp-120) REVERT: D 399 MET cc_start: 0.8718 (ttm) cc_final: 0.8482 (ttp) REVERT: D 409 GLU cc_start: 0.8573 (tt0) cc_final: 0.8232 (tt0) REVERT: D 428 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7520 (mptp) REVERT: D 431 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: D 490 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: D 572 ASP cc_start: 0.7453 (t0) cc_final: 0.7174 (t0) REVERT: D 597 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6702 (tp30) REVERT: D 600 LYS cc_start: 0.7161 (ttpt) cc_final: 0.6643 (ptmm) outliers start: 35 outliers final: 12 residues processed: 211 average time/residue: 0.7291 time to fit residues: 166.5541 Evaluate side-chains 178 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 451 LYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 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 534 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103870 restraints weight = 17745.134| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.13 r_work: 0.3060 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2016 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= 0.148 Angle : 0.488 5.626 21328 Z= 0.262 Chirality : 0.040 0.147 2368 Planarity : 0.003 0.030 2552 Dihedral : 11.181 76.447 2920 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.16 % Allowed : 10.84 % Favored : 87.01 % 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: 2.11 (0.20), residues: 1792 helix: 2.21 (0.15), residues: 1172 sheet: -1.94 (1.01), residues: 20 loop : -0.06 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.020 0.002 TYR A 349 PHE 0.015 0.002 PHE D 298 TRP 0.018 0.002 TRP C 168 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00341 (15812) covalent geometry : angle 0.48819 (21328) hydrogen bonds : bond 0.03645 ( 952) hydrogen bonds : angle 3.71146 ( 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 203 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.593 Fit side-chains REVERT: A 174 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 205 TYR cc_start: 0.6946 (m-10) cc_final: 0.6497 (t80) REVERT: A 226 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7444 (mp-120) REVERT: A 399 MET cc_start: 0.8801 (ttm) cc_final: 0.8566 (ttp) REVERT: A 409 GLU cc_start: 0.8628 (tt0) cc_final: 0.8289 (tt0) REVERT: A 428 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7514 (mptp) REVERT: A 431 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 490 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: A 551 ASN cc_start: 0.7132 (m-40) cc_final: 0.6512 (m110) REVERT: A 597 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6621 (tp30) REVERT: A 600 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6597 (ptmm) REVERT: B 174 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8388 (mp) REVERT: B 205 TYR cc_start: 0.6936 (m-10) cc_final: 0.6494 (t80) REVERT: B 226 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7454 (mp-120) REVERT: B 399 MET cc_start: 0.8803 (ttm) cc_final: 0.8571 (ttp) REVERT: B 409 GLU cc_start: 0.8623 (tt0) cc_final: 0.8283 (tt0) REVERT: B 428 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7549 (mptp) REVERT: B 431 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 572 ASP cc_start: 0.7547 (t0) cc_final: 0.7289 (t0) REVERT: B 597 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6665 (tp30) REVERT: B 600 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6588 (ptmm) REVERT: C 174 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8392 (mp) REVERT: C 205 TYR cc_start: 0.6966 (m-10) cc_final: 0.6491 (t80) REVERT: C 226 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7527 (mp-120) REVERT: C 399 MET cc_start: 0.8804 (ttm) cc_final: 0.8571 (ttp) REVERT: C 409 GLU cc_start: 0.8642 (tt0) cc_final: 0.8292 (tt0) REVERT: C 428 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7539 (mptp) REVERT: C 431 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: C 490 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: C 597 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6678 (tp30) REVERT: C 600 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6641 (ptmm) REVERT: D 174 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8395 (mp) REVERT: D 205 TYR cc_start: 0.6969 (m-10) cc_final: 0.6502 (t80) REVERT: D 226 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7431 (mp-120) REVERT: D 399 MET cc_start: 0.8811 (ttm) cc_final: 0.8576 (ttp) REVERT: D 409 GLU cc_start: 0.8645 (tt0) cc_final: 0.8293 (tt0) REVERT: D 428 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7513 (mptp) REVERT: D 431 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: D 490 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: D 572 ASP cc_start: 0.7499 (t0) cc_final: 0.7294 (t0) REVERT: D 597 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6672 (tp30) REVERT: D 600 LYS cc_start: 0.7161 (ttpt) cc_final: 0.6656 (ptmm) outliers start: 35 outliers final: 12 residues processed: 195 average time/residue: 0.6909 time to fit residues: 146.6681 Evaluate side-chains 184 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 chunk 62 optimal weight: 0.0980 chunk 82 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 329 ASN B 226 GLN B 286 GLN B 329 ASN C 226 GLN C 286 GLN C 329 ASN D 226 GLN D 286 GLN D 329 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108340 restraints weight = 17774.282| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.08 r_work: 0.3128 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15812 Z= 0.099 Angle : 0.445 6.844 21328 Z= 0.235 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.030 2552 Dihedral : 10.331 72.279 2920 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.16 % Allowed : 11.15 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1792 helix: 2.10 (0.15), residues: 1208 sheet: -1.84 (0.97), 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 0.012 0.001 TYR C 349 PHE 0.012 0.001 PHE D 298 TRP 0.018 0.002 TRP B 168 HIS 0.001 0.001 HIS D 470 Details of bonding type rmsd covalent geometry : bond 0.00219 (15812) covalent geometry : angle 0.44452 (21328) hydrogen bonds : bond 0.03140 ( 952) hydrogen bonds : angle 3.49683 ( 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 199 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.555 Fit side-chains REVERT: A 174 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8351 (mp) REVERT: A 198 GLU cc_start: 0.7343 (pm20) cc_final: 0.6704 (pm20) REVERT: A 399 MET cc_start: 0.8666 (ttm) cc_final: 0.8392 (ttp) REVERT: A 409 GLU cc_start: 0.8545 (tt0) cc_final: 0.8208 (tt0) REVERT: A 428 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7509 (mptp) REVERT: A 431 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 551 ASN cc_start: 0.7172 (m-40) cc_final: 0.6579 (m110) REVERT: A 597 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6628 (tp30) REVERT: A 600 LYS cc_start: 0.7167 (ttpt) cc_final: 0.6623 (ptmm) REVERT: B 174 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 198 GLU cc_start: 0.7334 (pm20) cc_final: 0.6695 (pm20) REVERT: B 399 MET cc_start: 0.8667 (ttm) cc_final: 0.8393 (ttp) REVERT: B 409 GLU cc_start: 0.8541 (tt0) cc_final: 0.8202 (tt0) REVERT: B 428 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7483 (mptp) REVERT: B 431 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: B 597 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6622 (tp30) REVERT: B 600 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6579 (ptmm) REVERT: C 174 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8362 (mp) REVERT: C 198 GLU cc_start: 0.7330 (pm20) cc_final: 0.6690 (pm20) REVERT: C 226 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7396 (mp-120) REVERT: C 399 MET cc_start: 0.8675 (ttm) cc_final: 0.8402 (ttp) REVERT: C 409 GLU cc_start: 0.8536 (tt0) cc_final: 0.8198 (tt0) REVERT: C 428 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7481 (mptp) REVERT: C 431 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: C 597 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6623 (tp30) REVERT: C 600 LYS cc_start: 0.7162 (ttpt) cc_final: 0.6662 (ptmm) REVERT: D 174 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8363 (mp) REVERT: D 198 GLU cc_start: 0.7343 (pm20) cc_final: 0.6704 (pm20) REVERT: D 399 MET cc_start: 0.8676 (ttm) cc_final: 0.8403 (ttp) REVERT: D 409 GLU cc_start: 0.8537 (tt0) cc_final: 0.8194 (tt0) REVERT: D 428 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7523 (mptp) REVERT: D 431 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: D 597 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6631 (tp30) REVERT: D 600 LYS cc_start: 0.7158 (ttpt) cc_final: 0.6646 (ptmm) outliers start: 35 outliers final: 12 residues processed: 194 average time/residue: 0.7019 time to fit residues: 147.4450 Evaluate side-chains 168 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU 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 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 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 286 GLN C 226 GLN C 286 GLN D 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105684 restraints weight = 18077.347| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.13 r_work: 0.3089 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2423 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= 0.114 Angle : 0.460 7.455 21328 Z= 0.244 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.030 2552 Dihedral : 10.338 74.037 2920 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.22 % Allowed : 11.39 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.20), residues: 1792 helix: 2.32 (0.15), residues: 1172 sheet: -1.54 (1.06), residues: 20 loop : 0.03 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 514 TYR 0.017 0.001 TYR D 349 PHE 0.013 0.001 PHE B 298 TRP 0.017 0.001 TRP B 168 HIS 0.002 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00258 (15812) covalent geometry : angle 0.45966 (21328) hydrogen bonds : bond 0.03306 ( 952) hydrogen bonds : angle 3.55333 ( 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 194 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.587 Fit side-chains REVERT: A 174 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 198 GLU cc_start: 0.7386 (pm20) cc_final: 0.7095 (mm-30) REVERT: A 399 MET cc_start: 0.8734 (ttm) cc_final: 0.8452 (ttp) REVERT: A 409 GLU cc_start: 0.8579 (tt0) cc_final: 0.8247 (tt0) REVERT: A 428 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7511 (mptp) REVERT: A 431 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: A 551 ASN cc_start: 0.7131 (m-40) cc_final: 0.6516 (m110) REVERT: A 597 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6662 (tp30) REVERT: A 600 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6642 (ptmm) REVERT: B 174 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 198 GLU cc_start: 0.7373 (pm20) cc_final: 0.7084 (mm-30) REVERT: B 399 MET cc_start: 0.8739 (ttm) cc_final: 0.8453 (ttp) REVERT: B 409 GLU cc_start: 0.8578 (tt0) cc_final: 0.8244 (tt0) REVERT: B 428 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7474 (mptp) REVERT: B 431 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: B 490 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (tp30) REVERT: B 597 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6589 (tp30) REVERT: B 600 LYS cc_start: 0.7124 (ttpt) cc_final: 0.6644 (ptmm) REVERT: C 174 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8351 (mp) REVERT: C 198 GLU cc_start: 0.7369 (pm20) cc_final: 0.7084 (mm-30) REVERT: C 226 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7514 (mp-120) REVERT: C 399 MET cc_start: 0.8746 (ttm) cc_final: 0.8459 (ttp) REVERT: C 409 GLU cc_start: 0.8581 (tt0) cc_final: 0.8242 (tt0) REVERT: C 428 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7470 (mptp) REVERT: C 431 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: C 490 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: C 597 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6632 (tp30) REVERT: C 600 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6773 (ptmt) REVERT: D 174 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8358 (mp) REVERT: D 198 GLU cc_start: 0.7374 (pm20) cc_final: 0.7097 (mm-30) REVERT: D 399 MET cc_start: 0.8754 (ttm) cc_final: 0.8470 (ttp) REVERT: D 409 GLU cc_start: 0.8583 (tt0) cc_final: 0.8241 (tt0) REVERT: D 428 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7525 (mptp) REVERT: D 431 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: D 490 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: D 597 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6598 (tp30) REVERT: D 600 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6698 (ptmm) outliers start: 36 outliers final: 20 residues processed: 186 average time/residue: 0.6416 time to fit residues: 130.3574 Evaluate side-chains 180 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU 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 539 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 174 LEU 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 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: 0.0050 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107488 restraints weight = 17664.715| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.08 r_work: 0.3114 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2541 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= 0.103 Angle : 0.451 8.454 21328 Z= 0.238 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.030 2552 Dihedral : 10.029 72.574 2920 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.59 % Allowed : 11.02 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.20), residues: 1792 helix: 2.24 (0.15), residues: 1180 sheet: -1.46 (1.06), residues: 20 loop : -0.10 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.015 0.001 TYR C 349 PHE 0.012 0.001 PHE D 298 TRP 0.018 0.001 TRP B 168 HIS 0.002 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00230 (15812) covalent geometry : angle 0.45117 (21328) hydrogen bonds : bond 0.03174 ( 952) hydrogen bonds : angle 3.49783 ( 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 196 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.552 Fit side-chains REVERT: A 174 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 198 GLU cc_start: 0.7365 (pm20) cc_final: 0.7078 (mm-30) REVERT: A 226 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7441 (mp-120) REVERT: A 399 MET cc_start: 0.8656 (ttm) cc_final: 0.8379 (ttp) REVERT: A 409 GLU cc_start: 0.8542 (tt0) cc_final: 0.8214 (tt0) REVERT: A 428 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7485 (mptp) REVERT: A 431 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: A 490 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: A 551 ASN cc_start: 0.7180 (m-40) cc_final: 0.6565 (m110) REVERT: A 597 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6767 (tp30) REVERT: A 600 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6971 (mtpt) REVERT: B 174 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 198 GLU cc_start: 0.7355 (pm20) cc_final: 0.7074 (mm-30) REVERT: B 226 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7436 (mp-120) REVERT: B 399 MET cc_start: 0.8674 (ttm) cc_final: 0.8399 (ttp) REVERT: B 409 GLU cc_start: 0.8529 (tt0) cc_final: 0.8203 (tt0) REVERT: B 428 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7442 (mptp) REVERT: B 431 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: B 597 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6726 (tp30) REVERT: B 600 LYS cc_start: 0.7115 (ttpt) cc_final: 0.6875 (mtpt) REVERT: C 174 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 198 GLU cc_start: 0.7348 (pm20) cc_final: 0.7068 (mm-30) REVERT: C 226 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7366 (mp-120) REVERT: C 399 MET cc_start: 0.8664 (ttm) cc_final: 0.8387 (ttp) REVERT: C 409 GLU cc_start: 0.8531 (tt0) cc_final: 0.8197 (tt0) REVERT: C 428 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7447 (mptp) REVERT: C 431 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: C 490 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: C 597 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6754 (tp30) REVERT: C 600 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6965 (mtpt) REVERT: D 174 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8349 (mp) REVERT: D 198 GLU cc_start: 0.7346 (pm20) cc_final: 0.7072 (mm-30) REVERT: D 226 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7430 (mp-120) REVERT: D 399 MET cc_start: 0.8661 (ttm) cc_final: 0.8381 (ttp) REVERT: D 409 GLU cc_start: 0.8542 (tt0) cc_final: 0.8204 (tt0) REVERT: D 428 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7508 (mptp) REVERT: D 431 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: D 490 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: D 597 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6599 (tp30) REVERT: D 600 LYS cc_start: 0.7193 (ttpt) cc_final: 0.6711 (ptmm) outliers start: 42 outliers final: 19 residues processed: 187 average time/residue: 0.6400 time to fit residues: 130.4938 Evaluate side-chains 185 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN A 534 GLN B 226 GLN B 286 GLN B 534 GLN C 226 GLN C 286 GLN D 226 GLN D 286 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107974 restraints weight = 17736.639| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.07 r_work: 0.3115 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15812 Z= 0.102 Angle : 0.455 9.773 21328 Z= 0.238 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.030 2552 Dihedral : 9.869 72.273 2920 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 11.64 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1792 helix: 2.28 (0.15), residues: 1180 sheet: -1.46 (1.07), residues: 20 loop : -0.06 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.014 0.001 TYR D 349 PHE 0.014 0.001 PHE B 423 TRP 0.018 0.001 TRP B 168 HIS 0.002 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00226 (15812) covalent geometry : angle 0.45501 (21328) hydrogen bonds : bond 0.03148 ( 952) hydrogen bonds : angle 3.47396 ( 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 197 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.565 Fit side-chains REVERT: A 174 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 198 GLU cc_start: 0.7345 (pm20) cc_final: 0.7070 (mm-30) REVERT: A 199 TYR cc_start: 0.8306 (m-80) cc_final: 0.7709 (m-80) REVERT: A 226 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7517 (mp-120) REVERT: A 399 MET cc_start: 0.8647 (ttm) cc_final: 0.8359 (ttp) REVERT: A 409 GLU cc_start: 0.8524 (tt0) cc_final: 0.8194 (tt0) REVERT: A 428 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7466 (mptp) REVERT: A 431 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: A 490 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: A 551 ASN cc_start: 0.7173 (m-40) cc_final: 0.6545 (m110) REVERT: A 597 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6788 (tp30) REVERT: A 600 LYS cc_start: 0.7202 (ttpt) cc_final: 0.6931 (mtpt) REVERT: B 174 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 198 GLU cc_start: 0.7326 (pm20) cc_final: 0.7060 (mm-30) REVERT: B 199 TYR cc_start: 0.8296 (m-80) cc_final: 0.7697 (m-80) REVERT: B 226 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7504 (mp-120) REVERT: B 399 MET cc_start: 0.8648 (ttm) cc_final: 0.8363 (ttp) REVERT: B 409 GLU cc_start: 0.8516 (tt0) cc_final: 0.8185 (tt0) REVERT: B 428 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7498 (mptp) REVERT: B 431 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: B 490 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: B 597 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6719 (tp30) REVERT: B 600 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6870 (mtpt) REVERT: C 174 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 198 GLU cc_start: 0.7318 (pm20) cc_final: 0.7056 (mm-30) REVERT: C 199 TYR cc_start: 0.8308 (m-80) cc_final: 0.7708 (m-80) REVERT: C 399 MET cc_start: 0.8655 (ttm) cc_final: 0.8374 (ttp) REVERT: C 409 GLU cc_start: 0.8531 (tt0) cc_final: 0.8197 (tt0) REVERT: C 428 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7517 (mptp) REVERT: C 431 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: C 490 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: C 597 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6775 (tp30) REVERT: D 174 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8346 (mp) REVERT: D 198 GLU cc_start: 0.7321 (pm20) cc_final: 0.7054 (mm-30) REVERT: D 226 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7506 (mp-120) REVERT: D 399 MET cc_start: 0.8654 (ttm) cc_final: 0.8370 (ttp) REVERT: D 409 GLU cc_start: 0.8538 (tt0) cc_final: 0.8200 (tt0) REVERT: D 428 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7506 (mptp) REVERT: D 431 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: D 490 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: D 597 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6745 (tp30) outliers start: 36 outliers final: 20 residues processed: 184 average time/residue: 0.6649 time to fit residues: 133.3003 Evaluate side-chains 192 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 A residue 594 MET 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 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 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: 0.7980 chunk 42 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 286 GLN B 226 GLN B 286 GLN C 286 GLN C 534 GLN D 226 GLN D 286 GLN D 534 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107485 restraints weight = 17593.876| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.08 r_work: 0.3117 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15812 Z= 0.108 Angle : 0.463 10.322 21328 Z= 0.241 Chirality : 0.039 0.145 2368 Planarity : 0.003 0.030 2552 Dihedral : 9.855 72.495 2920 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.59 % Allowed : 11.15 % Favored : 86.27 % 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: 2.19 (0.20), residues: 1792 helix: 2.25 (0.15), residues: 1180 sheet: -1.44 (1.07), residues: 20 loop : -0.04 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.015 0.001 TYR D 349 PHE 0.015 0.001 PHE A 423 TRP 0.018 0.001 TRP B 168 HIS 0.002 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00242 (15812) covalent geometry : angle 0.46333 (21328) hydrogen bonds : bond 0.03184 ( 952) hydrogen bonds : angle 3.49720 ( 2736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5100.58 seconds wall clock time: 87 minutes 40.56 seconds (5260.56 seconds total)