Starting phenix.real_space_refine on Mon Apr 6 15:29:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu4_60889/04_2026/9iu4_60889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu4_60889/04_2026/9iu4_60889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu4_60889/04_2026/9iu4_60889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu4_60889/04_2026/9iu4_60889.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu4_60889/04_2026/9iu4_60889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu4_60889/04_2026/9iu4_60889.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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 Zn 4 6.06 5 P 196 5.49 5 S 60 5.16 5 C 11579 2.51 5 N 3623 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19480 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Conformer: "B" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} bond proxies already assigned to first conformer: 3938 Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1066 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1066 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 38.859 163.315 76.522 1.00322.38 S ATOM 2447 SG CYS A 307 39.817 160.432 74.384 1.00322.20 S ATOM 2598 SG CYS A 326 41.883 161.218 76.746 1.00322.78 S ATOM 2670 SG CYS A 335 41.584 163.888 73.986 1.00323.88 S ATOM 6300 SG CYS B 304 71.498 36.924 120.961 1.00292.32 S ATOM 6318 SG CYS B 307 71.422 38.098 117.452 1.00291.66 S ATOM 6469 SG CYS B 326 68.605 38.067 118.982 1.00292.37 S ATOM 6541 SG CYS B 335 70.057 34.558 118.355 1.00294.19 S ATOM 10163 SG CYS C 304 77.497 129.433 17.503 1.00335.01 S ATOM 10181 SG CYS C 307 77.287 125.809 16.828 1.00334.63 S ATOM 10332 SG CYS C 326 79.350 126.630 19.152 1.00332.75 S ATOM 10404 SG CYS C 335 80.463 127.820 15.743 1.00332.40 S ATOM 14026 SG CYS D 304 59.437 26.461 40.810 1.00303.54 S ATOM 14044 SG CYS D 307 60.033 29.176 38.402 1.00302.91 S ATOM 14195 SG CYS D 326 57.122 29.179 39.726 1.00300.28 S ATOM 14267 SG CYS D 335 57.717 26.197 37.401 1.00300.56 S Time building chain proxies: 5.21, per 1000 atoms: 0.27 Number of scatterers: 19480 At special positions: 0 Unit cell: (119.935, 192.836, 156.385, 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) Zn 4 29.99 S 60 16.00 P 196 15.00 O 4018 8.00 N 3623 7.00 C 11579 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: 1.46 Conformation dependent library (CDL) restraints added in 728.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 307 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " Number of angles added : 24 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.7% alpha, 13.8% beta 95 base pairs and 165 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.613A pdb=" N TRP A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 117 through 151 removed outlier: 3.855A pdb=" N VAL A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.114A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.793A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 18 through 34 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.609A pdb=" N TRP B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 118 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.081A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.857A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.618A pdb=" N TRP C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 118 through 151 Processing helix chain 'C' and resid 177 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.685A pdb=" N LEU C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 478 through 486 Processing helix chain 'D' and resid 17 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.620A pdb=" N TRP D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'D' and resid 118 through 151 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.689A pdb=" N LEU D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 44 removed outlier: 7.488A pdb=" N VAL A 5 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 40 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 4 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 368 removed outlier: 7.089A pdb=" N ARG A 362 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 44 removed outlier: 7.484A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 4 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 368 removed outlier: 7.090A pdb=" N ARG B 362 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 44 removed outlier: 7.507A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU C 4 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 249 through 250 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB8, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 368 removed outlier: 7.099A pdb=" N ARG C 362 " --> pdb=" O THR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 44 removed outlier: 7.472A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 4 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AC3, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'D' and resid 302 through 304 Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'D' and resid 361 through 368 removed outlier: 7.124A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 246 hydrogen bonds 492 hydrogen bond angles 0 basepair planarities 95 basepair parallelities 165 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3547 1.33 - 1.45: 5957 1.45 - 1.57: 10313 1.57 - 1.70: 388 1.70 - 1.82: 92 Bond restraints: 20297 Sorted by residual: bond pdb=" CA SER A 157 " pdb=" CB SER A 157 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.21e+01 bond pdb=" CG HIS A 100 " pdb=" CD2 HIS A 100 " ideal model delta sigma weight residual 1.354 1.317 0.037 1.10e-02 8.26e+03 1.12e+01 bond pdb=" C SER D 18 " pdb=" O SER D 18 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" C HIS C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.330 1.366 -0.036 1.22e-02 6.72e+03 8.93e+00 bond pdb=" C ASP A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.19e-02 7.06e+03 8.22e+00 ... (remaining 20292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 26105 3.37 - 6.75: 2066 6.75 - 10.12: 160 10.12 - 13.50: 23 13.50 - 16.87: 5 Bond angle restraints: 28359 Sorted by residual: angle pdb=" O3' DG F 32 " pdb=" P DT F 33 " pdb=" O5' DT F 33 " ideal model delta sigma weight residual 104.00 87.13 16.87 1.50e+00 4.44e-01 1.26e+02 angle pdb=" O3' DG E 32 " pdb=" P DT E 33 " pdb=" O5' DT E 33 " ideal model delta sigma weight residual 104.00 87.58 16.42 1.50e+00 4.44e-01 1.20e+02 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 88.87 15.13 1.50e+00 4.44e-01 1.02e+02 angle pdb=" O3' DA F 20 " pdb=" P DC F 21 " pdb=" O5' DC F 21 " ideal model delta sigma weight residual 104.00 89.04 14.96 1.50e+00 4.44e-01 9.94e+01 angle pdb=" O3' DA E 20 " pdb=" P DC E 21 " pdb=" O5' DC E 21 " ideal model delta sigma weight residual 104.00 89.24 14.76 1.50e+00 4.44e-01 9.68e+01 ... (remaining 28354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 9475 17.87 - 35.74: 1070 35.74 - 53.61: 862 53.61 - 71.48: 199 71.48 - 89.36: 25 Dihedral angle restraints: 11631 sinusoidal: 6015 harmonic: 5616 Sorted by residual: dihedral pdb=" C ASP B 359 " pdb=" N ASP B 359 " pdb=" CA ASP B 359 " pdb=" CB ASP B 359 " ideal model delta harmonic sigma weight residual -122.60 -137.64 15.04 0 2.50e+00 1.60e-01 3.62e+01 dihedral pdb=" C ASP D 407 " pdb=" N ASP D 407 " pdb=" CA ASP D 407 " pdb=" CB ASP D 407 " ideal model delta harmonic sigma weight residual -122.60 -136.41 13.81 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C HIS C 199 " pdb=" N HIS C 199 " pdb=" CA HIS C 199 " pdb=" CB HIS C 199 " ideal model delta harmonic sigma weight residual -122.60 -136.12 13.52 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 11628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2744 0.130 - 0.260: 324 0.260 - 0.389: 30 0.389 - 0.519: 6 0.519 - 0.649: 5 Chirality restraints: 3109 Sorted by residual: chirality pdb=" P DT F 1 " pdb=" OP1 DT F 1 " pdb=" OP2 DT F 1 " pdb=" O5' DT F 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG E 1 " pdb=" OP1 DG E 1 " pdb=" OP2 DG E 1 " pdb=" O5' DG E 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 3106 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC E 30 " 0.061 2.00e-02 2.50e+03 3.06e-02 2.11e+01 pdb=" N1 DC E 30 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DC E 30 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DC E 30 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC E 30 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DC E 30 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC E 30 " 0.035 2.00e-02 2.50e+03 pdb=" C5 DC E 30 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC E 30 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 35 " -0.052 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP D 35 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 35 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 35 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP D 35 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 35 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 35 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 35 " -0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 35 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 35 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.031 2.00e-02 2.50e+03 1.89e-02 8.91e+00 pdb=" CG TRP A 432 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " -0.032 2.00e-02 2.50e+03 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 2 2.26 - 2.92: 6717 2.92 - 3.58: 28210 3.58 - 4.24: 47690 4.24 - 4.90: 77464 Nonbonded interactions: 160083 Sorted by model distance: nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.598 3.400 nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.598 3.400 nonbonded pdb=" OH TYR B 312 " pdb=" OP2 DT E 43 " model vdw 2.263 3.040 nonbonded pdb=" NH1 ARG B 58 " pdb=" O LEU B 83 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG A 58 " pdb=" O LEU A 83 " model vdw 2.284 3.120 ... (remaining 160078 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 1 through 141 or resid 143 through 1000)) selection = (chain 'B' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'C' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'D' and (resid 1 through 141 or resid 143 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.580 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 : 0.010 0.088 20313 Z= 0.590 Angle : 1.911 20.643 28383 Z= 1.215 Chirality : 0.091 0.649 3109 Planarity : 0.007 0.073 3022 Dihedral : 21.239 89.355 7997 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.05 % Allowed : 7.54 % Favored : 88.41 % Cbeta Deviations : 1.10 % 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: 0.34 (0.17), residues: 1937 helix: 0.55 (0.14), residues: 924 sheet: 0.09 (0.28), residues: 269 loop : 0.10 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.004 ARG C 461 TYR 0.032 0.006 TYR B 154 PHE 0.037 0.006 PHE A 112 TRP 0.052 0.006 TRP D 35 HIS 0.019 0.004 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00987 (20297) covalent geometry : angle 1.89155 (28359) hydrogen bonds : bond 0.16409 ( 1059) hydrogen bonds : angle 6.02006 ( 2792) metal coordination : bond 0.05615 ( 16) metal coordination : angle 9.46468 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 509 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7019 (mmm) cc_final: 0.6808 (tpt) REVERT: A 28 GLN cc_start: 0.9078 (tt0) cc_final: 0.8845 (tt0) REVERT: A 55 ARG cc_start: 0.6328 (mtt180) cc_final: 0.6089 (mtt180) REVERT: A 64 TRP cc_start: 0.7661 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: A 72 PHE cc_start: 0.6353 (p90) cc_final: 0.6029 (p90) REVERT: A 73 ASP cc_start: 0.7237 (m-30) cc_final: 0.6925 (m-30) REVERT: A 89 HIS cc_start: 0.7797 (m170) cc_final: 0.7429 (m170) REVERT: A 96 TRP cc_start: 0.6989 (t60) cc_final: 0.6575 (t60) REVERT: A 98 GLU cc_start: 0.7928 (tp30) cc_final: 0.7560 (tp30) REVERT: A 133 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 138 LYS cc_start: 0.7443 (mttm) cc_final: 0.7082 (mttp) REVERT: A 139 GLU cc_start: 0.7331 (tp30) cc_final: 0.7073 (tp30) REVERT: A 169 ASP cc_start: 0.7686 (t0) cc_final: 0.7200 (t0) REVERT: A 175 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6321 (m) REVERT: A 182 GLU cc_start: 0.8404 (tt0) cc_final: 0.8027 (tt0) REVERT: A 204 ASP cc_start: 0.6885 (t0) cc_final: 0.6622 (t0) REVERT: A 219 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7099 (mm110) REVERT: A 229 GLU cc_start: 0.7654 (pt0) cc_final: 0.7086 (pt0) REVERT: A 251 ASN cc_start: 0.7697 (m-40) cc_final: 0.7481 (m-40) REVERT: A 265 ARG cc_start: 0.7874 (ptt180) cc_final: 0.6733 (ptm160) REVERT: A 274 GLN cc_start: 0.7562 (mt0) cc_final: 0.7336 (mt0) REVERT: A 375 VAL cc_start: 0.8734 (t) cc_final: 0.8431 (t) REVERT: A 376 GLU cc_start: 0.8574 (tt0) cc_final: 0.8310 (tt0) REVERT: A 379 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 381 ASN cc_start: 0.8388 (t0) cc_final: 0.8054 (t0) REVERT: A 397 ARG cc_start: 0.0892 (OUTLIER) cc_final: -0.0868 (tpm170) REVERT: A 454 TRP cc_start: 0.8798 (t60) cc_final: 0.8355 (t60) REVERT: A 458 MET cc_start: 0.6633 (mmm) cc_final: 0.6061 (tmm) REVERT: B 6 VAL cc_start: 0.7645 (t) cc_final: 0.7260 (m) REVERT: B 24 GLU cc_start: 0.8006 (tt0) cc_final: 0.7644 (tt0) REVERT: B 28 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7774 (tp40) REVERT: B 32 GLN cc_start: 0.7634 (mt0) cc_final: 0.7319 (mt0) REVERT: B 64 TRP cc_start: 0.7995 (m100) cc_final: 0.7549 (m100) REVERT: B 73 ASP cc_start: 0.6100 (m-30) cc_final: 0.5686 (m-30) REVERT: B 81 ASP cc_start: 0.7565 (p0) cc_final: 0.7332 (p0) REVERT: B 82 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7417 (mmm160) REVERT: B 91 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7071 (tp40) REVERT: B 105 VAL cc_start: 0.7231 (t) cc_final: 0.6794 (p) REVERT: B 118 PHE cc_start: 0.7868 (m-80) cc_final: 0.7321 (m-10) REVERT: B 135 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 153 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (mtmp) REVERT: B 182 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 344 GLU cc_start: 0.9074 (tt0) cc_final: 0.8591 (tt0) REVERT: B 376 GLU cc_start: 0.8617 (tt0) cc_final: 0.7996 (tt0) REVERT: B 458 MET cc_start: 0.7727 (mmt) cc_final: 0.7485 (mmt) REVERT: B 459 ASN cc_start: 0.7572 (m-40) cc_final: 0.7312 (m-40) REVERT: B 466 VAL cc_start: 0.6357 (OUTLIER) cc_final: 0.6135 (t) REVERT: C 21 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7341 (mmm160) REVERT: C 22 GLN cc_start: 0.7847 (mt0) cc_final: 0.7461 (mt0) REVERT: C 24 GLU cc_start: 0.7661 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 25 SER cc_start: 0.7567 (t) cc_final: 0.7212 (m) REVERT: C 33 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6616 (tpp80) REVERT: C 42 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7409 (mt-10) REVERT: C 64 TRP cc_start: 0.7156 (m100) cc_final: 0.6529 (m100) REVERT: C 70 GLN cc_start: 0.7407 (mt0) cc_final: 0.7081 (mp10) REVERT: C 95 HIS cc_start: 0.6580 (t70) cc_final: 0.6073 (t70) REVERT: C 96 TRP cc_start: 0.6753 (t60) cc_final: 0.6451 (t60) REVERT: C 98 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5966 (pp20) REVERT: C 116 THR cc_start: 0.7543 (t) cc_final: 0.7186 (t) REVERT: C 135 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6769 (mp0) REVERT: C 140 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6893 (mpt-90) REVERT: C 163 TYR cc_start: 0.6605 (m-80) cc_final: 0.5900 (m-80) REVERT: C 173 ARG cc_start: 0.6293 (mtt90) cc_final: 0.5893 (mmt90) REVERT: C 186 GLU cc_start: 0.8884 (tp30) cc_final: 0.8496 (tp30) REVERT: C 193 ASP cc_start: 0.7988 (m-30) cc_final: 0.7664 (m-30) REVERT: C 198 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6002 (mm) REVERT: C 199 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6901 (p-80) REVERT: C 216 TYR cc_start: 0.8023 (t80) cc_final: 0.7640 (t80) REVERT: C 224 GLU cc_start: 0.7317 (tt0) cc_final: 0.7063 (tt0) REVERT: C 226 GLN cc_start: 0.7251 (mp10) cc_final: 0.6751 (mp10) REVERT: C 235 LEU cc_start: 0.8072 (mt) cc_final: 0.7570 (pp) REVERT: C 239 MET cc_start: 0.8587 (mmm) cc_final: 0.7956 (mmm) REVERT: C 244 MET cc_start: 0.7883 (mmt) cc_final: 0.6920 (tpp) REVERT: C 251 ASN cc_start: 0.7265 (m110) cc_final: 0.6989 (m110) REVERT: C 273 GLU cc_start: 0.8780 (pt0) cc_final: 0.8557 (pt0) REVERT: C 331 PHE cc_start: 0.7576 (m-80) cc_final: 0.6949 (m-80) REVERT: C 342 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.4129 (mmm) REVERT: C 384 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7131 (pp) REVERT: C 448 THR cc_start: 0.8169 (p) cc_final: 0.7847 (t) REVERT: C 452 ASN cc_start: 0.8112 (t0) cc_final: 0.7537 (t0) REVERT: C 454 TRP cc_start: 0.8594 (t60) cc_final: 0.7822 (t60) REVERT: C 464 PHE cc_start: 0.7257 (p90) cc_final: 0.7031 (p90) REVERT: D 21 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7439 (mtm180) REVERT: D 27 GLN cc_start: 0.7268 (mt0) cc_final: 0.6920 (mt0) REVERT: D 54 ASP cc_start: 0.5965 (t0) cc_final: 0.5467 (t0) REVERT: D 74 VAL cc_start: 0.6821 (p) cc_final: 0.6376 (m) REVERT: D 88 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7123 (ttm110) REVERT: D 101 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8071 (mmtt) REVERT: D 102 LYS cc_start: 0.6771 (mmtt) cc_final: 0.6341 (mmtp) REVERT: D 135 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7266 (mm-30) REVERT: D 150 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7817 (ttm-80) REVERT: D 153 LYS cc_start: 0.7478 (mttt) cc_final: 0.7042 (mttt) REVERT: D 158 LEU cc_start: 0.8616 (tp) cc_final: 0.8411 (tt) REVERT: D 164 LEU cc_start: 0.6597 (tp) cc_final: 0.6311 (mp) REVERT: D 173 ARG cc_start: 0.6990 (ttm110) cc_final: 0.6599 (mtp85) REVERT: D 182 GLU cc_start: 0.8118 (tt0) cc_final: 0.7841 (tt0) REVERT: D 216 TYR cc_start: 0.6731 (t80) cc_final: 0.6224 (t80) REVERT: D 224 GLU cc_start: 0.7482 (tp30) cc_final: 0.7195 (tp30) REVERT: D 228 ARG cc_start: 0.6429 (mtt-85) cc_final: 0.6181 (mtt90) REVERT: D 269 ILE cc_start: 0.7238 (mm) cc_final: 0.6804 (mm) REVERT: D 276 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8045 (mm-30) REVERT: D 331 PHE cc_start: 0.6355 (m-10) cc_final: 0.6139 (m-10) REVERT: D 452 ASN cc_start: 0.6928 (t0) cc_final: 0.6585 (t0) REVERT: D 457 SER cc_start: 0.8213 (p) cc_final: 0.7374 (p) outliers start: 65 outliers final: 17 residues processed: 545 average time/residue: 0.1695 time to fit residues: 130.4050 Evaluate side-chains 469 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 439 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 148 ASN A 446 GLN B 22 GLN B 27 GLN B 60 ASN B 91 GLN B 148 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 91 GLN C 480 GLN D 111 HIS D 189 HIS ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.190038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137272 restraints weight = 42599.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142346 restraints weight = 16955.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145401 restraints weight = 9948.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.147257 restraints weight = 7397.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148315 restraints weight = 6300.626| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20313 Z= 0.181 Angle : 0.609 10.595 28383 Z= 0.340 Chirality : 0.039 0.186 3109 Planarity : 0.005 0.047 3022 Dihedral : 22.943 83.614 4347 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.99 % Allowed : 12.90 % Favored : 84.11 % 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: 2.17 (0.19), residues: 1937 helix: 2.52 (0.16), residues: 921 sheet: 0.08 (0.28), residues: 290 loop : 0.73 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 58 TYR 0.016 0.002 TYR A 324 PHE 0.025 0.002 PHE C 314 TRP 0.038 0.002 TRP B 443 HIS 0.007 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00388 (20297) covalent geometry : angle 0.59901 (28359) hydrogen bonds : bond 0.04726 ( 1059) hydrogen bonds : angle 3.75841 ( 2792) metal coordination : bond 0.00575 ( 16) metal coordination : angle 3.82331 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 475 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8035 (t) cc_final: 0.7580 (m) REVERT: A 64 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: A 73 ASP cc_start: 0.6827 (m-30) cc_final: 0.6624 (m-30) REVERT: A 89 HIS cc_start: 0.7851 (m170) cc_final: 0.7517 (m170) REVERT: A 96 TRP cc_start: 0.8342 (t60) cc_final: 0.8008 (t60) REVERT: A 98 GLU cc_start: 0.7473 (tp30) cc_final: 0.6836 (tp30) REVERT: A 139 GLU cc_start: 0.7354 (tp30) cc_final: 0.7083 (tp30) REVERT: A 168 VAL cc_start: 0.8148 (t) cc_final: 0.7829 (m) REVERT: A 169 ASP cc_start: 0.7189 (t0) cc_final: 0.6622 (t0) REVERT: A 175 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7789 (m) REVERT: A 182 GLU cc_start: 0.7621 (tt0) cc_final: 0.7275 (tt0) REVERT: A 189 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7316 (t-90) REVERT: A 219 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7369 (mm-40) REVERT: A 241 SER cc_start: 0.8419 (t) cc_final: 0.7921 (p) REVERT: A 251 ASN cc_start: 0.8499 (m-40) cc_final: 0.8252 (m-40) REVERT: A 278 LEU cc_start: 0.8969 (tp) cc_final: 0.8510 (tp) REVERT: A 342 MET cc_start: 0.4398 (ttp) cc_final: 0.3909 (ttp) REVERT: A 375 VAL cc_start: 0.8823 (t) cc_final: 0.8387 (t) REVERT: A 376 GLU cc_start: 0.8363 (tt0) cc_final: 0.7794 (tt0) REVERT: A 379 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 381 ASN cc_start: 0.8162 (t0) cc_final: 0.7763 (t0) REVERT: A 397 ARG cc_start: 0.0057 (OUTLIER) cc_final: -0.2488 (tpm170) REVERT: B 6 VAL cc_start: 0.8209 (t) cc_final: 0.7798 (m) REVERT: B 22 GLN cc_start: 0.7143 (mt0) cc_final: 0.6867 (mt0) REVERT: B 24 GLU cc_start: 0.7611 (tt0) cc_final: 0.7214 (tt0) REVERT: B 28 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7332 (tp40) REVERT: B 64 TRP cc_start: 0.7363 (m100) cc_final: 0.6831 (m100) REVERT: B 91 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7493 (mm110) REVERT: B 102 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7879 (mmtt) REVERT: B 105 VAL cc_start: 0.8361 (t) cc_final: 0.8008 (p) REVERT: B 135 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 138 LYS cc_start: 0.8287 (mtmt) cc_final: 0.8083 (mtmt) REVERT: B 182 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 219 GLN cc_start: 0.6869 (tp40) cc_final: 0.6592 (tp40) REVERT: B 259 ASP cc_start: 0.8156 (p0) cc_final: 0.7888 (p0) REVERT: B 344 GLU cc_start: 0.8547 (tt0) cc_final: 0.8237 (tm-30) REVERT: B 376 GLU cc_start: 0.8350 (tt0) cc_final: 0.7669 (tt0) REVERT: B 381 ASN cc_start: 0.8669 (m-40) cc_final: 0.8369 (m-40) REVERT: B 458 MET cc_start: 0.8068 (mmt) cc_final: 0.7529 (mmt) REVERT: B 459 ASN cc_start: 0.8461 (m-40) cc_final: 0.8017 (m-40) REVERT: B 461 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7437 (mtp85) REVERT: C 9 LEU cc_start: 0.7829 (tp) cc_final: 0.7534 (mm) REVERT: C 21 ARG cc_start: 0.7570 (mmt90) cc_final: 0.7282 (mmm160) REVERT: C 43 ASP cc_start: 0.6761 (m-30) cc_final: 0.6381 (m-30) REVERT: C 51 ASP cc_start: 0.7500 (t0) cc_final: 0.7295 (t0) REVERT: C 135 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6653 (mp0) REVERT: C 140 ARG cc_start: 0.7391 (mpt-90) cc_final: 0.7058 (ttm110) REVERT: C 142 ARG cc_start: 0.7403 (ttp80) cc_final: 0.7092 (ttt-90) REVERT: C 173 ARG cc_start: 0.6759 (mtt90) cc_final: 0.6376 (mtt90) REVERT: C 181 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7365 (mtm110) REVERT: C 186 GLU cc_start: 0.8051 (tp30) cc_final: 0.7790 (tp30) REVERT: C 193 ASP cc_start: 0.7806 (m-30) cc_final: 0.7116 (m-30) REVERT: C 204 ASP cc_start: 0.7432 (t0) cc_final: 0.7107 (t0) REVERT: C 220 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 226 GLN cc_start: 0.7808 (mp10) cc_final: 0.7088 (mp10) REVERT: C 228 ARG cc_start: 0.7281 (mpt-90) cc_final: 0.6908 (mpt-90) REVERT: C 230 TRP cc_start: 0.7607 (m100) cc_final: 0.7400 (m100) REVERT: C 235 LEU cc_start: 0.7844 (mt) cc_final: 0.7511 (mm) REVERT: C 239 MET cc_start: 0.7674 (mmm) cc_final: 0.7250 (mmm) REVERT: C 244 MET cc_start: 0.7096 (mmt) cc_final: 0.6682 (mmt) REVERT: C 325 ARG cc_start: 0.6965 (ptm-80) cc_final: 0.6230 (ptm160) REVERT: C 331 PHE cc_start: 0.7308 (m-80) cc_final: 0.6875 (m-80) REVERT: C 384 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7495 (pp) REVERT: C 404 GLU cc_start: 0.8232 (pt0) cc_final: 0.7977 (pt0) REVERT: C 454 TRP cc_start: 0.8114 (t60) cc_final: 0.7543 (t60) REVERT: D 22 GLN cc_start: 0.8162 (mt0) cc_final: 0.7893 (mt0) REVERT: D 25 SER cc_start: 0.8067 (m) cc_final: 0.7769 (p) REVERT: D 32 GLN cc_start: 0.7743 (tp40) cc_final: 0.7381 (tt0) REVERT: D 42 GLU cc_start: 0.6986 (tt0) cc_final: 0.6770 (tt0) REVERT: D 50 VAL cc_start: 0.8658 (t) cc_final: 0.8272 (m) REVERT: D 54 ASP cc_start: 0.7730 (t0) cc_final: 0.7344 (t0) REVERT: D 74 VAL cc_start: 0.7905 (p) cc_final: 0.7558 (m) REVERT: D 109 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7235 (mt-10) REVERT: D 111 HIS cc_start: 0.8256 (p-80) cc_final: 0.7751 (p-80) REVERT: D 113 ASP cc_start: 0.7531 (t0) cc_final: 0.7217 (t0) REVERT: D 142 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7263 (ttt90) REVERT: D 150 ARG cc_start: 0.7916 (tpp-160) cc_final: 0.7590 (mtt-85) REVERT: D 164 LEU cc_start: 0.8141 (tp) cc_final: 0.7840 (mp) REVERT: D 173 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7297 (mtt-85) REVERT: D 265 ARG cc_start: 0.7938 (ptt180) cc_final: 0.6776 (ptt180) REVERT: D 276 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7069 (mm-30) REVERT: D 327 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7362 (ttp80) REVERT: D 331 PHE cc_start: 0.7237 (m-10) cc_final: 0.6368 (m-10) REVERT: D 351 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7775 (pp20) REVERT: D 409 ARG cc_start: 0.8567 (mmp80) cc_final: 0.8319 (mmp80) REVERT: D 452 ASN cc_start: 0.7561 (t0) cc_final: 0.7139 (t0) REVERT: D 458 MET cc_start: 0.7369 (mmt) cc_final: 0.7081 (mmt) outliers start: 48 outliers final: 22 residues processed: 501 average time/residue: 0.1608 time to fit residues: 115.3950 Evaluate side-chains 478 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 448 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 181 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS B 32 GLN B 60 ASN B 89 HIS B 100 HIS C 148 ASN C 452 ASN D 189 HIS D 459 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.187975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135685 restraints weight = 38785.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140548 restraints weight = 16075.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143546 restraints weight = 9657.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145283 restraints weight = 7266.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146270 restraints weight = 6242.859| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20313 Z= 0.193 Angle : 0.582 11.119 28383 Z= 0.325 Chirality : 0.039 0.192 3109 Planarity : 0.004 0.067 3022 Dihedral : 22.942 86.480 4311 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.43 % Allowed : 15.14 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 1937 helix: 2.56 (0.17), residues: 917 sheet: 0.11 (0.29), residues: 283 loop : 0.90 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 142 TYR 0.017 0.002 TYR A 154 PHE 0.016 0.001 PHE C 314 TRP 0.017 0.002 TRP B 443 HIS 0.022 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00416 (20297) covalent geometry : angle 0.57143 (28359) hydrogen bonds : bond 0.04182 ( 1059) hydrogen bonds : angle 3.67424 ( 2792) metal coordination : bond 0.00425 ( 16) metal coordination : angle 3.92633 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 467 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7139 (tm-30) REVERT: A 89 HIS cc_start: 0.7857 (m170) cc_final: 0.7521 (m170) REVERT: A 98 GLU cc_start: 0.7376 (tp30) cc_final: 0.6701 (tp30) REVERT: A 109 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6627 (mp0) REVERT: A 139 GLU cc_start: 0.7370 (tp30) cc_final: 0.7108 (tp30) REVERT: A 142 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7452 (ttp-110) REVERT: A 168 VAL cc_start: 0.8295 (t) cc_final: 0.8007 (m) REVERT: A 169 ASP cc_start: 0.7198 (t0) cc_final: 0.6558 (t0) REVERT: A 175 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7814 (m) REVERT: A 182 GLU cc_start: 0.7643 (tt0) cc_final: 0.7164 (tt0) REVERT: A 185 LEU cc_start: 0.8841 (mt) cc_final: 0.8594 (mm) REVERT: A 204 ASP cc_start: 0.7441 (t70) cc_final: 0.7068 (t0) REVERT: A 208 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.7158 (mtp-110) REVERT: A 219 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: A 241 SER cc_start: 0.8476 (t) cc_final: 0.7954 (p) REVERT: A 251 ASN cc_start: 0.8576 (m-40) cc_final: 0.8328 (m-40) REVERT: A 278 LEU cc_start: 0.9024 (tp) cc_final: 0.8741 (tp) REVERT: A 281 GLU cc_start: 0.8072 (tp30) cc_final: 0.7369 (tp30) REVERT: A 342 MET cc_start: 0.4561 (ttp) cc_final: 0.4033 (ttp) REVERT: A 375 VAL cc_start: 0.8836 (t) cc_final: 0.8297 (t) REVERT: A 376 GLU cc_start: 0.8354 (tt0) cc_final: 0.7861 (tt0) REVERT: A 379 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 381 ASN cc_start: 0.8085 (t0) cc_final: 0.7729 (t0) REVERT: A 397 ARG cc_start: 0.0428 (OUTLIER) cc_final: -0.2315 (tpm170) REVERT: A 419 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6274 (tm-30) REVERT: B 6 VAL cc_start: 0.8263 (t) cc_final: 0.7876 (m) REVERT: B 22 GLN cc_start: 0.7365 (mt0) cc_final: 0.7033 (mt0) REVERT: B 24 GLU cc_start: 0.7747 (tt0) cc_final: 0.7288 (tt0) REVERT: B 28 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7647 (tp40) REVERT: B 57 ARG cc_start: 0.7184 (mmm-85) cc_final: 0.6878 (mtm-85) REVERT: B 64 TRP cc_start: 0.7396 (m100) cc_final: 0.7051 (m100) REVERT: B 91 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7414 (tp40) REVERT: B 105 VAL cc_start: 0.8360 (t) cc_final: 0.7980 (p) REVERT: B 106 SER cc_start: 0.8186 (t) cc_final: 0.7918 (p) REVERT: B 135 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 138 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8112 (mtmt) REVERT: B 219 GLN cc_start: 0.6973 (tp40) cc_final: 0.6716 (tp40) REVERT: B 376 GLU cc_start: 0.8304 (tt0) cc_final: 0.7736 (tt0) REVERT: B 381 ASN cc_start: 0.8643 (m-40) cc_final: 0.8339 (m-40) REVERT: B 430 TRP cc_start: 0.9009 (m100) cc_final: 0.8524 (m100) REVERT: B 443 TRP cc_start: 0.7694 (t-100) cc_final: 0.6288 (t-100) REVERT: B 458 MET cc_start: 0.8033 (mmt) cc_final: 0.7504 (mmt) REVERT: B 459 ASN cc_start: 0.8519 (m-40) cc_final: 0.8122 (m-40) REVERT: C 9 LEU cc_start: 0.8023 (tp) cc_final: 0.7750 (mt) REVERT: C 21 ARG cc_start: 0.7579 (mmt90) cc_final: 0.7291 (mmm160) REVERT: C 26 CYS cc_start: 0.7131 (m) cc_final: 0.6861 (m) REVERT: C 29 LEU cc_start: 0.8068 (tp) cc_final: 0.7686 (tt) REVERT: C 43 ASP cc_start: 0.6797 (m-30) cc_final: 0.6523 (m-30) REVERT: C 57 ARG cc_start: 0.8099 (mpp80) cc_final: 0.7807 (mtm180) REVERT: C 92 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: C 98 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5711 (pp20) REVERT: C 135 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6574 (mp0) REVERT: C 140 ARG cc_start: 0.7326 (mpt-90) cc_final: 0.7030 (ttm110) REVERT: C 173 ARG cc_start: 0.6808 (mtt90) cc_final: 0.6404 (mtt90) REVERT: C 181 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7503 (mtm110) REVERT: C 186 GLU cc_start: 0.7999 (tp30) cc_final: 0.7771 (tp30) REVERT: C 193 ASP cc_start: 0.7738 (m-30) cc_final: 0.7502 (m-30) REVERT: C 199 HIS cc_start: 0.6416 (p-80) cc_final: 0.6181 (p-80) REVERT: C 204 ASP cc_start: 0.7534 (t0) cc_final: 0.7107 (t0) REVERT: C 226 GLN cc_start: 0.7842 (mp10) cc_final: 0.7093 (mp10) REVERT: C 228 ARG cc_start: 0.7462 (mpt-90) cc_final: 0.7132 (mpt-90) REVERT: C 235 LEU cc_start: 0.7863 (mt) cc_final: 0.7332 (pp) REVERT: C 239 MET cc_start: 0.7575 (mmm) cc_final: 0.7183 (mmm) REVERT: C 265 ARG cc_start: 0.7820 (ptt180) cc_final: 0.7593 (ptt180) REVERT: C 331 PHE cc_start: 0.7362 (m-80) cc_final: 0.6890 (m-80) REVERT: C 354 LEU cc_start: 0.8947 (mm) cc_final: 0.8500 (pp) REVERT: C 404 GLU cc_start: 0.8292 (pt0) cc_final: 0.8011 (pt0) REVERT: C 452 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8048 (m-40) REVERT: C 454 TRP cc_start: 0.8057 (t60) cc_final: 0.7480 (t60) REVERT: D 21 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7844 (mtm180) REVERT: D 25 SER cc_start: 0.8173 (m) cc_final: 0.7867 (p) REVERT: D 32 GLN cc_start: 0.7940 (tp40) cc_final: 0.7624 (tt0) REVERT: D 42 GLU cc_start: 0.6991 (tt0) cc_final: 0.6779 (tt0) REVERT: D 50 VAL cc_start: 0.8669 (t) cc_final: 0.8260 (m) REVERT: D 54 ASP cc_start: 0.7819 (t0) cc_final: 0.7564 (t0) REVERT: D 73 ASP cc_start: 0.6675 (m-30) cc_final: 0.6436 (m-30) REVERT: D 74 VAL cc_start: 0.7998 (p) cc_final: 0.7718 (m) REVERT: D 96 TRP cc_start: 0.8364 (t60) cc_final: 0.8144 (t60) REVERT: D 102 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7689 (mmtp) REVERT: D 111 HIS cc_start: 0.8379 (p-80) cc_final: 0.8000 (p-80) REVERT: D 113 ASP cc_start: 0.7400 (t0) cc_final: 0.7057 (t0) REVERT: D 142 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7321 (ttt-90) REVERT: D 173 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7464 (mtp85) REVERT: D 190 ARG cc_start: 0.8032 (mtp180) cc_final: 0.7671 (tpp80) REVERT: D 272 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7261 (mmm160) REVERT: D 276 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7707 (mm-30) REVERT: D 329 MET cc_start: 0.6796 (tpp) cc_final: 0.6429 (tpp) REVERT: D 331 PHE cc_start: 0.7246 (m-10) cc_final: 0.7027 (m-80) REVERT: D 452 ASN cc_start: 0.7679 (t0) cc_final: 0.7293 (t0) REVERT: D 458 MET cc_start: 0.7516 (mmt) cc_final: 0.7210 (mmt) outliers start: 55 outliers final: 30 residues processed: 495 average time/residue: 0.1597 time to fit residues: 113.9614 Evaluate side-chains 491 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 455 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 149 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN B 60 ASN B 89 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 452 ASN D 22 GLN D 226 GLN D 251 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.187903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.135277 restraints weight = 42041.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140271 restraints weight = 16856.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143405 restraints weight = 9953.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145228 restraints weight = 7354.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146273 restraints weight = 6251.846| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20313 Z= 0.174 Angle : 0.579 14.765 28383 Z= 0.315 Chirality : 0.038 0.162 3109 Planarity : 0.004 0.062 3022 Dihedral : 22.777 86.014 4302 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.36 % Allowed : 17.69 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 1937 helix: 2.54 (0.17), residues: 911 sheet: 0.17 (0.29), residues: 291 loop : 0.93 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 444 TYR 0.017 0.002 TYR A 154 PHE 0.032 0.001 PHE C 118 TRP 0.018 0.001 TRP D 345 HIS 0.011 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00375 (20297) covalent geometry : angle 0.56166 (28359) hydrogen bonds : bond 0.03941 ( 1059) hydrogen bonds : angle 3.64717 ( 2792) metal coordination : bond 0.00384 ( 16) metal coordination : angle 4.85338 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 453 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8230 (m-40) cc_final: 0.8003 (m-40) REVERT: A 89 HIS cc_start: 0.7874 (m170) cc_final: 0.7563 (m170) REVERT: A 98 GLU cc_start: 0.7393 (tp30) cc_final: 0.6720 (tp30) REVERT: A 109 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6635 (mp0) REVERT: A 139 GLU cc_start: 0.7381 (tp30) cc_final: 0.7066 (tp30) REVERT: A 168 VAL cc_start: 0.8377 (t) cc_final: 0.8131 (m) REVERT: A 169 ASP cc_start: 0.7236 (t0) cc_final: 0.6598 (t0) REVERT: A 175 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7789 (m) REVERT: A 182 GLU cc_start: 0.7623 (tt0) cc_final: 0.7176 (tt0) REVERT: A 185 LEU cc_start: 0.8813 (mt) cc_final: 0.8570 (mm) REVERT: A 219 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7056 (mm-40) REVERT: A 241 SER cc_start: 0.8395 (t) cc_final: 0.7601 (p) REVERT: A 251 ASN cc_start: 0.8598 (m-40) cc_final: 0.8336 (m-40) REVERT: A 278 LEU cc_start: 0.9028 (tp) cc_final: 0.8655 (tp) REVERT: A 281 GLU cc_start: 0.8097 (tp30) cc_final: 0.7407 (tp30) REVERT: A 342 MET cc_start: 0.4630 (ttp) cc_final: 0.4110 (ttp) REVERT: A 376 GLU cc_start: 0.8348 (tt0) cc_final: 0.7854 (tt0) REVERT: A 379 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 381 ASN cc_start: 0.7909 (t0) cc_final: 0.7594 (t0) REVERT: A 397 ARG cc_start: 0.1360 (OUTLIER) cc_final: -0.1209 (tpm170) REVERT: A 419 GLU cc_start: 0.6935 (tm-30) cc_final: 0.5684 (tm-30) REVERT: B 6 VAL cc_start: 0.8300 (t) cc_final: 0.7913 (m) REVERT: B 22 GLN cc_start: 0.7429 (mt0) cc_final: 0.6998 (mt0) REVERT: B 28 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7472 (tp-100) REVERT: B 57 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6860 (mtm-85) REVERT: B 60 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6424 (m-40) REVERT: B 64 TRP cc_start: 0.7548 (m100) cc_final: 0.7342 (m100) REVERT: B 91 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7486 (tp-100) REVERT: B 135 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 138 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8138 (mtmt) REVERT: B 219 GLN cc_start: 0.7007 (tp40) cc_final: 0.6765 (tp40) REVERT: B 292 VAL cc_start: 0.8695 (t) cc_final: 0.8299 (m) REVERT: B 376 GLU cc_start: 0.8249 (tt0) cc_final: 0.7762 (tt0) REVERT: B 381 ASN cc_start: 0.8670 (m-40) cc_final: 0.8385 (m-40) REVERT: B 430 TRP cc_start: 0.9023 (m100) cc_final: 0.8554 (m100) REVERT: B 458 MET cc_start: 0.8037 (mmt) cc_final: 0.7501 (mmt) REVERT: B 459 ASN cc_start: 0.8502 (m-40) cc_final: 0.8089 (m-40) REVERT: C 9 LEU cc_start: 0.8106 (tp) cc_final: 0.7860 (mt) REVERT: C 21 ARG cc_start: 0.7449 (mmt90) cc_final: 0.7153 (mmm160) REVERT: C 26 CYS cc_start: 0.7188 (m) cc_final: 0.6986 (m) REVERT: C 29 LEU cc_start: 0.7926 (tp) cc_final: 0.7509 (tt) REVERT: C 43 ASP cc_start: 0.6713 (m-30) cc_final: 0.6482 (m-30) REVERT: C 57 ARG cc_start: 0.8088 (mpp80) cc_final: 0.7801 (mpp80) REVERT: C 92 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: C 96 TRP cc_start: 0.8438 (t60) cc_final: 0.7849 (t60) REVERT: C 135 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6722 (mp0) REVERT: C 140 ARG cc_start: 0.7350 (mpt-90) cc_final: 0.7106 (ttm110) REVERT: C 142 ARG cc_start: 0.7403 (tmm-80) cc_final: 0.7123 (ttt-90) REVERT: C 181 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7499 (mtm110) REVERT: C 186 GLU cc_start: 0.7998 (tp30) cc_final: 0.7767 (tp30) REVERT: C 199 HIS cc_start: 0.6472 (p-80) cc_final: 0.6194 (p-80) REVERT: C 204 ASP cc_start: 0.7490 (t0) cc_final: 0.7075 (t0) REVERT: C 220 LEU cc_start: 0.8778 (mt) cc_final: 0.8559 (mp) REVERT: C 226 GLN cc_start: 0.7866 (mp10) cc_final: 0.6959 (mp10) REVERT: C 235 LEU cc_start: 0.8023 (mt) cc_final: 0.7370 (pp) REVERT: C 239 MET cc_start: 0.7668 (mmm) cc_final: 0.7288 (mmm) REVERT: C 331 PHE cc_start: 0.7371 (m-80) cc_final: 0.6869 (m-80) REVERT: C 384 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7501 (pp) REVERT: C 404 GLU cc_start: 0.8398 (pt0) cc_final: 0.8168 (pt0) REVERT: C 409 ARG cc_start: 0.8655 (mmp80) cc_final: 0.8333 (mmp80) REVERT: C 452 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8444 (m-40) REVERT: C 458 MET cc_start: 0.8249 (mmt) cc_final: 0.7681 (mpp) REVERT: D 25 SER cc_start: 0.8098 (m) cc_final: 0.7844 (p) REVERT: D 50 VAL cc_start: 0.8646 (t) cc_final: 0.8306 (m) REVERT: D 54 ASP cc_start: 0.7795 (t0) cc_final: 0.7554 (t0) REVERT: D 74 VAL cc_start: 0.8028 (p) cc_final: 0.7682 (m) REVERT: D 113 ASP cc_start: 0.7368 (t0) cc_final: 0.7070 (t0) REVERT: D 149 ILE cc_start: 0.8430 (mm) cc_final: 0.8159 (tp) REVERT: D 182 GLU cc_start: 0.7171 (pt0) cc_final: 0.6823 (pt0) REVERT: D 193 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7560 (p0) REVERT: D 216 TYR cc_start: 0.7720 (t80) cc_final: 0.7242 (t80) REVERT: D 221 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7847 (mm-40) REVERT: D 272 ARG cc_start: 0.7598 (mmm160) cc_final: 0.6970 (mmm160) REVERT: D 276 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7212 (mm-30) REVERT: D 279 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7865 (ttm110) REVERT: D 329 MET cc_start: 0.6821 (tpp) cc_final: 0.6388 (tpp) REVERT: D 350 GLU cc_start: 0.8752 (pt0) cc_final: 0.8502 (pt0) REVERT: D 351 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: D 404 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7880 (mp0) REVERT: D 452 ASN cc_start: 0.7817 (t0) cc_final: 0.7409 (t0) REVERT: D 458 MET cc_start: 0.7517 (mmt) cc_final: 0.7195 (mmt) outliers start: 54 outliers final: 31 residues processed: 482 average time/residue: 0.1543 time to fit residues: 107.5558 Evaluate side-chains 483 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 443 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS B 89 HIS C 452 ASN D 146 HIS D 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.183147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130320 restraints weight = 41732.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135227 restraints weight = 16872.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138234 restraints weight = 9965.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139892 restraints weight = 7421.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140953 restraints weight = 6357.016| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 20313 Z= 0.365 Angle : 0.699 14.241 28383 Z= 0.383 Chirality : 0.045 0.209 3109 Planarity : 0.005 0.073 3022 Dihedral : 23.061 100.057 4302 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.49 % Allowed : 17.63 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 1937 helix: 2.01 (0.17), residues: 911 sheet: 0.08 (0.29), residues: 277 loop : 0.60 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 150 TYR 0.031 0.002 TYR A 154 PHE 0.016 0.002 PHE A 476 TRP 0.028 0.002 TRP B 443 HIS 0.007 0.002 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00785 (20297) covalent geometry : angle 0.67956 (28359) hydrogen bonds : bond 0.05503 ( 1059) hydrogen bonds : angle 4.13659 ( 2792) metal coordination : bond 0.00693 ( 16) metal coordination : angle 5.67125 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 456 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 HIS cc_start: 0.7882 (m170) cc_final: 0.7519 (m90) REVERT: A 98 GLU cc_start: 0.7504 (tp30) cc_final: 0.6901 (tp30) REVERT: A 109 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6635 (mp0) REVERT: A 139 GLU cc_start: 0.7433 (tp30) cc_final: 0.6982 (tp30) REVERT: A 163 TYR cc_start: 0.8446 (m-80) cc_final: 0.8191 (m-80) REVERT: A 168 VAL cc_start: 0.8420 (t) cc_final: 0.8156 (m) REVERT: A 182 GLU cc_start: 0.7656 (tt0) cc_final: 0.7255 (tt0) REVERT: A 185 LEU cc_start: 0.8897 (mt) cc_final: 0.8657 (mm) REVERT: A 189 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7148 (t-90) REVERT: A 219 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7038 (mm-40) REVERT: A 229 GLU cc_start: 0.7559 (pt0) cc_final: 0.7194 (pt0) REVERT: A 241 SER cc_start: 0.8356 (t) cc_final: 0.7966 (p) REVERT: A 251 ASN cc_start: 0.8701 (m-40) cc_final: 0.8476 (m110) REVERT: A 278 LEU cc_start: 0.9079 (tp) cc_final: 0.8757 (tp) REVERT: A 281 GLU cc_start: 0.8236 (tp30) cc_final: 0.7993 (tp30) REVERT: A 286 SER cc_start: 0.8497 (t) cc_final: 0.8113 (p) REVERT: A 342 MET cc_start: 0.5011 (ttp) cc_final: 0.4540 (ttp) REVERT: A 376 GLU cc_start: 0.8437 (tt0) cc_final: 0.7868 (tt0) REVERT: A 379 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 381 ASN cc_start: 0.8058 (t0) cc_final: 0.7764 (t0) REVERT: A 397 ARG cc_start: 0.2216 (OUTLIER) cc_final: -0.0500 (tpm170) REVERT: A 419 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6089 (tm-30) REVERT: B 2 ARG cc_start: 0.6951 (ptm160) cc_final: 0.6393 (ptm160) REVERT: B 6 VAL cc_start: 0.8374 (t) cc_final: 0.8030 (m) REVERT: B 22 GLN cc_start: 0.7536 (mt0) cc_final: 0.7275 (mt0) REVERT: B 28 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7603 (tp40) REVERT: B 91 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7537 (mm-40) REVERT: B 101 LYS cc_start: 0.8176 (mptt) cc_final: 0.7866 (mptt) REVERT: B 118 PHE cc_start: 0.8365 (m-80) cc_final: 0.7792 (m-80) REVERT: B 135 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 220 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8463 (tt) REVERT: B 292 VAL cc_start: 0.8693 (t) cc_final: 0.8350 (m) REVERT: B 297 LEU cc_start: 0.8480 (tp) cc_final: 0.8180 (tp) REVERT: B 300 ARG cc_start: 0.8531 (tpt170) cc_final: 0.7943 (mmt-90) REVERT: B 376 GLU cc_start: 0.8314 (tt0) cc_final: 0.7845 (tt0) REVERT: B 381 ASN cc_start: 0.8704 (m-40) cc_final: 0.8447 (m-40) REVERT: B 416 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7566 (mmm160) REVERT: B 458 MET cc_start: 0.8206 (mmt) cc_final: 0.7591 (mmt) REVERT: B 459 ASN cc_start: 0.8659 (m-40) cc_final: 0.8294 (m-40) REVERT: C 21 ARG cc_start: 0.7592 (mmt90) cc_final: 0.7174 (mmm160) REVERT: C 24 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 26 CYS cc_start: 0.7523 (m) cc_final: 0.7312 (m) REVERT: C 43 ASP cc_start: 0.6711 (m-30) cc_final: 0.6503 (m-30) REVERT: C 57 ARG cc_start: 0.8122 (mpp80) cc_final: 0.7776 (mpp80) REVERT: C 60 ASN cc_start: 0.7550 (m-40) cc_final: 0.7152 (m-40) REVERT: C 73 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: C 79 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7156 (ttp80) REVERT: C 81 ASP cc_start: 0.7402 (p0) cc_final: 0.6820 (p0) REVERT: C 92 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: C 96 TRP cc_start: 0.8502 (t60) cc_final: 0.8084 (t60) REVERT: C 125 LEU cc_start: 0.8591 (mt) cc_final: 0.7971 (mp) REVERT: C 135 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: C 140 ARG cc_start: 0.7267 (mpt-90) cc_final: 0.7049 (ttm110) REVERT: C 181 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7499 (ttp-110) REVERT: C 204 ASP cc_start: 0.7571 (t0) cc_final: 0.7073 (t0) REVERT: C 220 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 226 GLN cc_start: 0.7866 (mp10) cc_final: 0.7049 (mp10) REVERT: C 228 ARG cc_start: 0.7848 (mpt180) cc_final: 0.7291 (mpt180) REVERT: C 239 MET cc_start: 0.7902 (mmm) cc_final: 0.7467 (mmm) REVERT: C 331 PHE cc_start: 0.7478 (m-80) cc_final: 0.6949 (m-80) REVERT: C 384 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7504 (pp) REVERT: C 404 GLU cc_start: 0.8518 (pt0) cc_final: 0.8317 (pt0) REVERT: C 409 ARG cc_start: 0.8609 (mmp80) cc_final: 0.8298 (mmp80) REVERT: C 452 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8512 (m-40) REVERT: C 458 MET cc_start: 0.8409 (mmt) cc_final: 0.8191 (mmt) REVERT: D 50 VAL cc_start: 0.8706 (t) cc_final: 0.8500 (m) REVERT: D 65 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.6863 (mp) REVERT: D 74 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7782 (m) REVERT: D 96 TRP cc_start: 0.8507 (t60) cc_final: 0.8270 (t60) REVERT: D 102 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7932 (mmtp) REVERT: D 113 ASP cc_start: 0.7422 (t0) cc_final: 0.7213 (t0) REVERT: D 182 GLU cc_start: 0.7312 (pt0) cc_final: 0.6980 (pt0) REVERT: D 193 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7244 (p0) REVERT: D 196 GLU cc_start: 0.7677 (tp30) cc_final: 0.7439 (tp30) REVERT: D 221 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8040 (mm-40) REVERT: D 242 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 244 MET cc_start: 0.6992 (mmm) cc_final: 0.6523 (mmm) REVERT: D 269 ILE cc_start: 0.7853 (mm) cc_final: 0.7639 (mm) REVERT: D 272 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7039 (mmm160) REVERT: D 276 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 279 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7891 (ttm110) REVERT: D 296 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7915 (t) REVERT: D 327 ARG cc_start: 0.8160 (ttt180) cc_final: 0.7458 (ttp80) REVERT: D 329 MET cc_start: 0.6972 (tpp) cc_final: 0.6429 (tpp) REVERT: D 331 PHE cc_start: 0.7312 (m-80) cc_final: 0.6203 (m-80) REVERT: D 350 GLU cc_start: 0.8821 (pt0) cc_final: 0.8390 (tp30) REVERT: D 367 TRP cc_start: 0.6331 (t-100) cc_final: 0.6054 (t-100) REVERT: D 452 ASN cc_start: 0.7959 (t0) cc_final: 0.7557 (t0) REVERT: D 458 MET cc_start: 0.7864 (mmt) cc_final: 0.7473 (mmt) outliers start: 72 outliers final: 41 residues processed: 491 average time/residue: 0.1618 time to fit residues: 113.6687 Evaluate side-chains 506 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 451 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 8 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 143 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 148 ASN C 189 HIS C 334 HIS C 452 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.188046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135206 restraints weight = 38802.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140181 restraints weight = 15925.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143281 restraints weight = 9436.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145057 restraints weight = 7000.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146108 restraints weight = 5966.071| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20313 Z= 0.162 Angle : 0.583 13.199 28383 Z= 0.317 Chirality : 0.038 0.174 3109 Planarity : 0.005 0.080 3022 Dihedral : 22.812 96.298 4299 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.61 % Allowed : 19.38 % Favored : 77.01 % 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: 1.97 (0.19), residues: 1937 helix: 2.25 (0.17), residues: 919 sheet: 0.09 (0.29), residues: 302 loop : 0.75 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 142 TYR 0.029 0.002 TYR D 154 PHE 0.027 0.001 PHE C 118 TRP 0.023 0.001 TRP B 64 HIS 0.011 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00349 (20297) covalent geometry : angle 0.57085 (28359) hydrogen bonds : bond 0.03959 ( 1059) hydrogen bonds : angle 3.73225 ( 2792) metal coordination : bond 0.00365 ( 16) metal coordination : angle 4.08798 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 447 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7542 (m) REVERT: A 89 HIS cc_start: 0.7797 (m170) cc_final: 0.7366 (m170) REVERT: A 98 GLU cc_start: 0.7493 (tp30) cc_final: 0.6746 (tp30) REVERT: A 109 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6564 (mp0) REVERT: A 139 GLU cc_start: 0.7440 (tp30) cc_final: 0.7044 (tp30) REVERT: A 148 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7834 (t0) REVERT: A 175 VAL cc_start: 0.8191 (t) cc_final: 0.7829 (m) REVERT: A 182 GLU cc_start: 0.7475 (tt0) cc_final: 0.7035 (tt0) REVERT: A 185 LEU cc_start: 0.8803 (mt) cc_final: 0.8585 (mm) REVERT: A 189 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: A 219 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6921 (mm-40) REVERT: A 229 GLU cc_start: 0.7465 (pt0) cc_final: 0.7080 (pt0) REVERT: A 241 SER cc_start: 0.8404 (t) cc_final: 0.7962 (p) REVERT: A 251 ASN cc_start: 0.8551 (m-40) cc_final: 0.8320 (m110) REVERT: A 278 LEU cc_start: 0.8991 (tp) cc_final: 0.8642 (tp) REVERT: A 286 SER cc_start: 0.8370 (t) cc_final: 0.7989 (p) REVERT: A 342 MET cc_start: 0.4773 (ttp) cc_final: 0.4285 (ttp) REVERT: A 376 GLU cc_start: 0.8296 (tt0) cc_final: 0.7714 (tt0) REVERT: A 379 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 381 ASN cc_start: 0.7988 (t0) cc_final: 0.7669 (t0) REVERT: A 397 ARG cc_start: 0.1866 (OUTLIER) cc_final: -0.0732 (tpm170) REVERT: A 419 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6211 (tm-30) REVERT: B 6 VAL cc_start: 0.8286 (t) cc_final: 0.7870 (m) REVERT: B 22 GLN cc_start: 0.7578 (mt0) cc_final: 0.6892 (mt0) REVERT: B 26 CYS cc_start: 0.7841 (m) cc_final: 0.7454 (m) REVERT: B 28 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7444 (tp40) REVERT: B 82 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7508 (mmm160) REVERT: B 91 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7456 (tp40) REVERT: B 101 LYS cc_start: 0.8178 (mptt) cc_final: 0.7819 (mptt) REVERT: B 105 VAL cc_start: 0.8267 (t) cc_final: 0.7886 (p) REVERT: B 135 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 181 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.7014 (ttm170) REVERT: B 220 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8498 (tt) REVERT: B 292 VAL cc_start: 0.8581 (t) cc_final: 0.8274 (m) REVERT: B 297 LEU cc_start: 0.8385 (tp) cc_final: 0.8149 (tp) REVERT: B 300 ARG cc_start: 0.8514 (tpt170) cc_final: 0.8101 (mmt-90) REVERT: B 372 ASP cc_start: 0.8176 (m-30) cc_final: 0.7652 (m-30) REVERT: B 376 GLU cc_start: 0.8289 (tt0) cc_final: 0.7809 (tt0) REVERT: B 381 ASN cc_start: 0.8653 (m-40) cc_final: 0.8404 (m-40) REVERT: B 407 ASP cc_start: 0.8167 (p0) cc_final: 0.7928 (p0) REVERT: B 416 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7558 (mmm160) REVERT: B 458 MET cc_start: 0.8132 (mmt) cc_final: 0.7525 (mmt) REVERT: B 459 ASN cc_start: 0.8639 (m-40) cc_final: 0.8276 (m-40) REVERT: C 9 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8147 (mt) REVERT: C 21 ARG cc_start: 0.7421 (mmt90) cc_final: 0.7092 (mmm160) REVERT: C 26 CYS cc_start: 0.7189 (m) cc_final: 0.6880 (m) REVERT: C 29 LEU cc_start: 0.7974 (tp) cc_final: 0.7551 (tt) REVERT: C 43 ASP cc_start: 0.6619 (m-30) cc_final: 0.6357 (m-30) REVERT: C 57 ARG cc_start: 0.8132 (mpp80) cc_final: 0.7797 (mpp80) REVERT: C 60 ASN cc_start: 0.7514 (m-40) cc_final: 0.7119 (m-40) REVERT: C 73 ASP cc_start: 0.6993 (m-30) cc_final: 0.6421 (m-30) REVERT: C 92 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: C 96 TRP cc_start: 0.8412 (t60) cc_final: 0.7845 (t60) REVERT: C 135 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: C 140 ARG cc_start: 0.7261 (mpt-90) cc_final: 0.7041 (ttm110) REVERT: C 154 TYR cc_start: 0.7853 (t80) cc_final: 0.7280 (t80) REVERT: C 172 TRP cc_start: 0.7896 (m100) cc_final: 0.7418 (m100) REVERT: C 181 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7500 (ttp-110) REVERT: C 204 ASP cc_start: 0.7523 (t0) cc_final: 0.7008 (t0) REVERT: C 220 LEU cc_start: 0.8764 (mt) cc_final: 0.8415 (mt) REVERT: C 226 GLN cc_start: 0.7751 (mp10) cc_final: 0.7358 (mp10) REVERT: C 228 ARG cc_start: 0.7665 (mpt180) cc_final: 0.7413 (mpt-90) REVERT: C 235 LEU cc_start: 0.8048 (mt) cc_final: 0.7432 (pp) REVERT: C 239 MET cc_start: 0.7782 (mmm) cc_final: 0.7343 (mmm) REVERT: C 331 PHE cc_start: 0.7394 (m-80) cc_final: 0.6873 (m-80) REVERT: C 384 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7494 (pp) REVERT: C 409 ARG cc_start: 0.8522 (mmp80) cc_final: 0.8231 (mmp80) REVERT: C 452 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8515 (m-40) REVERT: C 458 MET cc_start: 0.8200 (mmt) cc_final: 0.7959 (mmt) REVERT: D 50 VAL cc_start: 0.8702 (t) cc_final: 0.8360 (m) REVERT: D 74 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7787 (m) REVERT: D 102 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7996 (mmmm) REVERT: D 113 ASP cc_start: 0.7274 (t0) cc_final: 0.7004 (t0) REVERT: D 149 ILE cc_start: 0.8473 (mm) cc_final: 0.8153 (tt) REVERT: D 182 GLU cc_start: 0.7232 (pt0) cc_final: 0.6853 (pt0) REVERT: D 193 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7390 (p0) REVERT: D 196 GLU cc_start: 0.7608 (tp30) cc_final: 0.7338 (tp30) REVERT: D 221 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7979 (mm-40) REVERT: D 226 GLN cc_start: 0.7854 (mm110) cc_final: 0.7543 (mm110) REVERT: D 242 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7193 (mt-10) REVERT: D 279 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7843 (ttm110) REVERT: D 327 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7437 (ttp80) REVERT: D 329 MET cc_start: 0.6712 (tpp) cc_final: 0.6164 (tpp) REVERT: D 331 PHE cc_start: 0.7206 (m-80) cc_final: 0.6290 (m-80) REVERT: D 348 PHE cc_start: 0.8548 (t80) cc_final: 0.7765 (t80) REVERT: D 350 GLU cc_start: 0.8769 (pt0) cc_final: 0.8407 (tp30) REVERT: D 367 TRP cc_start: 0.6407 (t-100) cc_final: 0.6126 (t-100) REVERT: D 452 ASN cc_start: 0.7814 (t0) cc_final: 0.7461 (t0) REVERT: D 458 MET cc_start: 0.7785 (mmt) cc_final: 0.7375 (mmt) outliers start: 58 outliers final: 33 residues processed: 473 average time/residue: 0.1567 time to fit residues: 105.8968 Evaluate side-chains 483 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 437 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 56 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.0000 chunk 58 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 141 ASN B 148 ASN C 452 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.195863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142338 restraints weight = 47051.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147806 restraints weight = 17622.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151206 restraints weight = 9950.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153300 restraints weight = 7135.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154449 restraints weight = 5946.709| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20313 Z= 0.140 Angle : 0.568 12.301 28383 Z= 0.312 Chirality : 0.037 0.152 3109 Planarity : 0.004 0.067 3022 Dihedral : 22.734 95.428 4299 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.30 % Allowed : 20.56 % Favored : 76.14 % 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: 2.07 (0.20), residues: 1937 helix: 2.35 (0.17), residues: 919 sheet: 0.14 (0.28), residues: 322 loop : 0.81 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 142 TYR 0.025 0.002 TYR D 154 PHE 0.040 0.001 PHE B 348 TRP 0.034 0.001 TRP B 64 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00298 (20297) covalent geometry : angle 0.55891 (28359) hydrogen bonds : bond 0.03680 ( 1059) hydrogen bonds : angle 3.59224 ( 2792) metal coordination : bond 0.00373 ( 16) metal coordination : angle 3.61490 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 442 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7437 (m) REVERT: A 89 HIS cc_start: 0.7808 (m170) cc_final: 0.7405 (m170) REVERT: A 98 GLU cc_start: 0.7497 (tp30) cc_final: 0.6754 (tp30) REVERT: A 109 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6544 (mp0) REVERT: A 131 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7721 (tp-100) REVERT: A 137 ILE cc_start: 0.8544 (mt) cc_final: 0.8324 (tt) REVERT: A 139 GLU cc_start: 0.7453 (tp30) cc_final: 0.6940 (tp30) REVERT: A 148 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7779 (t0) REVERT: A 175 VAL cc_start: 0.8180 (t) cc_final: 0.7802 (m) REVERT: A 181 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7748 (ttm-80) REVERT: A 182 GLU cc_start: 0.7460 (tt0) cc_final: 0.7013 (tt0) REVERT: A 185 LEU cc_start: 0.8797 (mt) cc_final: 0.8577 (mm) REVERT: A 189 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7172 (t-90) REVERT: A 219 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6868 (mm-40) REVERT: A 229 GLU cc_start: 0.7468 (pt0) cc_final: 0.7094 (pt0) REVERT: A 241 SER cc_start: 0.8335 (t) cc_final: 0.7521 (p) REVERT: A 251 ASN cc_start: 0.8581 (m-40) cc_final: 0.8350 (m110) REVERT: A 286 SER cc_start: 0.8282 (t) cc_final: 0.7930 (p) REVERT: A 342 MET cc_start: 0.4756 (ttp) cc_final: 0.4296 (ttp) REVERT: A 376 GLU cc_start: 0.8277 (tt0) cc_final: 0.7803 (tt0) REVERT: A 379 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 381 ASN cc_start: 0.8081 (t0) cc_final: 0.7745 (t0) REVERT: A 397 ARG cc_start: 0.1233 (OUTLIER) cc_final: -0.1605 (tpm170) REVERT: A 419 GLU cc_start: 0.7118 (tm-30) cc_final: 0.5930 (tm-30) REVERT: B 6 VAL cc_start: 0.8204 (t) cc_final: 0.7795 (m) REVERT: B 22 GLN cc_start: 0.7531 (mt0) cc_final: 0.6910 (mt0) REVERT: B 26 CYS cc_start: 0.7834 (m) cc_final: 0.7381 (m) REVERT: B 28 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7539 (tp40) REVERT: B 91 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7385 (tp40) REVERT: B 101 LYS cc_start: 0.8204 (mptt) cc_final: 0.7967 (mptt) REVERT: B 105 VAL cc_start: 0.8244 (t) cc_final: 0.7824 (p) REVERT: B 135 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 181 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6995 (ttm170) REVERT: B 220 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 292 VAL cc_start: 0.8561 (t) cc_final: 0.8224 (m) REVERT: B 297 LEU cc_start: 0.8342 (tp) cc_final: 0.8110 (tp) REVERT: B 300 ARG cc_start: 0.8485 (tpt170) cc_final: 0.8106 (mmt-90) REVERT: B 372 ASP cc_start: 0.8201 (m-30) cc_final: 0.7668 (m-30) REVERT: B 376 GLU cc_start: 0.8307 (tt0) cc_final: 0.7887 (tt0) REVERT: B 381 ASN cc_start: 0.8657 (m-40) cc_final: 0.8390 (m110) REVERT: B 407 ASP cc_start: 0.8124 (p0) cc_final: 0.7885 (p0) REVERT: B 458 MET cc_start: 0.8086 (mmt) cc_final: 0.7522 (mmt) REVERT: B 459 ASN cc_start: 0.8607 (m-40) cc_final: 0.8062 (m-40) REVERT: C 21 ARG cc_start: 0.7411 (mmt90) cc_final: 0.7021 (mmm160) REVERT: C 24 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7505 (tm-30) REVERT: C 26 CYS cc_start: 0.7131 (m) cc_final: 0.6818 (m) REVERT: C 29 LEU cc_start: 0.7938 (tp) cc_final: 0.7518 (tt) REVERT: C 43 ASP cc_start: 0.6626 (m-30) cc_final: 0.6364 (m-30) REVERT: C 57 ARG cc_start: 0.8139 (mpp80) cc_final: 0.7790 (mpp80) REVERT: C 73 ASP cc_start: 0.7065 (m-30) cc_final: 0.6539 (m-30) REVERT: C 92 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: C 96 TRP cc_start: 0.8407 (t60) cc_final: 0.7877 (t60) REVERT: C 135 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: C 140 ARG cc_start: 0.7276 (mpt-90) cc_final: 0.7043 (ttm110) REVERT: C 154 TYR cc_start: 0.7842 (t80) cc_final: 0.7324 (t80) REVERT: C 172 TRP cc_start: 0.7929 (m100) cc_final: 0.7469 (m100) REVERT: C 181 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7408 (ttp-110) REVERT: C 204 ASP cc_start: 0.7513 (t0) cc_final: 0.6980 (t0) REVERT: C 220 LEU cc_start: 0.8788 (mt) cc_final: 0.8471 (mt) REVERT: C 226 GLN cc_start: 0.7730 (mp10) cc_final: 0.7361 (mp10) REVERT: C 228 ARG cc_start: 0.7624 (mpt180) cc_final: 0.7336 (mpt-90) REVERT: C 235 LEU cc_start: 0.8065 (mt) cc_final: 0.7420 (pp) REVERT: C 239 MET cc_start: 0.7740 (mmm) cc_final: 0.7312 (mmm) REVERT: C 331 PHE cc_start: 0.7366 (m-80) cc_final: 0.6846 (m-80) REVERT: C 384 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7440 (pp) REVERT: C 404 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: C 409 ARG cc_start: 0.8579 (mmp80) cc_final: 0.8272 (mmp80) REVERT: C 452 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: C 458 MET cc_start: 0.8148 (mmt) cc_final: 0.7859 (mmt) REVERT: D 50 VAL cc_start: 0.8638 (t) cc_final: 0.8345 (m) REVERT: D 74 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7795 (m) REVERT: D 102 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7982 (mmmm) REVERT: D 113 ASP cc_start: 0.7295 (t0) cc_final: 0.7085 (t0) REVERT: D 149 ILE cc_start: 0.8527 (mm) cc_final: 0.8166 (tt) REVERT: D 196 GLU cc_start: 0.7533 (tp30) cc_final: 0.7255 (tp30) REVERT: D 216 TYR cc_start: 0.7648 (t80) cc_final: 0.7412 (t80) REVERT: D 221 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7946 (mm-40) REVERT: D 226 GLN cc_start: 0.7640 (mm110) cc_final: 0.7390 (mm110) REVERT: D 242 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: D 279 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7856 (ttm110) REVERT: D 327 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7479 (ttp80) REVERT: D 329 MET cc_start: 0.6465 (tpp) cc_final: 0.5929 (tpp) REVERT: D 331 PHE cc_start: 0.7116 (m-80) cc_final: 0.6150 (m-80) REVERT: D 350 GLU cc_start: 0.8672 (pt0) cc_final: 0.8327 (tp30) REVERT: D 367 TRP cc_start: 0.6400 (t-100) cc_final: 0.6146 (t-100) REVERT: D 452 ASN cc_start: 0.7819 (t0) cc_final: 0.7454 (t0) REVERT: D 458 MET cc_start: 0.7759 (mmt) cc_final: 0.7339 (mmt) outliers start: 53 outliers final: 37 residues processed: 463 average time/residue: 0.1664 time to fit residues: 110.0030 Evaluate side-chains 487 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 437 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130048 restraints weight = 57096.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135494 restraints weight = 20111.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139000 restraints weight = 11081.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141030 restraints weight = 7831.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142150 restraints weight = 6484.373| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20313 Z= 0.271 Angle : 0.636 13.071 28383 Z= 0.350 Chirality : 0.042 0.236 3109 Planarity : 0.005 0.071 3022 Dihedral : 22.898 93.511 4299 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.61 % Allowed : 20.44 % Favored : 75.95 % 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: 1.79 (0.19), residues: 1937 helix: 2.08 (0.17), residues: 922 sheet: 0.09 (0.28), residues: 324 loop : 0.67 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 272 TYR 0.028 0.002 TYR D 154 PHE 0.038 0.002 PHE B 348 TRP 0.047 0.002 TRP B 64 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00588 (20297) covalent geometry : angle 0.62347 (28359) hydrogen bonds : bond 0.04692 ( 1059) hydrogen bonds : angle 3.90075 ( 2792) metal coordination : bond 0.00509 ( 16) metal coordination : angle 4.37665 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 447 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7524 (m) REVERT: A 89 HIS cc_start: 0.7844 (m170) cc_final: 0.7459 (m90) REVERT: A 98 GLU cc_start: 0.7509 (tp30) cc_final: 0.6765 (tp30) REVERT: A 109 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6619 (mp0) REVERT: A 139 GLU cc_start: 0.7383 (tp30) cc_final: 0.6894 (tp30) REVERT: A 168 VAL cc_start: 0.8473 (t) cc_final: 0.8235 (m) REVERT: A 175 VAL cc_start: 0.8216 (t) cc_final: 0.7828 (m) REVERT: A 182 GLU cc_start: 0.7602 (tt0) cc_final: 0.7101 (tt0) REVERT: A 185 LEU cc_start: 0.8880 (mt) cc_final: 0.8638 (mm) REVERT: A 219 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6966 (mm-40) REVERT: A 229 GLU cc_start: 0.7574 (pt0) cc_final: 0.7154 (pt0) REVERT: A 241 SER cc_start: 0.8397 (t) cc_final: 0.8013 (p) REVERT: A 286 SER cc_start: 0.8372 (t) cc_final: 0.8004 (p) REVERT: A 342 MET cc_start: 0.4916 (ttp) cc_final: 0.4548 (ttp) REVERT: A 376 GLU cc_start: 0.8439 (tt0) cc_final: 0.7894 (tt0) REVERT: A 379 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 381 ASN cc_start: 0.7962 (t0) cc_final: 0.7644 (t0) REVERT: A 397 ARG cc_start: 0.1755 (OUTLIER) cc_final: -0.1142 (tpm170) REVERT: A 419 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6087 (tm-30) REVERT: B 6 VAL cc_start: 0.8378 (t) cc_final: 0.7945 (m) REVERT: B 22 GLN cc_start: 0.7621 (mt0) cc_final: 0.6963 (mt0) REVERT: B 26 CYS cc_start: 0.7845 (m) cc_final: 0.7472 (m) REVERT: B 27 GLN cc_start: 0.7753 (mt0) cc_final: 0.7550 (mt0) REVERT: B 28 GLN cc_start: 0.7695 (tp-100) cc_final: 0.7445 (tp40) REVERT: B 82 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7379 (mmm160) REVERT: B 91 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7315 (tp40) REVERT: B 101 LYS cc_start: 0.8290 (mptt) cc_final: 0.8079 (mptt) REVERT: B 118 PHE cc_start: 0.8387 (m-80) cc_final: 0.7790 (m-80) REVERT: B 135 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 220 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 292 VAL cc_start: 0.8619 (t) cc_final: 0.8326 (m) REVERT: B 297 LEU cc_start: 0.8459 (tp) cc_final: 0.8197 (tp) REVERT: B 300 ARG cc_start: 0.8530 (tpt170) cc_final: 0.8054 (mmt-90) REVERT: B 372 ASP cc_start: 0.8214 (m-30) cc_final: 0.7647 (m-30) REVERT: B 376 GLU cc_start: 0.8300 (tt0) cc_final: 0.7923 (tt0) REVERT: B 381 ASN cc_start: 0.8705 (m-40) cc_final: 0.8428 (m-40) REVERT: B 407 ASP cc_start: 0.8177 (p0) cc_final: 0.7916 (p0) REVERT: B 458 MET cc_start: 0.8201 (mmt) cc_final: 0.7575 (mmt) REVERT: B 459 ASN cc_start: 0.8665 (m-40) cc_final: 0.8302 (m-40) REVERT: C 21 ARG cc_start: 0.7462 (mmt90) cc_final: 0.7141 (mmm160) REVERT: C 26 CYS cc_start: 0.7402 (m) cc_final: 0.7147 (m) REVERT: C 29 LEU cc_start: 0.7958 (tp) cc_final: 0.7531 (tt) REVERT: C 43 ASP cc_start: 0.6595 (m-30) cc_final: 0.6393 (m-30) REVERT: C 54 ASP cc_start: 0.7885 (t0) cc_final: 0.6114 (p0) REVERT: C 57 ARG cc_start: 0.8147 (mpp80) cc_final: 0.7854 (mpp80) REVERT: C 60 ASN cc_start: 0.7470 (m-40) cc_final: 0.7116 (m-40) REVERT: C 92 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: C 96 TRP cc_start: 0.8458 (t60) cc_final: 0.7981 (t60) REVERT: C 113 ASP cc_start: 0.7595 (t0) cc_final: 0.7316 (t0) REVERT: C 135 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: C 181 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7459 (mtm110) REVERT: C 204 ASP cc_start: 0.7480 (t0) cc_final: 0.7253 (t0) REVERT: C 220 LEU cc_start: 0.8893 (mt) cc_final: 0.8521 (mt) REVERT: C 226 GLN cc_start: 0.7834 (mp10) cc_final: 0.7367 (mp10) REVERT: C 228 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7513 (mpt-90) REVERT: C 235 LEU cc_start: 0.8088 (mt) cc_final: 0.7467 (pp) REVERT: C 239 MET cc_start: 0.7906 (mmm) cc_final: 0.7434 (mmm) REVERT: C 331 PHE cc_start: 0.7420 (m-80) cc_final: 0.6864 (m-80) REVERT: C 384 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7461 (pp) REVERT: C 404 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: C 407 ASP cc_start: 0.7947 (m-30) cc_final: 0.7560 (m-30) REVERT: C 409 ARG cc_start: 0.8570 (mmp80) cc_final: 0.8268 (mmp80) REVERT: C 452 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: C 458 MET cc_start: 0.8317 (mmt) cc_final: 0.7990 (mmt) REVERT: D 74 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7830 (m) REVERT: D 149 ILE cc_start: 0.8503 (mm) cc_final: 0.8201 (tt) REVERT: D 182 GLU cc_start: 0.7265 (pt0) cc_final: 0.6899 (pt0) REVERT: D 189 HIS cc_start: 0.7469 (m90) cc_final: 0.6812 (m90) REVERT: D 196 GLU cc_start: 0.7685 (tp30) cc_final: 0.7402 (tp30) REVERT: D 216 TYR cc_start: 0.7900 (t80) cc_final: 0.7589 (t80) REVERT: D 226 GLN cc_start: 0.7734 (mm110) cc_final: 0.7489 (mm110) REVERT: D 242 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: D 269 ILE cc_start: 0.7749 (mm) cc_final: 0.7494 (mm) REVERT: D 279 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7807 (ttm110) REVERT: D 296 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7747 (t) REVERT: D 327 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7338 (ttp80) REVERT: D 329 MET cc_start: 0.6897 (tpp) cc_final: 0.6223 (tpp) REVERT: D 331 PHE cc_start: 0.7033 (m-80) cc_final: 0.5997 (m-80) REVERT: D 350 GLU cc_start: 0.8686 (pt0) cc_final: 0.8249 (tp30) REVERT: D 367 TRP cc_start: 0.6320 (t-100) cc_final: 0.5748 (t-100) REVERT: D 409 ARG cc_start: 0.8597 (mmp80) cc_final: 0.8241 (mmp80) REVERT: D 452 ASN cc_start: 0.7927 (t0) cc_final: 0.7531 (t0) REVERT: D 458 MET cc_start: 0.8015 (mmt) cc_final: 0.7602 (mmt) REVERT: D 459 ASN cc_start: 0.8578 (m-40) cc_final: 0.8359 (m-40) outliers start: 58 outliers final: 39 residues processed: 477 average time/residue: 0.1651 time to fit residues: 112.6134 Evaluate side-chains 495 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 444 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.185718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133115 restraints weight = 41400.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138096 restraints weight = 16760.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141206 restraints weight = 9898.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143001 restraints weight = 7321.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144040 restraints weight = 6227.910| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20313 Z= 0.207 Angle : 0.600 12.908 28383 Z= 0.331 Chirality : 0.040 0.251 3109 Planarity : 0.005 0.071 3022 Dihedral : 22.830 93.076 4292 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.99 % Allowed : 21.43 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 1937 helix: 2.10 (0.17), residues: 923 sheet: 0.09 (0.28), residues: 324 loop : 0.67 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 272 TYR 0.026 0.002 TYR D 154 PHE 0.039 0.001 PHE B 348 TRP 0.052 0.002 TRP B 64 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00450 (20297) covalent geometry : angle 0.58848 (28359) hydrogen bonds : bond 0.04183 ( 1059) hydrogen bonds : angle 3.77436 ( 2792) metal coordination : bond 0.00425 ( 16) metal coordination : angle 3.99909 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 440 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8555 (m) cc_final: 0.8319 (p) REVERT: A 37 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7513 (m) REVERT: A 89 HIS cc_start: 0.7799 (m170) cc_final: 0.7377 (m170) REVERT: A 98 GLU cc_start: 0.7476 (tp30) cc_final: 0.6728 (tp30) REVERT: A 109 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6577 (mp0) REVERT: A 139 GLU cc_start: 0.7402 (tp30) cc_final: 0.6900 (tp30) REVERT: A 163 TYR cc_start: 0.8359 (m-80) cc_final: 0.7944 (m-10) REVERT: A 175 VAL cc_start: 0.8192 (t) cc_final: 0.7915 (m) REVERT: A 181 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: A 182 GLU cc_start: 0.7462 (tt0) cc_final: 0.7004 (tt0) REVERT: A 185 LEU cc_start: 0.8827 (mt) cc_final: 0.8596 (mm) REVERT: A 189 HIS cc_start: 0.7560 (m-70) cc_final: 0.7077 (t-90) REVERT: A 219 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6860 (mm-40) REVERT: A 229 GLU cc_start: 0.7479 (pt0) cc_final: 0.7055 (pt0) REVERT: A 241 SER cc_start: 0.8386 (t) cc_final: 0.8031 (p) REVERT: A 286 SER cc_start: 0.8349 (t) cc_final: 0.8026 (p) REVERT: A 342 MET cc_start: 0.4959 (ttp) cc_final: 0.4601 (ttp) REVERT: A 376 GLU cc_start: 0.8376 (tt0) cc_final: 0.7858 (tt0) REVERT: A 379 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 381 ASN cc_start: 0.8146 (t0) cc_final: 0.7765 (t0) REVERT: A 397 ARG cc_start: 0.1653 (OUTLIER) cc_final: -0.1014 (tpm170) REVERT: A 419 GLU cc_start: 0.7170 (tm-30) cc_final: 0.5995 (tm-30) REVERT: B 2 ARG cc_start: 0.7012 (ptt180) cc_final: 0.6788 (ptt180) REVERT: B 6 VAL cc_start: 0.8330 (t) cc_final: 0.7929 (m) REVERT: B 22 GLN cc_start: 0.7547 (mt0) cc_final: 0.6924 (mt0) REVERT: B 26 CYS cc_start: 0.7765 (m) cc_final: 0.7385 (m) REVERT: B 27 GLN cc_start: 0.7750 (mt0) cc_final: 0.7536 (mt0) REVERT: B 28 GLN cc_start: 0.7643 (tp-100) cc_final: 0.7410 (tp40) REVERT: B 82 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7388 (mmm160) REVERT: B 91 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7323 (tp40) REVERT: B 105 VAL cc_start: 0.8288 (t) cc_final: 0.7900 (p) REVERT: B 135 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 220 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 292 VAL cc_start: 0.8592 (t) cc_final: 0.8315 (m) REVERT: B 297 LEU cc_start: 0.8414 (tp) cc_final: 0.8173 (tp) REVERT: B 300 ARG cc_start: 0.8508 (tpt170) cc_final: 0.8040 (mmt-90) REVERT: B 348 PHE cc_start: 0.7979 (t80) cc_final: 0.7621 (t80) REVERT: B 372 ASP cc_start: 0.8131 (m-30) cc_final: 0.7621 (m-30) REVERT: B 376 GLU cc_start: 0.8287 (tt0) cc_final: 0.7932 (tt0) REVERT: B 381 ASN cc_start: 0.8681 (m-40) cc_final: 0.8406 (m110) REVERT: B 407 ASP cc_start: 0.8150 (p0) cc_final: 0.7888 (p0) REVERT: B 458 MET cc_start: 0.8128 (mmt) cc_final: 0.7575 (mmt) REVERT: B 459 ASN cc_start: 0.8668 (m-40) cc_final: 0.8124 (m-40) REVERT: C 21 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7072 (mmm160) REVERT: C 26 CYS cc_start: 0.7197 (m) cc_final: 0.6911 (m) REVERT: C 29 LEU cc_start: 0.7956 (tp) cc_final: 0.7529 (tt) REVERT: C 43 ASP cc_start: 0.6576 (m-30) cc_final: 0.6345 (m-30) REVERT: C 54 ASP cc_start: 0.7826 (t0) cc_final: 0.6120 (p0) REVERT: C 57 ARG cc_start: 0.8118 (mpp80) cc_final: 0.7842 (mpp80) REVERT: C 60 ASN cc_start: 0.7388 (m-40) cc_final: 0.6974 (m-40) REVERT: C 92 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: C 96 TRP cc_start: 0.8442 (t60) cc_final: 0.7856 (t60) REVERT: C 113 ASP cc_start: 0.7511 (t0) cc_final: 0.7272 (t0) REVERT: C 135 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: C 161 TRP cc_start: 0.8608 (t60) cc_final: 0.8395 (t60) REVERT: C 181 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7438 (ttp-110) REVERT: C 204 ASP cc_start: 0.7442 (t0) cc_final: 0.7178 (t0) REVERT: C 220 LEU cc_start: 0.8859 (mt) cc_final: 0.8495 (mt) REVERT: C 226 GLN cc_start: 0.7763 (mp10) cc_final: 0.7336 (mp10) REVERT: C 228 ARG cc_start: 0.7684 (mpt180) cc_final: 0.7434 (mpt-90) REVERT: C 235 LEU cc_start: 0.8024 (mt) cc_final: 0.7438 (pp) REVERT: C 239 MET cc_start: 0.7843 (mmm) cc_final: 0.7369 (mmm) REVERT: C 331 PHE cc_start: 0.7325 (m-80) cc_final: 0.6733 (m-80) REVERT: C 342 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.5095 (mmm) REVERT: C 384 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7467 (pp) REVERT: C 404 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: C 407 ASP cc_start: 0.7850 (m-30) cc_final: 0.7504 (m-30) REVERT: C 409 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8202 (mmp80) REVERT: C 458 MET cc_start: 0.8339 (mmt) cc_final: 0.8056 (mmt) REVERT: D 74 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7807 (m) REVERT: D 102 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8116 (mmmm) REVERT: D 109 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7295 (mt-10) REVERT: D 149 ILE cc_start: 0.8516 (mm) cc_final: 0.8210 (tt) REVERT: D 189 HIS cc_start: 0.7441 (m90) cc_final: 0.6854 (m90) REVERT: D 196 GLU cc_start: 0.7651 (tp30) cc_final: 0.7379 (tp30) REVERT: D 216 TYR cc_start: 0.7812 (t80) cc_final: 0.7539 (t80) REVERT: D 267 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6532 (tm-30) REVERT: D 269 ILE cc_start: 0.7927 (mm) cc_final: 0.7651 (mm) REVERT: D 279 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7762 (ttm110) REVERT: D 296 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7722 (t) REVERT: D 327 ARG cc_start: 0.8101 (ttt180) cc_final: 0.7403 (ttp80) REVERT: D 329 MET cc_start: 0.6817 (tpp) cc_final: 0.6122 (tpp) REVERT: D 331 PHE cc_start: 0.6941 (m-80) cc_final: 0.6057 (m-80) REVERT: D 350 GLU cc_start: 0.8668 (pt0) cc_final: 0.8258 (tp30) REVERT: D 367 TRP cc_start: 0.6331 (t-100) cc_final: 0.5688 (t-100) REVERT: D 452 ASN cc_start: 0.7903 (t0) cc_final: 0.7513 (t0) REVERT: D 458 MET cc_start: 0.7966 (mmt) cc_final: 0.7560 (mmt) REVERT: D 459 ASN cc_start: 0.8481 (m-40) cc_final: 0.8265 (m-40) outliers start: 48 outliers final: 34 residues processed: 464 average time/residue: 0.1628 time to fit residues: 108.5544 Evaluate side-chains 484 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 439 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 0.0030 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.187986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134603 restraints weight = 45223.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139899 restraints weight = 17457.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143127 restraints weight = 10010.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145059 restraints weight = 7274.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146118 restraints weight = 6102.443| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20313 Z= 0.165 Angle : 0.597 12.968 28383 Z= 0.328 Chirality : 0.039 0.229 3109 Planarity : 0.004 0.065 3022 Dihedral : 22.804 93.052 4292 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.05 % Allowed : 21.43 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 1937 helix: 2.16 (0.17), residues: 924 sheet: 0.11 (0.29), residues: 324 loop : 0.71 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 272 TYR 0.027 0.002 TYR D 154 PHE 0.039 0.001 PHE B 348 TRP 0.063 0.002 TRP D 345 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00355 (20297) covalent geometry : angle 0.58729 (28359) hydrogen bonds : bond 0.03971 ( 1059) hydrogen bonds : angle 3.67555 ( 2792) metal coordination : bond 0.00373 ( 16) metal coordination : angle 3.68087 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 449 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8423 (m) cc_final: 0.8149 (p) REVERT: A 37 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7475 (m) REVERT: A 89 HIS cc_start: 0.7815 (m170) cc_final: 0.7351 (m170) REVERT: A 98 GLU cc_start: 0.7492 (tp30) cc_final: 0.6711 (tp30) REVERT: A 109 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6572 (mp0) REVERT: A 139 GLU cc_start: 0.7420 (tp30) cc_final: 0.6929 (tp30) REVERT: A 148 ASN cc_start: 0.8115 (m-40) cc_final: 0.7845 (t0) REVERT: A 175 VAL cc_start: 0.8160 (t) cc_final: 0.7771 (m) REVERT: A 181 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7851 (ttm-80) REVERT: A 182 GLU cc_start: 0.7460 (tt0) cc_final: 0.6954 (tt0) REVERT: A 185 LEU cc_start: 0.8808 (mt) cc_final: 0.8585 (mm) REVERT: A 189 HIS cc_start: 0.7544 (m-70) cc_final: 0.7047 (t-90) REVERT: A 219 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6863 (mm-40) REVERT: A 229 GLU cc_start: 0.7459 (pt0) cc_final: 0.7052 (pt0) REVERT: A 233 THR cc_start: 0.7847 (m) cc_final: 0.7542 (t) REVERT: A 241 SER cc_start: 0.8403 (t) cc_final: 0.8024 (p) REVERT: A 276 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 286 SER cc_start: 0.8311 (t) cc_final: 0.8005 (p) REVERT: A 342 MET cc_start: 0.4937 (ttp) cc_final: 0.4556 (ttp) REVERT: A 376 GLU cc_start: 0.8341 (tt0) cc_final: 0.7816 (tt0) REVERT: A 379 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 381 ASN cc_start: 0.7985 (t0) cc_final: 0.7626 (t0) REVERT: A 397 ARG cc_start: 0.1556 (OUTLIER) cc_final: -0.1136 (tpm170) REVERT: A 419 GLU cc_start: 0.7088 (tm-30) cc_final: 0.5881 (tm-30) REVERT: B 6 VAL cc_start: 0.8310 (t) cc_final: 0.7878 (m) REVERT: B 26 CYS cc_start: 0.7759 (m) cc_final: 0.7396 (m) REVERT: B 27 GLN cc_start: 0.7715 (mt0) cc_final: 0.7499 (mt0) REVERT: B 28 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7400 (tp40) REVERT: B 69 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.5826 (mt-10) REVERT: B 82 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7433 (mmm160) REVERT: B 91 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7439 (tp40) REVERT: B 105 VAL cc_start: 0.8270 (t) cc_final: 0.7876 (p) REVERT: B 135 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 220 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8509 (tt) REVERT: B 292 VAL cc_start: 0.8559 (t) cc_final: 0.8277 (m) REVERT: B 297 LEU cc_start: 0.8400 (tp) cc_final: 0.8159 (tp) REVERT: B 300 ARG cc_start: 0.8494 (tpt170) cc_final: 0.8059 (mmt-90) REVERT: B 348 PHE cc_start: 0.7867 (t80) cc_final: 0.7397 (t80) REVERT: B 351 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 372 ASP cc_start: 0.8159 (m-30) cc_final: 0.7660 (m-30) REVERT: B 376 GLU cc_start: 0.8302 (tt0) cc_final: 0.7940 (tt0) REVERT: B 381 ASN cc_start: 0.8684 (m-40) cc_final: 0.8407 (m110) REVERT: B 407 ASP cc_start: 0.8148 (p0) cc_final: 0.7880 (p0) REVERT: B 458 MET cc_start: 0.8111 (mmt) cc_final: 0.7562 (mmt) REVERT: B 459 ASN cc_start: 0.8653 (m-40) cc_final: 0.8115 (m-40) REVERT: C 21 ARG cc_start: 0.7372 (mmt90) cc_final: 0.7048 (mmm160) REVERT: C 26 CYS cc_start: 0.7097 (m) cc_final: 0.6818 (m) REVERT: C 43 ASP cc_start: 0.6590 (m-30) cc_final: 0.6333 (m-30) REVERT: C 54 ASP cc_start: 0.7845 (t0) cc_final: 0.6187 (p0) REVERT: C 57 ARG cc_start: 0.8128 (mpp80) cc_final: 0.7856 (mpp80) REVERT: C 60 ASN cc_start: 0.7369 (m-40) cc_final: 0.6950 (m-40) REVERT: C 96 TRP cc_start: 0.8394 (t60) cc_final: 0.7809 (t60) REVERT: C 113 ASP cc_start: 0.7553 (t0) cc_final: 0.7290 (t0) REVERT: C 135 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: C 154 TYR cc_start: 0.7801 (t80) cc_final: 0.7196 (t80) REVERT: C 181 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7453 (ttp-110) REVERT: C 204 ASP cc_start: 0.7430 (t0) cc_final: 0.7194 (t0) REVERT: C 220 LEU cc_start: 0.8801 (mt) cc_final: 0.8453 (mt) REVERT: C 226 GLN cc_start: 0.7746 (mp10) cc_final: 0.7324 (mp10) REVERT: C 228 ARG cc_start: 0.7660 (mpt180) cc_final: 0.7405 (mpt-90) REVERT: C 235 LEU cc_start: 0.8016 (mt) cc_final: 0.7420 (pp) REVERT: C 239 MET cc_start: 0.7799 (mmm) cc_final: 0.7301 (mmm) REVERT: C 331 PHE cc_start: 0.7313 (m-80) cc_final: 0.6706 (m-80) REVERT: C 384 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (pp) REVERT: C 404 GLU cc_start: 0.8411 (pt0) cc_final: 0.8046 (pp20) REVERT: C 407 ASP cc_start: 0.7816 (m-30) cc_final: 0.7472 (m-30) REVERT: C 409 ARG cc_start: 0.8480 (mmp80) cc_final: 0.8164 (mmp80) REVERT: C 458 MET cc_start: 0.8293 (mmt) cc_final: 0.8020 (mmt) REVERT: D 74 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7804 (m) REVERT: D 102 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8071 (mmmm) REVERT: D 149 ILE cc_start: 0.8533 (mm) cc_final: 0.8218 (tt) REVERT: D 189 HIS cc_start: 0.7468 (m90) cc_final: 0.7031 (m90) REVERT: D 196 GLU cc_start: 0.7623 (tp30) cc_final: 0.7328 (tp30) REVERT: D 216 TYR cc_start: 0.7798 (t80) cc_final: 0.7525 (t80) REVERT: D 221 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7988 (mm-40) REVERT: D 267 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6477 (tm-30) REVERT: D 269 ILE cc_start: 0.7939 (mm) cc_final: 0.7673 (mm) REVERT: D 279 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7572 (ttm-80) REVERT: D 296 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7709 (t) REVERT: D 329 MET cc_start: 0.6612 (tpp) cc_final: 0.5846 (tpp) REVERT: D 350 GLU cc_start: 0.8663 (pt0) cc_final: 0.8184 (tp30) REVERT: D 367 TRP cc_start: 0.6388 (t-100) cc_final: 0.5785 (t-100) REVERT: D 452 ASN cc_start: 0.7845 (t0) cc_final: 0.7483 (t0) REVERT: D 458 MET cc_start: 0.7942 (mmt) cc_final: 0.7545 (mmt) REVERT: D 459 ASN cc_start: 0.8459 (m-40) cc_final: 0.8249 (m-40) outliers start: 49 outliers final: 39 residues processed: 473 average time/residue: 0.1590 time to fit residues: 108.7619 Evaluate side-chains 491 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 443 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 113 optimal weight: 0.0370 chunk 151 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 165 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 100 HIS ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.187065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133914 restraints weight = 50049.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139287 restraints weight = 18631.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142666 restraints weight = 10464.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144614 restraints weight = 7507.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145569 restraints weight = 6271.634| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20313 Z= 0.161 Angle : 0.597 12.861 28383 Z= 0.329 Chirality : 0.039 0.275 3109 Planarity : 0.005 0.118 3022 Dihedral : 22.784 91.576 4292 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.18 % Allowed : 21.50 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 1937 helix: 2.12 (0.17), residues: 925 sheet: 0.08 (0.29), residues: 324 loop : 0.74 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG D 272 TYR 0.026 0.002 TYR D 154 PHE 0.039 0.002 PHE B 348 TRP 0.043 0.001 TRP B 64 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00348 (20297) covalent geometry : angle 0.58840 (28359) hydrogen bonds : bond 0.04003 ( 1059) hydrogen bonds : angle 3.70964 ( 2792) metal coordination : bond 0.00350 ( 16) metal coordination : angle 3.57117 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4903.26 seconds wall clock time: 84 minutes 18.02 seconds (5058.02 seconds total)