Starting phenix.real_space_refine on Sun Sep 13 02:10:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu4_60889/09_2026/9iu4_60889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu4_60889/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iu4_60889/09_2026/9iu4_60889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu4_60889/09_2026/9iu4_60889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu4_60889/09_2026/9iu4_60889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu4_60889/09_2026/9iu4_60889.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.61, per 1000 atoms: 0.24 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: 2.07 Conformation dependent library (CDL) restraints added in 946.9 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: 3.12 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: 4.67 Time building geometry restraints manager: 2.73 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=" N1 DC F 30 " pdb=" C6 DC F 30 " ideal model delta sigma weight residual 1.367 1.330 0.037 6.00e-03 2.78e+04 3.71e+01 bond pdb=" N1 DC E 30 " pdb=" C6 DC E 30 " ideal model delta sigma weight residual 1.367 1.332 0.035 6.00e-03 2.78e+04 3.38e+01 bond pdb=" N1 DC F 21 " pdb=" C6 DC F 21 " ideal model delta sigma weight residual 1.367 1.336 0.031 6.00e-03 2.78e+04 2.60e+01 bond pdb=" C4 DC F 30 " pdb=" C5 DC F 30 " ideal model delta sigma weight residual 1.425 1.387 0.038 8.00e-03 1.56e+04 2.27e+01 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 ... (remaining 20292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 26180 3.37 - 6.75: 1994 6.75 - 10.12: 157 10.12 - 13.50: 23 13.50 - 16.87: 5 Bond angle restraints: 28359 Sorted by residual: angle pdb=" O4' DGG2 36 " pdb=" C1' DGG2 36 " pdb=" N9 DGG2 36 " ideal model delta sigma weight residual 108.00 115.11 -7.11 7.00e-01 2.04e+00 1.03e+02 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 1.90e+00 2.77e-01 7.88e+01 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 1.90e+00 2.77e-01 7.47e+01 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 1.90e+00 2.77e-01 6.34e+01 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 1.90e+00 2.77e-01 6.20e+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 - 0.132: 2749 0.132 - 0.264: 321 0.264 - 0.396: 29 0.396 - 0.527: 5 0.527 - 0.659: 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 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.09e+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 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+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 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 26.120 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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= 0.687 Angle : 1.890 20.643 28383 Z= 1.295 Chirality : 0.091 0.659 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/Z covalent geometry : bond 0.01023 / 0.68 (20297) covalent geometry : angle 1.87022 / 1.29 (28359) hydrogen bonds : bond 0.16409 / 10.99 ( 1059) hydrogen bonds : angle 6.02006 / 4.41 ( 2792) metal coordination : bond 0.05615 / 3.45 ( 16) metal coordination : angle 9.46468 / 6.40 ( 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 : 0.604 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: 0.6030 (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: 0.6574 (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: 0.7079 (mttp) REVERT: A 139 GLU cc_start: 0.7331 (tp30) cc_final: 0.7073 (tp30) REVERT: A 155 ARG cc_start: 0.7487 (ptt180) cc_final: 0.6508 (ttp80) REVERT: A 169 ASP cc_start: 0.7686 (t0) cc_final: 0.7199 (t0) REVERT: A 175 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6318 (m) REVERT: A 182 GLU cc_start: 0.8404 (tt0) cc_final: 0.8026 (tt0) REVERT: A 204 ASP cc_start: 0.6885 (t0) cc_final: 0.6623 (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: 0.7083 (pt0) REVERT: A 251 ASN cc_start: 0.7697 (m-40) cc_final: 0.7468 (m-40) REVERT: A 265 ARG cc_start: 0.7874 (ptt180) cc_final: 0.6743 (ptm160) REVERT: A 274 GLN cc_start: 0.7562 (mt0) cc_final: 0.7341 (mt0) REVERT: A 375 VAL cc_start: 0.8734 (t) cc_final: 0.8428 (t) REVERT: A 376 GLU cc_start: 0.8574 (tt0) cc_final: 0.8309 (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: -0.0867 (tpm170) REVERT: A 454 TRP cc_start: 0.8798 (t60) cc_final: 0.8356 (t60) REVERT: A 458 MET cc_start: 0.6633 (mmm) cc_final: 0.6062 (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: 0.5685 (m-30) REVERT: B 81 ASP cc_start: 0.7565 (p0) cc_final: 0.7331 (p0) REVERT: B 82 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7418 (mmm160) REVERT: B 91 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7072 (tp40) REVERT: B 105 VAL cc_start: 0.7231 (t) cc_final: 0.6793 (p) REVERT: B 118 PHE cc_start: 0.7868 (m-80) cc_final: 0.7319 (m-10) REVERT: B 135 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7079 (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: 0.7311 (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: 0.6983 (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: 0.6615 (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: 0.7187 (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: 0.6892 (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: 0.6001 (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: 0.7641 (t80) REVERT: C 224 GLU cc_start: 0.7317 (tt0) cc_final: 0.7086 (tt0) REVERT: C 226 GLN cc_start: 0.7251 (mp10) cc_final: 0.6933 (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: 0.6990 (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: 0.7846 (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: 0.7032 (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: 0.5466 (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: 0.6340 (mmtp) REVERT: D 135 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7265 (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: 0.8410 (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: 0.6223 (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: 0.6586 (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: 0.1828 time to fit residues: 142.3530 Evaluate side-chains 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 440 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 100 HIS B 27 GLN B 89 HIS B 91 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 100 HIS C 148 ASN D 91 GLN D 95 HIS D 111 HIS D 189 HIS D 452 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.189556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136290 restraints weight = 42670.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141279 restraints weight = 17213.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144392 restraints weight = 10189.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146196 restraints weight = 7575.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.147172 restraints weight = 6462.004| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20313 Z= 0.202 Angle : 0.798 13.938 28383 Z= 0.440 Chirality : 0.055 0.245 3109 Planarity : 0.005 0.051 3022 Dihedral : 23.578 87.503 4347 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.55 % Allowed : 12.40 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 1937 helix: 2.22 (0.16), residues: 911 sheet: -0.09 (0.27), residues: 287 loop : 0.65 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.026 0.002 TYR B 482 PHE 0.025 0.002 PHE C 314 TRP 0.029 0.002 TRP B 443 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (20297) covalent geometry : angle 0.78101 / 0.44 (28359) hydrogen bonds : bond 0.05888 / 4.09 ( 1059) hydrogen bonds : angle 4.04786 / 3.00 ( 2792) metal coordination : bond 0.01454 / 0.76 ( 16) metal coordination : angle 5.69117 / 3.97 ( 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 524 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 467 time to evaluate : 0.698 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: A 6 VAL cc_start: 0.7759 (t) cc_final: 0.7213 (m) REVERT: A 64 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: A 89 HIS cc_start: 0.7959 (m-70) cc_final: 0.7476 (m170) REVERT: A 96 TRP cc_start: 0.8323 (t60) cc_final: 0.7840 (t60) REVERT: A 98 GLU cc_start: 0.7496 (tp30) cc_final: 0.7029 (tp30) REVERT: A 138 LYS cc_start: 0.8037 (mttm) cc_final: 0.7782 (mtmm) REVERT: A 168 VAL cc_start: 0.8004 (t) cc_final: 0.7765 (m) REVERT: A 169 ASP cc_start: 0.7227 (t0) cc_final: 0.6639 (t0) REVERT: A 175 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7772 (m) REVERT: A 182 GLU cc_start: 0.7671 (tt0) cc_final: 0.7351 (tt0) REVERT: A 204 ASP cc_start: 0.7136 (t0) cc_final: 0.6854 (t0) REVERT: A 219 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7259 (mm110) REVERT: A 228 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7763 (mtt180) REVERT: A 239 MET cc_start: 0.7713 (tpp) cc_final: 0.7339 (mmm) REVERT: A 241 SER cc_start: 0.8365 (t) cc_final: 0.7870 (p) REVERT: A 251 ASN cc_start: 0.8451 (m-40) cc_final: 0.8209 (m-40) REVERT: A 257 ASP cc_start: 0.5719 (p0) cc_final: 0.5233 (p0) REVERT: A 265 ARG cc_start: 0.8471 (ptt180) cc_final: 0.7960 (ptt90) REVERT: A 342 MET cc_start: 0.4337 (ttp) cc_final: 0.3900 (ttp) REVERT: A 375 VAL cc_start: 0.8811 (t) cc_final: 0.8265 (t) REVERT: A 376 GLU cc_start: 0.8407 (tt0) cc_final: 0.7832 (tt0) REVERT: A 379 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 381 ASN cc_start: 0.8150 (t0) cc_final: 0.7893 (t0) REVERT: A 397 ARG cc_start: 0.0072 (OUTLIER) cc_final: -0.2321 (tpm170) REVERT: B 6 VAL cc_start: 0.8265 (t) cc_final: 0.7804 (m) REVERT: B 21 ARG cc_start: 0.7562 (ttp-110) cc_final: 0.7344 (ttm110) REVERT: B 24 GLU cc_start: 0.7487 (tt0) cc_final: 0.7127 (tt0) REVERT: B 28 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7407 (tp40) REVERT: B 64 TRP cc_start: 0.7346 (m100) cc_final: 0.7061 (m100) REVERT: B 82 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7331 (mmm160) REVERT: B 91 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7367 (mm110) REVERT: B 105 VAL cc_start: 0.8334 (t) cc_final: 0.7968 (p) REVERT: B 118 PHE cc_start: 0.8298 (m-80) cc_final: 0.7661 (m-10) REVERT: B 135 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 138 LYS cc_start: 0.8265 (mtmt) cc_final: 0.8061 (mtmt) REVERT: B 153 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7631 (mtmp) REVERT: B 164 LEU cc_start: 0.8093 (tt) cc_final: 0.7880 (tt) REVERT: B 219 GLN cc_start: 0.6661 (tp40) cc_final: 0.6421 (tp40) REVERT: B 365 LYS cc_start: 0.8342 (tttt) cc_final: 0.7931 (tttt) REVERT: B 376 GLU cc_start: 0.8263 (tt0) cc_final: 0.7108 (tt0) REVERT: B 381 ASN cc_start: 0.8639 (m-40) cc_final: 0.8432 (m110) REVERT: B 430 TRP cc_start: 0.8867 (m100) cc_final: 0.8438 (m100) REVERT: B 432 TRP cc_start: 0.7476 (m100) cc_final: 0.7189 (m100) REVERT: B 447 ASP cc_start: 0.8042 (t0) cc_final: 0.7616 (p0) REVERT: B 458 MET cc_start: 0.7924 (mmt) cc_final: 0.7476 (mmt) REVERT: B 459 ASN cc_start: 0.8367 (m-40) cc_final: 0.7839 (m-40) REVERT: B 461 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7440 (mtp85) REVERT: C 21 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7346 (mmm160) REVERT: C 22 GLN cc_start: 0.7768 (mt0) cc_final: 0.7508 (mt0) REVERT: C 84 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8031 (t) REVERT: C 88 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7719 (mtp85) REVERT: C 95 HIS cc_start: 0.7605 (t70) cc_final: 0.6921 (t-90) REVERT: C 98 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5549 (pp20) REVERT: C 135 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: C 140 ARG cc_start: 0.7386 (mpt-90) cc_final: 0.6946 (ttm110) REVERT: C 158 LEU cc_start: 0.8817 (tp) cc_final: 0.8553 (tp) REVERT: C 163 TYR cc_start: 0.6624 (m-80) cc_final: 0.6307 (m-80) REVERT: C 167 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7368 (tpp80) REVERT: C 173 ARG cc_start: 0.6768 (mtt90) cc_final: 0.6434 (mtt90) REVERT: C 181 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7573 (mtm110) REVERT: C 186 GLU cc_start: 0.8055 (tp30) cc_final: 0.7835 (tp30) REVERT: C 193 ASP cc_start: 0.7786 (m-30) cc_final: 0.7062 (m-30) REVERT: C 204 ASP cc_start: 0.7365 (t0) cc_final: 0.7160 (t0) REVERT: C 216 TYR cc_start: 0.8320 (t80) cc_final: 0.8006 (t80) REVERT: C 224 GLU cc_start: 0.7724 (tt0) cc_final: 0.7405 (tt0) REVERT: C 226 GLN cc_start: 0.7805 (mp10) cc_final: 0.7056 (mp10) REVERT: C 228 ARG cc_start: 0.7326 (mpt-90) cc_final: 0.7075 (mpt-90) REVERT: C 235 LEU cc_start: 0.7828 (mt) cc_final: 0.7504 (mm) REVERT: C 239 MET cc_start: 0.7683 (mmm) cc_final: 0.7254 (mmm) REVERT: C 244 MET cc_start: 0.7014 (mmt) cc_final: 0.6660 (mmp) REVERT: C 276 GLU cc_start: 0.8054 (pt0) cc_final: 0.7763 (mt-10) REVERT: C 331 PHE cc_start: 0.7274 (m-80) cc_final: 0.6778 (m-80) REVERT: C 342 MET cc_start: 0.5080 (OUTLIER) cc_final: 0.4711 (mmm) REVERT: C 352 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8717 (tp-100) REVERT: C 384 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7508 (pp) REVERT: C 404 GLU cc_start: 0.8340 (pt0) cc_final: 0.7664 (mp0) REVERT: C 452 ASN cc_start: 0.8073 (t0) cc_final: 0.7807 (t0) REVERT: C 454 TRP cc_start: 0.8141 (t60) cc_final: 0.7512 (t60) REVERT: D 22 GLN cc_start: 0.8022 (mt0) cc_final: 0.7793 (mt0) REVERT: D 25 SER cc_start: 0.8027 (m) cc_final: 0.7687 (p) REVERT: D 32 GLN cc_start: 0.7770 (tp40) cc_final: 0.7305 (tt0) REVERT: D 74 VAL cc_start: 0.7926 (p) cc_final: 0.7589 (m) REVERT: D 101 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8123 (mmtt) REVERT: D 111 HIS cc_start: 0.8134 (p-80) cc_final: 0.7718 (p-80) REVERT: D 150 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7600 (mtt-85) REVERT: D 216 TYR cc_start: 0.7814 (t80) cc_final: 0.7282 (t80) REVERT: D 327 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7439 (ttp80) REVERT: D 329 MET cc_start: 0.7154 (tpp) cc_final: 0.6817 (tpp) REVERT: D 331 PHE cc_start: 0.7162 (m-10) cc_final: 0.6257 (m-10) REVERT: D 351 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: D 452 ASN cc_start: 0.7573 (t0) cc_final: 0.7183 (t0) REVERT: D 458 MET cc_start: 0.7460 (mmt) cc_final: 0.7171 (mmt) outliers start: 57 outliers final: 28 residues processed: 500 average time/residue: 0.1837 time to fit residues: 132.1429 Evaluate side-chains 463 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 425 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 64 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL 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 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 182 GLU 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 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 231 SER 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: 0.0070 chunk 51 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 206 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 81 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.0837 > 50:) chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS A 131 GLN B 32 GLN B 60 ASN B 89 HIS B 141 ASN B 148 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN D 189 HIS ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134340 restraints weight = 39001.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139192 restraints weight = 16256.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142156 restraints weight = 9799.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143867 restraints weight = 7392.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144545 restraints weight = 6349.561| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20313 Z= 0.222 Angle : 0.701 10.501 28383 Z= 0.396 Chirality : 0.048 0.292 3109 Planarity : 0.005 0.071 3022 Dihedral : 23.364 85.473 4319 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.49 % Allowed : 14.77 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1937 helix: 2.19 (0.17), residues: 913 sheet: -0.20 (0.28), residues: 286 loop : 0.65 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 228 TYR 0.021 0.002 TYR A 154 PHE 0.030 0.002 PHE D 147 TRP 0.047 0.002 TRP B 443 HIS 0.009 0.001 HIS D 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.22 (20297) covalent geometry : angle 0.69003 / 0.40 (28359) hydrogen bonds : bond 0.05481 / 3.81 ( 1059) hydrogen bonds : angle 4.01479 / 2.96 ( 2792) metal coordination : bond 0.00638 / 0.36 ( 16) metal coordination : angle 4.25590 / 2.83 ( 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: 56 poor density : 466 time to evaluate : 0.604 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 55 ARG cc_start: 0.6325 (ttm110) cc_final: 0.6026 (mtp-110) REVERT: A 64 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7698 (m-10) REVERT: A 89 HIS cc_start: 0.8042 (m-70) cc_final: 0.7734 (m-70) REVERT: A 96 TRP cc_start: 0.8349 (t60) cc_final: 0.7987 (t60) REVERT: A 98 GLU cc_start: 0.7445 (tp30) cc_final: 0.6635 (tp30) REVERT: A 109 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6633 (mp0) REVERT: A 139 GLU cc_start: 0.7250 (tp30) cc_final: 0.7019 (tp30) REVERT: A 142 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7453 (ttm110) REVERT: A 168 VAL cc_start: 0.8176 (t) cc_final: 0.7812 (m) REVERT: A 169 ASP cc_start: 0.7230 (t0) cc_final: 0.6640 (t0) REVERT: A 175 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7831 (p) REVERT: A 182 GLU cc_start: 0.7739 (tt0) cc_final: 0.7330 (tt0) REVERT: A 204 ASP cc_start: 0.7253 (t0) cc_final: 0.6923 (t0) REVERT: A 208 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.7060 (mtp-110) REVERT: A 219 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7300 (mm-40) REVERT: A 241 SER cc_start: 0.8488 (t) cc_final: 0.8000 (p) REVERT: A 251 ASN cc_start: 0.8544 (m-40) cc_final: 0.8298 (m-40) REVERT: A 257 ASP cc_start: 0.5896 (p0) cc_final: 0.5657 (p0) REVERT: A 278 LEU cc_start: 0.9027 (tp) cc_final: 0.8606 (tp) REVERT: A 342 MET cc_start: 0.4371 (ttp) cc_final: 0.3988 (ttp) REVERT: A 376 GLU cc_start: 0.8427 (tt0) cc_final: 0.7831 (tt0) REVERT: A 379 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 381 ASN cc_start: 0.8195 (t0) cc_final: 0.7844 (t0) REVERT: A 383 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8450 (mt-10) REVERT: A 397 ARG cc_start: 0.0316 (OUTLIER) cc_final: -0.2335 (ttm170) REVERT: B 6 VAL cc_start: 0.8261 (t) cc_final: 0.7887 (m) REVERT: B 22 GLN cc_start: 0.7130 (mt0) cc_final: 0.6773 (mt0) REVERT: B 24 GLU cc_start: 0.7618 (tt0) cc_final: 0.7216 (tt0) REVERT: B 28 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7773 (tp40) REVERT: B 51 ASP cc_start: 0.7917 (t0) cc_final: 0.7576 (t0) REVERT: B 56 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7766 (mtmm) REVERT: B 57 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.7163 (mtm-85) REVERT: B 64 TRP cc_start: 0.7486 (m100) cc_final: 0.6952 (m100) REVERT: B 91 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7350 (tp-100) REVERT: B 102 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7864 (mmtp) REVERT: B 118 PHE cc_start: 0.8382 (m-80) cc_final: 0.7674 (m-10) REVERT: B 135 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7203 (mm-30) REVERT: B 138 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8125 (mtmt) REVERT: B 376 GLU cc_start: 0.8151 (tt0) cc_final: 0.7468 (tt0) REVERT: B 381 ASN cc_start: 0.8706 (m-40) cc_final: 0.8386 (m-40) REVERT: B 430 TRP cc_start: 0.8933 (m100) cc_final: 0.8484 (m100) REVERT: B 432 TRP cc_start: 0.7628 (m100) cc_final: 0.7141 (m100) REVERT: B 458 MET cc_start: 0.8088 (mmt) cc_final: 0.7581 (mmt) REVERT: B 459 ASN cc_start: 0.8512 (m-40) cc_final: 0.8038 (m-40) REVERT: C 9 LEU cc_start: 0.7998 (tp) cc_final: 0.7687 (mt) REVERT: C 21 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7378 (mmm160) REVERT: C 29 LEU cc_start: 0.7995 (tp) cc_final: 0.7639 (tt) REVERT: C 51 ASP cc_start: 0.7379 (t0) cc_final: 0.7016 (t70) REVERT: C 88 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7642 (mmm-85) REVERT: C 92 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: C 95 HIS cc_start: 0.7631 (t70) cc_final: 0.7047 (t-90) REVERT: C 96 TRP cc_start: 0.8405 (t60) cc_final: 0.7994 (t60) REVERT: C 98 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5575 (pp20) REVERT: C 135 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6672 (mp0) REVERT: C 140 ARG cc_start: 0.7329 (mpt-90) cc_final: 0.7026 (ttm110) REVERT: C 142 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7129 (ttt-90) REVERT: C 158 LEU cc_start: 0.8700 (tp) cc_final: 0.8469 (tp) REVERT: C 163 TYR cc_start: 0.6669 (m-80) cc_final: 0.6276 (m-80) REVERT: C 173 ARG cc_start: 0.6764 (mtt90) cc_final: 0.6392 (mtt90) REVERT: C 181 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7595 (mtm110) REVERT: C 186 GLU cc_start: 0.8085 (tp30) cc_final: 0.7845 (tp30) REVERT: C 189 HIS cc_start: 0.7173 (t-90) cc_final: 0.6962 (t-90) REVERT: C 193 ASP cc_start: 0.7609 (m-30) cc_final: 0.7338 (m-30) REVERT: C 204 ASP cc_start: 0.7406 (t0) cc_final: 0.7141 (t0) REVERT: C 220 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8532 (mm) REVERT: C 224 GLU cc_start: 0.7801 (tt0) cc_final: 0.7476 (tt0) REVERT: C 226 GLN cc_start: 0.7873 (mp10) cc_final: 0.7105 (mp10) REVERT: C 228 ARG cc_start: 0.7621 (mpt-90) cc_final: 0.7408 (mpt-90) REVERT: C 235 LEU cc_start: 0.7858 (mt) cc_final: 0.7549 (mm) REVERT: C 239 MET cc_start: 0.7733 (mmm) cc_final: 0.7302 (mmm) REVERT: C 331 PHE cc_start: 0.7312 (m-80) cc_final: 0.6816 (m-80) REVERT: C 342 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4869 (mmm) REVERT: C 352 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8720 (tp-100) REVERT: C 384 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7518 (pp) REVERT: C 404 GLU cc_start: 0.8384 (pt0) cc_final: 0.8151 (pt0) REVERT: C 452 ASN cc_start: 0.8113 (t0) cc_final: 0.7816 (t0) REVERT: C 454 TRP cc_start: 0.8117 (t60) cc_final: 0.7528 (t60) REVERT: D 21 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7706 (mtm180) REVERT: D 22 GLN cc_start: 0.8100 (mt0) cc_final: 0.7895 (mt0) REVERT: D 25 SER cc_start: 0.8125 (m) cc_final: 0.7805 (p) REVERT: D 32 GLN cc_start: 0.7828 (tp40) cc_final: 0.7443 (tt0) REVERT: D 42 GLU cc_start: 0.7019 (tt0) cc_final: 0.6760 (tt0) REVERT: D 54 ASP cc_start: 0.7759 (t0) cc_final: 0.7374 (t0) REVERT: D 74 VAL cc_start: 0.7959 (p) cc_final: 0.7642 (m) REVERT: D 111 HIS cc_start: 0.8231 (p-80) cc_final: 0.7816 (p-80) REVERT: D 113 ASP cc_start: 0.7574 (t0) cc_final: 0.7349 (t0) REVERT: D 142 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7293 (ttt90) REVERT: D 182 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6098 (mm-30) REVERT: D 190 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7651 (tpp80) REVERT: D 296 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7830 (t) REVERT: D 331 PHE cc_start: 0.7351 (m-10) cc_final: 0.7075 (m-10) REVERT: D 350 GLU cc_start: 0.8960 (pt0) cc_final: 0.8330 (tp30) REVERT: D 452 ASN cc_start: 0.7669 (t0) cc_final: 0.7297 (t0) REVERT: D 458 MET cc_start: 0.7604 (mmt) cc_final: 0.7186 (mmt) outliers start: 56 outliers final: 29 residues processed: 500 average time/residue: 0.1781 time to fit residues: 128.2195 Evaluate side-chains 496 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 457 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 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 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 149 ILE 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 283 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 69 GLU 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 182 GLU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 249 THR 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 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 296 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 149 optimal weight: 0.9980 chunk 99 optimal weight: 0.0670 chunk 153 optimal weight: 1.9990 chunk 192 optimal weight: 40.0000 chunk 209 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 36 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 133 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 100 HIS B 60 ASN B 89 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.190259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136175 restraints weight = 42021.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141369 restraints weight = 16765.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144562 restraints weight = 9805.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146434 restraints weight = 7227.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147422 restraints weight = 6133.620| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20313 Z= 0.150 Angle : 0.632 16.801 28383 Z= 0.352 Chirality : 0.043 0.226 3109 Planarity : 0.005 0.062 3022 Dihedral : 23.295 84.052 4314 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 16.39 % Favored : 80.69 % 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: 1.92 (0.19), residues: 1937 helix: 2.32 (0.17), residues: 914 sheet: -0.18 (0.28), residues: 285 loop : 0.70 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 167 TYR 0.017 0.001 TYR A 188 PHE 0.015 0.001 PHE A 72 TRP 0.041 0.002 TRP B 443 HIS 0.005 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (20297) covalent geometry : angle 0.61038 / 0.35 (28359) hydrogen bonds : bond 0.04614 / 3.19 ( 1059) hydrogen bonds : angle 3.79780 / 2.80 ( 2792) metal coordination : bond 0.01357 / 0.67 ( 16) metal coordination : angle 5.72625 / 4.19 ( 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 494 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 447 time to evaluate : 0.638 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: A 1 MET cc_start: 0.6177 (tpt) cc_final: 0.5930 (tpt) REVERT: A 37 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7544 (m) REVERT: A 89 HIS cc_start: 0.7869 (m170) cc_final: 0.7462 (m170) REVERT: A 142 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7519 (ttm-80) REVERT: A 168 VAL cc_start: 0.8202 (t) cc_final: 0.7868 (m) REVERT: A 169 ASP cc_start: 0.7187 (t0) cc_final: 0.6534 (t0) REVERT: A 177 ASP cc_start: 0.7616 (t0) cc_final: 0.7359 (t0) REVERT: A 182 GLU cc_start: 0.7700 (tt0) cc_final: 0.7249 (tt0) REVERT: A 204 ASP cc_start: 0.7298 (t0) cc_final: 0.6955 (t0) REVERT: A 208 ARG cc_start: 0.7376 (mtp-110) cc_final: 0.7028 (mtp-110) REVERT: A 241 SER cc_start: 0.8467 (t) cc_final: 0.7978 (p) REVERT: A 251 ASN cc_start: 0.8548 (m-40) cc_final: 0.8310 (m-40) REVERT: A 278 LEU cc_start: 0.9006 (tp) cc_final: 0.8579 (tp) REVERT: A 342 MET cc_start: 0.4433 (ttp) cc_final: 0.4010 (ttp) REVERT: A 376 GLU cc_start: 0.8344 (tt0) cc_final: 0.7723 (tt0) REVERT: A 379 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 381 ASN cc_start: 0.8083 (t0) cc_final: 0.7720 (t0) REVERT: A 383 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 397 ARG cc_start: 0.0321 (OUTLIER) cc_final: -0.2367 (ttm170) REVERT: B 6 VAL cc_start: 0.8257 (t) cc_final: 0.7887 (m) REVERT: B 22 GLN cc_start: 0.7034 (mt0) cc_final: 0.6705 (mt0) REVERT: B 24 GLU cc_start: 0.7556 (tt0) cc_final: 0.7180 (tt0) REVERT: B 28 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7610 (tp40) REVERT: B 64 TRP cc_start: 0.7409 (m100) cc_final: 0.6850 (m100) REVERT: B 91 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7320 (tp-100) REVERT: B 102 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7890 (mmtp) REVERT: B 105 VAL cc_start: 0.8336 (t) cc_final: 0.7987 (p) REVERT: B 135 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 138 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8075 (mtmt) REVERT: B 164 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 300 ARG cc_start: 0.8581 (tpt170) cc_final: 0.8020 (mmt-90) REVERT: B 376 GLU cc_start: 0.8062 (tt0) cc_final: 0.7495 (tt0) REVERT: B 430 TRP cc_start: 0.8960 (m100) cc_final: 0.8476 (m100) REVERT: B 432 TRP cc_start: 0.7636 (m100) cc_final: 0.7151 (m100) REVERT: B 458 MET cc_start: 0.8025 (mmt) cc_final: 0.7578 (mmt) REVERT: B 459 ASN cc_start: 0.8514 (m-40) cc_final: 0.8063 (m-40) REVERT: C 9 LEU cc_start: 0.7954 (tp) cc_final: 0.7597 (mm) REVERT: C 21 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7277 (mmm160) REVERT: C 26 CYS cc_start: 0.7281 (m) cc_final: 0.7028 (m) REVERT: C 51 ASP cc_start: 0.7351 (t0) cc_final: 0.7115 (t0) REVERT: C 92 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: C 95 HIS cc_start: 0.7664 (t70) cc_final: 0.7081 (t-90) REVERT: C 96 TRP cc_start: 0.8380 (t60) cc_final: 0.7928 (t60) REVERT: C 98 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5470 (pp20) REVERT: C 135 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6661 (mp0) REVERT: C 140 ARG cc_start: 0.7316 (mpt-90) cc_final: 0.7023 (ttm110) REVERT: C 142 ARG cc_start: 0.7418 (ttp80) cc_final: 0.7125 (ttt-90) REVERT: C 181 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7545 (mtm110) REVERT: C 186 GLU cc_start: 0.8058 (tp30) cc_final: 0.7830 (tp30) REVERT: C 193 ASP cc_start: 0.7620 (m-30) cc_final: 0.7332 (m-30) REVERT: C 204 ASP cc_start: 0.7457 (t0) cc_final: 0.7106 (t0) REVERT: C 224 GLU cc_start: 0.7813 (tt0) cc_final: 0.7492 (tt0) REVERT: C 226 GLN cc_start: 0.7867 (mp10) cc_final: 0.7142 (mp10) REVERT: C 228 ARG cc_start: 0.7602 (mpt-90) cc_final: 0.7352 (mpt-90) REVERT: C 239 MET cc_start: 0.7642 (mmm) cc_final: 0.7201 (mmm) REVERT: C 250 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7765 (tt) REVERT: C 331 PHE cc_start: 0.7345 (m-80) cc_final: 0.6882 (m-80) REVERT: C 352 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8739 (tp-100) REVERT: C 384 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7520 (pp) REVERT: C 404 GLU cc_start: 0.8285 (pt0) cc_final: 0.8018 (pt0) REVERT: C 452 ASN cc_start: 0.8079 (t0) cc_final: 0.7747 (t0) REVERT: C 454 TRP cc_start: 0.8034 (t60) cc_final: 0.7541 (t60) REVERT: D 25 SER cc_start: 0.8110 (m) cc_final: 0.7764 (p) REVERT: D 42 GLU cc_start: 0.7033 (tt0) cc_final: 0.6828 (tt0) REVERT: D 54 ASP cc_start: 0.7814 (t0) cc_final: 0.7414 (t0) REVERT: D 74 VAL cc_start: 0.7944 (p) cc_final: 0.7633 (m) REVERT: D 96 TRP cc_start: 0.8350 (t60) cc_final: 0.8118 (t60) REVERT: D 111 HIS cc_start: 0.8246 (p-80) cc_final: 0.7803 (p-80) REVERT: D 142 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7343 (ttt-90) REVERT: D 186 GLU cc_start: 0.8035 (tt0) cc_final: 0.7644 (pt0) REVERT: D 190 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7681 (tpp80) REVERT: D 206 ASN cc_start: 0.8190 (m-40) cc_final: 0.7874 (m-40) REVERT: D 226 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7684 (mm-40) REVERT: D 279 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7989 (ttm110) REVERT: D 296 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7773 (t) REVERT: D 327 ARG cc_start: 0.8020 (ttt180) cc_final: 0.7355 (ttp80) REVERT: D 329 MET cc_start: 0.6590 (tpp) cc_final: 0.6065 (tpp) REVERT: D 331 PHE cc_start: 0.7176 (m-10) cc_final: 0.6328 (m-10) REVERT: D 350 GLU cc_start: 0.8891 (pt0) cc_final: 0.8259 (tp30) REVERT: D 452 ASN cc_start: 0.7664 (t0) cc_final: 0.7269 (t0) REVERT: D 458 MET cc_start: 0.7453 (mmt) cc_final: 0.7138 (mmt) outliers start: 47 outliers final: 27 residues processed: 472 average time/residue: 0.1754 time to fit residues: 119.3424 Evaluate side-chains 482 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 447 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 LEU 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 283 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 384 LEU 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 204 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 296 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 144 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN B 89 HIS B 100 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN D 32 GLN D 92 GLN D 251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.187905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133909 restraints weight = 41374.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138995 restraints weight = 16679.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142131 restraints weight = 9834.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143922 restraints weight = 7273.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144976 restraints weight = 6193.556| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20313 Z= 0.209 Angle : 0.655 13.966 28383 Z= 0.363 Chirality : 0.044 0.204 3109 Planarity : 0.005 0.065 3022 Dihedral : 23.310 85.644 4308 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.93 % Allowed : 16.32 % Favored : 79.75 % 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: 2.20 (0.17), residues: 915 sheet: -0.17 (0.29), residues: 280 loop : 0.62 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 444 TYR 0.023 0.002 TYR A 154 PHE 0.017 0.001 PHE A 72 TRP 0.043 0.002 TRP B 443 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 (20297) covalent geometry : angle 0.63674 / 0.36 (28359) hydrogen bonds : bond 0.04883 / 3.40 ( 1059) hydrogen bonds : angle 3.87141 / 2.86 ( 2792) metal coordination : bond 0.00813 / 0.40 ( 16) metal coordination : angle 5.37068 / 3.88 ( 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 514 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 451 time to evaluate : 0.640 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: A 60 ASN cc_start: 0.8166 (m-40) cc_final: 0.7763 (m-40) REVERT: A 89 HIS cc_start: 0.7951 (m170) cc_final: 0.7442 (m170) REVERT: A 109 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6611 (mp0) REVERT: A 138 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8119 (mtmt) REVERT: A 142 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7514 (ttp-110) REVERT: A 168 VAL cc_start: 0.8306 (t) cc_final: 0.7986 (m) REVERT: A 169 ASP cc_start: 0.7239 (t0) cc_final: 0.6578 (t0) REVERT: A 182 GLU cc_start: 0.7690 (tt0) cc_final: 0.7247 (tt0) REVERT: A 204 ASP cc_start: 0.7312 (t0) cc_final: 0.6974 (t0) REVERT: A 208 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.7097 (mtp-110) REVERT: A 241 SER cc_start: 0.8398 (t) cc_final: 0.7922 (p) REVERT: A 251 ASN cc_start: 0.8577 (m-40) cc_final: 0.8328 (m-40) REVERT: A 278 LEU cc_start: 0.9053 (tp) cc_final: 0.8670 (tp) REVERT: A 342 MET cc_start: 0.4559 (ttp) cc_final: 0.4308 (ttp) REVERT: A 376 GLU cc_start: 0.8336 (tt0) cc_final: 0.7711 (tt0) REVERT: A 379 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7908 (mm-30) REVERT: A 381 ASN cc_start: 0.8105 (t0) cc_final: 0.7747 (t0) REVERT: A 383 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8398 (mt-10) REVERT: A 397 ARG cc_start: 0.0490 (OUTLIER) cc_final: -0.2283 (ttm170) REVERT: B 6 VAL cc_start: 0.8318 (t) cc_final: 0.7948 (m) REVERT: B 22 GLN cc_start: 0.7311 (mt0) cc_final: 0.7021 (mt0) REVERT: B 24 GLU cc_start: 0.7664 (tt0) cc_final: 0.7301 (tt0) REVERT: B 28 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7622 (tp40) REVERT: B 57 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7179 (mtm-85) REVERT: B 64 TRP cc_start: 0.7612 (m100) cc_final: 0.7183 (m100) REVERT: B 91 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7384 (tp40) REVERT: B 102 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7879 (mmtt) REVERT: B 135 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 138 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8127 (mtmt) REVERT: B 300 ARG cc_start: 0.8599 (tpt170) cc_final: 0.8133 (mmt-90) REVERT: B 376 GLU cc_start: 0.8140 (tt0) cc_final: 0.7606 (tt0) REVERT: B 381 ASN cc_start: 0.8686 (m-40) cc_final: 0.8368 (m-40) REVERT: B 416 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7453 (mmm160) REVERT: B 430 TRP cc_start: 0.8993 (m100) cc_final: 0.8577 (m100) REVERT: B 458 MET cc_start: 0.8066 (mmt) cc_final: 0.7515 (mmt) REVERT: B 459 ASN cc_start: 0.8552 (m-40) cc_final: 0.8118 (m-40) REVERT: C 1 MET cc_start: 0.6951 (ttm) cc_final: 0.6715 (ttt) REVERT: C 9 LEU cc_start: 0.8097 (tp) cc_final: 0.7821 (mt) REVERT: C 21 ARG cc_start: 0.7601 (mmt90) cc_final: 0.7316 (mmm160) REVERT: C 26 CYS cc_start: 0.7297 (m) cc_final: 0.7059 (m) REVERT: C 29 LEU cc_start: 0.8065 (tp) cc_final: 0.7741 (tt) REVERT: C 92 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: C 95 HIS cc_start: 0.7683 (t70) cc_final: 0.7152 (t-90) REVERT: C 96 TRP cc_start: 0.8461 (t60) cc_final: 0.8000 (t60) REVERT: C 98 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5787 (pp20) REVERT: C 109 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7081 (mt-10) REVERT: C 135 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: C 140 ARG cc_start: 0.7345 (mpt-90) cc_final: 0.7062 (tpp80) REVERT: C 186 GLU cc_start: 0.8061 (tp30) cc_final: 0.7840 (tp30) REVERT: C 204 ASP cc_start: 0.7449 (t0) cc_final: 0.7059 (t0) REVERT: C 220 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 224 GLU cc_start: 0.7864 (tt0) cc_final: 0.7652 (tt0) REVERT: C 226 GLN cc_start: 0.7869 (mp10) cc_final: 0.7109 (mp10) REVERT: C 228 ARG cc_start: 0.7748 (mpt-90) cc_final: 0.7519 (mpt-90) REVERT: C 239 MET cc_start: 0.7672 (mmm) cc_final: 0.7283 (mmm) REVERT: C 265 ARG cc_start: 0.7942 (ptt180) cc_final: 0.7523 (ptt180) REVERT: C 331 PHE cc_start: 0.7378 (m-80) cc_final: 0.6904 (m-80) REVERT: C 352 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8751 (tp-100) REVERT: C 384 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7569 (pp) REVERT: C 404 GLU cc_start: 0.8329 (pt0) cc_final: 0.8084 (pt0) REVERT: C 452 ASN cc_start: 0.8075 (t0) cc_final: 0.7682 (t0) REVERT: D 1 MET cc_start: 0.5116 (mtm) cc_final: 0.4893 (mtm) REVERT: D 25 SER cc_start: 0.8182 (m) cc_final: 0.7856 (p) REVERT: D 54 ASP cc_start: 0.7788 (t0) cc_final: 0.7501 (t0) REVERT: D 74 VAL cc_start: 0.8018 (p) cc_final: 0.7721 (m) REVERT: D 109 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7358 (mt-10) REVERT: D 111 HIS cc_start: 0.8389 (p-80) cc_final: 0.8004 (p-80) REVERT: D 142 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7299 (ttt-90) REVERT: D 164 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7954 (mp) REVERT: D 224 GLU cc_start: 0.6968 (pp20) cc_final: 0.6257 (pp20) REVERT: D 226 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7687 (mm-40) REVERT: D 229 GLU cc_start: 0.7120 (pt0) cc_final: 0.6842 (pt0) REVERT: D 242 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: D 272 ARG cc_start: 0.7670 (mmm160) cc_final: 0.7432 (tpt90) REVERT: D 279 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7852 (ttm110) REVERT: D 296 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7767 (t) REVERT: D 325 ARG cc_start: 0.7474 (ttm110) cc_final: 0.6861 (ptm160) REVERT: D 327 ARG cc_start: 0.8025 (ttt180) cc_final: 0.7393 (ttp80) REVERT: D 331 PHE cc_start: 0.7210 (m-10) cc_final: 0.6375 (m-80) REVERT: D 350 GLU cc_start: 0.8844 (pt0) cc_final: 0.8349 (pt0) REVERT: D 452 ASN cc_start: 0.7690 (t0) cc_final: 0.7323 (t0) REVERT: D 458 MET cc_start: 0.7641 (mmt) cc_final: 0.7230 (mmt) outliers start: 63 outliers final: 39 residues processed: 480 average time/residue: 0.1774 time to fit residues: 122.5226 Evaluate side-chains 496 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 446 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 219 GLN 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 57 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 LEU 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 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 VAL 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 188 TYR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 249 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 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 35 TRP Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 273 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 8 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 208 optimal weight: 30.0000 chunk 54 optimal weight: 0.1980 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.189548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136642 restraints weight = 39060.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141631 restraints weight = 16103.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144706 restraints weight = 9593.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146506 restraints weight = 7134.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.147506 restraints weight = 6093.336| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20313 Z= 0.145 Angle : 0.621 13.517 28383 Z= 0.344 Chirality : 0.042 0.193 3109 Planarity : 0.005 0.067 3022 Dihedral : 23.301 85.034 4307 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.49 % Allowed : 18.01 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1937 helix: 2.21 (0.17), residues: 918 sheet: -0.15 (0.29), residues: 274 loop : 0.62 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 325 TYR 0.020 0.002 TYR A 188 PHE 0.025 0.001 PHE B 314 TRP 0.035 0.002 TRP B 443 HIS 0.006 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (20297) covalent geometry : angle 0.60410 / 0.34 (28359) hydrogen bonds : bond 0.04367 / 3.04 ( 1059) hydrogen bonds : angle 3.77705 / 2.79 ( 2792) metal coordination : bond 0.00444 / 0.25 ( 16) metal coordination : angle 4.99009 / 3.65 ( 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 504 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 448 time to evaluate : 0.574 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: A 37 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7553 (m) REVERT: A 40 VAL cc_start: 0.7846 (m) cc_final: 0.7571 (t) REVERT: A 60 ASN cc_start: 0.8164 (m-40) cc_final: 0.7914 (m-40) REVERT: A 89 HIS cc_start: 0.7888 (m170) cc_final: 0.7557 (m170) REVERT: A 109 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6554 (mp0) REVERT: A 142 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7483 (ttp-110) REVERT: A 168 VAL cc_start: 0.8313 (t) cc_final: 0.8017 (m) REVERT: A 169 ASP cc_start: 0.7205 (t0) cc_final: 0.6562 (t0) REVERT: A 182 GLU cc_start: 0.7667 (tt0) cc_final: 0.7218 (tt0) REVERT: A 204 ASP cc_start: 0.7309 (t0) cc_final: 0.6953 (t0) REVERT: A 208 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.7091 (mtp-110) REVERT: A 241 SER cc_start: 0.8397 (t) cc_final: 0.7933 (p) REVERT: A 251 ASN cc_start: 0.8571 (m-40) cc_final: 0.8320 (m-40) REVERT: A 278 LEU cc_start: 0.9033 (tp) cc_final: 0.8656 (tp) REVERT: A 342 MET cc_start: 0.4468 (ttp) cc_final: 0.4239 (ttp) REVERT: A 376 GLU cc_start: 0.8296 (tt0) cc_final: 0.7684 (tt0) REVERT: A 379 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 381 ASN cc_start: 0.8045 (t0) cc_final: 0.7691 (t0) REVERT: A 383 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 397 ARG cc_start: 0.0486 (OUTLIER) cc_final: -0.2291 (tpm170) REVERT: B 6 VAL cc_start: 0.8336 (t) cc_final: 0.7943 (m) REVERT: B 22 GLN cc_start: 0.7329 (mt0) cc_final: 0.7023 (mt0) REVERT: B 24 GLU cc_start: 0.7610 (tt0) cc_final: 0.7255 (tt0) REVERT: B 28 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7515 (tp40) REVERT: B 57 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6969 (mtm-85) REVERT: B 64 TRP cc_start: 0.7534 (m100) cc_final: 0.7169 (m100) REVERT: B 91 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7330 (tp40) REVERT: B 135 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 138 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8111 (mtmt) REVERT: B 164 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7916 (tt) REVERT: B 300 ARG cc_start: 0.8551 (tpt170) cc_final: 0.8224 (mmt-90) REVERT: B 345 TRP cc_start: 0.8095 (m100) cc_final: 0.7885 (m100) REVERT: B 376 GLU cc_start: 0.8086 (tt0) cc_final: 0.7710 (tt0) REVERT: B 381 ASN cc_start: 0.8604 (m-40) cc_final: 0.8273 (m-40) REVERT: B 430 TRP cc_start: 0.9003 (m100) cc_final: 0.8522 (m100) REVERT: B 444 ARG cc_start: 0.7949 (mmp80) cc_final: 0.7643 (mmp80) REVERT: B 458 MET cc_start: 0.8003 (mmt) cc_final: 0.7511 (mmt) REVERT: B 459 ASN cc_start: 0.8546 (m-40) cc_final: 0.7943 (m-40) REVERT: C 1 MET cc_start: 0.6977 (ttm) cc_final: 0.6617 (ttt) REVERT: C 9 LEU cc_start: 0.8048 (tp) cc_final: 0.7718 (mm) REVERT: C 21 ARG cc_start: 0.7565 (mmt90) cc_final: 0.7258 (mmm160) REVERT: C 26 CYS cc_start: 0.7258 (m) cc_final: 0.7010 (m) REVERT: C 29 LEU cc_start: 0.8043 (tp) cc_final: 0.7632 (tt) REVERT: C 92 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: C 95 HIS cc_start: 0.7677 (t70) cc_final: 0.7074 (t-90) REVERT: C 96 TRP cc_start: 0.8374 (t60) cc_final: 0.7873 (t60) REVERT: C 98 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5512 (pp20) REVERT: C 109 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7037 (mt-10) REVERT: C 135 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: C 140 ARG cc_start: 0.7339 (mpt-90) cc_final: 0.7059 (tpp80) REVERT: C 186 GLU cc_start: 0.8039 (tp30) cc_final: 0.7810 (tp30) REVERT: C 204 ASP cc_start: 0.7436 (t0) cc_final: 0.7021 (t0) REVERT: C 220 LEU cc_start: 0.8600 (mm) cc_final: 0.8299 (mp) REVERT: C 226 GLN cc_start: 0.7879 (mp10) cc_final: 0.7181 (mp10) REVERT: C 228 ARG cc_start: 0.7705 (mpt-90) cc_final: 0.7451 (mpt-90) REVERT: C 235 LEU cc_start: 0.7890 (mt) cc_final: 0.7341 (pp) REVERT: C 239 MET cc_start: 0.7666 (mmm) cc_final: 0.7277 (mmm) REVERT: C 265 ARG cc_start: 0.7891 (ptt180) cc_final: 0.7488 (ptt180) REVERT: C 331 PHE cc_start: 0.7389 (m-80) cc_final: 0.6932 (m-80) REVERT: C 352 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8764 (tp-100) REVERT: C 384 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7551 (pp) REVERT: C 404 GLU cc_start: 0.8279 (pt0) cc_final: 0.7952 (pt0) REVERT: C 409 ARG cc_start: 0.8619 (mmp80) cc_final: 0.8214 (mmp80) REVERT: C 452 ASN cc_start: 0.8031 (t0) cc_final: 0.7627 (t0) REVERT: D 1 MET cc_start: 0.5050 (mtm) cc_final: 0.4781 (mtm) REVERT: D 25 SER cc_start: 0.8192 (m) cc_final: 0.7919 (p) REVERT: D 54 ASP cc_start: 0.7771 (t0) cc_final: 0.7432 (t0) REVERT: D 74 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7767 (m) REVERT: D 96 TRP cc_start: 0.8439 (t60) cc_final: 0.8172 (t60) REVERT: D 102 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7853 (mmtp) REVERT: D 111 HIS cc_start: 0.8362 (p-80) cc_final: 0.7953 (p-80) REVERT: D 190 ARG cc_start: 0.8218 (mtp180) cc_final: 0.8006 (mtp180) REVERT: D 224 GLU cc_start: 0.7020 (pp20) cc_final: 0.6732 (pp20) REVERT: D 242 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7249 (mm-30) REVERT: D 296 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7931 (t) REVERT: D 327 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7393 (ttp80) REVERT: D 329 MET cc_start: 0.6817 (ttp) cc_final: 0.6548 (ttm) REVERT: D 331 PHE cc_start: 0.7315 (m-10) cc_final: 0.6528 (m-80) REVERT: D 350 GLU cc_start: 0.8837 (pt0) cc_final: 0.8210 (tp30) REVERT: D 452 ASN cc_start: 0.7704 (t0) cc_final: 0.7318 (t0) REVERT: D 458 MET cc_start: 0.7588 (mmt) cc_final: 0.7181 (mmt) outliers start: 56 outliers final: 38 residues processed: 474 average time/residue: 0.1746 time to fit residues: 119.0996 Evaluate side-chains 487 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 203 HIS 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 46 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 LEU 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 283 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 250 LEU 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 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 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 273 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 56 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS D 146 HIS D 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.186880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133714 restraints weight = 47591.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138957 restraints weight = 18159.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142187 restraints weight = 10361.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144126 restraints weight = 7521.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145232 restraints weight = 6302.674| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20313 Z= 0.187 Angle : 0.634 11.274 28383 Z= 0.352 Chirality : 0.042 0.206 3109 Planarity : 0.005 0.074 3022 Dihedral : 23.297 85.512 4305 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.12 % Allowed : 19.50 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1937 helix: 2.08 (0.17), residues: 918 sheet: -0.13 (0.29), residues: 274 loop : 0.56 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 325 TYR 0.023 0.002 TYR A 188 PHE 0.017 0.001 PHE C 147 TRP 0.032 0.002 TRP B 443 HIS 0.009 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (20297) covalent geometry : angle 0.61933 / 0.35 (28359) hydrogen bonds : bond 0.04573 / 3.19 ( 1059) hydrogen bonds : angle 3.82360 / 2.82 ( 2792) metal coordination : bond 0.00492 / 0.29 ( 16) metal coordination : angle 4.66603 / 3.44 ( 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 490 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 440 time to evaluate : 0.601 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: A 37 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7554 (m) REVERT: A 40 VAL cc_start: 0.7864 (m) cc_final: 0.7614 (t) REVERT: A 89 HIS cc_start: 0.7937 (m170) cc_final: 0.7475 (m170) REVERT: A 109 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6587 (mp0) REVERT: A 131 GLN cc_start: 0.8136 (tp40) cc_final: 0.7866 (tp-100) REVERT: A 142 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7462 (ttp-110) REVERT: A 168 VAL cc_start: 0.8348 (t) cc_final: 0.8065 (m) REVERT: A 169 ASP cc_start: 0.7245 (t0) cc_final: 0.6599 (t0) REVERT: A 182 GLU cc_start: 0.7650 (tt0) cc_final: 0.7197 (tt0) REVERT: A 204 ASP cc_start: 0.7262 (t0) cc_final: 0.6908 (t0) REVERT: A 208 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.7064 (mtp-110) REVERT: A 241 SER cc_start: 0.8416 (t) cc_final: 0.7963 (p) REVERT: A 251 ASN cc_start: 0.8598 (m-40) cc_final: 0.8345 (m-40) REVERT: A 278 LEU cc_start: 0.9042 (tp) cc_final: 0.8743 (tp) REVERT: A 342 MET cc_start: 0.4534 (ttp) cc_final: 0.4285 (ttp) REVERT: A 376 GLU cc_start: 0.8360 (tt0) cc_final: 0.7794 (tt0) REVERT: A 379 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 381 ASN cc_start: 0.8088 (t0) cc_final: 0.7744 (t0) REVERT: A 383 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8407 (mt-10) REVERT: A 397 ARG cc_start: 0.1282 (OUTLIER) cc_final: -0.1310 (tpm170) REVERT: A 419 GLU cc_start: 0.6877 (tm-30) cc_final: 0.5654 (tm-30) REVERT: B 6 VAL cc_start: 0.8360 (t) cc_final: 0.7987 (m) REVERT: B 22 GLN cc_start: 0.7391 (mt0) cc_final: 0.7106 (mt0) REVERT: B 24 GLU cc_start: 0.7657 (tt0) cc_final: 0.7283 (tt0) REVERT: B 28 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7606 (tp40) REVERT: B 91 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7360 (tp40) REVERT: B 101 LYS cc_start: 0.8089 (mptt) cc_final: 0.7693 (mptt) REVERT: B 106 SER cc_start: 0.8184 (t) cc_final: 0.7905 (p) REVERT: B 135 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 138 LYS cc_start: 0.8355 (mtmt) cc_final: 0.8138 (mtmt) REVERT: B 164 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7905 (tt) REVERT: B 300 ARG cc_start: 0.8570 (tpt170) cc_final: 0.8080 (mmt-90) REVERT: B 348 PHE cc_start: 0.8265 (t80) cc_final: 0.7837 (t80) REVERT: B 376 GLU cc_start: 0.8218 (tt0) cc_final: 0.7848 (tt0) REVERT: B 381 ASN cc_start: 0.8669 (m-40) cc_final: 0.8356 (m-40) REVERT: B 430 TRP cc_start: 0.9012 (m100) cc_final: 0.8585 (m100) REVERT: B 458 MET cc_start: 0.8045 (mmt) cc_final: 0.7562 (mmt) REVERT: B 459 ASN cc_start: 0.8595 (m-40) cc_final: 0.7996 (m-40) REVERT: C 1 MET cc_start: 0.6940 (ttm) cc_final: 0.6703 (ttt) REVERT: C 9 LEU cc_start: 0.8134 (tp) cc_final: 0.7880 (mt) REVERT: C 21 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7271 (mmm160) REVERT: C 26 CYS cc_start: 0.7273 (m) cc_final: 0.7001 (m) REVERT: C 29 LEU cc_start: 0.8056 (tp) cc_final: 0.7707 (tt) REVERT: C 92 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: C 95 HIS cc_start: 0.7699 (t70) cc_final: 0.7105 (t-90) REVERT: C 96 TRP cc_start: 0.8417 (t60) cc_final: 0.7939 (t60) REVERT: C 98 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5832 (pp20) REVERT: C 109 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 135 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: C 140 ARG cc_start: 0.7359 (mpt-90) cc_final: 0.7072 (tpp80) REVERT: C 142 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7239 (tmm-80) REVERT: C 172 TRP cc_start: 0.7596 (m100) cc_final: 0.7176 (m100) REVERT: C 186 GLU cc_start: 0.7996 (tp30) cc_final: 0.7740 (tp30) REVERT: C 189 HIS cc_start: 0.7746 (m90) cc_final: 0.7261 (m90) REVERT: C 204 ASP cc_start: 0.7466 (t0) cc_final: 0.7046 (t0) REVERT: C 226 GLN cc_start: 0.7833 (mp10) cc_final: 0.7096 (mp10) REVERT: C 228 ARG cc_start: 0.7758 (mpt-90) cc_final: 0.7517 (mpt-90) REVERT: C 235 LEU cc_start: 0.7972 (mt) cc_final: 0.7395 (pp) REVERT: C 239 MET cc_start: 0.7645 (mmm) cc_final: 0.7290 (mmm) REVERT: C 331 PHE cc_start: 0.7397 (m-80) cc_final: 0.6899 (m-80) REVERT: C 352 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8747 (tp-100) REVERT: C 384 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7577 (pp) REVERT: C 404 GLU cc_start: 0.8347 (pt0) cc_final: 0.8030 (pt0) REVERT: C 409 ARG cc_start: 0.8646 (mmp80) cc_final: 0.8222 (mmp80) REVERT: C 452 ASN cc_start: 0.8066 (t0) cc_final: 0.7700 (m-40) REVERT: D 1 MET cc_start: 0.5061 (mtm) cc_final: 0.4778 (mtm) REVERT: D 25 SER cc_start: 0.8200 (m) cc_final: 0.7920 (p) REVERT: D 51 ASP cc_start: 0.7918 (t0) cc_final: 0.7699 (t0) REVERT: D 54 ASP cc_start: 0.7769 (t0) cc_final: 0.7471 (t0) REVERT: D 74 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7790 (m) REVERT: D 102 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7871 (mmtp) REVERT: D 149 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8217 (tp) REVERT: D 190 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7614 (tpp80) REVERT: D 226 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7682 (mm-40) REVERT: D 242 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7241 (mm-30) REVERT: D 279 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7683 (ttm-80) REVERT: D 296 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7937 (t) REVERT: D 327 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7413 (ttp80) REVERT: D 331 PHE cc_start: 0.7389 (m-10) cc_final: 0.6637 (m-80) REVERT: D 350 GLU cc_start: 0.8858 (pt0) cc_final: 0.8198 (tp30) REVERT: D 409 ARG cc_start: 0.8560 (mmp80) cc_final: 0.8282 (mmp80) REVERT: D 452 ASN cc_start: 0.7710 (t0) cc_final: 0.7270 (t0) REVERT: D 458 MET cc_start: 0.7684 (mmt) cc_final: 0.7262 (mmt) outliers start: 50 outliers final: 34 residues processed: 467 average time/residue: 0.1761 time to fit residues: 118.9772 Evaluate side-chains 481 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 437 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 203 HIS 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 46 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 VAL 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 129 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 249 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 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 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 273 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 202 optimal weight: 50.0000 chunk 86 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 148 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.186813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132412 restraints weight = 58600.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138034 restraints weight = 20296.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141465 restraints weight = 11058.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143613 restraints weight = 7850.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144719 restraints weight = 6471.046| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20313 Z= 0.184 Angle : 0.634 10.602 28383 Z= 0.352 Chirality : 0.042 0.204 3109 Planarity : 0.005 0.076 3022 Dihedral : 23.262 86.082 4302 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.80 % Allowed : 20.19 % 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: 1.71 (0.19), residues: 1937 helix: 2.11 (0.17), residues: 912 sheet: -0.06 (0.30), residues: 272 loop : 0.51 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 325 TYR 0.024 0.002 TYR A 188 PHE 0.060 0.002 PHE B 348 TRP 0.054 0.002 TRP B 64 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (20297) covalent geometry : angle 0.61904 / 0.35 (28359) hydrogen bonds : bond 0.04554 / 3.16 ( 1059) hydrogen bonds : angle 3.85246 / 2.85 ( 2792) metal coordination : bond 0.00666 / 0.47 ( 16) metal coordination : angle 4.82712 / 3.47 ( 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 480 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 435 time to evaluate : 0.640 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: A 37 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7544 (m) REVERT: A 40 VAL cc_start: 0.7878 (m) cc_final: 0.7641 (t) REVERT: A 89 HIS cc_start: 0.7924 (m170) cc_final: 0.7460 (m170) REVERT: A 109 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6577 (mp0) REVERT: A 131 GLN cc_start: 0.8147 (tp40) cc_final: 0.7833 (tp-100) REVERT: A 142 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7460 (ttp-110) REVERT: A 168 VAL cc_start: 0.8365 (t) cc_final: 0.8080 (m) REVERT: A 169 ASP cc_start: 0.7258 (t0) cc_final: 0.6603 (t0) REVERT: A 182 GLU cc_start: 0.7551 (tt0) cc_final: 0.7119 (tt0) REVERT: A 204 ASP cc_start: 0.7283 (t0) cc_final: 0.6919 (t0) REVERT: A 208 ARG cc_start: 0.7372 (mtp-110) cc_final: 0.7034 (mtp-110) REVERT: A 219 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7174 (tm-30) REVERT: A 241 SER cc_start: 0.8444 (t) cc_final: 0.7999 (p) REVERT: A 251 ASN cc_start: 0.8607 (m-40) cc_final: 0.8352 (m-40) REVERT: A 278 LEU cc_start: 0.9040 (tp) cc_final: 0.8770 (tp) REVERT: A 342 MET cc_start: 0.4496 (ttp) cc_final: 0.4249 (ttp) REVERT: A 376 GLU cc_start: 0.8363 (tt0) cc_final: 0.7795 (tt0) REVERT: A 379 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 381 ASN cc_start: 0.8092 (t0) cc_final: 0.7748 (t0) REVERT: A 383 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8413 (mt-10) REVERT: A 397 ARG cc_start: 0.1426 (OUTLIER) cc_final: -0.1219 (tpm170) REVERT: A 419 GLU cc_start: 0.6961 (tm-30) cc_final: 0.5731 (tm-30) REVERT: B 6 VAL cc_start: 0.8370 (t) cc_final: 0.7992 (m) REVERT: B 22 GLN cc_start: 0.7434 (mt0) cc_final: 0.7170 (mt0) REVERT: B 28 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7599 (tp40) REVERT: B 91 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7346 (tp40) REVERT: B 101 LYS cc_start: 0.8178 (mptt) cc_final: 0.7789 (mptt) REVERT: B 106 SER cc_start: 0.8172 (t) cc_final: 0.7893 (p) REVERT: B 135 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 138 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8124 (mtmt) REVERT: B 164 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7918 (tt) REVERT: B 219 GLN cc_start: 0.6883 (tp40) cc_final: 0.6626 (mm110) REVERT: B 300 ARG cc_start: 0.8557 (tpt170) cc_final: 0.8084 (mmt-90) REVERT: B 348 PHE cc_start: 0.8008 (t80) cc_final: 0.7713 (t80) REVERT: B 376 GLU cc_start: 0.8225 (tt0) cc_final: 0.7912 (tt0) REVERT: B 381 ASN cc_start: 0.8669 (m-40) cc_final: 0.8355 (m-40) REVERT: B 430 TRP cc_start: 0.9015 (m100) cc_final: 0.8578 (m100) REVERT: B 444 ARG cc_start: 0.8062 (mmp80) cc_final: 0.7627 (mmp80) REVERT: B 458 MET cc_start: 0.8055 (mmt) cc_final: 0.7554 (mmt) REVERT: B 459 ASN cc_start: 0.8591 (m-40) cc_final: 0.7999 (m-40) REVERT: C 9 LEU cc_start: 0.8159 (tp) cc_final: 0.7843 (mm) REVERT: C 21 ARG cc_start: 0.7571 (mmt90) cc_final: 0.7279 (mmm160) REVERT: C 26 CYS cc_start: 0.7240 (m) cc_final: 0.6936 (m) REVERT: C 29 LEU cc_start: 0.7950 (tp) cc_final: 0.7608 (tt) REVERT: C 92 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: C 96 TRP cc_start: 0.8401 (t60) cc_final: 0.7923 (t60) REVERT: C 109 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 135 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: C 140 ARG cc_start: 0.7339 (mpt-90) cc_final: 0.7049 (tpp80) REVERT: C 142 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7264 (ttt-90) REVERT: C 172 TRP cc_start: 0.7611 (m100) cc_final: 0.7273 (m100) REVERT: C 181 ARG cc_start: 0.7887 (ptp90) cc_final: 0.7481 (mtm110) REVERT: C 186 GLU cc_start: 0.7990 (tp30) cc_final: 0.7740 (tp30) REVERT: C 189 HIS cc_start: 0.7635 (m90) cc_final: 0.7291 (m90) REVERT: C 204 ASP cc_start: 0.7472 (t0) cc_final: 0.7028 (t0) REVERT: C 226 GLN cc_start: 0.7837 (mp10) cc_final: 0.7103 (mp10) REVERT: C 228 ARG cc_start: 0.7754 (mpt-90) cc_final: 0.7522 (mpt-90) REVERT: C 235 LEU cc_start: 0.7982 (mt) cc_final: 0.7384 (pp) REVERT: C 239 MET cc_start: 0.7681 (mmm) cc_final: 0.7305 (mmm) REVERT: C 331 PHE cc_start: 0.7413 (m-80) cc_final: 0.6868 (m-80) REVERT: C 352 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8762 (tp-100) REVERT: C 404 GLU cc_start: 0.8422 (pt0) cc_final: 0.8108 (pt0) REVERT: C 409 ARG cc_start: 0.8651 (mmp80) cc_final: 0.8326 (mmp80) REVERT: C 452 ASN cc_start: 0.8136 (t0) cc_final: 0.7758 (m-40) REVERT: D 1 MET cc_start: 0.5027 (mtm) cc_final: 0.4741 (mtm) REVERT: D 25 SER cc_start: 0.8218 (m) cc_final: 0.7958 (p) REVERT: D 54 ASP cc_start: 0.7771 (t0) cc_final: 0.7551 (t0) REVERT: D 74 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7809 (m) REVERT: D 102 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7899 (mmtp) REVERT: D 242 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7252 (mm-30) REVERT: D 244 MET cc_start: 0.6869 (mmm) cc_final: 0.6537 (mmm) REVERT: D 279 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7822 (ttm110) REVERT: D 296 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7898 (t) REVERT: D 327 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7386 (ttp80) REVERT: D 331 PHE cc_start: 0.7457 (m-10) cc_final: 0.6699 (m-80) REVERT: D 350 GLU cc_start: 0.8876 (pt0) cc_final: 0.8204 (tp30) REVERT: D 409 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8288 (mmp80) REVERT: D 452 ASN cc_start: 0.7778 (t0) cc_final: 0.7342 (t0) REVERT: D 458 MET cc_start: 0.7747 (mmt) cc_final: 0.7290 (mmt) outliers start: 45 outliers final: 33 residues processed: 460 average time/residue: 0.1763 time to fit residues: 116.8512 Evaluate side-chains 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 430 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 203 HIS 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 153 LYS Chi-restraints excluded: chain B residue 164 LEU 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 283 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 342 MET 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 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 204 ASP 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: 10.0000 chunk 6 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.185112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132495 restraints weight = 41305.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137404 restraints weight = 16754.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140466 restraints weight = 9908.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142253 restraints weight = 7349.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143132 restraints weight = 6259.594| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20313 Z= 0.253 Angle : 0.679 10.479 28383 Z= 0.375 Chirality : 0.045 0.214 3109 Planarity : 0.005 0.076 3022 Dihedral : 23.290 88.343 4300 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.05 % Allowed : 19.63 % Favored : 77.32 % 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: 1.44 (0.19), residues: 1937 helix: 1.89 (0.17), residues: 912 sheet: -0.23 (0.29), residues: 284 loop : 0.40 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 57 TYR 0.026 0.002 TYR D 154 PHE 0.042 0.002 PHE B 348 TRP 0.073 0.003 TRP B 64 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (20297) covalent geometry : angle 0.66598 / 0.37 (28359) hydrogen bonds : bond 0.05101 / 3.52 ( 1059) hydrogen bonds : angle 4.00097 / 2.96 ( 2792) metal coordination : bond 0.00559 / 0.34 ( 16) metal coordination : angle 4.63705 / 3.37 ( 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 490 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 441 time to evaluate : 0.636 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: A 89 HIS cc_start: 0.7891 (m170) cc_final: 0.7505 (m170) REVERT: A 109 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6605 (mp0) REVERT: A 163 TYR cc_start: 0.8262 (m-80) cc_final: 0.7838 (m-10) REVERT: A 168 VAL cc_start: 0.8412 (t) cc_final: 0.8149 (m) REVERT: A 169 ASP cc_start: 0.7271 (t0) cc_final: 0.6620 (t0) REVERT: A 182 GLU cc_start: 0.7625 (tt0) cc_final: 0.7145 (tt0) REVERT: A 219 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7165 (tm-30) REVERT: A 241 SER cc_start: 0.8398 (t) cc_final: 0.7989 (p) REVERT: A 251 ASN cc_start: 0.8638 (m-40) cc_final: 0.8418 (m110) REVERT: A 342 MET cc_start: 0.4642 (ttp) cc_final: 0.4377 (ttp) REVERT: A 376 GLU cc_start: 0.8362 (tt0) cc_final: 0.7776 (tt0) REVERT: A 379 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 381 ASN cc_start: 0.8119 (t0) cc_final: 0.7785 (t0) REVERT: A 383 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8427 (mt-10) REVERT: A 397 ARG cc_start: 0.1642 (OUTLIER) cc_final: -0.1103 (tpm170) REVERT: A 419 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6252 (tm-30) REVERT: B 6 VAL cc_start: 0.8354 (t) cc_final: 0.8009 (m) REVERT: B 22 GLN cc_start: 0.7550 (mt0) cc_final: 0.7251 (mt0) REVERT: B 28 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7614 (tp40) REVERT: B 91 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7382 (tp40) REVERT: B 101 LYS cc_start: 0.8219 (mptt) cc_final: 0.7730 (mptt) REVERT: B 106 SER cc_start: 0.8200 (t) cc_final: 0.7900 (p) REVERT: B 135 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 138 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7996 (mtmt) REVERT: B 164 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7945 (tt) REVERT: B 219 GLN cc_start: 0.6967 (tp40) cc_final: 0.6536 (mm110) REVERT: B 292 VAL cc_start: 0.8753 (t) cc_final: 0.8386 (m) REVERT: B 297 LEU cc_start: 0.8385 (tp) cc_final: 0.8107 (tp) REVERT: B 300 ARG cc_start: 0.8605 (tpt170) cc_final: 0.8112 (mmt-90) REVERT: B 348 PHE cc_start: 0.8141 (t80) cc_final: 0.7834 (t80) REVERT: B 376 GLU cc_start: 0.8254 (tt0) cc_final: 0.7888 (tt0) REVERT: B 381 ASN cc_start: 0.8683 (m-40) cc_final: 0.8389 (m-40) REVERT: B 416 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7674 (mmm160) REVERT: B 430 TRP cc_start: 0.9016 (m100) cc_final: 0.8637 (m100) REVERT: B 444 ARG cc_start: 0.8017 (mmp80) cc_final: 0.7602 (mmp80) REVERT: B 458 MET cc_start: 0.8160 (mmt) cc_final: 0.7571 (mmt) REVERT: B 459 ASN cc_start: 0.8652 (m-40) cc_final: 0.8081 (m-40) REVERT: C 9 LEU cc_start: 0.8232 (tp) cc_final: 0.7963 (mt) REVERT: C 21 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7208 (mmm160) REVERT: C 26 CYS cc_start: 0.7314 (m) cc_final: 0.7021 (m) REVERT: C 29 LEU cc_start: 0.7962 (tp) cc_final: 0.7645 (tt) REVERT: C 57 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7856 (mtm180) REVERT: C 92 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: C 96 TRP cc_start: 0.8432 (t60) cc_final: 0.7994 (t60) REVERT: C 135 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: C 140 ARG cc_start: 0.7297 (mpt-90) cc_final: 0.6949 (tpp80) REVERT: C 172 TRP cc_start: 0.7815 (m100) cc_final: 0.7221 (m100) REVERT: C 181 ARG cc_start: 0.7925 (ptp90) cc_final: 0.7490 (mtm110) REVERT: C 186 GLU cc_start: 0.7997 (tp30) cc_final: 0.7766 (tp30) REVERT: C 189 HIS cc_start: 0.7626 (m90) cc_final: 0.7101 (m90) REVERT: C 204 ASP cc_start: 0.7520 (t0) cc_final: 0.7038 (t0) REVERT: C 226 GLN cc_start: 0.7853 (mp10) cc_final: 0.7130 (mp10) REVERT: C 228 ARG cc_start: 0.7897 (mpt-90) cc_final: 0.7676 (mpt-90) REVERT: C 235 LEU cc_start: 0.8049 (mt) cc_final: 0.7423 (pp) REVERT: C 239 MET cc_start: 0.7743 (mmm) cc_final: 0.7338 (mmm) REVERT: C 331 PHE cc_start: 0.7382 (m-80) cc_final: 0.6828 (m-80) REVERT: C 352 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8797 (tp-100) REVERT: C 384 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7486 (pp) REVERT: C 404 GLU cc_start: 0.8470 (pt0) cc_final: 0.8178 (pt0) REVERT: C 409 ARG cc_start: 0.8650 (mmp80) cc_final: 0.8338 (mmp80) REVERT: C 452 ASN cc_start: 0.8129 (t0) cc_final: 0.7752 (m-40) REVERT: D 1 MET cc_start: 0.4957 (mtm) cc_final: 0.4644 (mtm) REVERT: D 25 SER cc_start: 0.8208 (m) cc_final: 0.7970 (p) REVERT: D 74 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7805 (m) REVERT: D 149 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8136 (tt) REVERT: D 216 TYR cc_start: 0.7924 (t80) cc_final: 0.7381 (t80) REVERT: D 226 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7501 (mm-40) REVERT: D 242 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7253 (mm-30) REVERT: D 244 MET cc_start: 0.6913 (mmm) cc_final: 0.6546 (mmm) REVERT: D 296 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.7917 (t) REVERT: D 327 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7360 (ttp80) REVERT: D 331 PHE cc_start: 0.7405 (m-10) cc_final: 0.6639 (m-80) REVERT: D 350 GLU cc_start: 0.8930 (pt0) cc_final: 0.8305 (tp30) REVERT: D 404 GLU cc_start: 0.8937 (pt0) cc_final: 0.8444 (mp0) REVERT: D 409 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8241 (mmp80) REVERT: D 452 ASN cc_start: 0.7823 (t0) cc_final: 0.7395 (t0) REVERT: D 458 MET cc_start: 0.7836 (mmt) cc_final: 0.7354 (mmt) outliers start: 49 outliers final: 34 residues processed: 466 average time/residue: 0.1738 time to fit residues: 116.9716 Evaluate side-chains 475 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 433 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 92 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 199 HIS 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 153 LYS Chi-restraints excluded: chain B residue 164 LEU 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 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain C residue 80 VAL 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 129 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 384 LEU 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 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 273 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 138 optimal weight: 40.0000 chunk 181 optimal weight: 0.0010 chunk 146 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.187939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135052 restraints weight = 45796.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140271 restraints weight = 17673.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143478 restraints weight = 10143.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145439 restraints weight = 7379.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146355 restraints weight = 6224.981| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 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 = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20313 Z= 0.140 Angle : 0.641 11.857 28383 Z= 0.354 Chirality : 0.041 0.185 3109 Planarity : 0.005 0.079 3022 Dihedral : 23.243 87.317 4297 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.18 % Allowed : 20.93 % Favored : 76.88 % 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: 1.63 (0.19), residues: 1937 helix: 2.04 (0.17), residues: 909 sheet: -0.13 (0.30), residues: 278 loop : 0.51 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 325 TYR 0.055 0.002 TYR C 324 PHE 0.044 0.002 PHE B 348 TRP 0.077 0.002 TRP B 64 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (20297) covalent geometry : angle 0.62730 / 0.35 (28359) hydrogen bonds : bond 0.04331 / 2.99 ( 1059) hydrogen bonds : angle 3.90004 / 2.87 ( 2792) metal coordination : bond 0.00362 / 0.22 ( 16) metal coordination : angle 4.60098 / 3.40 ( 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 475 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 440 time to evaluate : 0.626 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 37 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7532 (m) REVERT: A 89 HIS cc_start: 0.7824 (m170) cc_final: 0.7528 (m170) REVERT: A 91 GLN cc_start: 0.8379 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 109 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6570 (mp0) REVERT: A 131 GLN cc_start: 0.8081 (tp40) cc_final: 0.7865 (tp-100) REVERT: A 137 ILE cc_start: 0.8462 (mt) cc_final: 0.8225 (tt) REVERT: A 168 VAL cc_start: 0.8408 (t) cc_final: 0.8149 (m) REVERT: A 181 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7635 (ttm-80) REVERT: A 182 GLU cc_start: 0.7509 (tt0) cc_final: 0.7028 (tt0) REVERT: A 219 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7108 (tm-30) REVERT: A 229 GLU cc_start: 0.7615 (pt0) cc_final: 0.7174 (pt0) REVERT: A 241 SER cc_start: 0.8394 (t) cc_final: 0.7947 (p) REVERT: A 251 ASN cc_start: 0.8632 (m-40) cc_final: 0.8417 (m110) REVERT: A 278 LEU cc_start: 0.8955 (mt) cc_final: 0.8582 (mm) REVERT: A 342 MET cc_start: 0.4566 (ttp) cc_final: 0.4302 (ttp) REVERT: A 376 GLU cc_start: 0.8330 (tt0) cc_final: 0.7746 (tt0) REVERT: A 379 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 381 ASN cc_start: 0.8046 (t0) cc_final: 0.7738 (t0) REVERT: A 397 ARG cc_start: 0.1547 (OUTLIER) cc_final: -0.1131 (tpm170) REVERT: A 419 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6361 (tm-30) REVERT: B 6 VAL cc_start: 0.8336 (t) cc_final: 0.7977 (m) REVERT: B 22 GLN cc_start: 0.7480 (mt0) cc_final: 0.7267 (mt0) REVERT: B 28 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7569 (tp40) REVERT: B 69 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.5607 (mt-10) REVERT: B 82 ARG cc_start: 0.7772 (mmt180) cc_final: 0.7462 (mmm160) REVERT: B 91 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7328 (tp40) REVERT: B 101 LYS cc_start: 0.8220 (mptt) cc_final: 0.7882 (mptt) REVERT: B 106 SER cc_start: 0.8144 (t) cc_final: 0.7869 (p) REVERT: B 135 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 138 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8095 (mtmt) REVERT: B 164 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7910 (tt) REVERT: B 219 GLN cc_start: 0.6885 (tp40) cc_final: 0.6614 (mm110) REVERT: B 220 LEU cc_start: 0.8604 (tp) cc_final: 0.8176 (tt) REVERT: B 257 ASP cc_start: 0.7760 (p0) cc_final: 0.7181 (p0) REVERT: B 292 VAL cc_start: 0.8713 (t) cc_final: 0.8343 (m) REVERT: B 300 ARG cc_start: 0.8488 (tpt170) cc_final: 0.8083 (mmt-90) REVERT: B 348 PHE cc_start: 0.8031 (t80) cc_final: 0.7718 (t80) REVERT: B 376 GLU cc_start: 0.8239 (tt0) cc_final: 0.7919 (tt0) REVERT: B 381 ASN cc_start: 0.8656 (m-40) cc_final: 0.8357 (m-40) REVERT: B 454 TRP cc_start: 0.8412 (t60) cc_final: 0.7543 (t60) REVERT: B 458 MET cc_start: 0.8089 (mmt) cc_final: 0.7582 (mmt) REVERT: B 459 ASN cc_start: 0.8621 (m-40) cc_final: 0.8046 (m-40) REVERT: C 9 LEU cc_start: 0.8153 (tp) cc_final: 0.7863 (mt) REVERT: C 21 ARG cc_start: 0.7500 (mmt90) cc_final: 0.7026 (mmm160) REVERT: C 24 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7366 (tm-30) REVERT: C 26 CYS cc_start: 0.7247 (m) cc_final: 0.6982 (m) REVERT: C 29 LEU cc_start: 0.8088 (tp) cc_final: 0.7661 (tt) REVERT: C 57 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7836 (mtm180) REVERT: C 81 ASP cc_start: 0.7382 (p0) cc_final: 0.6827 (t0) REVERT: C 92 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: C 96 TRP cc_start: 0.8317 (t60) cc_final: 0.7745 (t60) REVERT: C 135 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: C 140 ARG cc_start: 0.7322 (mpt-90) cc_final: 0.7057 (tpp80) REVERT: C 142 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7287 (ttt-90) REVERT: C 172 TRP cc_start: 0.7594 (m100) cc_final: 0.7096 (m100) REVERT: C 181 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7396 (ptt-90) REVERT: C 186 GLU cc_start: 0.7982 (tp30) cc_final: 0.7731 (tp30) REVERT: C 189 HIS cc_start: 0.7696 (m90) cc_final: 0.7217 (m90) REVERT: C 204 ASP cc_start: 0.7511 (t0) cc_final: 0.7038 (t0) REVERT: C 226 GLN cc_start: 0.7850 (mp10) cc_final: 0.7180 (mp10) REVERT: C 228 ARG cc_start: 0.7769 (mpt-90) cc_final: 0.7542 (mpt-90) REVERT: C 235 LEU cc_start: 0.8007 (mt) cc_final: 0.7365 (pp) REVERT: C 239 MET cc_start: 0.7695 (mmm) cc_final: 0.7326 (mmm) REVERT: C 331 PHE cc_start: 0.7397 (m-80) cc_final: 0.6822 (m-80) REVERT: C 352 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8795 (tp-100) REVERT: C 404 GLU cc_start: 0.8446 (pt0) cc_final: 0.8179 (pt0) REVERT: C 409 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8326 (mmp80) REVERT: C 452 ASN cc_start: 0.8137 (t0) cc_final: 0.7649 (t0) REVERT: D 1 MET cc_start: 0.4958 (mtm) cc_final: 0.4592 (mtm) REVERT: D 25 SER cc_start: 0.8191 (m) cc_final: 0.7978 (p) REVERT: D 74 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7792 (m) REVERT: D 102 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8020 (mmmm) REVERT: D 149 ILE cc_start: 0.8506 (mm) cc_final: 0.8285 (tp) REVERT: D 190 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7776 (mmm-85) REVERT: D 196 GLU cc_start: 0.7411 (tp30) cc_final: 0.7134 (tp30) REVERT: D 216 TYR cc_start: 0.7770 (t80) cc_final: 0.7276 (t80) REVERT: D 226 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7203 (mm-40) REVERT: D 242 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7210 (mm-30) REVERT: D 244 MET cc_start: 0.6860 (mmm) cc_final: 0.6507 (mmm) REVERT: D 279 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7817 (ttm110) REVERT: D 296 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7858 (t) REVERT: D 327 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7326 (ttp80) REVERT: D 331 PHE cc_start: 0.7274 (m-10) cc_final: 0.6475 (m-80) REVERT: D 350 GLU cc_start: 0.8849 (pt0) cc_final: 0.8230 (tp30) REVERT: D 404 GLU cc_start: 0.8868 (pt0) cc_final: 0.8376 (mp0) REVERT: D 409 ARG cc_start: 0.8516 (mmp80) cc_final: 0.8237 (mmp80) REVERT: D 452 ASN cc_start: 0.7811 (t0) cc_final: 0.7377 (t0) REVERT: D 458 MET cc_start: 0.7765 (mmt) cc_final: 0.7278 (mmt) outliers start: 35 outliers final: 27 residues processed: 458 average time/residue: 0.1763 time to fit residues: 116.0034 Evaluate side-chains 466 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 431 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 92 GLN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 203 HIS 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 164 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 445 GLU 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 129 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 249 THR 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 35 TRP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 273 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.187550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134185 restraints weight = 50227.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139554 restraints weight = 18617.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142885 restraints weight = 10481.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144854 restraints weight = 7523.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145980 restraints weight = 6309.329| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 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 = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20313 Z= 0.151 Angle : 0.645 18.117 28383 Z= 0.354 Chirality : 0.041 0.202 3109 Planarity : 0.005 0.109 3022 Dihedral : 23.230 85.870 4296 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.18 % Allowed : 21.12 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1937 helix: 1.98 (0.17), residues: 909 sheet: -0.07 (0.30), residues: 278 loop : 0.50 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 416 TYR 0.060 0.002 TYR C 324 PHE 0.050 0.002 PHE B 348 TRP 0.065 0.002 TRP B 64 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20297) covalent geometry : angle 0.63420 / 0.35 (28359) hydrogen bonds : bond 0.04392 / 3.04 ( 1059) hydrogen bonds : angle 3.94058 / 2.89 ( 2792) metal coordination : bond 0.00358 / 0.21 ( 16) metal coordination : angle 4.11354 / 3.02 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5325.45 seconds wall clock time: 91 minutes 29.29 seconds (5489.29 seconds total)