Starting phenix.real_space_refine on Sat Jul 4 10:01:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu4_60889/07_2026/9iu4_60889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu4_60889/07_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_60889/07_2026/9iu4_60889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu4_60889/07_2026/9iu4_60889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu4_60889/07_2026/9iu4_60889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu4_60889/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19480 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Conformer: "B" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} bond proxies already assigned to first conformer: 3938 Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1066 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1066 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 38.859 163.315 76.522 1.00322.38 S ATOM 2447 SG CYS A 307 39.817 160.432 74.384 1.00322.20 S ATOM 2598 SG CYS A 326 41.883 161.218 76.746 1.00322.78 S ATOM 2670 SG CYS A 335 41.584 163.888 73.986 1.00323.88 S ATOM 6300 SG CYS B 304 71.498 36.924 120.961 1.00292.32 S ATOM 6318 SG CYS B 307 71.422 38.098 117.452 1.00291.66 S ATOM 6469 SG CYS B 326 68.605 38.067 118.982 1.00292.37 S ATOM 6541 SG CYS B 335 70.057 34.558 118.355 1.00294.19 S ATOM 10163 SG CYS C 304 77.497 129.433 17.503 1.00335.01 S ATOM 10181 SG CYS C 307 77.287 125.809 16.828 1.00334.63 S ATOM 10332 SG CYS C 326 79.350 126.630 19.152 1.00332.75 S ATOM 10404 SG CYS C 335 80.463 127.820 15.743 1.00332.40 S ATOM 14026 SG CYS D 304 59.437 26.461 40.810 1.00303.54 S ATOM 14044 SG CYS D 307 60.033 29.176 38.402 1.00302.91 S ATOM 14195 SG CYS D 326 57.122 29.179 39.726 1.00300.28 S ATOM 14267 SG CYS D 335 57.717 26.197 37.401 1.00300.56 S Time building chain proxies: 5.11, per 1000 atoms: 0.26 Number of scatterers: 19480 At special positions: 0 Unit cell: (119.935, 192.836, 156.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 60 16.00 P 196 15.00 O 4018 8.00 N 3623 7.00 C 11579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 811.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 307 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " Number of angles added : 24 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.7% alpha, 13.8% beta 95 base pairs and 165 stacking pairs defined. Time for finding SS restraints: 2.51 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: 3.69 Time building geometry restraints manager: 2.25 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: 26203 3.37 - 6.75: 1971 6.75 - 10.12: 157 10.12 - 13.50: 23 13.50 - 16.87: 5 Bond angle restraints: 28359 Sorted by residual: angle pdb=" O3' DG F 32 " pdb=" P DT F 33 " pdb=" O5' DT F 33 " ideal model delta sigma weight residual 104.00 87.13 16.87 1.50e+00 4.44e-01 1.26e+02 angle pdb=" O3' DG E 32 " pdb=" P DT E 33 " pdb=" O5' DT E 33 " ideal model delta sigma weight residual 104.00 87.58 16.42 1.50e+00 4.44e-01 1.20e+02 angle pdb=" 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' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 88.87 15.13 1.50e+00 4.44e-01 1.02e+02 angle pdb=" O3' DA F 20 " pdb=" P DC F 21 " pdb=" O5' DC F 21 " ideal model delta sigma weight residual 104.00 89.04 14.96 1.50e+00 4.44e-01 9.94e+01 ... (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: 0.990 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.500 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- 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= 0.686 Angle : 1.886 20.643 28383 Z= 1.304 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 1.86701 / 1.30 (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 : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7019 (mmm) cc_final: 0.6808 (tpt) REVERT: A 28 GLN cc_start: 0.9078 (tt0) cc_final: 0.8845 (tt0) REVERT: A 55 ARG cc_start: 0.6328 (mtt180) cc_final: 0.6089 (mtt180) REVERT: A 64 TRP cc_start: 0.7661 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: A 72 PHE cc_start: 0.6353 (p90) cc_final: 0.6029 (p90) REVERT: A 73 ASP cc_start: 0.7237 (m-30) cc_final: 0.6925 (m-30) REVERT: A 89 HIS cc_start: 0.7797 (m170) cc_final: 0.7429 (m170) REVERT: A 96 TRP cc_start: 0.6989 (t60) cc_final: 0.6575 (t60) REVERT: A 98 GLU cc_start: 0.7928 (tp30) cc_final: 0.7560 (tp30) REVERT: A 133 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 138 LYS cc_start: 0.7443 (mttm) cc_final: 0.7082 (mttp) REVERT: A 139 GLU cc_start: 0.7331 (tp30) cc_final: 0.7073 (tp30) REVERT: A 169 ASP cc_start: 0.7686 (t0) cc_final: 0.7200 (t0) REVERT: A 175 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6321 (m) REVERT: A 182 GLU cc_start: 0.8404 (tt0) cc_final: 0.8027 (tt0) REVERT: A 204 ASP cc_start: 0.6885 (t0) cc_final: 0.6622 (t0) REVERT: A 219 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7099 (mm110) REVERT: A 229 GLU cc_start: 0.7654 (pt0) cc_final: 0.7086 (pt0) REVERT: A 251 ASN cc_start: 0.7697 (m-40) cc_final: 0.7481 (m-40) REVERT: A 265 ARG cc_start: 0.7874 (ptt180) cc_final: 0.6733 (ptm160) REVERT: A 274 GLN cc_start: 0.7562 (mt0) cc_final: 0.7336 (mt0) REVERT: A 375 VAL cc_start: 0.8734 (t) cc_final: 0.8431 (t) REVERT: A 376 GLU cc_start: 0.8574 (tt0) cc_final: 0.8310 (tt0) REVERT: A 379 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 381 ASN cc_start: 0.8388 (t0) cc_final: 0.8054 (t0) REVERT: A 397 ARG cc_start: 0.0892 (OUTLIER) cc_final: -0.0868 (tpm170) REVERT: A 454 TRP cc_start: 0.8798 (t60) cc_final: 0.8355 (t60) REVERT: A 458 MET cc_start: 0.6633 (mmm) cc_final: 0.6061 (tmm) REVERT: B 6 VAL cc_start: 0.7645 (t) cc_final: 0.7260 (m) REVERT: B 24 GLU cc_start: 0.8006 (tt0) cc_final: 0.7644 (tt0) REVERT: B 28 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7774 (tp40) REVERT: B 32 GLN cc_start: 0.7634 (mt0) cc_final: 0.7319 (mt0) REVERT: B 64 TRP cc_start: 0.7995 (m100) cc_final: 0.7549 (m100) REVERT: B 73 ASP cc_start: 0.6100 (m-30) cc_final: 0.5686 (m-30) REVERT: B 81 ASP cc_start: 0.7565 (p0) cc_final: 0.7332 (p0) REVERT: B 82 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7417 (mmm160) REVERT: B 91 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7071 (tp40) REVERT: B 105 VAL cc_start: 0.7231 (t) cc_final: 0.6794 (p) REVERT: B 118 PHE cc_start: 0.7868 (m-80) cc_final: 0.7321 (m-10) REVERT: B 135 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 153 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (mtmp) REVERT: B 182 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 344 GLU cc_start: 0.9074 (tt0) cc_final: 0.8591 (tt0) REVERT: B 376 GLU cc_start: 0.8617 (tt0) cc_final: 0.7996 (tt0) REVERT: B 458 MET cc_start: 0.7727 (mmt) cc_final: 0.7485 (mmt) REVERT: B 459 ASN cc_start: 0.7572 (m-40) cc_final: 0.7312 (m-40) REVERT: B 466 VAL cc_start: 0.6357 (OUTLIER) cc_final: 0.6135 (t) REVERT: C 21 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7341 (mmm160) REVERT: C 22 GLN cc_start: 0.7847 (mt0) cc_final: 0.7461 (mt0) REVERT: C 24 GLU cc_start: 0.7661 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 25 SER cc_start: 0.7567 (t) cc_final: 0.7212 (m) REVERT: C 33 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6616 (tpp80) REVERT: C 42 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7409 (mt-10) REVERT: C 64 TRP cc_start: 0.7156 (m100) cc_final: 0.6529 (m100) REVERT: C 70 GLN cc_start: 0.7407 (mt0) cc_final: 0.7081 (mp10) REVERT: C 95 HIS cc_start: 0.6580 (t70) cc_final: 0.6073 (t70) REVERT: C 96 TRP cc_start: 0.6753 (t60) cc_final: 0.6451 (t60) REVERT: C 98 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5966 (pp20) REVERT: C 116 THR cc_start: 0.7543 (t) cc_final: 0.7186 (t) REVERT: C 135 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6769 (mp0) REVERT: C 140 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6893 (mpt-90) REVERT: C 163 TYR cc_start: 0.6605 (m-80) cc_final: 0.5900 (m-80) REVERT: C 173 ARG cc_start: 0.6293 (mtt90) cc_final: 0.5893 (mmt90) REVERT: C 186 GLU cc_start: 0.8884 (tp30) cc_final: 0.8496 (tp30) REVERT: C 193 ASP cc_start: 0.7988 (m-30) cc_final: 0.7664 (m-30) REVERT: C 198 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6002 (mm) REVERT: C 199 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6901 (p-80) REVERT: C 216 TYR cc_start: 0.8023 (t80) cc_final: 0.7640 (t80) REVERT: C 224 GLU cc_start: 0.7317 (tt0) cc_final: 0.7063 (tt0) REVERT: C 226 GLN cc_start: 0.7251 (mp10) cc_final: 0.6751 (mp10) REVERT: C 235 LEU cc_start: 0.8072 (mt) cc_final: 0.7570 (pp) REVERT: C 239 MET cc_start: 0.8587 (mmm) cc_final: 0.7956 (mmm) REVERT: C 244 MET cc_start: 0.7883 (mmt) cc_final: 0.6920 (tpp) REVERT: C 251 ASN cc_start: 0.7265 (m110) cc_final: 0.6989 (m110) REVERT: C 273 GLU cc_start: 0.8780 (pt0) cc_final: 0.8557 (pt0) REVERT: C 331 PHE cc_start: 0.7576 (m-80) cc_final: 0.6949 (m-80) REVERT: C 342 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.4129 (mmm) REVERT: C 384 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7131 (pp) REVERT: C 448 THR cc_start: 0.8169 (p) cc_final: 0.7847 (t) REVERT: C 452 ASN cc_start: 0.8112 (t0) cc_final: 0.7537 (t0) REVERT: C 454 TRP cc_start: 0.8594 (t60) cc_final: 0.7822 (t60) REVERT: C 464 PHE cc_start: 0.7257 (p90) cc_final: 0.7031 (p90) REVERT: D 21 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7439 (mtm180) REVERT: D 27 GLN cc_start: 0.7268 (mt0) cc_final: 0.6920 (mt0) REVERT: D 54 ASP cc_start: 0.5965 (t0) cc_final: 0.5467 (t0) REVERT: D 74 VAL cc_start: 0.6821 (p) cc_final: 0.6376 (m) REVERT: D 88 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7123 (ttm110) REVERT: D 101 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8071 (mmtt) REVERT: D 102 LYS cc_start: 0.6771 (mmtt) cc_final: 0.6341 (mmtp) REVERT: D 135 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7266 (mm-30) REVERT: D 150 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7817 (ttm-80) REVERT: D 153 LYS cc_start: 0.7478 (mttt) cc_final: 0.7042 (mttt) REVERT: D 158 LEU cc_start: 0.8616 (tp) cc_final: 0.8411 (tt) REVERT: D 164 LEU cc_start: 0.6597 (tp) cc_final: 0.6311 (mp) REVERT: D 173 ARG cc_start: 0.6990 (ttm110) cc_final: 0.6599 (mtp85) REVERT: D 182 GLU cc_start: 0.8118 (tt0) cc_final: 0.7841 (tt0) REVERT: D 216 TYR cc_start: 0.6731 (t80) cc_final: 0.6224 (t80) REVERT: D 224 GLU cc_start: 0.7482 (tp30) cc_final: 0.7195 (tp30) REVERT: D 228 ARG cc_start: 0.6429 (mtt-85) cc_final: 0.6181 (mtt90) REVERT: D 269 ILE cc_start: 0.7238 (mm) cc_final: 0.6804 (mm) REVERT: D 276 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8045 (mm-30) REVERT: D 331 PHE cc_start: 0.6355 (m-10) cc_final: 0.6139 (m-10) REVERT: D 452 ASN cc_start: 0.6928 (t0) cc_final: 0.6585 (t0) REVERT: D 457 SER cc_start: 0.8213 (p) cc_final: 0.7374 (p) outliers start: 65 outliers final: 17 residues processed: 545 average time/residue: 0.1817 time to fit residues: 141.2051 Evaluate side-chains 469 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 439 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 111 HIS D 189 HIS D 452 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.189517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136020 restraints weight = 42731.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141038 restraints weight = 17236.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144131 restraints weight = 10203.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145930 restraints weight = 7608.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146752 restraints weight = 6501.801| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 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 = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2221 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= 0.210 Angle : 0.795 13.561 28383 Z= 0.438 Chirality : 0.056 0.250 3109 Planarity : 0.005 0.047 3022 Dihedral : 23.604 87.897 4347 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.61 % Allowed : 12.27 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1937 helix: 2.18 (0.16), residues: 912 sheet: -0.12 (0.27), residues: 287 loop : 0.64 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 167 TYR 0.027 0.002 TYR B 482 PHE 0.028 0.002 PHE C 314 TRP 0.030 0.002 TRP B 443 HIS 0.007 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (20297) covalent geometry : angle 0.77855 / 0.44 (28359) hydrogen bonds : bond 0.05921 / 4.11 ( 1059) hydrogen bonds : angle 4.03547 / 2.99 ( 2792) metal coordination : bond 0.00973 / 0.54 ( 16) metal coordination : angle 5.50764 / 3.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 465 time to evaluate : 0.617 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: A 6 VAL cc_start: 0.7778 (t) cc_final: 0.7232 (m) REVERT: A 64 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: A 89 HIS cc_start: 0.7949 (m-70) cc_final: 0.7468 (m170) REVERT: A 96 TRP cc_start: 0.8320 (t60) cc_final: 0.7857 (t60) REVERT: A 98 GLU cc_start: 0.7499 (tp30) cc_final: 0.6753 (tp30) REVERT: A 138 LYS cc_start: 0.8061 (mttm) cc_final: 0.7786 (mtmm) REVERT: A 139 GLU cc_start: 0.7279 (tp30) cc_final: 0.7011 (tp30) REVERT: A 168 VAL cc_start: 0.8006 (t) cc_final: 0.7757 (m) REVERT: A 169 ASP cc_start: 0.7236 (t0) cc_final: 0.6651 (t0) REVERT: A 175 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7780 (m) REVERT: A 182 GLU cc_start: 0.7612 (tt0) cc_final: 0.7288 (tt0) REVERT: A 204 ASP cc_start: 0.7132 (t0) cc_final: 0.6842 (t0) REVERT: A 219 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7257 (mm110) REVERT: A 228 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7754 (mtt180) REVERT: A 239 MET cc_start: 0.7700 (tpp) cc_final: 0.7329 (mmm) REVERT: A 241 SER cc_start: 0.8368 (t) cc_final: 0.7880 (p) REVERT: A 251 ASN cc_start: 0.8452 (m-40) cc_final: 0.8212 (m-40) REVERT: A 257 ASP cc_start: 0.5636 (p0) cc_final: 0.5209 (p0) REVERT: A 265 ARG cc_start: 0.8474 (ptt180) cc_final: 0.7951 (ptt90) REVERT: A 342 MET cc_start: 0.4348 (ttp) cc_final: 0.3894 (ttp) REVERT: A 375 VAL cc_start: 0.8814 (t) cc_final: 0.8265 (t) REVERT: A 376 GLU cc_start: 0.8416 (tt0) cc_final: 0.7840 (tt0) REVERT: A 379 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 381 ASN cc_start: 0.8160 (t0) cc_final: 0.7905 (t0) REVERT: A 397 ARG cc_start: 0.0130 (OUTLIER) cc_final: -0.2282 (tpm170) REVERT: A 458 MET cc_start: 0.6250 (mmm) cc_final: 0.5380 (tmm) REVERT: B 6 VAL cc_start: 0.8265 (t) cc_final: 0.7804 (m) REVERT: B 24 GLU cc_start: 0.7525 (tt0) cc_final: 0.7143 (tt0) REVERT: B 28 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7422 (tp40) REVERT: B 64 TRP cc_start: 0.7374 (m100) cc_final: 0.7085 (m100) REVERT: B 82 ARG cc_start: 0.7653 (mmt180) cc_final: 0.7321 (mmm160) REVERT: B 91 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7384 (mm110) REVERT: B 105 VAL cc_start: 0.8315 (t) cc_final: 0.7962 (p) REVERT: B 118 PHE cc_start: 0.8286 (m-80) cc_final: 0.7655 (m-10) REVERT: B 135 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7190 (mm-30) REVERT: B 138 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8060 (mtmt) REVERT: B 153 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7621 (mtmp) REVERT: B 164 LEU cc_start: 0.8095 (tt) cc_final: 0.7876 (tt) REVERT: B 344 GLU cc_start: 0.8567 (tt0) cc_final: 0.8330 (tm-30) REVERT: B 376 GLU cc_start: 0.8270 (tt0) cc_final: 0.7614 (tt0) REVERT: B 381 ASN cc_start: 0.8645 (m-40) cc_final: 0.8342 (m-40) REVERT: B 430 TRP cc_start: 0.8866 (m100) cc_final: 0.8305 (m100) REVERT: B 447 ASP cc_start: 0.8048 (t0) cc_final: 0.7610 (p0) REVERT: B 458 MET cc_start: 0.7938 (mmt) cc_final: 0.7469 (mmt) REVERT: B 459 ASN cc_start: 0.8371 (m-40) cc_final: 0.7857 (m-40) REVERT: B 461 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7497 (mtp85) REVERT: C 21 ARG cc_start: 0.7570 (mmt90) cc_final: 0.7342 (mmm160) REVERT: C 22 GLN cc_start: 0.7788 (mt0) cc_final: 0.7504 (mt0) REVERT: C 43 ASP cc_start: 0.6611 (m-30) cc_final: 0.6385 (m-30) REVERT: C 84 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8053 (t) REVERT: C 88 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7597 (mmm-85) REVERT: C 95 HIS cc_start: 0.7606 (t70) cc_final: 0.6929 (t-90) REVERT: C 98 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5542 (pp20) REVERT: C 135 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: C 140 ARG cc_start: 0.7377 (mpt-90) cc_final: 0.6950 (ttm110) REVERT: C 163 TYR cc_start: 0.6647 (m-80) cc_final: 0.6316 (m-80) REVERT: C 167 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7314 (tpp80) REVERT: C 173 ARG cc_start: 0.6768 (mtt90) cc_final: 0.6428 (mtt90) REVERT: C 181 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7579 (mtm110) REVERT: C 186 GLU cc_start: 0.8067 (tp30) cc_final: 0.7841 (tp30) REVERT: C 193 ASP cc_start: 0.7801 (m-30) cc_final: 0.7099 (m-30) REVERT: C 204 ASP cc_start: 0.7370 (t0) cc_final: 0.7143 (t0) REVERT: C 216 TYR cc_start: 0.8329 (t80) cc_final: 0.8014 (t80) REVERT: C 224 GLU cc_start: 0.7740 (tt0) cc_final: 0.7426 (tt0) REVERT: C 226 GLN cc_start: 0.7687 (mp10) cc_final: 0.6908 (mp10) REVERT: C 228 ARG cc_start: 0.7177 (mpt-90) cc_final: 0.6755 (mpt-90) REVERT: C 235 LEU cc_start: 0.7833 (mt) cc_final: 0.7508 (mm) REVERT: C 239 MET cc_start: 0.7699 (mmm) cc_final: 0.7265 (mmm) REVERT: C 244 MET cc_start: 0.7038 (mmt) cc_final: 0.6665 (mmp) REVERT: C 276 GLU cc_start: 0.8056 (pt0) cc_final: 0.7849 (mt-10) REVERT: C 331 PHE cc_start: 0.7306 (m-80) cc_final: 0.6813 (m-80) REVERT: C 342 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4705 (mmm) REVERT: C 352 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8734 (tp-100) REVERT: C 384 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7506 (pp) REVERT: C 404 GLU cc_start: 0.8342 (pt0) cc_final: 0.7694 (mp0) REVERT: C 452 ASN cc_start: 0.8077 (t0) cc_final: 0.7816 (t0) REVERT: C 454 TRP cc_start: 0.8167 (t60) cc_final: 0.7525 (t60) REVERT: D 25 SER cc_start: 0.8032 (m) cc_final: 0.7687 (p) REVERT: D 74 VAL cc_start: 0.7928 (p) cc_final: 0.7608 (m) REVERT: D 101 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8116 (mmtt) REVERT: D 111 HIS cc_start: 0.8146 (p-80) cc_final: 0.7727 (p-80) REVERT: D 150 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7588 (mtt-85) REVERT: D 164 LEU cc_start: 0.8118 (tp) cc_final: 0.7780 (mp) REVERT: D 216 TYR cc_start: 0.7813 (t80) cc_final: 0.7299 (t80) REVERT: D 327 ARG cc_start: 0.8117 (ttt180) cc_final: 0.7439 (ttp80) REVERT: D 329 MET cc_start: 0.7152 (tpp) cc_final: 0.6824 (tpp) REVERT: D 331 PHE cc_start: 0.7179 (m-10) cc_final: 0.6278 (m-10) REVERT: D 351 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: D 452 ASN cc_start: 0.7585 (t0) cc_final: 0.7199 (t0) REVERT: D 458 MET cc_start: 0.7490 (mmt) cc_final: 0.7161 (mmt) outliers start: 58 outliers final: 31 residues processed: 499 average time/residue: 0.1596 time to fit residues: 114.3858 Evaluate side-chains 466 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 425 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 80 VAL 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 273 GLU Chi-restraints excluded: chain B residue 281 GLU 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: 0.4980 chunk 51 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 100 HIS A 131 GLN A 334 HIS 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 92 GLN D 95 HIS D 189 HIS D 274 GLN D 381 ASN D 459 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.186547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133565 restraints weight = 38663.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138370 restraints weight = 16163.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141254 restraints weight = 9763.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142985 restraints weight = 7374.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143974 restraints weight = 6356.007| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20313 Z= 0.254 Angle : 0.705 9.886 28383 Z= 0.398 Chirality : 0.048 0.296 3109 Planarity : 0.005 0.072 3022 Dihedral : 23.417 86.111 4322 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.49 % Allowed : 14.45 % Favored : 82.06 % 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: 1.68 (0.19), residues: 1937 helix: 2.12 (0.17), residues: 910 sheet: -0.28 (0.28), residues: 286 loop : 0.58 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 228 TYR 0.023 0.002 TYR A 154 PHE 0.030 0.002 PHE D 147 TRP 0.052 0.002 TRP B 443 HIS 0.011 0.002 HIS D 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.25 (20297) covalent geometry : angle 0.69356 / 0.40 (28359) hydrogen bonds : bond 0.05604 / 3.89 ( 1059) hydrogen bonds : angle 4.03165 / 2.96 ( 2792) metal coordination : bond 0.00678 / 0.38 ( 16) metal coordination : angle 4.38911 / 2.92 ( 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 510 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 454 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.6320 (ttm110) cc_final: 0.6020 (mtp-110) REVERT: A 64 TRP cc_start: 0.7930 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: A 89 HIS cc_start: 0.7888 (m170) cc_final: 0.7411 (m170) REVERT: A 98 GLU cc_start: 0.7436 (tp30) cc_final: 0.6808 (tp30) REVERT: A 109 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6642 (mp0) REVERT: A 168 VAL cc_start: 0.8219 (t) cc_final: 0.7853 (m) REVERT: A 169 ASP cc_start: 0.7213 (t0) cc_final: 0.6621 (t0) REVERT: A 175 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7862 (p) REVERT: A 182 GLU cc_start: 0.7717 (tt0) cc_final: 0.7325 (tt0) REVERT: A 204 ASP cc_start: 0.7272 (t0) cc_final: 0.6840 (t0) REVERT: A 208 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.6742 (ttm110) REVERT: A 219 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7309 (mm-40) REVERT: A 239 MET cc_start: 0.7658 (tpp) cc_final: 0.7399 (mmm) REVERT: A 241 SER cc_start: 0.8477 (t) cc_final: 0.8009 (p) REVERT: A 251 ASN cc_start: 0.8565 (m-40) cc_final: 0.8311 (m-40) REVERT: A 342 MET cc_start: 0.4456 (ttp) cc_final: 0.3975 (ttp) REVERT: A 376 GLU cc_start: 0.8396 (tt0) cc_final: 0.7857 (tt0) REVERT: A 379 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 381 ASN cc_start: 0.8123 (t0) cc_final: 0.7795 (t0) REVERT: A 383 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 397 ARG cc_start: 0.0287 (OUTLIER) cc_final: -0.2419 (ttm170) REVERT: A 419 GLU cc_start: 0.6675 (tm-30) cc_final: 0.5863 (tm-30) REVERT: B 6 VAL cc_start: 0.8272 (t) cc_final: 0.7888 (m) REVERT: B 22 GLN cc_start: 0.7108 (mt0) cc_final: 0.6758 (mt0) REVERT: B 24 GLU cc_start: 0.7609 (tt0) cc_final: 0.7217 (tt0) REVERT: B 28 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7772 (tp40) REVERT: B 56 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7689 (mtmm) REVERT: B 64 TRP cc_start: 0.7481 (m100) cc_final: 0.6912 (m100) REVERT: B 89 HIS cc_start: 0.7775 (m90) cc_final: 0.7560 (m-70) REVERT: B 91 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7386 (tp40) REVERT: B 102 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7862 (mmtp) REVERT: B 118 PHE cc_start: 0.8414 (m-80) cc_final: 0.7770 (m-80) REVERT: B 135 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 138 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8160 (mtmt) REVERT: B 285 THR cc_start: 0.7625 (m) cc_final: 0.7299 (p) REVERT: B 376 GLU cc_start: 0.8306 (tt0) cc_final: 0.7642 (tt0) REVERT: B 381 ASN cc_start: 0.8674 (m-40) cc_final: 0.8374 (m-40) REVERT: B 430 TRP cc_start: 0.8949 (m100) cc_final: 0.8508 (m100) REVERT: B 443 TRP cc_start: 0.7894 (t-100) cc_final: 0.7527 (t-100) REVERT: B 458 MET cc_start: 0.8122 (mmt) cc_final: 0.7582 (mmt) REVERT: B 459 ASN cc_start: 0.8544 (m-40) cc_final: 0.8080 (m-40) REVERT: C 9 LEU cc_start: 0.8083 (tp) cc_final: 0.7777 (mt) REVERT: C 21 ARG cc_start: 0.7602 (mmt90) cc_final: 0.7372 (mmm160) REVERT: C 29 LEU cc_start: 0.8022 (tp) cc_final: 0.7666 (tt) REVERT: C 43 ASP cc_start: 0.6740 (m-30) cc_final: 0.6409 (m-30) REVERT: C 84 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8194 (t) REVERT: C 88 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7806 (mmm-85) REVERT: C 92 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: C 95 HIS cc_start: 0.7647 (t70) cc_final: 0.7092 (t-90) REVERT: C 96 TRP cc_start: 0.8434 (t60) cc_final: 0.8047 (t60) REVERT: C 98 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5605 (pp20) REVERT: C 135 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6687 (mp0) REVERT: C 140 ARG cc_start: 0.7329 (mpt-90) cc_final: 0.7001 (ttm110) REVERT: C 142 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7106 (ttt-90) REVERT: C 158 LEU cc_start: 0.8678 (tp) cc_final: 0.8451 (tp) REVERT: C 163 TYR cc_start: 0.6678 (m-80) cc_final: 0.6297 (m-80) REVERT: C 173 ARG cc_start: 0.6733 (mtt90) cc_final: 0.6400 (mtt90) REVERT: C 186 GLU cc_start: 0.8030 (tp30) cc_final: 0.7815 (tp30) REVERT: C 189 HIS cc_start: 0.7123 (t-90) cc_final: 0.6918 (t-90) REVERT: C 193 ASP cc_start: 0.7590 (m-30) cc_final: 0.7333 (m-30) REVERT: C 204 ASP cc_start: 0.7381 (t0) cc_final: 0.7104 (t0) REVERT: C 220 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8542 (mm) REVERT: C 224 GLU cc_start: 0.7793 (tt0) cc_final: 0.7458 (tt0) REVERT: C 226 GLN cc_start: 0.7772 (mp10) cc_final: 0.7112 (mp10) REVERT: C 228 ARG cc_start: 0.7569 (mpt-90) cc_final: 0.7252 (mpt-90) REVERT: C 235 LEU cc_start: 0.7849 (mt) cc_final: 0.7539 (mm) REVERT: C 239 MET cc_start: 0.7704 (mmm) cc_final: 0.7288 (mmm) REVERT: C 276 GLU cc_start: 0.8023 (pt0) cc_final: 0.7784 (mt-10) REVERT: C 331 PHE cc_start: 0.7272 (m-80) cc_final: 0.6785 (m-80) REVERT: C 342 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4894 (mmm) REVERT: C 352 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8737 (tp-100) REVERT: C 384 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7533 (pp) REVERT: C 404 GLU cc_start: 0.8360 (pt0) cc_final: 0.8139 (pt0) REVERT: C 452 ASN cc_start: 0.8080 (t0) cc_final: 0.7768 (t0) REVERT: C 454 TRP cc_start: 0.8103 (t60) cc_final: 0.7525 (t60) REVERT: D 21 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7749 (mtm180) REVERT: D 25 SER cc_start: 0.8135 (m) cc_final: 0.7823 (p) REVERT: D 42 GLU cc_start: 0.7026 (tt0) cc_final: 0.6758 (tt0) REVERT: D 74 VAL cc_start: 0.7967 (p) cc_final: 0.7676 (m) REVERT: D 111 HIS cc_start: 0.8262 (p-80) cc_final: 0.7861 (p-80) REVERT: D 142 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7328 (ttt90) REVERT: D 164 LEU cc_start: 0.8263 (tp) cc_final: 0.8061 (mt) REVERT: D 186 GLU cc_start: 0.8028 (tt0) cc_final: 0.7621 (pt0) REVERT: D 190 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7602 (tpp80) REVERT: D 216 TYR cc_start: 0.7788 (t80) cc_final: 0.7246 (t80) REVERT: D 228 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7341 (mtt90) REVERT: D 296 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7832 (t) REVERT: D 331 PHE cc_start: 0.7356 (m-10) cc_final: 0.7107 (m-80) REVERT: D 351 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: D 452 ASN cc_start: 0.7657 (t0) cc_final: 0.7306 (t0) REVERT: D 458 MET cc_start: 0.7599 (mmt) cc_final: 0.7164 (mmt) outliers start: 56 outliers final: 28 residues processed: 486 average time/residue: 0.1687 time to fit residues: 117.6672 Evaluate side-chains 483 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 443 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 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 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 445 GLU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS 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 Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 149 optimal weight: 0.0570 chunk 99 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 192 optimal weight: 30.0000 chunk 209 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 133 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN D 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.190298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136427 restraints weight = 42011.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141611 restraints weight = 16711.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.144806 restraints weight = 9769.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146665 restraints weight = 7211.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147656 restraints weight = 6121.276| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20313 Z= 0.140 Angle : 0.624 17.772 28383 Z= 0.348 Chirality : 0.043 0.234 3109 Planarity : 0.005 0.061 3022 Dihedral : 23.358 84.366 4315 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.30 % Allowed : 16.14 % Favored : 80.56 % 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: 1.90 (0.19), residues: 1937 helix: 2.30 (0.17), residues: 912 sheet: -0.17 (0.29), residues: 285 loop : 0.67 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 57 TYR 0.017 0.002 TYR D 396 PHE 0.015 0.001 PHE A 72 TRP 0.023 0.001 TRP B 443 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (20297) covalent geometry : angle 0.59808 / 0.35 (28359) hydrogen bonds : bond 0.04550 / 3.16 ( 1059) hydrogen bonds : angle 3.74233 / 2.76 ( 2792) metal coordination : bond 0.01421 / 0.63 ( 16) metal coordination : angle 6.17324 / 4.62 ( 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 500 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 447 time to evaluate : 0.664 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: 0.6159 (tpt) cc_final: 0.5914 (tpt) REVERT: A 4 LEU cc_start: 0.7529 (tp) cc_final: 0.7154 (tt) REVERT: A 37 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7539 (m) REVERT: A 89 HIS cc_start: 0.7869 (m170) cc_final: 0.7456 (m170) REVERT: A 168 VAL cc_start: 0.8195 (t) cc_final: 0.7862 (m) REVERT: A 169 ASP cc_start: 0.7170 (t0) cc_final: 0.6518 (t0) REVERT: A 182 GLU cc_start: 0.7673 (tt0) cc_final: 0.7246 (tt0) REVERT: A 228 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7918 (mtt180) REVERT: A 241 SER cc_start: 0.8438 (t) cc_final: 0.7948 (p) REVERT: A 251 ASN cc_start: 0.8573 (m-40) cc_final: 0.8337 (m-40) REVERT: A 278 LEU cc_start: 0.8998 (tp) cc_final: 0.8608 (tp) REVERT: A 342 MET cc_start: 0.4294 (ttp) cc_final: 0.3873 (ttp) REVERT: A 376 GLU cc_start: 0.8333 (tt0) cc_final: 0.7712 (tt0) REVERT: A 379 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 381 ASN cc_start: 0.8079 (t0) cc_final: 0.7718 (t0) REVERT: A 383 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 397 ARG cc_start: 0.0296 (OUTLIER) cc_final: -0.2382 (ttm170) REVERT: B 6 VAL cc_start: 0.8249 (t) cc_final: 0.7875 (m) REVERT: B 22 GLN cc_start: 0.7018 (mt0) cc_final: 0.6692 (mt0) REVERT: B 24 GLU cc_start: 0.7545 (tt0) cc_final: 0.7160 (tt0) REVERT: B 28 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7618 (tp40) REVERT: B 57 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7091 (mtm-85) REVERT: B 64 TRP cc_start: 0.7397 (m100) cc_final: 0.6842 (m100) REVERT: B 91 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7329 (tp-100) REVERT: B 102 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7864 (mmtp) REVERT: B 105 VAL cc_start: 0.8338 (t) cc_final: 0.7977 (p) REVERT: B 135 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 138 LYS cc_start: 0.8306 (mtmt) cc_final: 0.8063 (mtmt) REVERT: B 164 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7919 (tt) REVERT: B 376 GLU cc_start: 0.8286 (tt0) cc_final: 0.7626 (tt0) REVERT: B 381 ASN cc_start: 0.8641 (m-40) cc_final: 0.8317 (m-40) REVERT: B 430 TRP cc_start: 0.8956 (m100) cc_final: 0.8473 (m100) REVERT: B 444 ARG cc_start: 0.8105 (mmp80) cc_final: 0.7651 (mmp80) REVERT: B 458 MET cc_start: 0.8029 (mmt) cc_final: 0.7531 (mmt) REVERT: B 459 ASN cc_start: 0.8530 (m-40) cc_final: 0.8078 (m-40) REVERT: C 9 LEU cc_start: 0.7975 (tp) cc_final: 0.7608 (mm) REVERT: C 21 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7276 (mmm160) REVERT: C 26 CYS cc_start: 0.7225 (m) cc_final: 0.6950 (m) REVERT: C 43 ASP cc_start: 0.6629 (m-30) cc_final: 0.6356 (m-30) REVERT: C 70 GLN cc_start: 0.7987 (mp10) cc_final: 0.7786 (mp10) REVERT: C 92 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: C 95 HIS cc_start: 0.7656 (t70) cc_final: 0.7071 (t-90) REVERT: C 96 TRP cc_start: 0.8345 (t60) cc_final: 0.7860 (t60) REVERT: C 98 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5462 (pp20) REVERT: C 135 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6651 (mp0) REVERT: C 140 ARG cc_start: 0.7317 (mpt-90) cc_final: 0.7024 (ttm110) REVERT: C 142 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7096 (ttt-90) REVERT: C 167 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7326 (ttm110) REVERT: C 173 ARG cc_start: 0.6749 (mtt90) cc_final: 0.6417 (mtt90) REVERT: C 186 GLU cc_start: 0.8045 (tp30) cc_final: 0.7825 (tp30) REVERT: C 193 ASP cc_start: 0.7616 (m-30) cc_final: 0.7321 (m-30) REVERT: C 204 ASP cc_start: 0.7455 (t0) cc_final: 0.7104 (t0) REVERT: C 224 GLU cc_start: 0.7809 (tt0) cc_final: 0.7474 (tt0) REVERT: C 226 GLN cc_start: 0.7783 (mp10) cc_final: 0.7109 (mp10) REVERT: C 228 ARG cc_start: 0.7386 (mpt-90) cc_final: 0.7028 (mpt-90) REVERT: C 239 MET cc_start: 0.7645 (mmm) cc_final: 0.7202 (mmm) REVERT: C 247 TYR cc_start: 0.7649 (m-10) cc_final: 0.7383 (m-10) REVERT: C 265 ARG cc_start: 0.7880 (ptt180) cc_final: 0.7087 (ptt180) REVERT: C 331 PHE cc_start: 0.7353 (m-80) cc_final: 0.6885 (m-80) REVERT: C 352 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8711 (tp-100) REVERT: C 384 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7518 (pp) REVERT: C 404 GLU cc_start: 0.8252 (pt0) cc_final: 0.7962 (pt0) REVERT: C 409 ARG cc_start: 0.8626 (mmp80) cc_final: 0.8321 (mmp80) REVERT: C 452 ASN cc_start: 0.8050 (t0) cc_final: 0.7722 (t0) REVERT: C 454 TRP cc_start: 0.8038 (t60) cc_final: 0.7458 (t60) REVERT: D 25 SER cc_start: 0.8120 (m) cc_final: 0.7788 (p) REVERT: D 33 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7479 (mtp85) REVERT: D 42 GLU cc_start: 0.7012 (tt0) cc_final: 0.6790 (tt0) REVERT: D 74 VAL cc_start: 0.7968 (p) cc_final: 0.7628 (m) REVERT: D 111 HIS cc_start: 0.8251 (p-80) cc_final: 0.7840 (p-80) REVERT: D 164 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7886 (mt) REVERT: D 186 GLU cc_start: 0.7936 (tt0) cc_final: 0.7390 (pt0) REVERT: D 216 TYR cc_start: 0.7794 (t80) cc_final: 0.7077 (t80) REVERT: D 220 LEU cc_start: 0.8524 (mm) cc_final: 0.8146 (mt) REVERT: D 226 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7779 (mm-40) REVERT: D 279 ARG cc_start: 0.8243 (ttm110) cc_final: 0.8031 (ttm110) REVERT: D 296 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7753 (t) REVERT: D 329 MET cc_start: 0.6744 (tpp) cc_final: 0.6232 (tpp) REVERT: D 331 PHE cc_start: 0.7178 (m-10) cc_final: 0.6950 (m-80) REVERT: D 351 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: D 452 ASN cc_start: 0.7657 (t0) cc_final: 0.7266 (t0) REVERT: D 458 MET cc_start: 0.7449 (mmt) cc_final: 0.7137 (mmt) outliers start: 53 outliers final: 28 residues processed: 475 average time/residue: 0.1704 time to fit residues: 115.9029 Evaluate side-chains 476 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 438 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 267 GLU 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 132 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 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 241 SER Chi-restraints excluded: chain C residue 249 THR 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 164 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 Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 144 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 122 optimal weight: 0.0020 chunk 32 optimal weight: 1.9990 overall best weight: 1.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS B 60 ASN B 89 HIS B 141 ASN C 27 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.187990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133735 restraints weight = 41811.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138854 restraints weight = 16820.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142004 restraints weight = 9893.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143847 restraints weight = 7329.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144882 restraints weight = 6244.307| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20313 Z= 0.191 Angle : 0.624 13.818 28383 Z= 0.348 Chirality : 0.043 0.200 3109 Planarity : 0.005 0.071 3022 Dihedral : 23.348 84.953 4308 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.43 % Allowed : 17.57 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 1937 helix: 2.26 (0.17), residues: 912 sheet: -0.18 (0.29), residues: 286 loop : 0.68 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 167 TYR 0.020 0.002 TYR A 154 PHE 0.012 0.001 PHE A 72 TRP 0.023 0.002 TRP C 172 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (20297) covalent geometry : angle 0.60500 / 0.35 (28359) hydrogen bonds : bond 0.04686 / 3.27 ( 1059) hydrogen bonds : angle 3.77242 / 2.77 ( 2792) metal coordination : bond 0.00655 / 0.36 ( 16) metal coordination : angle 5.31766 / 3.84 ( 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 499 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 444 time to evaluate : 0.649 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: A 5 VAL cc_start: 0.8095 (t) cc_final: 0.7868 (m) REVERT: A 60 ASN cc_start: 0.8121 (m-40) cc_final: 0.7878 (m-40) REVERT: A 89 HIS cc_start: 0.7939 (m170) cc_final: 0.7557 (m170) REVERT: A 109 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6584 (mp0) REVERT: A 138 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8108 (mtmt) REVERT: A 168 VAL cc_start: 0.8265 (t) cc_final: 0.7936 (m) REVERT: A 169 ASP cc_start: 0.7223 (t0) cc_final: 0.6564 (t0) REVERT: A 182 GLU cc_start: 0.7673 (tt0) cc_final: 0.7244 (tt0) REVERT: A 204 ASP cc_start: 0.7450 (t70) cc_final: 0.7085 (t0) REVERT: A 219 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7236 (mm110) REVERT: A 241 SER cc_start: 0.8412 (t) cc_final: 0.7936 (p) REVERT: A 251 ASN cc_start: 0.8595 (m-40) cc_final: 0.8355 (m-40) REVERT: A 274 GLN cc_start: 0.7590 (mt0) cc_final: 0.7352 (mt0) REVERT: A 278 LEU cc_start: 0.9014 (tp) cc_final: 0.8628 (tp) REVERT: A 342 MET cc_start: 0.4442 (ttp) cc_final: 0.4197 (ttp) REVERT: A 376 GLU cc_start: 0.8345 (tt0) cc_final: 0.7716 (tt0) REVERT: A 379 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 381 ASN cc_start: 0.8126 (t0) cc_final: 0.7774 (t0) REVERT: A 397 ARG cc_start: 0.0449 (OUTLIER) cc_final: -0.2316 (ttm170) REVERT: B 2 ARG cc_start: 0.6772 (ptm160) cc_final: 0.6381 (ptm160) REVERT: B 6 VAL cc_start: 0.8307 (t) cc_final: 0.7915 (m) REVERT: B 22 GLN cc_start: 0.7300 (mt0) cc_final: 0.7007 (mt0) REVERT: B 24 GLU cc_start: 0.7673 (tt0) cc_final: 0.7312 (tt0) REVERT: B 28 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7626 (tp40) REVERT: B 64 TRP cc_start: 0.7557 (m100) cc_final: 0.7132 (m100) REVERT: B 91 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7371 (tp40) REVERT: B 135 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 138 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8116 (mtmt) REVERT: B 164 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 376 GLU cc_start: 0.8331 (tt0) cc_final: 0.7699 (tt0) REVERT: B 381 ASN cc_start: 0.8693 (m-40) cc_final: 0.8382 (m-40) REVERT: B 430 TRP cc_start: 0.8977 (m100) cc_final: 0.8476 (m100) REVERT: B 444 ARG cc_start: 0.8169 (mmp80) cc_final: 0.7680 (mmp80) REVERT: B 458 MET cc_start: 0.8065 (mmt) cc_final: 0.7560 (mmt) REVERT: B 459 ASN cc_start: 0.8547 (m-40) cc_final: 0.8101 (m-40) REVERT: C 1 MET cc_start: 0.6948 (ttm) cc_final: 0.6640 (ttt) REVERT: C 9 LEU cc_start: 0.8097 (tp) cc_final: 0.7806 (mm) REVERT: C 21 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7319 (mmm160) REVERT: C 26 CYS cc_start: 0.7275 (m) cc_final: 0.6994 (m) REVERT: C 29 LEU cc_start: 0.8048 (tp) cc_final: 0.7651 (tt) REVERT: C 43 ASP cc_start: 0.6703 (m-30) cc_final: 0.6436 (m-30) REVERT: C 45 ASP cc_start: 0.7462 (t0) cc_final: 0.7201 (t0) REVERT: C 92 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: C 95 HIS cc_start: 0.7683 (t70) cc_final: 0.7154 (t-90) REVERT: C 96 TRP cc_start: 0.8441 (t60) cc_final: 0.8018 (t60) REVERT: C 98 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5764 (pp20) REVERT: C 135 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: C 140 ARG cc_start: 0.7342 (mpt-90) cc_final: 0.7037 (ttm110) REVERT: C 181 ARG cc_start: 0.7776 (ptp90) cc_final: 0.7380 (mtm110) REVERT: C 186 GLU cc_start: 0.8075 (tp30) cc_final: 0.7853 (tp30) REVERT: C 204 ASP cc_start: 0.7453 (t0) cc_final: 0.7072 (t0) REVERT: C 220 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 224 GLU cc_start: 0.7873 (tt0) cc_final: 0.7586 (tt0) REVERT: C 226 GLN cc_start: 0.7794 (mp10) cc_final: 0.7073 (mp10) REVERT: C 228 ARG cc_start: 0.7576 (mpt-90) cc_final: 0.7202 (mpt-90) REVERT: C 239 MET cc_start: 0.7684 (mmm) cc_final: 0.7246 (mmm) REVERT: C 247 TYR cc_start: 0.7837 (m-10) cc_final: 0.7627 (m-10) REVERT: C 265 ARG cc_start: 0.7966 (ptt180) cc_final: 0.7714 (ptt180) REVERT: C 331 PHE cc_start: 0.7351 (m-80) cc_final: 0.6857 (m-80) REVERT: C 352 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8761 (tp-100) REVERT: C 384 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7565 (pp) REVERT: C 404 GLU cc_start: 0.8320 (pt0) cc_final: 0.8043 (pt0) REVERT: C 452 ASN cc_start: 0.8079 (t0) cc_final: 0.7740 (t0) REVERT: C 454 TRP cc_start: 0.8077 (t60) cc_final: 0.7591 (t60) REVERT: D 20 GLU cc_start: 0.7408 (mp0) cc_final: 0.7153 (mp0) REVERT: D 25 SER cc_start: 0.8145 (m) cc_final: 0.7804 (p) REVERT: D 74 VAL cc_start: 0.8014 (p) cc_final: 0.7719 (m) REVERT: D 96 TRP cc_start: 0.8417 (t60) cc_final: 0.8170 (t60) REVERT: D 102 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7850 (mmtp) REVERT: D 111 HIS cc_start: 0.8360 (p-80) cc_final: 0.7925 (p-80) REVERT: D 164 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8133 (mt) REVERT: D 216 TYR cc_start: 0.7783 (t80) cc_final: 0.7227 (t80) REVERT: D 224 GLU cc_start: 0.7024 (pp20) cc_final: 0.6338 (pp20) REVERT: D 226 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7815 (mm-40) REVERT: D 229 GLU cc_start: 0.6981 (pt0) cc_final: 0.6568 (pm20) REVERT: D 242 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: D 296 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7757 (t) REVERT: D 327 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7401 (ttp80) REVERT: D 329 MET cc_start: 0.6768 (tpp) cc_final: 0.6303 (tpp) REVERT: D 331 PHE cc_start: 0.7256 (m-10) cc_final: 0.6378 (m-80) REVERT: D 350 GLU cc_start: 0.8858 (pt0) cc_final: 0.8290 (pt0) REVERT: D 351 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7852 (pp20) REVERT: D 404 GLU cc_start: 0.8866 (pt0) cc_final: 0.8641 (pt0) REVERT: D 452 ASN cc_start: 0.7697 (t0) cc_final: 0.7312 (t0) REVERT: D 458 MET cc_start: 0.7617 (mmt) cc_final: 0.7213 (mmt) outliers start: 55 outliers final: 35 residues processed: 469 average time/residue: 0.1642 time to fit residues: 111.3213 Evaluate side-chains 487 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 440 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 69 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 109 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 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 98 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 204 ASP 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 Chi-restraints excluded: chain D residue 351 GLU 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: 7.9990 chunk 9 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 208 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS B 89 HIS B 100 HIS D 91 GLN D 206 ASN D 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.186052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133580 restraints weight = 39181.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138388 restraints weight = 16216.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141369 restraints weight = 9694.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143027 restraints weight = 7275.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144077 restraints weight = 6258.385| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20313 Z= 0.234 Angle : 0.642 13.304 28383 Z= 0.359 Chirality : 0.044 0.205 3109 Planarity : 0.005 0.071 3022 Dihedral : 23.357 86.606 4307 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.80 % Allowed : 18.01 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 1937 helix: 2.11 (0.17), residues: 909 sheet: -0.28 (0.28), residues: 290 loop : 0.55 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 325 TYR 0.021 0.002 TYR A 154 PHE 0.024 0.002 PHE B 348 TRP 0.035 0.002 TRP B 345 HIS 0.007 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (20297) covalent geometry : angle 0.62567 / 0.36 (28359) hydrogen bonds : bond 0.04928 / 3.42 ( 1059) hydrogen bonds : angle 3.87983 / 2.84 ( 2792) metal coordination : bond 0.00646 / 0.40 ( 16) metal coordination : angle 4.96377 / 3.52 ( 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 501 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 440 time to evaluate : 0.554 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: 0.6378 (tpt) cc_final: 0.6108 (tpt) REVERT: A 5 VAL cc_start: 0.8104 (t) cc_final: 0.7842 (m) REVERT: A 60 ASN cc_start: 0.8026 (m-40) cc_final: 0.7810 (m-40) REVERT: A 89 HIS cc_start: 0.7980 (m170) cc_final: 0.7470 (m170) REVERT: A 109 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6567 (mp0) REVERT: A 163 TYR cc_start: 0.8246 (m-80) cc_final: 0.7859 (m-80) REVERT: A 168 VAL cc_start: 0.8345 (t) cc_final: 0.8044 (m) REVERT: A 169 ASP cc_start: 0.7208 (t0) cc_final: 0.6561 (t0) REVERT: A 182 GLU cc_start: 0.7693 (tt0) cc_final: 0.7258 (tt0) REVERT: A 204 ASP cc_start: 0.7486 (t70) cc_final: 0.7181 (t0) REVERT: A 241 SER cc_start: 0.8406 (t) cc_final: 0.7959 (p) REVERT: A 251 ASN cc_start: 0.8619 (m-40) cc_final: 0.8375 (m-40) REVERT: A 342 MET cc_start: 0.4596 (ttp) cc_final: 0.4350 (ttp) REVERT: A 376 GLU cc_start: 0.8347 (tt0) cc_final: 0.7771 (tt0) REVERT: A 379 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 381 ASN cc_start: 0.8114 (t0) cc_final: 0.7769 (t0) REVERT: A 383 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8455 (mt-10) REVERT: A 397 ARG cc_start: 0.1092 (OUTLIER) cc_final: -0.1427 (ttm170) REVERT: A 419 GLU cc_start: 0.7024 (tm-30) cc_final: 0.5788 (tm-30) REVERT: B 2 ARG cc_start: 0.6823 (ptm160) cc_final: 0.6397 (ptm160) REVERT: B 6 VAL cc_start: 0.8334 (t) cc_final: 0.7942 (m) REVERT: B 22 GLN cc_start: 0.7385 (mt0) cc_final: 0.7091 (mt0) REVERT: B 24 GLU cc_start: 0.7678 (tt0) cc_final: 0.7295 (tt0) REVERT: B 28 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7567 (tp40) REVERT: B 91 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7369 (tp40) REVERT: B 106 SER cc_start: 0.8163 (t) cc_final: 0.7908 (p) REVERT: B 135 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 138 LYS cc_start: 0.8355 (mtmt) cc_final: 0.8133 (mtmt) REVERT: B 164 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7953 (tt) REVERT: B 219 GLN cc_start: 0.6958 (tp40) cc_final: 0.6497 (mm110) REVERT: B 300 ARG cc_start: 0.8516 (tpt170) cc_final: 0.7933 (mmt-90) REVERT: B 376 GLU cc_start: 0.8321 (tt0) cc_final: 0.7742 (tt0) REVERT: B 381 ASN cc_start: 0.8714 (m-40) cc_final: 0.8426 (m-40) REVERT: B 430 TRP cc_start: 0.9001 (m100) cc_final: 0.8588 (m100) REVERT: B 458 MET cc_start: 0.8097 (mmt) cc_final: 0.7521 (mmt) REVERT: B 459 ASN cc_start: 0.8614 (m-40) cc_final: 0.8192 (m-40) REVERT: C 9 LEU cc_start: 0.8189 (tp) cc_final: 0.7898 (mt) REVERT: C 21 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7317 (mmm160) REVERT: C 26 CYS cc_start: 0.7299 (m) cc_final: 0.7034 (m) REVERT: C 29 LEU cc_start: 0.8060 (tp) cc_final: 0.7708 (tt) REVERT: C 43 ASP cc_start: 0.6702 (m-30) cc_final: 0.6443 (m-30) REVERT: C 57 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7838 (mtm180) REVERT: C 92 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: C 96 TRP cc_start: 0.8431 (t60) cc_final: 0.7993 (t60) REVERT: C 109 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7256 (mt-10) REVERT: C 135 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: C 140 ARG cc_start: 0.7328 (mpt-90) cc_final: 0.7042 (ttm110) REVERT: C 142 ARG cc_start: 0.7493 (ttp80) cc_final: 0.7245 (tmm-80) REVERT: C 204 ASP cc_start: 0.7541 (t0) cc_final: 0.7095 (t0) REVERT: C 224 GLU cc_start: 0.7929 (tt0) cc_final: 0.7695 (tt0) REVERT: C 226 GLN cc_start: 0.7768 (mp10) cc_final: 0.7049 (mp10) REVERT: C 228 ARG cc_start: 0.7659 (mpt-90) cc_final: 0.7363 (mpt-90) REVERT: C 239 MET cc_start: 0.7684 (mmm) cc_final: 0.7290 (mmm) REVERT: C 331 PHE cc_start: 0.7354 (m-80) cc_final: 0.6846 (m-80) REVERT: C 352 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8782 (tp-100) REVERT: C 384 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7566 (pp) REVERT: C 404 GLU cc_start: 0.8389 (pt0) cc_final: 0.8105 (pt0) REVERT: C 452 ASN cc_start: 0.8109 (t0) cc_final: 0.7687 (t0) REVERT: D 20 GLU cc_start: 0.7333 (mp0) cc_final: 0.7076 (mp0) REVERT: D 21 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7417 (mtm180) REVERT: D 25 SER cc_start: 0.8311 (m) cc_final: 0.8044 (p) REVERT: D 74 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7731 (m) REVERT: D 109 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7268 (mt-10) REVERT: D 190 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7661 (tpp80) REVERT: D 216 TYR cc_start: 0.7846 (t80) cc_final: 0.7087 (t80) REVERT: D 220 LEU cc_start: 0.8635 (mm) cc_final: 0.8256 (mt) REVERT: D 226 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7790 (mm-40) REVERT: D 242 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: D 244 MET cc_start: 0.6786 (mmm) cc_final: 0.6539 (mmm) REVERT: D 279 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7862 (ttm110) REVERT: D 296 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7929 (t) REVERT: D 325 ARG cc_start: 0.7490 (ttm110) cc_final: 0.6879 (ptm160) REVERT: D 327 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7458 (ttp80) REVERT: D 331 PHE cc_start: 0.7300 (m-10) cc_final: 0.6446 (m-80) REVERT: D 350 GLU cc_start: 0.8897 (pt0) cc_final: 0.8688 (pt0) REVERT: D 351 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7865 (pp20) REVERT: D 404 GLU cc_start: 0.8873 (pt0) cc_final: 0.8534 (pp20) REVERT: D 409 ARG cc_start: 0.8557 (mmp80) cc_final: 0.8299 (mmp80) REVERT: D 452 ASN cc_start: 0.7753 (t0) cc_final: 0.7340 (t0) REVERT: D 458 MET cc_start: 0.7752 (mmt) cc_final: 0.7343 (mmt) outliers start: 61 outliers final: 39 residues processed: 468 average time/residue: 0.1670 time to fit residues: 112.4772 Evaluate side-chains 480 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 432 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 109 GLU Chi-restraints excluded: chain B residue 149 ILE 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 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 72 PHE 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 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 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 242 GLU Chi-restraints excluded: chain D residue 263 LEU 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 Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 56 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 0.0030 chunk 149 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.0030 chunk 74 optimal weight: 0.0870 chunk 170 optimal weight: 0.7980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS B 89 HIS C 189 HIS D 251 ASN D 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.188904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135761 restraints weight = 47459.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141038 restraints weight = 17999.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144295 restraints weight = 10264.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146215 restraints weight = 7458.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.147153 restraints weight = 6279.827| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20313 Z= 0.127 Angle : 0.602 13.607 28383 Z= 0.333 Chirality : 0.040 0.182 3109 Planarity : 0.005 0.071 3022 Dihedral : 23.293 85.537 4304 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.05 % Allowed : 19.56 % 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: 1.89 (0.19), residues: 1937 helix: 2.30 (0.17), residues: 910 sheet: -0.17 (0.29), residues: 286 loop : 0.67 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 409 TYR 0.025 0.002 TYR A 188 PHE 0.024 0.001 PHE B 348 TRP 0.051 0.002 TRP B 64 HIS 0.009 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (20297) covalent geometry : angle 0.58680 / 0.33 (28359) hydrogen bonds : bond 0.04195 / 2.92 ( 1059) hydrogen bonds : angle 3.72141 / 2.73 ( 2792) metal coordination : bond 0.00362 / 0.19 ( 16) metal coordination : angle 4.63426 / 3.43 ( 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 478 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 429 time to evaluate : 0.521 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 1 MET cc_start: 0.6079 (tpt) cc_final: 0.5795 (tpt) REVERT: A 5 VAL cc_start: 0.8090 (t) cc_final: 0.7766 (m) REVERT: A 40 VAL cc_start: 0.7829 (m) cc_final: 0.7530 (t) REVERT: A 89 HIS cc_start: 0.7887 (m170) cc_final: 0.7376 (m170) REVERT: A 109 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6514 (mp0) REVERT: A 131 GLN cc_start: 0.8137 (tp40) cc_final: 0.7743 (tp-100) REVERT: A 168 VAL cc_start: 0.8340 (t) cc_final: 0.8061 (m) REVERT: A 169 ASP cc_start: 0.7200 (t0) cc_final: 0.6552 (t0) REVERT: A 182 GLU cc_start: 0.7519 (tt0) cc_final: 0.7068 (tt0) REVERT: A 204 ASP cc_start: 0.7448 (t70) cc_final: 0.7151 (t0) REVERT: A 229 GLU cc_start: 0.7589 (pt0) cc_final: 0.7151 (pt0) REVERT: A 241 SER cc_start: 0.8413 (t) cc_final: 0.7955 (p) REVERT: A 251 ASN cc_start: 0.8616 (m-40) cc_final: 0.8365 (m-40) REVERT: A 278 LEU cc_start: 0.9037 (tp) cc_final: 0.8766 (mt) REVERT: A 342 MET cc_start: 0.4452 (ttp) cc_final: 0.4208 (ttp) REVERT: A 376 GLU cc_start: 0.8311 (tt0) cc_final: 0.7699 (tt0) REVERT: A 379 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 381 ASN cc_start: 0.8049 (t0) cc_final: 0.7704 (t0) REVERT: A 383 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 397 ARG cc_start: 0.1299 (OUTLIER) cc_final: -0.1264 (tpm170) REVERT: B 6 VAL cc_start: 0.8320 (t) cc_final: 0.7947 (m) REVERT: B 21 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7423 (ttm110) REVERT: B 22 GLN cc_start: 0.7383 (mt0) cc_final: 0.7170 (mt0) REVERT: B 28 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7606 (tp40) REVERT: B 68 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6868 (mt-10) REVERT: B 82 ARG cc_start: 0.7774 (mmt180) cc_final: 0.7439 (mmm160) REVERT: B 91 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7312 (tp-100) REVERT: B 106 SER cc_start: 0.8139 (t) cc_final: 0.7862 (p) REVERT: B 135 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 138 LYS cc_start: 0.8310 (mtmt) cc_final: 0.8081 (mtmt) REVERT: B 164 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7875 (tt) REVERT: B 219 GLN cc_start: 0.6850 (tp40) cc_final: 0.6538 (mm110) REVERT: B 300 ARG cc_start: 0.8478 (tpt170) cc_final: 0.8022 (mmt-90) REVERT: B 376 GLU cc_start: 0.8291 (tt0) cc_final: 0.7800 (tt0) REVERT: B 381 ASN cc_start: 0.8693 (m-40) cc_final: 0.8401 (m-40) REVERT: B 444 ARG cc_start: 0.8083 (mmp80) cc_final: 0.7783 (mmp80) REVERT: B 458 MET cc_start: 0.8040 (mmt) cc_final: 0.7514 (mmt) REVERT: B 459 ASN cc_start: 0.8566 (m-40) cc_final: 0.7967 (m-40) REVERT: C 9 LEU cc_start: 0.8085 (tp) cc_final: 0.7783 (mt) REVERT: C 21 ARG cc_start: 0.7501 (mmt90) cc_final: 0.7179 (mmm160) REVERT: C 26 CYS cc_start: 0.7321 (m) cc_final: 0.7025 (m) REVERT: C 29 LEU cc_start: 0.8038 (tp) cc_final: 0.7603 (tt) REVERT: C 43 ASP cc_start: 0.6620 (m-30) cc_final: 0.6380 (m-30) REVERT: C 92 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: C 96 TRP cc_start: 0.8313 (t60) cc_final: 0.7784 (t60) REVERT: C 98 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5802 (pp20) REVERT: C 109 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7097 (mt-10) REVERT: C 135 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: C 140 ARG cc_start: 0.7325 (mpt-90) cc_final: 0.7088 (ttm110) REVERT: C 142 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7192 (tmm-80) REVERT: C 181 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7221 (ptt-90) REVERT: C 189 HIS cc_start: 0.7724 (m90) cc_final: 0.7385 (m90) REVERT: C 204 ASP cc_start: 0.7493 (t0) cc_final: 0.7059 (t0) REVERT: C 224 GLU cc_start: 0.7892 (tt0) cc_final: 0.7672 (tt0) REVERT: C 226 GLN cc_start: 0.7777 (mp10) cc_final: 0.7115 (mp10) REVERT: C 228 ARG cc_start: 0.7467 (mpt-90) cc_final: 0.7141 (mpt-90) REVERT: C 235 LEU cc_start: 0.7961 (mt) cc_final: 0.7377 (pp) REVERT: C 239 MET cc_start: 0.7653 (mmm) cc_final: 0.7254 (mmm) REVERT: C 331 PHE cc_start: 0.7372 (m-80) cc_final: 0.6829 (m-80) REVERT: C 352 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8745 (tp-100) REVERT: C 384 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7562 (pp) REVERT: C 404 GLU cc_start: 0.8326 (pt0) cc_final: 0.8063 (pt0) REVERT: C 452 ASN cc_start: 0.8072 (t0) cc_final: 0.7712 (m-40) REVERT: D 21 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7354 (mtm180) REVERT: D 25 SER cc_start: 0.8171 (m) cc_final: 0.7931 (p) REVERT: D 42 GLU cc_start: 0.7133 (tt0) cc_final: 0.6858 (tt0) REVERT: D 74 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7762 (m) REVERT: D 102 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7859 (mmtp) REVERT: D 164 LEU cc_start: 0.8117 (mt) cc_final: 0.7648 (mt) REVERT: D 182 GLU cc_start: 0.7168 (pt0) cc_final: 0.6909 (pt0) REVERT: D 186 GLU cc_start: 0.7911 (tt0) cc_final: 0.7317 (pt0) REVERT: D 190 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7606 (tpp80) REVERT: D 216 TYR cc_start: 0.7786 (t80) cc_final: 0.7104 (t80) REVERT: D 220 LEU cc_start: 0.8551 (mm) cc_final: 0.8152 (mt) REVERT: D 242 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7251 (mm-30) REVERT: D 244 MET cc_start: 0.6809 (mmm) cc_final: 0.6429 (mmm) REVERT: D 279 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7853 (ttm110) REVERT: D 296 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7912 (t) REVERT: D 325 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6923 (mtm180) REVERT: D 327 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7420 (ttp80) REVERT: D 331 PHE cc_start: 0.7288 (m-10) cc_final: 0.6381 (m-80) REVERT: D 348 PHE cc_start: 0.8488 (t80) cc_final: 0.8004 (t80) REVERT: D 351 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: D 409 ARG cc_start: 0.8529 (mmp80) cc_final: 0.8253 (mmp80) REVERT: D 452 ASN cc_start: 0.7708 (t0) cc_final: 0.7263 (t0) REVERT: D 458 MET cc_start: 0.7706 (mmt) cc_final: 0.7203 (mmt) outliers start: 49 outliers final: 32 residues processed: 451 average time/residue: 0.1656 time to fit residues: 107.3797 Evaluate side-chains 473 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 432 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 189 HIS 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 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 135 GLU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 249 THR 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 Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 121 optimal weight: 0.0070 chunk 202 optimal weight: 50.0000 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS B 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.187465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133290 restraints weight = 58385.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138924 restraints weight = 20239.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142416 restraints weight = 11009.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144437 restraints weight = 7766.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145693 restraints weight = 6443.329| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 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 = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20313 Z= 0.162 Angle : 0.605 12.484 28383 Z= 0.336 Chirality : 0.041 0.197 3109 Planarity : 0.005 0.073 3022 Dihedral : 23.281 85.486 4302 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 20.56 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 1937 helix: 2.18 (0.17), residues: 917 sheet: -0.17 (0.29), residues: 282 loop : 0.62 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 57 TYR 0.023 0.002 TYR D 154 PHE 0.028 0.001 PHE B 348 TRP 0.072 0.002 TRP B 64 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (20297) covalent geometry : angle 0.59247 / 0.34 (28359) hydrogen bonds : bond 0.04354 / 3.04 ( 1059) hydrogen bonds : angle 3.72515 / 2.73 ( 2792) metal coordination : bond 0.00412 / 0.23 ( 16) metal coordination : angle 4.30102 / 3.13 ( 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 467 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 424 time to evaluate : 0.395 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 1 MET cc_start: 0.6086 (tpt) cc_final: 0.5780 (tpt) REVERT: A 5 VAL cc_start: 0.8100 (t) cc_final: 0.7769 (m) REVERT: A 40 VAL cc_start: 0.7868 (m) cc_final: 0.7582 (t) REVERT: A 89 HIS cc_start: 0.7885 (m170) cc_final: 0.7591 (m170) REVERT: A 109 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6563 (mp0) REVERT: A 168 VAL cc_start: 0.8360 (t) cc_final: 0.8078 (m) REVERT: A 169 ASP cc_start: 0.7219 (t0) cc_final: 0.6567 (t0) REVERT: A 182 GLU cc_start: 0.7551 (tt0) cc_final: 0.7106 (tt0) REVERT: A 196 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 219 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7175 (tm-30) REVERT: A 241 SER cc_start: 0.8437 (t) cc_final: 0.7999 (p) REVERT: A 251 ASN cc_start: 0.8639 (m-40) cc_final: 0.8390 (m-40) REVERT: A 278 LEU cc_start: 0.9058 (tp) cc_final: 0.8729 (tp) REVERT: A 281 GLU cc_start: 0.8042 (tp30) cc_final: 0.7572 (tp30) REVERT: A 342 MET cc_start: 0.4510 (ttp) cc_final: 0.4253 (ttp) REVERT: A 376 GLU cc_start: 0.8342 (tt0) cc_final: 0.7780 (tt0) REVERT: A 379 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 381 ASN cc_start: 0.8074 (t0) cc_final: 0.7736 (t0) REVERT: A 383 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 397 ARG cc_start: 0.1363 (OUTLIER) cc_final: -0.1267 (tpm170) REVERT: B 6 VAL cc_start: 0.8340 (t) cc_final: 0.7966 (m) REVERT: B 21 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7451 (ttm110) REVERT: B 22 GLN cc_start: 0.7404 (mt0) cc_final: 0.7181 (mt0) REVERT: B 28 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7603 (tp40) REVERT: B 82 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7446 (mmm160) REVERT: B 91 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7329 (tp40) REVERT: B 106 SER cc_start: 0.8179 (t) cc_final: 0.7892 (p) REVERT: B 135 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 138 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8118 (mtmt) REVERT: B 164 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7885 (tt) REVERT: B 292 VAL cc_start: 0.8706 (t) cc_final: 0.8332 (m) REVERT: B 300 ARG cc_start: 0.8465 (tpt170) cc_final: 0.7966 (mmt-90) REVERT: B 376 GLU cc_start: 0.8281 (tt0) cc_final: 0.7810 (tt0) REVERT: B 381 ASN cc_start: 0.8720 (m-40) cc_final: 0.8443 (m-40) REVERT: B 430 TRP cc_start: 0.9012 (m100) cc_final: 0.8532 (m100) REVERT: B 444 ARG cc_start: 0.8094 (mmp80) cc_final: 0.7769 (mmp80) REVERT: B 458 MET cc_start: 0.8070 (mmt) cc_final: 0.7545 (mmt) REVERT: B 459 ASN cc_start: 0.8582 (m-40) cc_final: 0.7992 (m-40) REVERT: C 9 LEU cc_start: 0.8158 (tp) cc_final: 0.7881 (mt) REVERT: C 21 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7170 (mmm160) REVERT: C 26 CYS cc_start: 0.7223 (m) cc_final: 0.6949 (m) REVERT: C 29 LEU cc_start: 0.7912 (tp) cc_final: 0.7566 (tt) REVERT: C 43 ASP cc_start: 0.6660 (m-30) cc_final: 0.6426 (m-30) REVERT: C 92 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: C 96 TRP cc_start: 0.8395 (t60) cc_final: 0.7910 (t60) REVERT: C 109 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7141 (mt-10) REVERT: C 135 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: C 140 ARG cc_start: 0.7322 (mpt-90) cc_final: 0.7097 (ttm110) REVERT: C 142 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7243 (tmm-80) REVERT: C 181 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7213 (ptt-90) REVERT: C 189 HIS cc_start: 0.7773 (m90) cc_final: 0.7304 (m90) REVERT: C 204 ASP cc_start: 0.7490 (t0) cc_final: 0.7054 (t0) REVERT: C 224 GLU cc_start: 0.7915 (tt0) cc_final: 0.7703 (tt0) REVERT: C 226 GLN cc_start: 0.7810 (mp10) cc_final: 0.7110 (mp10) REVERT: C 228 ARG cc_start: 0.7549 (mpt-90) cc_final: 0.7216 (mpt-90) REVERT: C 235 LEU cc_start: 0.7993 (mt) cc_final: 0.7407 (pp) REVERT: C 239 MET cc_start: 0.7679 (mmm) cc_final: 0.7284 (mmm) REVERT: C 331 PHE cc_start: 0.7380 (m-80) cc_final: 0.6839 (m-80) REVERT: C 352 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8779 (tp-100) REVERT: C 404 GLU cc_start: 0.8328 (pt0) cc_final: 0.7989 (pt0) REVERT: C 409 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8351 (mmp80) REVERT: C 452 ASN cc_start: 0.8087 (t0) cc_final: 0.7730 (m-40) REVERT: D 20 GLU cc_start: 0.7450 (mp0) cc_final: 0.7179 (mp0) REVERT: D 21 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7453 (mtm180) REVERT: D 25 SER cc_start: 0.8239 (m) cc_final: 0.7982 (p) REVERT: D 74 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7776 (m) REVERT: D 96 TRP cc_start: 0.8471 (t60) cc_final: 0.8232 (t60) REVERT: D 102 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7901 (mmtp) REVERT: D 164 LEU cc_start: 0.8188 (mt) cc_final: 0.7717 (mt) REVERT: D 182 GLU cc_start: 0.7231 (pt0) cc_final: 0.6973 (pt0) REVERT: D 186 GLU cc_start: 0.7923 (tt0) cc_final: 0.7399 (pt0) REVERT: D 216 TYR cc_start: 0.7803 (t80) cc_final: 0.7267 (t80) REVERT: D 224 GLU cc_start: 0.6967 (pp20) cc_final: 0.6079 (pp20) REVERT: D 226 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7128 (mm-40) REVERT: D 228 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7619 (mtt90) REVERT: D 242 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7201 (mm-30) REVERT: D 244 MET cc_start: 0.6807 (mmm) cc_final: 0.6435 (mmm) REVERT: D 279 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7839 (ttm110) REVERT: D 296 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7906 (t) REVERT: D 327 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7491 (ttp80) REVERT: D 329 MET cc_start: 0.7782 (ppp) cc_final: 0.7014 (ppp) REVERT: D 331 PHE cc_start: 0.7343 (m-10) cc_final: 0.6499 (m-80) REVERT: D 348 PHE cc_start: 0.8477 (t80) cc_final: 0.7986 (t80) REVERT: D 351 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: D 409 ARG cc_start: 0.8564 (mmp80) cc_final: 0.8279 (mmp80) REVERT: D 452 ASN cc_start: 0.7752 (t0) cc_final: 0.7330 (t0) REVERT: D 458 MET cc_start: 0.7694 (mmt) cc_final: 0.7275 (mmt) outliers start: 43 outliers final: 29 residues processed: 446 average time/residue: 0.1634 time to fit residues: 104.3889 Evaluate side-chains 456 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 420 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 164 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 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 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 Chi-restraints excluded: chain D residue 351 GLU 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: 10.0000 chunk 201 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS B 89 HIS D 251 ASN D 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.184789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132065 restraints weight = 41108.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136962 restraints weight = 16665.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140037 restraints weight = 9859.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141828 restraints weight = 7320.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142849 restraints weight = 6230.431| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 20313 Z= 0.271 Angle : 0.679 15.286 28383 Z= 0.373 Chirality : 0.045 0.221 3109 Planarity : 0.005 0.072 3022 Dihedral : 23.331 87.429 4300 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.93 % Allowed : 20.37 % 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: 1.52 (0.19), residues: 1937 helix: 1.93 (0.17), residues: 919 sheet: -0.23 (0.29), residues: 283 loop : 0.48 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 416 TYR 0.026 0.002 TYR A 188 PHE 0.027 0.002 PHE B 348 TRP 0.060 0.003 TRP B 64 HIS 0.010 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.27 (20297) covalent geometry : angle 0.66636 / 0.37 (28359) hydrogen bonds : bond 0.05144 / 3.56 ( 1059) hydrogen bonds : angle 3.94545 / 2.90 ( 2792) metal coordination : bond 0.00602 / 0.36 ( 16) metal coordination : angle 4.55202 / 3.26 ( 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 486 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 439 time to evaluate : 0.567 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 1 MET cc_start: 0.6417 (tpt) cc_final: 0.6140 (tpt) REVERT: A 89 HIS cc_start: 0.7871 (m170) cc_final: 0.7537 (m90) REVERT: A 109 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6624 (mp0) REVERT: A 131 GLN cc_start: 0.8145 (tp40) cc_final: 0.7871 (tp-100) REVERT: A 168 VAL cc_start: 0.8408 (t) cc_final: 0.8134 (m) REVERT: A 169 ASP cc_start: 0.7232 (t0) cc_final: 0.6588 (t0) REVERT: A 182 GLU cc_start: 0.7626 (tt0) cc_final: 0.7151 (tt0) REVERT: A 196 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 204 ASP cc_start: 0.7408 (t70) cc_final: 0.7138 (t0) REVERT: A 219 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7174 (tm-30) REVERT: A 241 SER cc_start: 0.8385 (t) cc_final: 0.7981 (p) REVERT: A 251 ASN cc_start: 0.8665 (m-40) cc_final: 0.8460 (m110) REVERT: A 342 MET cc_start: 0.4655 (ttp) cc_final: 0.4364 (ttp) REVERT: A 376 GLU cc_start: 0.8344 (tt0) cc_final: 0.7766 (tt0) REVERT: A 379 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7797 (mm-30) REVERT: A 381 ASN cc_start: 0.7924 (t0) cc_final: 0.7618 (t0) REVERT: A 383 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8456 (mt-10) REVERT: A 397 ARG cc_start: 0.1619 (OUTLIER) cc_final: -0.1129 (tpm170) REVERT: B 6 VAL cc_start: 0.8339 (t) cc_final: 0.7991 (m) REVERT: B 22 GLN cc_start: 0.7477 (mt0) cc_final: 0.7223 (mt0) REVERT: B 28 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7567 (tp40) REVERT: B 91 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7399 (tp40) REVERT: B 106 SER cc_start: 0.8161 (t) cc_final: 0.7949 (p) REVERT: B 118 PHE cc_start: 0.8402 (m-80) cc_final: 0.7818 (m-80) REVERT: B 135 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 138 LYS cc_start: 0.8209 (mtmt) cc_final: 0.8002 (mtmt) REVERT: B 164 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 219 GLN cc_start: 0.7020 (tp40) cc_final: 0.6514 (mm110) REVERT: B 292 VAL cc_start: 0.8731 (t) cc_final: 0.8391 (m) REVERT: B 297 LEU cc_start: 0.8352 (tp) cc_final: 0.8072 (tp) REVERT: B 300 ARG cc_start: 0.8523 (tpt170) cc_final: 0.8006 (mmt-90) REVERT: B 376 GLU cc_start: 0.8301 (tt0) cc_final: 0.7834 (tt0) REVERT: B 381 ASN cc_start: 0.8723 (m-40) cc_final: 0.8453 (m-40) REVERT: B 430 TRP cc_start: 0.9026 (m100) cc_final: 0.8619 (m100) REVERT: B 444 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7829 (mmp80) REVERT: B 458 MET cc_start: 0.8127 (mmt) cc_final: 0.7618 (mmt) REVERT: B 459 ASN cc_start: 0.8612 (m-40) cc_final: 0.8038 (m-40) REVERT: C 9 LEU cc_start: 0.8277 (tp) cc_final: 0.8034 (mt) REVERT: C 21 ARG cc_start: 0.7535 (mmt90) cc_final: 0.7207 (mmm160) REVERT: C 26 CYS cc_start: 0.7249 (m) cc_final: 0.6954 (m) REVERT: C 29 LEU cc_start: 0.7969 (tp) cc_final: 0.7666 (tt) REVERT: C 43 ASP cc_start: 0.6659 (m-30) cc_final: 0.6420 (m-30) REVERT: C 81 ASP cc_start: 0.7427 (p0) cc_final: 0.6853 (t0) REVERT: C 92 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: C 96 TRP cc_start: 0.8464 (t60) cc_final: 0.7986 (t60) REVERT: C 135 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: C 140 ARG cc_start: 0.7279 (mpt-90) cc_final: 0.7031 (ttm110) REVERT: C 142 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7207 (ttt-90) REVERT: C 172 TRP cc_start: 0.7923 (m100) cc_final: 0.7416 (m100) REVERT: C 181 ARG cc_start: 0.7770 (ptp90) cc_final: 0.7232 (ptt-90) REVERT: C 189 HIS cc_start: 0.7650 (m90) cc_final: 0.7127 (m90) REVERT: C 204 ASP cc_start: 0.7520 (t0) cc_final: 0.7079 (t0) REVERT: C 224 GLU cc_start: 0.7947 (tt0) cc_final: 0.7733 (tt0) REVERT: C 226 GLN cc_start: 0.7834 (mp10) cc_final: 0.7124 (mp10) REVERT: C 228 ARG cc_start: 0.7790 (mpt-90) cc_final: 0.7469 (mpt-90) REVERT: C 235 LEU cc_start: 0.8060 (mt) cc_final: 0.7713 (mm) REVERT: C 239 MET cc_start: 0.7741 (mmm) cc_final: 0.7350 (mmm) REVERT: C 250 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7701 (tt) REVERT: C 331 PHE cc_start: 0.7379 (m-80) cc_final: 0.6836 (m-80) REVERT: C 342 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.4776 (mmm) REVERT: C 352 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8802 (tp-100) REVERT: C 384 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7517 (pp) REVERT: C 404 GLU cc_start: 0.8432 (pt0) cc_final: 0.8116 (pt0) REVERT: C 452 ASN cc_start: 0.8167 (t0) cc_final: 0.7797 (m-40) REVERT: D 21 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7450 (mtm180) REVERT: D 25 SER cc_start: 0.8291 (m) cc_final: 0.8060 (p) REVERT: D 74 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7791 (m) REVERT: D 190 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7642 (tpp80) REVERT: D 216 TYR cc_start: 0.7889 (t80) cc_final: 0.7140 (t80) REVERT: D 220 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8280 (mp) REVERT: D 221 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7947 (mm-40) REVERT: D 242 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7203 (mm-30) REVERT: D 244 MET cc_start: 0.6850 (mmm) cc_final: 0.6376 (mmm) REVERT: D 279 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7713 (ttm110) REVERT: D 296 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7921 (t) REVERT: D 325 ARG cc_start: 0.7068 (ptm160) cc_final: 0.6780 (ptm160) REVERT: D 327 ARG cc_start: 0.8261 (ttt180) cc_final: 0.7515 (ttp80) REVERT: D 329 MET cc_start: 0.8191 (ppp) cc_final: 0.7510 (ppp) REVERT: D 331 PHE cc_start: 0.7406 (m-10) cc_final: 0.6533 (m-80) REVERT: D 409 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8232 (mmp80) REVERT: D 452 ASN cc_start: 0.7803 (t0) cc_final: 0.7399 (t0) REVERT: D 458 MET cc_start: 0.7842 (mmt) cc_final: 0.7454 (mmt) outliers start: 47 outliers final: 31 residues processed: 460 average time/residue: 0.1701 time to fit residues: 111.8718 Evaluate side-chains 472 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 431 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 185 LEU 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 153 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 ASP 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 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 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 29 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 220 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 138 optimal weight: 40.0000 chunk 181 optimal weight: 0.0050 chunk 146 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133400 restraints weight = 45136.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138718 restraints weight = 17303.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141975 restraints weight = 9945.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143881 restraints weight = 7257.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144976 restraints weight = 6135.310| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 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 = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20313 Z= 0.154 Angle : 0.621 12.439 28383 Z= 0.344 Chirality : 0.041 0.206 3109 Planarity : 0.005 0.080 3022 Dihedral : 23.317 88.806 4300 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.37 % Allowed : 20.69 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 1937 helix: 2.17 (0.17), residues: 904 sheet: -0.13 (0.29), residues: 288 loop : 0.54 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 57 TYR 0.028 0.002 TYR A 188 PHE 0.029 0.001 PHE B 348 TRP 0.062 0.002 TRP B 64 HIS 0.006 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (20297) covalent geometry : angle 0.60922 / 0.34 (28359) hydrogen bonds : bond 0.04362 / 3.02 ( 1059) hydrogen bonds : angle 3.80009 / 2.78 ( 2792) metal coordination : bond 0.00383 / 0.21 ( 16) metal coordination : angle 4.19582 / 3.03 ( 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 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 432 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6260 (tpt) cc_final: 0.5968 (tpt) REVERT: A 89 HIS cc_start: 0.7810 (m170) cc_final: 0.7420 (m170) REVERT: A 109 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6605 (mp0) REVERT: A 131 GLN cc_start: 0.8122 (tp40) cc_final: 0.7861 (tp-100) REVERT: A 168 VAL cc_start: 0.8402 (t) cc_final: 0.8126 (m) REVERT: A 182 GLU cc_start: 0.7597 (tt0) cc_final: 0.7072 (tt0) REVERT: A 204 ASP cc_start: 0.7394 (t70) cc_final: 0.7102 (t0) REVERT: A 208 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.7126 (mtp85) REVERT: A 219 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7129 (tm-30) REVERT: A 241 SER cc_start: 0.8422 (t) cc_final: 0.7971 (p) REVERT: A 251 ASN cc_start: 0.8649 (m-40) cc_final: 0.8440 (m110) REVERT: A 272 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7709 (mmm-85) REVERT: A 278 LEU cc_start: 0.9053 (tp) cc_final: 0.8823 (tp) REVERT: A 281 GLU cc_start: 0.8049 (tp30) cc_final: 0.7500 (tp30) REVERT: A 342 MET cc_start: 0.4582 (ttp) cc_final: 0.4307 (ttp) REVERT: A 376 GLU cc_start: 0.8307 (tt0) cc_final: 0.7731 (tt0) REVERT: A 379 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 381 ASN cc_start: 0.8034 (t0) cc_final: 0.7703 (t0) REVERT: A 383 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 397 ARG cc_start: 0.1300 (OUTLIER) cc_final: -0.1303 (tpm170) REVERT: B 6 VAL cc_start: 0.8318 (t) cc_final: 0.7946 (m) REVERT: B 21 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7534 (ttp80) REVERT: B 22 GLN cc_start: 0.7467 (mt0) cc_final: 0.7258 (mt0) REVERT: B 28 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7629 (tp40) REVERT: B 82 ARG cc_start: 0.7747 (mmt180) cc_final: 0.7426 (mmm160) REVERT: B 91 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7316 (tp40) REVERT: B 135 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 138 LYS cc_start: 0.8362 (mtmt) cc_final: 0.8139 (mtmt) REVERT: B 164 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 292 VAL cc_start: 0.8625 (t) cc_final: 0.8280 (m) REVERT: B 300 ARG cc_start: 0.8440 (tpt170) cc_final: 0.8012 (mmt-90) REVERT: B 376 GLU cc_start: 0.8274 (tt0) cc_final: 0.7792 (tt0) REVERT: B 381 ASN cc_start: 0.8702 (m-40) cc_final: 0.8454 (m-40) REVERT: B 407 ASP cc_start: 0.8229 (p0) cc_final: 0.7917 (p0) REVERT: B 430 TRP cc_start: 0.9033 (m100) cc_final: 0.8554 (m100) REVERT: B 458 MET cc_start: 0.8139 (mmt) cc_final: 0.7545 (mmt) REVERT: B 459 ASN cc_start: 0.8601 (m-40) cc_final: 0.8037 (m-40) REVERT: C 9 LEU cc_start: 0.8214 (tp) cc_final: 0.7943 (mt) REVERT: C 21 ARG cc_start: 0.7489 (mmt90) cc_final: 0.7062 (mmm160) REVERT: C 24 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7386 (tm-30) REVERT: C 26 CYS cc_start: 0.7199 (m) cc_final: 0.6947 (m) REVERT: C 29 LEU cc_start: 0.7953 (tp) cc_final: 0.7531 (tt) REVERT: C 43 ASP cc_start: 0.6621 (m-30) cc_final: 0.6328 (m-30) REVERT: C 51 ASP cc_start: 0.7464 (t0) cc_final: 0.7242 (t0) REVERT: C 57 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7761 (mtm110) REVERT: C 92 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: C 96 TRP cc_start: 0.8362 (t60) cc_final: 0.7855 (t60) REVERT: C 135 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: C 142 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7167 (ttt-90) REVERT: C 172 TRP cc_start: 0.7798 (m100) cc_final: 0.7400 (m100) REVERT: C 181 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7201 (ptt-90) REVERT: C 189 HIS cc_start: 0.7718 (m90) cc_final: 0.7271 (m90) REVERT: C 204 ASP cc_start: 0.7493 (t0) cc_final: 0.7022 (t0) REVERT: C 226 GLN cc_start: 0.7824 (mp10) cc_final: 0.7161 (mp10) REVERT: C 228 ARG cc_start: 0.7628 (mpt-90) cc_final: 0.7349 (mpt-90) REVERT: C 235 LEU cc_start: 0.8038 (mt) cc_final: 0.7310 (pp) REVERT: C 239 MET cc_start: 0.7835 (mmm) cc_final: 0.7386 (mmm) REVERT: C 250 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7679 (tt) REVERT: C 325 ARG cc_start: 0.7751 (ptm-80) cc_final: 0.7088 (ttt90) REVERT: C 331 PHE cc_start: 0.7382 (m-80) cc_final: 0.6825 (m-80) REVERT: C 352 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8783 (tp-100) REVERT: C 404 GLU cc_start: 0.8387 (pt0) cc_final: 0.8113 (pt0) REVERT: C 452 ASN cc_start: 0.8125 (t0) cc_final: 0.7731 (m-40) REVERT: D 21 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7405 (mtm180) REVERT: D 25 SER cc_start: 0.8213 (m) cc_final: 0.7983 (p) REVERT: D 74 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7781 (m) REVERT: D 102 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8066 (mmmm) REVERT: D 164 LEU cc_start: 0.8185 (mt) cc_final: 0.7597 (mt) REVERT: D 182 GLU cc_start: 0.7256 (pt0) cc_final: 0.6921 (mm-30) REVERT: D 190 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7653 (tpp80) REVERT: D 216 TYR cc_start: 0.7829 (t80) cc_final: 0.7279 (t80) REVERT: D 220 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8302 (mp) REVERT: D 221 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7847 (mm-40) REVERT: D 226 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7132 (mm-40) REVERT: D 242 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7199 (mm-30) REVERT: D 244 MET cc_start: 0.6807 (mmm) cc_final: 0.6349 (mmm) REVERT: D 279 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7545 (ttm-80) REVERT: D 296 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7857 (t) REVERT: D 327 ARG cc_start: 0.8185 (ttt180) cc_final: 0.7442 (ttp80) REVERT: D 329 MET cc_start: 0.8079 (ppp) cc_final: 0.7381 (ppp) REVERT: D 331 PHE cc_start: 0.7327 (m-10) cc_final: 0.6440 (m-80) REVERT: D 351 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: D 404 GLU cc_start: 0.8882 (pt0) cc_final: 0.8219 (mp0) REVERT: D 452 ASN cc_start: 0.7848 (t0) cc_final: 0.7427 (t0) REVERT: D 458 MET cc_start: 0.7881 (mmt) cc_final: 0.7405 (mmt) outliers start: 38 outliers final: 26 residues processed: 448 average time/residue: 0.1567 time to fit residues: 100.3627 Evaluate side-chains 469 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 434 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 239 MET 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 153 LYS Chi-restraints excluded: chain B residue 164 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 418 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 250 LEU 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 220 LEU 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 351 GLU 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: 3.9990 chunk 168 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 122 optimal weight: 0.1980 chunk 165 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 446 GLN D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.188370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134272 restraints weight = 49446.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139745 restraints weight = 18123.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143081 restraints weight = 10160.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145095 restraints weight = 7321.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146226 restraints weight = 6118.787| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 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 = 0.3750 r_free = 0.3750 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 (3 function evaluations) r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20313 Z= 0.140 Angle : 0.620 11.976 28383 Z= 0.342 Chirality : 0.041 0.212 3109 Planarity : 0.005 0.079 3022 Dihedral : 23.298 93.567 4299 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.06 % Allowed : 21.50 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 1937 helix: 2.18 (0.17), residues: 908 sheet: -0.09 (0.29), residues: 290 loop : 0.53 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 444 TYR 0.029 0.002 TYR A 188 PHE 0.030 0.001 PHE B 348 TRP 0.052 0.002 TRP B 64 HIS 0.008 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (20297) covalent geometry : angle 0.60966 / 0.34 (28359) hydrogen bonds : bond 0.04193 / 2.91 ( 1059) hydrogen bonds : angle 3.75678 / 2.74 ( 2792) metal coordination : bond 0.00355 / 0.19 ( 16) metal coordination : angle 3.89677 / 2.81 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5062.18 seconds wall clock time: 87 minutes 1.22 seconds (5221.22 seconds total)