Starting phenix.real_space_refine on Mon Apr 6 15:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu5_60890/04_2026/9iu5_60890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu5_60890/04_2026/9iu5_60890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iu5_60890/04_2026/9iu5_60890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu5_60890/04_2026/9iu5_60890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu5_60890/04_2026/9iu5_60890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu5_60890/04_2026/9iu5_60890.map" } resolution = 3.63 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= 0.027 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 11574 2.51 5 N 3620 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 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19472 Number of models: 1 Model: "" Number of chains: 16 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: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} 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: "E1" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E2" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F1" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F2" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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 304 100.701 146.761 33.299 1.00365.26 S ATOM 2447 SG CYS A 307 98.291 145.285 35.705 1.00365.18 S ATOM 2598 SG CYS A 326 97.388 145.304 32.599 1.00365.36 S ATOM 2670 SG CYS A 335 97.660 148.814 34.160 1.00366.12 S ATOM 6292 SG CYS B 304 61.272 33.418 128.399 1.00287.61 S ATOM 6310 SG CYS B 307 61.341 34.617 124.898 1.00287.11 S ATOM 6461 SG CYS B 326 58.498 34.765 126.377 1.00287.63 S ATOM 6533 SG CYS B 335 59.718 31.166 125.753 1.00289.25 S ATOM 10155 SG CYS C 304 42.887 149.001 86.057 1.00250.96 S ATOM 10173 SG CYS C 307 42.551 146.234 88.478 1.00249.47 S ATOM 10324 SG CYS C 326 40.509 146.113 85.992 1.00243.67 S ATOM 10396 SG CYS C 335 39.815 149.032 88.302 1.00243.88 S ATOM 14018 SG CYS D 304 54.254 24.971 51.138 1.00300.38 S ATOM 14036 SG CYS D 307 55.235 27.485 48.640 1.00299.96 S ATOM 14187 SG CYS D 326 52.212 27.723 49.674 1.00298.18 S ATOM 14259 SG CYS D 335 52.858 24.559 47.608 1.00298.54 S Time building chain proxies: 4.19, per 1000 atoms: 0.22 Number of scatterers: 19472 At special positions: 0 Unit cell: (135.22, 175.199, 164.616, 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 3620 7.00 C 11574 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: 1.49 Conformation dependent library (CDL) restraints added in 748.2 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 304 " 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 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 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.6% alpha, 13.9% beta 93 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.630A 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 118 through 151 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: 4.121A 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: 3.819A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.679A 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 19 through 34 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.626A 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: 4.095A 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: 3.812A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.625A 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: 3.693A 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 18 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.630A 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: 3.678A 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: 7.520A pdb=" N VAL A 5 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 40 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.184A 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: 7.087A 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: 7.507A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.174A 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: 7.089A 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: 7.513A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.179A 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: 7.105A 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: 7.482A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.191A 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: 7.109A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 241 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.11 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: 3730 1.33 - 1.45: 6023 1.45 - 1.57: 10057 1.57 - 1.70: 384 1.70 - 1.82: 92 Bond restraints: 20286 Sorted by residual: bond pdb=" C SER B 18 " pdb=" N PRO B 19 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.06e-02 8.90e+03 9.82e+00 bond pdb=" NE ARG B 426 " pdb=" CZ ARG B 426 " ideal model delta sigma weight residual 1.326 1.358 -0.032 1.10e-02 8.26e+03 8.72e+00 bond pdb=" C HIS C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.330 1.366 -0.036 1.22e-02 6.72e+03 8.68e+00 bond pdb=" CA SER B 106 " pdb=" CB SER B 106 " ideal model delta sigma weight residual 1.530 1.485 0.046 1.55e-02 4.16e+03 8.64e+00 bond pdb=" C GLU A 196 " pdb=" N PRO A 197 " ideal model delta sigma weight residual 1.331 1.367 -0.036 1.31e-02 5.83e+03 7.66e+00 ... (remaining 20281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 26301 3.45 - 6.89: 1878 6.89 - 10.34: 137 10.34 - 13.79: 15 13.79 - 17.23: 7 Bond angle restraints: 28338 Sorted by residual: angle pdb=" O3' DGF1 32 " pdb=" P DTF1 33 " pdb=" O5' DTF1 33 " ideal model delta sigma weight residual 104.00 86.77 17.23 1.50e+00 4.44e-01 1.32e+02 angle pdb=" O3' DGE2 32 " pdb=" P DTE2 33 " pdb=" O5' DTE2 33 " ideal model delta sigma weight residual 104.00 88.81 15.19 1.50e+00 4.44e-01 1.03e+02 angle pdb=" C ARG C 140 " pdb=" CA ARG C 140 " pdb=" CB ARG C 140 " ideal model delta sigma weight residual 110.88 95.26 15.62 1.57e+00 4.06e-01 9.90e+01 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.49 14.51 1.50e+00 4.44e-01 9.36e+01 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 89.82 14.18 1.50e+00 4.44e-01 8.94e+01 ... (remaining 28333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9457 17.91 - 35.82: 1062 35.82 - 53.73: 871 53.73 - 71.64: 198 71.64 - 89.55: 28 Dihedral angle restraints: 11616 sinusoidal: 6004 harmonic: 5612 Sorted by residual: dihedral pdb=" N LEU D 125 " pdb=" C LEU D 125 " pdb=" CA LEU D 125 " pdb=" CB LEU D 125 " ideal model delta harmonic sigma weight residual 122.80 139.10 -16.30 0 2.50e+00 1.60e-01 4.25e+01 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 -137.71 15.11 0 2.50e+00 1.60e-01 3.65e+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 -136.44 13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2708 0.130 - 0.260: 368 0.260 - 0.390: 24 0.390 - 0.520: 2 0.520 - 0.649: 6 Chirality restraints: 3108 Sorted by residual: chirality pdb=" P DTF2 1 " pdb=" OP1 DTF2 1 " pdb=" OP2 DTF2 1 " pdb=" O5' DTF2 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DGE1 1 " pdb=" OP1 DGE1 1 " pdb=" OP2 DGE1 1 " pdb=" O5' DGE1 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3105 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCF2 27 " -0.112 2.00e-02 2.50e+03 5.23e-02 6.16e+01 pdb=" N1 DCF2 27 " 0.073 2.00e-02 2.50e+03 pdb=" C2 DCF2 27 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DCF2 27 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DCF2 27 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DCF2 27 " -0.020 2.00e-02 2.50e+03 pdb=" N4 DCF2 27 " -0.046 2.00e-02 2.50e+03 pdb=" C5 DCF2 27 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DCF2 27 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 35 " -0.053 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP D 35 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 35 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 35 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP D 35 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 35 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 35 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 35 " 0.011 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=" C1' DAF2 24 " -0.025 2.00e-02 2.50e+03 2.38e-02 1.56e+01 pdb=" N9 DAF2 24 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DAF2 24 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DAF2 24 " 0.042 2.00e-02 2.50e+03 pdb=" C5 DAF2 24 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DAF2 24 " -0.030 2.00e-02 2.50e+03 pdb=" N6 DAF2 24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DAF2 24 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DAF2 24 " 0.025 2.00e-02 2.50e+03 pdb=" N3 DAF2 24 " 0.027 2.00e-02 2.50e+03 pdb=" C4 DAF2 24 " -0.005 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 6 2.26 - 2.92: 6804 2.92 - 3.58: 28325 3.58 - 4.24: 47767 4.24 - 4.90: 77603 Nonbonded interactions: 160505 Sorted by model distance: nonbonded pdb=" OG SER A 10 " pdb=" P DCF1 28 " model vdw 1.603 3.400 nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.605 3.400 nonbonded pdb=" OG SER B 10 " pdb=" P DCE2 28 " model vdw 1.608 3.400 nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.618 3.400 nonbonded pdb=" OP1 DCE2 28 " pdb=" O3' DAG1 24 " model vdw 2.144 3.040 ... (remaining 160500 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.860 Find NCS groups from input model: 0.330 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 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 0.070 20302 Z= 0.580 Angle : 1.882 20.416 28362 Z= 1.196 Chirality : 0.090 0.649 3108 Planarity : 0.007 0.078 3020 Dihedral : 21.338 89.554 7984 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 4.18 % Allowed : 6.67 % Favored : 89.15 % Cbeta Deviations : 0.77 % 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: 0.42 (0.17), residues: 1936 helix: 0.55 (0.14), residues: 920 sheet: 0.12 (0.28), residues: 261 loop : 0.24 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.005 ARG C 287 TYR 0.028 0.006 TYR A 482 PHE 0.036 0.006 PHE C 118 TRP 0.053 0.005 TRP D 35 HIS 0.019 0.004 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00971 (20286) covalent geometry : angle 1.86291 (28338) hydrogen bonds : bond 0.16284 ( 1053) hydrogen bonds : angle 6.00215 ( 2783) metal coordination : bond 0.05536 ( 16) metal coordination : angle 9.43780 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 475 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8103 (tpt-90) cc_final: 0.7856 (mmt180) REVERT: A 24 GLU cc_start: 0.7652 (tp30) cc_final: 0.7073 (tp30) REVERT: A 25 SER cc_start: 0.7362 (m) cc_final: 0.7022 (p) REVERT: A 33 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7675 (tpp80) REVERT: A 46 VAL cc_start: 0.7465 (t) cc_final: 0.7056 (p) REVERT: A 54 ASP cc_start: 0.5719 (t0) cc_final: 0.5363 (t0) REVERT: A 63 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.6764 (mtm-85) REVERT: A 68 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 72 PHE cc_start: 0.7278 (p90) cc_final: 0.6836 (p90) REVERT: A 73 ASP cc_start: 0.7420 (m-30) cc_final: 0.7164 (m-30) REVERT: A 102 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7040 (mmtp) REVERT: A 135 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 137 ILE cc_start: 0.6951 (mt) cc_final: 0.6736 (mm) REVERT: A 161 TRP cc_start: 0.6828 (t60) cc_final: 0.5861 (t60) REVERT: A 163 TYR cc_start: 0.4922 (m-80) cc_final: 0.4636 (m-80) REVERT: A 181 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7869 (ptp90) REVERT: A 182 GLU cc_start: 0.8804 (tt0) cc_final: 0.8492 (tt0) REVERT: A 199 HIS cc_start: 0.7480 (p-80) cc_final: 0.7035 (p-80) REVERT: A 204 ASP cc_start: 0.8450 (t0) cc_final: 0.8074 (t0) REVERT: A 216 TYR cc_start: 0.8035 (t80) cc_final: 0.7677 (t80) REVERT: A 220 LEU cc_start: 0.8186 (mt) cc_final: 0.7945 (mt) REVERT: A 270 LEU cc_start: 0.7856 (mt) cc_final: 0.7606 (mt) REVERT: A 276 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7829 (tp30) REVERT: A 342 MET cc_start: 0.5621 (ttp) cc_final: 0.5404 (ttp) REVERT: A 397 ARG cc_start: 0.0965 (OUTLIER) cc_final: 0.0058 (ttm170) REVERT: B 17 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7609 (p) REVERT: B 20 GLU cc_start: 0.7673 (mp0) cc_final: 0.7105 (mp0) REVERT: B 42 GLU cc_start: 0.7524 (tt0) cc_final: 0.7158 (tt0) REVERT: B 68 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7326 (tt0) REVERT: B 73 ASP cc_start: 0.7326 (m-30) cc_final: 0.7083 (m-30) REVERT: B 74 VAL cc_start: 0.7817 (t) cc_final: 0.7423 (p) REVERT: B 98 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 125 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6700 (tp) REVERT: B 128 THR cc_start: 0.7529 (m) cc_final: 0.7028 (p) REVERT: B 153 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7783 (mtmp) REVERT: B 155 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: B 175 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7437 (p) REVERT: B 250 LEU cc_start: 0.7709 (tp) cc_final: 0.7467 (tt) REVERT: B 255 VAL cc_start: 0.7312 (t) cc_final: 0.7067 (p) REVERT: B 269 ILE cc_start: 0.7641 (mm) cc_final: 0.7352 (mm) REVERT: B 281 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: B 351 GLU cc_start: 0.9427 (tt0) cc_final: 0.9185 (tp30) REVERT: B 376 GLU cc_start: 0.8762 (tt0) cc_final: 0.8460 (tt0) REVERT: B 379 GLU cc_start: 0.8520 (pt0) cc_final: 0.8291 (pt0) REVERT: B 454 TRP cc_start: 0.8935 (t60) cc_final: 0.8482 (t60) REVERT: B 466 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6808 (m) REVERT: B 480 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6322 (mp10) REVERT: C 1 MET cc_start: 0.5801 (tpp) cc_final: 0.5592 (tpp) REVERT: C 24 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 26 CYS cc_start: 0.7871 (m) cc_final: 0.7583 (m) REVERT: C 28 GLN cc_start: 0.7920 (tt0) cc_final: 0.7656 (tt0) REVERT: C 57 ARG cc_start: 0.7539 (mmt90) cc_final: 0.7248 (mpp-170) REVERT: C 79 ARG cc_start: 0.7292 (mtp85) cc_final: 0.7020 (mtp85) REVERT: C 96 TRP cc_start: 0.7403 (t60) cc_final: 0.7115 (t60) REVERT: C 109 GLU cc_start: 0.6387 (mt-10) cc_final: 0.5559 (mt-10) REVERT: C 140 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7339 (ttm170) REVERT: C 142 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6905 (ttp80) REVERT: C 149 ILE cc_start: 0.8029 (mm) cc_final: 0.7601 (mt) REVERT: C 183 ARG cc_start: 0.7589 (mmt-90) cc_final: 0.7384 (tpp80) REVERT: C 186 GLU cc_start: 0.8068 (tp30) cc_final: 0.7628 (tp30) REVERT: C 196 GLU cc_start: 0.5204 (tt0) cc_final: 0.4784 (tt0) REVERT: C 200 LEU cc_start: 0.7846 (mt) cc_final: 0.7473 (mt) REVERT: C 267 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6661 (tm-30) REVERT: C 272 ARG cc_start: 0.6736 (tpt90) cc_final: 0.6215 (tpt90) REVERT: C 274 GLN cc_start: 0.7712 (mt0) cc_final: 0.7491 (mt0) REVERT: C 275 LEU cc_start: 0.7606 (tp) cc_final: 0.7332 (tp) REVERT: C 300 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7727 (ttm-80) REVERT: C 314 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4673 (p90) REVERT: C 325 ARG cc_start: 0.6742 (ptt180) cc_final: 0.6303 (ttp80) REVERT: C 344 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 351 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 355 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7120 (p0) REVERT: D 9 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6834 (mt) REVERT: D 11 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6360 (mmm-85) REVERT: D 20 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: D 22 GLN cc_start: 0.7480 (mt0) cc_final: 0.6866 (mt0) REVERT: D 32 GLN cc_start: 0.8244 (tp40) cc_final: 0.8001 (tp40) REVERT: D 56 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7820 (ttmt) REVERT: D 68 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6604 (mt-10) REVERT: D 73 ASP cc_start: 0.7134 (m-30) cc_final: 0.6651 (m-30) REVERT: D 81 ASP cc_start: 0.7355 (p0) cc_final: 0.7097 (p0) REVERT: D 88 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7094 (ttm-80) REVERT: D 98 GLU cc_start: 0.7593 (pt0) cc_final: 0.7172 (pt0) REVERT: D 101 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7602 (mmtt) REVERT: D 135 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 155 ARG cc_start: 0.4818 (ptt180) cc_final: 0.3882 (tmm-80) REVERT: D 199 HIS cc_start: 0.7652 (t-90) cc_final: 0.7067 (t-90) REVERT: D 204 ASP cc_start: 0.7925 (t70) cc_final: 0.7650 (t0) REVERT: D 214 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7561 (ttmm) REVERT: D 228 ARG cc_start: 0.6952 (mtt-85) cc_final: 0.6609 (mtm180) REVERT: D 235 LEU cc_start: 0.8257 (mt) cc_final: 0.7924 (mt) REVERT: D 238 SER cc_start: 0.6439 (m) cc_final: 0.6103 (t) REVERT: D 241 SER cc_start: 0.6905 (t) cc_final: 0.5593 (p) REVERT: D 242 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7918 (mt-10) REVERT: D 244 MET cc_start: 0.7745 (mmt) cc_final: 0.7382 (mmp) REVERT: D 276 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6231 (mm-30) REVERT: D 279 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7469 (ptp90) REVERT: D 339 THR cc_start: 0.6942 (p) cc_final: 0.5278 (m) REVERT: D 348 PHE cc_start: 0.8216 (t80) cc_final: 0.7856 (t80) REVERT: D 457 SER cc_start: 0.8606 (p) cc_final: 0.8312 (p) outliers start: 67 outliers final: 21 residues processed: 521 average time/residue: 0.1850 time to fit residues: 133.8233 Evaluate side-chains 457 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 421 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 155 ARG 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 441 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 32 GLN A 95 HIS A 446 GLN B 22 GLN B 131 GLN B 352 GLN B 446 GLN C 95 HIS C 251 ASN C 480 GLN D 141 ASN D 189 HIS D 199 HIS D 226 GLN D 251 ASN D 352 GLN D 452 ASN D 459 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.191740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138208 restraints weight = 36801.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142278 restraints weight = 16610.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142898 restraints weight = 10278.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144216 restraints weight = 8568.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144185 restraints weight = 7311.591| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20302 Z= 0.202 Angle : 0.623 12.079 28362 Z= 0.348 Chirality : 0.040 0.186 3108 Planarity : 0.005 0.049 3020 Dihedral : 22.980 87.996 4358 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % Rotamer: Outliers : 3.87 % Allowed : 12.28 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.19), residues: 1936 helix: 2.47 (0.16), residues: 912 sheet: -0.06 (0.29), residues: 263 loop : 0.85 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 409 TYR 0.020 0.002 TYR B 154 PHE 0.016 0.002 PHE C 53 TRP 0.032 0.002 TRP D 230 HIS 0.016 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00433 (20286) covalent geometry : angle 0.61242 (28338) hydrogen bonds : bond 0.04795 ( 1053) hydrogen bonds : angle 3.94537 ( 2783) metal coordination : bond 0.00397 ( 16) metal coordination : angle 3.89940 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 436 time to evaluate : 0.595 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 9 LEU cc_start: 0.7484 (mt) cc_final: 0.7216 (pp) REVERT: A 24 GLU cc_start: 0.7110 (tp30) cc_final: 0.6628 (tp30) REVERT: A 51 ASP cc_start: 0.7961 (t0) cc_final: 0.7752 (t0) REVERT: A 88 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6604 (tpp-160) REVERT: A 140 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7314 (ttp80) REVERT: A 182 GLU cc_start: 0.8168 (tt0) cc_final: 0.7812 (tt0) REVERT: A 186 GLU cc_start: 0.8289 (tt0) cc_final: 0.7773 (tp30) REVERT: A 189 HIS cc_start: 0.8426 (m-70) cc_final: 0.8213 (m-70) REVERT: A 190 ARG cc_start: 0.8882 (mtm180) cc_final: 0.8565 (mtp180) REVERT: A 205 LEU cc_start: 0.9031 (mt) cc_final: 0.8830 (mp) REVERT: A 220 LEU cc_start: 0.8428 (mt) cc_final: 0.8195 (mt) REVERT: A 235 LEU cc_start: 0.8521 (mt) cc_final: 0.7897 (mt) REVERT: A 239 MET cc_start: 0.7685 (mmm) cc_final: 0.6931 (mmm) REVERT: A 250 LEU cc_start: 0.7258 (tp) cc_final: 0.6903 (mt) REVERT: A 267 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 342 MET cc_start: 0.6261 (ttp) cc_final: 0.5927 (ttp) REVERT: A 397 ARG cc_start: 0.0354 (OUTLIER) cc_final: -0.0872 (ttm170) REVERT: B 17 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7435 (p) REVERT: B 135 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 140 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6929 (mtp-110) REVERT: B 143 SER cc_start: 0.8204 (t) cc_final: 0.7955 (p) REVERT: B 219 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 250 LEU cc_start: 0.8117 (tp) cc_final: 0.7900 (tt) REVERT: B 251 ASN cc_start: 0.8584 (m-40) cc_final: 0.8347 (m-40) REVERT: B 299 LEU cc_start: 0.8216 (tp) cc_final: 0.7869 (tp) REVERT: B 350 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 351 GLU cc_start: 0.9104 (tt0) cc_final: 0.8477 (tp30) REVERT: B 376 GLU cc_start: 0.8476 (tt0) cc_final: 0.7993 (tt0) REVERT: B 379 GLU cc_start: 0.8239 (pt0) cc_final: 0.7968 (pt0) REVERT: B 466 VAL cc_start: 0.6914 (OUTLIER) cc_final: 0.6634 (m) REVERT: B 480 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.6252 (mp10) REVERT: C 1 MET cc_start: 0.6958 (tpp) cc_final: 0.6651 (tpt) REVERT: C 22 GLN cc_start: 0.7808 (mt0) cc_final: 0.7088 (mt0) REVERT: C 26 CYS cc_start: 0.8011 (m) cc_final: 0.7701 (m) REVERT: C 87 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8028 (pt) REVERT: C 101 LYS cc_start: 0.7030 (ttmm) cc_final: 0.6825 (ttmm) REVERT: C 109 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6784 (mt-10) REVERT: C 118 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7343 (t80) REVERT: C 141 ASN cc_start: 0.8145 (m-40) cc_final: 0.7938 (m-40) REVERT: C 186 GLU cc_start: 0.7652 (tp30) cc_final: 0.7324 (tp30) REVERT: C 194 ASN cc_start: 0.8751 (m-40) cc_final: 0.8475 (m-40) REVERT: C 196 GLU cc_start: 0.6597 (tt0) cc_final: 0.6270 (tt0) REVERT: C 241 SER cc_start: 0.8251 (m) cc_final: 0.8002 (t) REVERT: C 251 ASN cc_start: 0.8526 (m-40) cc_final: 0.8299 (m-40) REVERT: C 274 GLN cc_start: 0.8176 (mt0) cc_final: 0.7858 (mt0) REVERT: C 300 ARG cc_start: 0.8242 (mmt180) cc_final: 0.7833 (tpp80) REVERT: C 314 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6455 (p90) REVERT: C 325 ARG cc_start: 0.7256 (ptt180) cc_final: 0.6544 (ttp-170) REVERT: C 342 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.5624 (tpp) REVERT: C 344 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 351 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7358 (tm-30) REVERT: C 379 GLU cc_start: 0.7481 (tp30) cc_final: 0.6478 (tp30) REVERT: D 9 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (mt) REVERT: D 11 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7726 (mmm-85) REVERT: D 32 GLN cc_start: 0.7940 (tp40) cc_final: 0.7586 (tp40) REVERT: D 56 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8374 (ttmt) REVERT: D 65 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 73 ASP cc_start: 0.7179 (m-30) cc_final: 0.6849 (m-30) REVERT: D 85 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7492 (mmm160) REVERT: D 86 SER cc_start: 0.8378 (t) cc_final: 0.8001 (m) REVERT: D 99 ASP cc_start: 0.7354 (m-30) cc_final: 0.6944 (t0) REVERT: D 101 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8042 (mmtt) REVERT: D 102 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7296 (mmtm) REVERT: D 109 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6632 (mt-10) REVERT: D 131 GLN cc_start: 0.7853 (tt0) cc_final: 0.7647 (tt0) REVERT: D 150 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7781 (ttm170) REVERT: D 155 ARG cc_start: 0.6653 (ptt180) cc_final: 0.6304 (tmm-80) REVERT: D 164 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7752 (mt) REVERT: D 214 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7729 (ttmm) REVERT: D 228 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7664 (mtm-85) REVERT: D 229 GLU cc_start: 0.7642 (pt0) cc_final: 0.7318 (pt0) REVERT: D 235 LEU cc_start: 0.8585 (mt) cc_final: 0.8328 (mt) REVERT: D 244 MET cc_start: 0.7356 (mmt) cc_final: 0.7153 (mmp) REVERT: D 270 LEU cc_start: 0.8049 (mp) cc_final: 0.7667 (tp) REVERT: D 271 THR cc_start: 0.7956 (p) cc_final: 0.7617 (p) REVERT: D 276 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6057 (mm-30) REVERT: D 279 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7367 (ptp90) REVERT: D 329 MET cc_start: 0.7449 (tpp) cc_final: 0.7205 (tpp) REVERT: D 346 ASP cc_start: 0.7176 (m-30) cc_final: 0.6868 (m-30) REVERT: D 348 PHE cc_start: 0.8104 (t80) cc_final: 0.7526 (t80) REVERT: D 350 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8492 (tp30) REVERT: D 351 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: D 454 TRP cc_start: 0.8061 (t60) cc_final: 0.7518 (t60) REVERT: D 458 MET cc_start: 0.7523 (mmt) cc_final: 0.6799 (mmt) outliers start: 62 outliers final: 28 residues processed: 472 average time/residue: 0.1826 time to fit residues: 119.1900 Evaluate side-chains 454 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 413 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 129 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 181 optimal weight: 30.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS B 194 ASN C 27 GLN C 131 GLN D 189 HIS D 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.189516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135930 restraints weight = 36611.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139768 restraints weight = 16610.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140728 restraints weight = 10104.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141909 restraints weight = 8589.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141844 restraints weight = 7205.624| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20302 Z= 0.203 Angle : 0.591 11.805 28362 Z= 0.329 Chirality : 0.039 0.189 3108 Planarity : 0.005 0.055 3020 Dihedral : 23.080 82.901 4314 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 3.93 % Allowed : 15.09 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.19), residues: 1936 helix: 2.54 (0.17), residues: 914 sheet: -0.02 (0.30), residues: 257 loop : 0.93 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 416 TYR 0.021 0.002 TYR C 154 PHE 0.016 0.002 PHE B 348 TRP 0.024 0.001 TRP A 454 HIS 0.028 0.002 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00438 (20286) covalent geometry : angle 0.58215 (28338) hydrogen bonds : bond 0.04324 ( 1053) hydrogen bonds : angle 3.73418 ( 2783) metal coordination : bond 0.00386 ( 16) metal coordination : angle 3.60699 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 438 time to evaluate : 0.511 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 33 ARG cc_start: 0.7710 (mmt180) cc_final: 0.7356 (tpp80) REVERT: A 51 ASP cc_start: 0.7962 (t0) cc_final: 0.7744 (t0) REVERT: A 54 ASP cc_start: 0.7572 (t0) cc_final: 0.5461 (t0) REVERT: A 138 LYS cc_start: 0.8330 (mttm) cc_final: 0.8073 (mttm) REVERT: A 140 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7153 (ttp-170) REVERT: A 150 ARG cc_start: 0.7300 (ttm170) cc_final: 0.7100 (mmm-85) REVERT: A 182 GLU cc_start: 0.8124 (tt0) cc_final: 0.7737 (tt0) REVERT: A 186 GLU cc_start: 0.8266 (tt0) cc_final: 0.7854 (tt0) REVERT: A 189 HIS cc_start: 0.8410 (m-70) cc_final: 0.8194 (m-70) REVERT: A 233 THR cc_start: 0.8668 (m) cc_final: 0.8443 (p) REVERT: A 235 LEU cc_start: 0.8625 (mt) cc_final: 0.7957 (mt) REVERT: A 239 MET cc_start: 0.7755 (mmm) cc_final: 0.7001 (mmm) REVERT: A 270 LEU cc_start: 0.7900 (mt) cc_final: 0.7667 (mt) REVERT: A 342 MET cc_start: 0.6294 (ttp) cc_final: 0.5916 (ttp) REVERT: A 383 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 423 LEU cc_start: 0.6479 (mm) cc_final: 0.6003 (mm) REVERT: B 17 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7529 (p) REVERT: B 32 GLN cc_start: 0.7620 (mt0) cc_final: 0.7376 (mt0) REVERT: B 88 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6916 (mmt180) REVERT: B 98 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 135 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 140 ARG cc_start: 0.7321 (mtp180) cc_final: 0.6938 (mtp-110) REVERT: B 142 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6640 (ttp-110) REVERT: B 143 SER cc_start: 0.8175 (t) cc_final: 0.7925 (p) REVERT: B 153 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7487 (mtmp) REVERT: B 185 LEU cc_start: 0.8263 (mt) cc_final: 0.8020 (mm) REVERT: B 190 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7643 (ttm110) REVERT: B 215 ASP cc_start: 0.7427 (m-30) cc_final: 0.7032 (t70) REVERT: B 251 ASN cc_start: 0.8537 (m-40) cc_final: 0.8267 (m-40) REVERT: B 276 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 281 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 351 GLU cc_start: 0.9039 (tt0) cc_final: 0.8791 (tt0) REVERT: B 352 GLN cc_start: 0.8576 (mm110) cc_final: 0.8175 (mm110) REVERT: B 376 GLU cc_start: 0.8390 (tt0) cc_final: 0.8189 (tt0) REVERT: B 466 VAL cc_start: 0.6725 (OUTLIER) cc_final: 0.6487 (m) REVERT: C 20 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 22 GLN cc_start: 0.7900 (mt0) cc_final: 0.7282 (mt0) REVERT: C 26 CYS cc_start: 0.8066 (m) cc_final: 0.7778 (m) REVERT: C 28 GLN cc_start: 0.7832 (tt0) cc_final: 0.7399 (mt0) REVERT: C 118 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7165 (t80) REVERT: C 181 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7978 (mtp85) REVERT: C 186 GLU cc_start: 0.7618 (tp30) cc_final: 0.7209 (tp30) REVERT: C 196 GLU cc_start: 0.6893 (tt0) cc_final: 0.6653 (tt0) REVERT: C 231 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8075 (t) REVERT: C 241 SER cc_start: 0.8455 (m) cc_final: 0.7935 (p) REVERT: C 267 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: C 274 GLN cc_start: 0.8204 (mt0) cc_final: 0.7931 (mt0) REVERT: C 300 ARG cc_start: 0.8347 (mmt180) cc_final: 0.7971 (tpp80) REVERT: C 325 ARG cc_start: 0.7294 (ptt180) cc_final: 0.6801 (ptm160) REVERT: C 344 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 351 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 355 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.6914 (p0) REVERT: C 367 TRP cc_start: 0.7632 (t-100) cc_final: 0.6921 (t-100) REVERT: C 486 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.5055 (pp) REVERT: D 9 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 25 SER cc_start: 0.7871 (p) cc_final: 0.7554 (t) REVERT: D 32 GLN cc_start: 0.7853 (tp40) cc_final: 0.7542 (tp40) REVERT: D 63 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7552 (ttp80) REVERT: D 65 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7878 (mp) REVERT: D 68 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7168 (mt-10) REVERT: D 73 ASP cc_start: 0.7161 (m-30) cc_final: 0.6885 (m-30) REVERT: D 85 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7539 (mmm160) REVERT: D 95 HIS cc_start: 0.7383 (m170) cc_final: 0.7169 (m-70) REVERT: D 98 GLU cc_start: 0.7056 (pt0) cc_final: 0.6695 (pt0) REVERT: D 99 ASP cc_start: 0.7289 (m-30) cc_final: 0.6795 (m-30) REVERT: D 102 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7422 (mmtm) REVERT: D 109 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6571 (mt-10) REVERT: D 150 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7880 (ttm170) REVERT: D 164 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7838 (mt) REVERT: D 182 GLU cc_start: 0.8239 (tt0) cc_final: 0.7960 (tt0) REVERT: D 199 HIS cc_start: 0.7257 (t70) cc_final: 0.6679 (t70) REVERT: D 214 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7927 (ttmm) REVERT: D 220 LEU cc_start: 0.8186 (mm) cc_final: 0.7874 (mm) REVERT: D 226 GLN cc_start: 0.7688 (mt0) cc_final: 0.7430 (mt0) REVERT: D 229 GLU cc_start: 0.7686 (pt0) cc_final: 0.7329 (pt0) REVERT: D 235 LEU cc_start: 0.8528 (mt) cc_final: 0.8275 (mt) REVERT: D 244 MET cc_start: 0.7507 (mmt) cc_final: 0.6987 (mmt) REVERT: D 276 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6461 (mm-30) REVERT: D 331 PHE cc_start: 0.7333 (m-10) cc_final: 0.7031 (m-10) REVERT: D 348 PHE cc_start: 0.7939 (t80) cc_final: 0.7494 (t80) REVERT: D 351 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: D 409 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8547 (tpp-160) REVERT: D 454 TRP cc_start: 0.7991 (t60) cc_final: 0.7257 (t60) REVERT: D 458 MET cc_start: 0.7523 (mmt) cc_final: 0.6686 (mmt) outliers start: 63 outliers final: 27 residues processed: 467 average time/residue: 0.1819 time to fit residues: 117.7789 Evaluate side-chains 455 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 415 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN 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 276 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 474 ILE 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 116 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 194 ASN C 27 GLN D 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.191253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138457 restraints weight = 36465.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142657 restraints weight = 16642.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143167 restraints weight = 9610.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144327 restraints weight = 8400.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144366 restraints weight = 7199.922| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20302 Z= 0.146 Angle : 0.550 11.083 28362 Z= 0.303 Chirality : 0.037 0.222 3108 Planarity : 0.004 0.053 3020 Dihedral : 22.969 79.753 4298 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Rotamer: Outliers : 3.18 % Allowed : 16.71 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.20), residues: 1936 helix: 2.64 (0.17), residues: 915 sheet: 0.04 (0.30), residues: 270 loop : 0.93 (0.25), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 272 TYR 0.017 0.002 TYR C 216 PHE 0.011 0.001 PHE D 67 TRP 0.019 0.001 TRP A 454 HIS 0.024 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00311 (20286) covalent geometry : angle 0.54310 (28338) hydrogen bonds : bond 0.03749 ( 1053) hydrogen bonds : angle 3.53350 ( 2783) metal coordination : bond 0.00261 ( 16) metal coordination : angle 3.06781 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 418 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7662 (mmt180) cc_final: 0.7348 (tpp80) REVERT: A 88 ARG cc_start: 0.6921 (tpp-160) cc_final: 0.6638 (tpp-160) REVERT: A 131 GLN cc_start: 0.7623 (tp40) cc_final: 0.7358 (tt0) REVERT: A 135 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6619 (tm-30) REVERT: A 140 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7360 (ttp80) REVERT: A 182 GLU cc_start: 0.8091 (tt0) cc_final: 0.7717 (tt0) REVERT: A 186 GLU cc_start: 0.8169 (tt0) cc_final: 0.7875 (tt0) REVERT: A 189 HIS cc_start: 0.8425 (m-70) cc_final: 0.8198 (m-70) REVERT: A 233 THR cc_start: 0.8663 (m) cc_final: 0.8416 (p) REVERT: A 235 LEU cc_start: 0.8618 (mt) cc_final: 0.7958 (mt) REVERT: A 239 MET cc_start: 0.7773 (mmm) cc_final: 0.7121 (mmm) REVERT: A 250 LEU cc_start: 0.7293 (tp) cc_final: 0.7055 (mt) REVERT: A 270 LEU cc_start: 0.7915 (mt) cc_final: 0.7701 (mt) REVERT: A 342 MET cc_start: 0.6314 (ttp) cc_final: 0.5928 (ttp) REVERT: A 383 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7984 (mt-10) REVERT: A 423 LEU cc_start: 0.6470 (mm) cc_final: 0.6037 (mm) REVERT: B 17 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7486 (p) REVERT: B 32 GLN cc_start: 0.7595 (mt0) cc_final: 0.7382 (mt0) REVERT: B 88 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6501 (mtt180) REVERT: B 98 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 140 ARG cc_start: 0.7340 (mtp180) cc_final: 0.6934 (mtp-110) REVERT: B 142 ARG cc_start: 0.6983 (ttp-110) cc_final: 0.6656 (ttp-110) REVERT: B 143 SER cc_start: 0.8137 (t) cc_final: 0.7934 (p) REVERT: B 185 LEU cc_start: 0.8211 (mt) cc_final: 0.7999 (mm) REVERT: B 208 ARG cc_start: 0.7355 (mtp180) cc_final: 0.7101 (ttp-110) REVERT: B 215 ASP cc_start: 0.7449 (m-30) cc_final: 0.7205 (t0) REVERT: B 251 ASN cc_start: 0.8537 (m-40) cc_final: 0.8281 (m-40) REVERT: B 276 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: B 351 GLU cc_start: 0.8940 (tt0) cc_final: 0.8732 (tt0) REVERT: B 352 GLN cc_start: 0.8677 (mm110) cc_final: 0.8171 (mm110) REVERT: B 466 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.6620 (m) REVERT: C 2 ARG cc_start: 0.6664 (mtp180) cc_final: 0.6330 (ptm160) REVERT: C 14 ASP cc_start: 0.8253 (t0) cc_final: 0.7936 (t0) REVERT: C 20 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 22 GLN cc_start: 0.7834 (mt0) cc_final: 0.7180 (mt0) REVERT: C 26 CYS cc_start: 0.8155 (m) cc_final: 0.7758 (m) REVERT: C 28 GLN cc_start: 0.7759 (tt0) cc_final: 0.7379 (mt0) REVERT: C 69 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7624 (tp30) REVERT: C 109 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6984 (mt-10) REVERT: C 118 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7071 (t80) REVERT: C 139 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7347 (tp30) REVERT: C 175 VAL cc_start: 0.7585 (p) cc_final: 0.7178 (m) REVERT: C 182 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6521 (tm-30) REVERT: C 196 GLU cc_start: 0.6884 (tt0) cc_final: 0.6616 (tt0) REVERT: C 231 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.8027 (t) REVERT: C 241 SER cc_start: 0.8400 (m) cc_final: 0.7907 (p) REVERT: C 263 LEU cc_start: 0.8581 (tp) cc_final: 0.8308 (tt) REVERT: C 267 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 300 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7823 (tpp80) REVERT: C 325 ARG cc_start: 0.7240 (ptt180) cc_final: 0.5249 (ptm160) REVERT: C 342 MET cc_start: 0.6291 (tpt) cc_final: 0.6023 (tpt) REVERT: C 351 GLU cc_start: 0.7682 (tm-30) cc_final: 0.6948 (tm-30) REVERT: C 355 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.6788 (p0) REVERT: C 367 TRP cc_start: 0.7668 (t-100) cc_final: 0.7128 (t-100) REVERT: C 383 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6570 (mp0) REVERT: D 9 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7674 (mt) REVERT: D 25 SER cc_start: 0.7915 (p) cc_final: 0.7635 (t) REVERT: D 32 GLN cc_start: 0.7809 (tp40) cc_final: 0.7495 (tp40) REVERT: D 65 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 73 ASP cc_start: 0.7091 (m-30) cc_final: 0.6868 (m-30) REVERT: D 85 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7623 (mmm160) REVERT: D 86 SER cc_start: 0.8413 (t) cc_final: 0.8007 (m) REVERT: D 95 HIS cc_start: 0.7474 (m170) cc_final: 0.6916 (m90) REVERT: D 98 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6447 (pt0) REVERT: D 101 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7846 (mmtt) REVERT: D 102 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7328 (mmtm) REVERT: D 109 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6547 (mt-10) REVERT: D 139 GLU cc_start: 0.7231 (tp30) cc_final: 0.7027 (tp30) REVERT: D 164 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (mt) REVERT: D 182 GLU cc_start: 0.8211 (tt0) cc_final: 0.7928 (tt0) REVERT: D 199 HIS cc_start: 0.7407 (t70) cc_final: 0.6680 (t70) REVERT: D 214 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7877 (mtpp) REVERT: D 216 TYR cc_start: 0.7576 (t80) cc_final: 0.7309 (t80) REVERT: D 220 LEU cc_start: 0.8197 (mm) cc_final: 0.7750 (mm) REVERT: D 229 GLU cc_start: 0.7648 (pt0) cc_final: 0.7296 (pt0) REVERT: D 235 LEU cc_start: 0.8520 (mt) cc_final: 0.8268 (mt) REVERT: D 244 MET cc_start: 0.7596 (mmt) cc_final: 0.7070 (mmt) REVERT: D 276 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6647 (mm-30) REVERT: D 329 MET cc_start: 0.7142 (tpp) cc_final: 0.6871 (ttp) REVERT: D 331 PHE cc_start: 0.7210 (m-10) cc_final: 0.6910 (m-10) REVERT: D 348 PHE cc_start: 0.7781 (t80) cc_final: 0.7248 (t80) REVERT: D 351 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: D 409 ARG cc_start: 0.8874 (mmm160) cc_final: 0.8637 (tpp-160) REVERT: D 454 TRP cc_start: 0.7967 (t60) cc_final: 0.7239 (t60) REVERT: D 458 MET cc_start: 0.7430 (mmt) cc_final: 0.6641 (mmt) REVERT: D 476 PHE cc_start: 0.6145 (m-80) cc_final: 0.5802 (m-80) outliers start: 51 outliers final: 26 residues processed: 443 average time/residue: 0.1761 time to fit residues: 108.8771 Evaluate side-chains 436 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 398 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 0.0020 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN B 131 GLN B 194 ASN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 194 ASN D 221 GLN D 446 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137455 restraints weight = 36284.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141437 restraints weight = 16393.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142011 restraints weight = 10137.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143391 restraints weight = 8413.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143344 restraints weight = 7050.774| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20302 Z= 0.166 Angle : 0.550 13.396 28362 Z= 0.302 Chirality : 0.037 0.200 3108 Planarity : 0.004 0.052 3020 Dihedral : 22.949 79.032 4297 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 3.12 % Allowed : 17.83 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.20), residues: 1936 helix: 2.63 (0.17), residues: 916 sheet: 0.03 (0.30), residues: 276 loop : 0.85 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.019 0.002 TYR C 216 PHE 0.012 0.001 PHE D 53 TRP 0.022 0.001 TRP A 454 HIS 0.020 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00355 (20286) covalent geometry : angle 0.54369 (28338) hydrogen bonds : bond 0.03876 ( 1053) hydrogen bonds : angle 3.50495 ( 2783) metal coordination : bond 0.00299 ( 16) metal coordination : angle 2.81460 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 415 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7662 (mmt180) cc_final: 0.7237 (tpp80) REVERT: A 70 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 131 GLN cc_start: 0.7683 (tp40) cc_final: 0.7395 (tt0) REVERT: A 135 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6709 (tm-30) REVERT: A 182 GLU cc_start: 0.8070 (tt0) cc_final: 0.7482 (tm-30) REVERT: A 186 GLU cc_start: 0.8268 (tt0) cc_final: 0.7941 (tt0) REVERT: A 205 LEU cc_start: 0.8956 (mp) cc_final: 0.8739 (mp) REVERT: A 233 THR cc_start: 0.8683 (m) cc_final: 0.8471 (p) REVERT: A 235 LEU cc_start: 0.8678 (mt) cc_final: 0.8044 (mt) REVERT: A 239 MET cc_start: 0.7805 (mmm) cc_final: 0.7290 (mmm) REVERT: A 250 LEU cc_start: 0.7307 (tp) cc_final: 0.7019 (mt) REVERT: A 270 LEU cc_start: 0.7931 (mt) cc_final: 0.7714 (mt) REVERT: A 342 MET cc_start: 0.6346 (ttp) cc_final: 0.5908 (ttp) REVERT: A 423 LEU cc_start: 0.6563 (mm) cc_final: 0.6130 (mm) REVERT: B 17 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7535 (p) REVERT: B 88 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7088 (mtp85) REVERT: B 98 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7018 (mt-10) REVERT: B 140 ARG cc_start: 0.7272 (mtp180) cc_final: 0.6827 (mtp-110) REVERT: B 142 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6567 (ttp-110) REVERT: B 185 LEU cc_start: 0.8249 (mt) cc_final: 0.8035 (mm) REVERT: B 215 ASP cc_start: 0.7429 (m-30) cc_final: 0.7205 (t0) REVERT: B 251 ASN cc_start: 0.8575 (m-40) cc_final: 0.8322 (m-40) REVERT: B 273 GLU cc_start: 0.7508 (tt0) cc_final: 0.7026 (tt0) REVERT: B 276 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 352 GLN cc_start: 0.8780 (mm110) cc_final: 0.8400 (mm-40) REVERT: B 466 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6658 (m) REVERT: C 14 ASP cc_start: 0.8371 (t0) cc_final: 0.8078 (t0) REVERT: C 20 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 22 GLN cc_start: 0.7887 (mt0) cc_final: 0.7263 (mt0) REVERT: C 26 CYS cc_start: 0.8150 (m) cc_final: 0.7774 (m) REVERT: C 28 GLN cc_start: 0.7823 (tt0) cc_final: 0.7431 (mt0) REVERT: C 69 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7513 (tp30) REVERT: C 118 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7005 (t80) REVERT: C 139 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7325 (tp30) REVERT: C 182 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6511 (tm-30) REVERT: C 196 GLU cc_start: 0.6879 (tt0) cc_final: 0.6633 (tt0) REVERT: C 231 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8038 (t) REVERT: C 241 SER cc_start: 0.8448 (m) cc_final: 0.7964 (p) REVERT: C 263 LEU cc_start: 0.8556 (tp) cc_final: 0.8335 (tt) REVERT: C 267 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: C 300 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7969 (tpp80) REVERT: C 351 GLU cc_start: 0.7684 (tm-30) cc_final: 0.6917 (tm-30) REVERT: C 355 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.6715 (p0) REVERT: C 367 TRP cc_start: 0.7631 (t-100) cc_final: 0.7108 (t-100) REVERT: D 9 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7650 (mt) REVERT: D 25 SER cc_start: 0.7840 (p) cc_final: 0.7467 (t) REVERT: D 32 GLN cc_start: 0.7800 (tp40) cc_final: 0.7469 (tp40) REVERT: D 57 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7263 (ttm110) REVERT: D 63 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7594 (ttp80) REVERT: D 65 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7991 (mp) REVERT: D 68 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7029 (mt-10) REVERT: D 73 ASP cc_start: 0.7133 (m-30) cc_final: 0.6889 (m-30) REVERT: D 74 VAL cc_start: 0.8289 (p) cc_final: 0.7987 (m) REVERT: D 86 SER cc_start: 0.8399 (t) cc_final: 0.8011 (m) REVERT: D 101 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7851 (mmtt) REVERT: D 102 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7359 (mmtm) REVERT: D 109 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6553 (mt-10) REVERT: D 164 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8023 (mt) REVERT: D 182 GLU cc_start: 0.8240 (tt0) cc_final: 0.7919 (tt0) REVERT: D 199 HIS cc_start: 0.7404 (t70) cc_final: 0.6655 (t70) REVERT: D 214 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7884 (mtpp) REVERT: D 216 TYR cc_start: 0.7582 (t80) cc_final: 0.7345 (t80) REVERT: D 220 LEU cc_start: 0.8222 (mm) cc_final: 0.7756 (mm) REVERT: D 229 GLU cc_start: 0.7670 (pt0) cc_final: 0.7325 (pt0) REVERT: D 244 MET cc_start: 0.7538 (mmt) cc_final: 0.7152 (mmt) REVERT: D 272 ARG cc_start: 0.7921 (mmp80) cc_final: 0.7627 (mmp80) REVERT: D 276 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6685 (mm-30) REVERT: D 329 MET cc_start: 0.7172 (tpp) cc_final: 0.6890 (ttp) REVERT: D 331 PHE cc_start: 0.7203 (m-10) cc_final: 0.6913 (m-10) REVERT: D 348 PHE cc_start: 0.7743 (t80) cc_final: 0.7209 (t80) REVERT: D 351 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: D 409 ARG cc_start: 0.8885 (mmm160) cc_final: 0.8683 (tpp-160) REVERT: D 454 TRP cc_start: 0.7965 (t60) cc_final: 0.7254 (t60) REVERT: D 458 MET cc_start: 0.7481 (mmt) cc_final: 0.6745 (mmt) outliers start: 50 outliers final: 27 residues processed: 436 average time/residue: 0.1738 time to fit residues: 106.0000 Evaluate side-chains 432 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 394 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS B 32 GLN B 131 GLN B 194 ASN B 274 GLN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.189702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136225 restraints weight = 36209.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140526 restraints weight = 16679.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141710 restraints weight = 9380.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142442 restraints weight = 7704.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142588 restraints weight = 7050.556| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20302 Z= 0.180 Angle : 0.567 14.301 28362 Z= 0.311 Chirality : 0.038 0.170 3108 Planarity : 0.004 0.053 3020 Dihedral : 22.905 79.070 4293 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.43 % Allowed : 18.83 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1936 helix: 2.53 (0.17), residues: 916 sheet: 0.04 (0.30), residues: 276 loop : 0.76 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 208 TYR 0.018 0.002 TYR C 216 PHE 0.030 0.001 PHE B 348 TRP 0.024 0.001 TRP A 454 HIS 0.022 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00387 (20286) covalent geometry : angle 0.56183 (28338) hydrogen bonds : bond 0.03965 ( 1053) hydrogen bonds : angle 3.59399 ( 2783) metal coordination : bond 0.00285 ( 16) metal coordination : angle 2.72838 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 403 time to evaluate : 0.579 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 33 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7304 (tpp80) REVERT: A 70 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 85 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.6684 (mmm-85) REVERT: A 131 GLN cc_start: 0.7711 (tp40) cc_final: 0.7415 (tt0) REVERT: A 135 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6697 (tm-30) REVERT: A 140 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7356 (ttm-80) REVERT: A 182 GLU cc_start: 0.8100 (tt0) cc_final: 0.7497 (tm-30) REVERT: A 186 GLU cc_start: 0.8329 (tt0) cc_final: 0.7978 (tt0) REVERT: A 235 LEU cc_start: 0.8729 (mt) cc_final: 0.8075 (mt) REVERT: A 239 MET cc_start: 0.7789 (mmm) cc_final: 0.7243 (mmm) REVERT: A 250 LEU cc_start: 0.7342 (tp) cc_final: 0.7089 (mt) REVERT: A 265 ARG cc_start: 0.7082 (ptt180) cc_final: 0.6826 (ptt180) REVERT: A 270 LEU cc_start: 0.8024 (mt) cc_final: 0.7780 (mt) REVERT: A 342 MET cc_start: 0.6338 (ttp) cc_final: 0.5912 (ttp) REVERT: A 423 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6149 (mm) REVERT: B 17 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7533 (p) REVERT: B 69 GLU cc_start: 0.7672 (tp30) cc_final: 0.7070 (tp30) REVERT: B 88 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7010 (mtp85) REVERT: B 92 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7517 (tp40) REVERT: B 98 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7062 (mt-10) REVERT: B 140 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6908 (mtp85) REVERT: B 142 ARG cc_start: 0.6990 (ttp-110) cc_final: 0.6533 (ttp-110) REVERT: B 185 LEU cc_start: 0.8298 (mt) cc_final: 0.8076 (mm) REVERT: B 215 ASP cc_start: 0.7442 (m-30) cc_final: 0.7186 (t0) REVERT: B 221 GLN cc_start: 0.7901 (mm110) cc_final: 0.7583 (tp40) REVERT: B 251 ASN cc_start: 0.8605 (m-40) cc_final: 0.8321 (m-40) REVERT: B 276 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 352 GLN cc_start: 0.8759 (mm110) cc_final: 0.8322 (mm110) REVERT: B 466 VAL cc_start: 0.6856 (OUTLIER) cc_final: 0.6631 (m) REVERT: C 14 ASP cc_start: 0.8427 (t0) cc_final: 0.8105 (t0) REVERT: C 20 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 22 GLN cc_start: 0.7907 (mt0) cc_final: 0.7277 (mt0) REVERT: C 26 CYS cc_start: 0.8160 (m) cc_final: 0.7820 (m) REVERT: C 28 GLN cc_start: 0.7813 (tt0) cc_final: 0.7477 (mt0) REVERT: C 69 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 109 GLU cc_start: 0.7220 (mt-10) cc_final: 0.7001 (mt-10) REVERT: C 118 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7046 (t80) REVERT: C 139 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7447 (tp30) REVERT: C 164 LEU cc_start: 0.8359 (mt) cc_final: 0.8049 (mp) REVERT: C 175 VAL cc_start: 0.7574 (p) cc_final: 0.7179 (m) REVERT: C 181 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7564 (mtp85) REVERT: C 196 GLU cc_start: 0.6896 (tt0) cc_final: 0.6629 (tt0) REVERT: C 231 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8019 (t) REVERT: C 241 SER cc_start: 0.8471 (m) cc_final: 0.7986 (p) REVERT: C 263 LEU cc_start: 0.8547 (tp) cc_final: 0.8347 (tt) REVERT: C 267 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: C 300 ARG cc_start: 0.8362 (mmt180) cc_final: 0.8017 (tpp80) REVERT: C 351 GLU cc_start: 0.7717 (tm-30) cc_final: 0.6919 (tm-30) REVERT: C 355 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6705 (p0) REVERT: C 367 TRP cc_start: 0.7509 (t-100) cc_final: 0.6842 (t-100) REVERT: D 9 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7690 (mt) REVERT: D 17 THR cc_start: 0.7290 (p) cc_final: 0.7044 (p) REVERT: D 25 SER cc_start: 0.7837 (p) cc_final: 0.7471 (t) REVERT: D 32 GLN cc_start: 0.7802 (tp40) cc_final: 0.7495 (tp40) REVERT: D 63 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7415 (ttp-110) REVERT: D 68 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7089 (mt-10) REVERT: D 73 ASP cc_start: 0.7056 (m-30) cc_final: 0.6841 (m-30) REVERT: D 74 VAL cc_start: 0.8300 (p) cc_final: 0.8014 (m) REVERT: D 86 SER cc_start: 0.8388 (t) cc_final: 0.7998 (m) REVERT: D 101 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7906 (mmtt) REVERT: D 102 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7419 (mmtm) REVERT: D 109 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6475 (mt-10) REVERT: D 132 MET cc_start: 0.7107 (mmm) cc_final: 0.6905 (mmm) REVERT: D 138 LYS cc_start: 0.8087 (mttp) cc_final: 0.7836 (mtpp) REVERT: D 164 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8040 (mt) REVERT: D 182 GLU cc_start: 0.8238 (tt0) cc_final: 0.7916 (tt0) REVERT: D 199 HIS cc_start: 0.7199 (t70) cc_final: 0.6493 (t70) REVERT: D 229 GLU cc_start: 0.7765 (pt0) cc_final: 0.7409 (pt0) REVERT: D 244 MET cc_start: 0.7557 (mmt) cc_final: 0.7233 (mmt) REVERT: D 276 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6859 (mm-30) REVERT: D 329 MET cc_start: 0.7204 (tpp) cc_final: 0.6968 (tpp) REVERT: D 331 PHE cc_start: 0.7344 (m-10) cc_final: 0.7038 (m-10) REVERT: D 348 PHE cc_start: 0.7569 (t80) cc_final: 0.7021 (t80) REVERT: D 350 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: D 351 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: D 409 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8565 (tpp-160) outliers start: 55 outliers final: 32 residues processed: 426 average time/residue: 0.1735 time to fit residues: 103.0096 Evaluate side-chains 447 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 401 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS B 131 GLN B 194 ASN B 274 GLN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.189840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136671 restraints weight = 36328.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140399 restraints weight = 16428.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141393 restraints weight = 10144.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142504 restraints weight = 8280.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142452 restraints weight = 7228.904| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20302 Z= 0.168 Angle : 0.568 15.408 28362 Z= 0.309 Chirality : 0.038 0.153 3108 Planarity : 0.004 0.053 3020 Dihedral : 22.842 78.895 4293 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.30 % Allowed : 19.39 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 1936 helix: 2.52 (0.17), residues: 915 sheet: 0.06 (0.30), residues: 279 loop : 0.78 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 444 TYR 0.016 0.002 TYR C 216 PHE 0.018 0.001 PHE C 314 TRP 0.024 0.001 TRP B 454 HIS 0.026 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00362 (20286) covalent geometry : angle 0.56294 (28338) hydrogen bonds : bond 0.03825 ( 1053) hydrogen bonds : angle 3.54599 ( 2783) metal coordination : bond 0.00242 ( 16) metal coordination : angle 2.63932 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 397 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7625 (mmt180) cc_final: 0.7296 (tpp80) REVERT: A 85 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.6660 (mmm-85) REVERT: A 131 GLN cc_start: 0.7710 (tp40) cc_final: 0.7403 (tt0) REVERT: A 135 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6705 (tm-30) REVERT: A 140 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7391 (ttm-80) REVERT: A 182 GLU cc_start: 0.8152 (tt0) cc_final: 0.7508 (tm-30) REVERT: A 186 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 205 LEU cc_start: 0.8911 (mp) cc_final: 0.8686 (mp) REVERT: A 235 LEU cc_start: 0.8763 (mt) cc_final: 0.8086 (mt) REVERT: A 239 MET cc_start: 0.7707 (mmm) cc_final: 0.7133 (mmm) REVERT: A 250 LEU cc_start: 0.7328 (tp) cc_final: 0.7017 (mt) REVERT: A 265 ARG cc_start: 0.7232 (ptt180) cc_final: 0.6833 (ptt180) REVERT: A 270 LEU cc_start: 0.7860 (mt) cc_final: 0.7635 (mt) REVERT: A 342 MET cc_start: 0.6411 (ttp) cc_final: 0.5953 (ttp) REVERT: A 419 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 423 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5988 (mm) REVERT: B 17 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 98 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 140 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6958 (mtp85) REVERT: B 142 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6509 (ttp-110) REVERT: B 182 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7169 (mm-30) REVERT: B 185 LEU cc_start: 0.8301 (mt) cc_final: 0.8095 (mm) REVERT: B 215 ASP cc_start: 0.7437 (m-30) cc_final: 0.7215 (t0) REVERT: B 219 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 221 GLN cc_start: 0.7877 (mm110) cc_final: 0.7606 (tp40) REVERT: B 231 SER cc_start: 0.8222 (m) cc_final: 0.7456 (p) REVERT: B 251 ASN cc_start: 0.8615 (m-40) cc_final: 0.8310 (m-40) REVERT: B 276 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 350 GLU cc_start: 0.8677 (mt-10) cc_final: 0.7954 (tp30) REVERT: B 351 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: B 352 GLN cc_start: 0.8741 (mm110) cc_final: 0.8505 (mm110) REVERT: B 466 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6821 (m) REVERT: C 14 ASP cc_start: 0.8448 (t0) cc_final: 0.8140 (t0) REVERT: C 20 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7309 (mm-30) REVERT: C 22 GLN cc_start: 0.7887 (mt0) cc_final: 0.7253 (mt0) REVERT: C 26 CYS cc_start: 0.8181 (m) cc_final: 0.7803 (m) REVERT: C 28 GLN cc_start: 0.7811 (tt0) cc_final: 0.7490 (mt0) REVERT: C 69 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7422 (tp30) REVERT: C 118 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7072 (t80) REVERT: C 139 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7310 (tp30) REVERT: C 164 LEU cc_start: 0.8324 (mt) cc_final: 0.7927 (mt) REVERT: C 175 VAL cc_start: 0.7562 (p) cc_final: 0.7183 (m) REVERT: C 181 ARG cc_start: 0.8359 (mtp85) cc_final: 0.7933 (mtp85) REVERT: C 186 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7178 (tm-30) REVERT: C 226 GLN cc_start: 0.7265 (mp10) cc_final: 0.6879 (mp10) REVERT: C 231 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.8020 (t) REVERT: C 241 SER cc_start: 0.8524 (m) cc_final: 0.8015 (p) REVERT: C 263 LEU cc_start: 0.8530 (tp) cc_final: 0.8314 (tt) REVERT: C 267 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: C 367 TRP cc_start: 0.7641 (t-100) cc_final: 0.6900 (t-100) REVERT: C 458 MET cc_start: 0.7663 (mmm) cc_final: 0.7066 (mtt) REVERT: D 9 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7657 (mt) REVERT: D 17 THR cc_start: 0.7345 (p) cc_final: 0.7063 (p) REVERT: D 25 SER cc_start: 0.7867 (p) cc_final: 0.7497 (t) REVERT: D 32 GLN cc_start: 0.7827 (tp40) cc_final: 0.7559 (tp40) REVERT: D 68 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7079 (mt-10) REVERT: D 74 VAL cc_start: 0.8307 (p) cc_final: 0.7998 (m) REVERT: D 86 SER cc_start: 0.8383 (t) cc_final: 0.8012 (m) REVERT: D 101 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7957 (mmtt) REVERT: D 102 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7483 (mmmt) REVERT: D 109 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6458 (mt-10) REVERT: D 132 MET cc_start: 0.7163 (mmm) cc_final: 0.6879 (mmm) REVERT: D 138 LYS cc_start: 0.8053 (mttp) cc_final: 0.7810 (mtpp) REVERT: D 142 ARG cc_start: 0.7841 (ttt90) cc_final: 0.7640 (ptm-80) REVERT: D 164 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8092 (mt) REVERT: D 182 GLU cc_start: 0.8213 (tt0) cc_final: 0.7896 (tt0) REVERT: D 199 HIS cc_start: 0.7174 (t70) cc_final: 0.6305 (t70) REVERT: D 229 GLU cc_start: 0.7739 (pt0) cc_final: 0.7423 (pt0) REVERT: D 272 ARG cc_start: 0.7975 (mmp80) cc_final: 0.7723 (mmp80) REVERT: D 276 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6692 (mm-30) REVERT: D 279 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7412 (ptp-110) REVERT: D 281 GLU cc_start: 0.7688 (tp30) cc_final: 0.7222 (tt0) REVERT: D 329 MET cc_start: 0.7184 (tpp) cc_final: 0.6922 (tpp) REVERT: D 331 PHE cc_start: 0.7374 (m-10) cc_final: 0.7009 (m-10) REVERT: D 348 PHE cc_start: 0.7630 (t80) cc_final: 0.7042 (t80) REVERT: D 351 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: D 409 ARG cc_start: 0.8966 (mmm160) cc_final: 0.8735 (tpp-160) REVERT: D 454 TRP cc_start: 0.7949 (t60) cc_final: 0.7539 (t60) REVERT: D 458 MET cc_start: 0.7680 (mmt) cc_final: 0.6990 (mmt) outliers start: 53 outliers final: 33 residues processed: 418 average time/residue: 0.1717 time to fit residues: 100.8018 Evaluate side-chains 437 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 391 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 172 optimal weight: 0.0470 chunk 187 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 0.0010 chunk 93 optimal weight: 6.9990 overall best weight: 0.9288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS B 32 GLN B 131 GLN B 194 ASN B 226 GLN B 274 GLN C 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.189839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143259 restraints weight = 36040.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142218 restraints weight = 18023.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142541 restraints weight = 13141.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143914 restraints weight = 10400.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143786 restraints weight = 8741.381| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20302 Z= 0.159 Angle : 0.566 16.522 28362 Z= 0.307 Chirality : 0.037 0.136 3108 Planarity : 0.004 0.053 3020 Dihedral : 22.811 78.872 4290 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.62 % Allowed : 19.51 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.19), residues: 1936 helix: 2.47 (0.17), residues: 915 sheet: 0.11 (0.29), residues: 297 loop : 0.82 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 208 TYR 0.022 0.002 TYR C 188 PHE 0.016 0.001 PHE C 314 TRP 0.025 0.001 TRP B 454 HIS 0.027 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00344 (20286) covalent geometry : angle 0.56138 (28338) hydrogen bonds : bond 0.03739 ( 1053) hydrogen bonds : angle 3.53576 ( 2783) metal coordination : bond 0.00246 ( 16) metal coordination : angle 2.55917 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 401 time to evaluate : 0.620 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 24 GLU cc_start: 0.7020 (tp30) cc_final: 0.6469 (tp30) REVERT: A 33 ARG cc_start: 0.7693 (mmt180) cc_final: 0.7335 (tpp80) REVERT: A 70 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 85 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.6593 (mmm-85) REVERT: A 131 GLN cc_start: 0.7700 (tp40) cc_final: 0.7421 (tt0) REVERT: A 135 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6695 (tm-30) REVERT: A 140 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7420 (ttm-80) REVERT: A 157 SER cc_start: 0.7446 (p) cc_final: 0.7239 (p) REVERT: A 163 TYR cc_start: 0.8137 (m-80) cc_final: 0.7720 (m-80) REVERT: A 182 GLU cc_start: 0.7965 (tt0) cc_final: 0.7374 (tm-30) REVERT: A 186 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 235 LEU cc_start: 0.8678 (mt) cc_final: 0.7998 (mt) REVERT: A 239 MET cc_start: 0.7507 (mmm) cc_final: 0.7003 (mmm) REVERT: A 250 LEU cc_start: 0.7342 (tp) cc_final: 0.7004 (mt) REVERT: A 342 MET cc_start: 0.6175 (ttp) cc_final: 0.5792 (ttp) REVERT: A 419 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 423 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6013 (mm) REVERT: B 17 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7466 (p) REVERT: B 69 GLU cc_start: 0.7919 (tp30) cc_final: 0.7095 (tp30) REVERT: B 98 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 140 ARG cc_start: 0.7428 (mtp180) cc_final: 0.7031 (mtp85) REVERT: B 142 ARG cc_start: 0.7031 (ttp-110) cc_final: 0.6454 (ttp-110) REVERT: B 182 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 215 ASP cc_start: 0.7439 (m-30) cc_final: 0.7231 (t0) REVERT: B 219 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 231 SER cc_start: 0.8237 (m) cc_final: 0.7656 (t) REVERT: B 251 ASN cc_start: 0.8590 (m-40) cc_final: 0.8305 (m-40) REVERT: B 352 GLN cc_start: 0.8533 (mm110) cc_final: 0.8161 (mm-40) REVERT: B 448 THR cc_start: 0.8821 (p) cc_final: 0.8539 (t) REVERT: B 466 VAL cc_start: 0.7048 (OUTLIER) cc_final: 0.6818 (m) REVERT: C 14 ASP cc_start: 0.8468 (t0) cc_final: 0.8111 (t0) REVERT: C 20 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 26 CYS cc_start: 0.8210 (m) cc_final: 0.7792 (m) REVERT: C 28 GLN cc_start: 0.7848 (tt0) cc_final: 0.7523 (mt0) REVERT: C 69 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7311 (tp30) REVERT: C 118 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7026 (t80) REVERT: C 139 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7239 (tp30) REVERT: C 175 VAL cc_start: 0.7480 (p) cc_final: 0.7098 (m) REVERT: C 181 ARG cc_start: 0.8371 (mtp85) cc_final: 0.7915 (mtp85) REVERT: C 186 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 226 GLN cc_start: 0.7339 (mp10) cc_final: 0.7037 (mp10) REVERT: C 231 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (t) REVERT: C 241 SER cc_start: 0.8422 (m) cc_final: 0.7974 (p) REVERT: C 267 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: C 355 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.6941 (p0) REVERT: C 367 TRP cc_start: 0.7466 (t-100) cc_final: 0.6965 (t-100) REVERT: D 9 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7664 (mt) REVERT: D 17 THR cc_start: 0.7413 (p) cc_final: 0.7137 (p) REVERT: D 25 SER cc_start: 0.7896 (p) cc_final: 0.7600 (t) REVERT: D 68 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7047 (mt-10) REVERT: D 73 ASP cc_start: 0.7084 (m-30) cc_final: 0.6605 (p0) REVERT: D 86 SER cc_start: 0.8400 (t) cc_final: 0.8037 (m) REVERT: D 101 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7899 (mmtt) REVERT: D 102 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7441 (mmtm) REVERT: D 109 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6501 (mt-10) REVERT: D 132 MET cc_start: 0.7279 (mmm) cc_final: 0.6904 (mmm) REVERT: D 139 GLU cc_start: 0.7224 (tp30) cc_final: 0.6831 (tp30) REVERT: D 142 ARG cc_start: 0.7820 (ttt90) cc_final: 0.7594 (ptm-80) REVERT: D 182 GLU cc_start: 0.8152 (tt0) cc_final: 0.7833 (tt0) REVERT: D 183 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7067 (mtm-85) REVERT: D 199 HIS cc_start: 0.6894 (t70) cc_final: 0.6136 (t70) REVERT: D 229 GLU cc_start: 0.7677 (pt0) cc_final: 0.7396 (pt0) REVERT: D 230 TRP cc_start: 0.7389 (m100) cc_final: 0.7047 (m100) REVERT: D 244 MET cc_start: 0.7540 (mmt) cc_final: 0.7046 (mmt) REVERT: D 276 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6572 (mm-30) REVERT: D 279 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7351 (ptp-110) REVERT: D 281 GLU cc_start: 0.7575 (tp30) cc_final: 0.7117 (tt0) REVERT: D 329 MET cc_start: 0.7050 (tpp) cc_final: 0.6697 (tpp) REVERT: D 331 PHE cc_start: 0.7248 (m-10) cc_final: 0.6995 (m-10) REVERT: D 348 PHE cc_start: 0.7429 (t80) cc_final: 0.6799 (t80) REVERT: D 351 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7722 (pt0) outliers start: 58 outliers final: 34 residues processed: 420 average time/residue: 0.1763 time to fit residues: 104.2228 Evaluate side-chains 445 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 400 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 207 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS B 32 GLN B 131 GLN B 194 ASN B 226 GLN B 274 GLN C 27 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.188110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141419 restraints weight = 35813.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139724 restraints weight = 18789.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140491 restraints weight = 12947.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141403 restraints weight = 10760.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141428 restraints weight = 9391.044| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20302 Z= 0.238 Angle : 0.625 16.799 28362 Z= 0.338 Chirality : 0.040 0.186 3108 Planarity : 0.005 0.056 3020 Dihedral : 22.854 81.354 4287 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.93 % Allowed : 20.95 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 1936 helix: 2.38 (0.17), residues: 913 sheet: -0.00 (0.30), residues: 281 loop : 0.69 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 325 TYR 0.025 0.002 TYR C 188 PHE 0.017 0.002 PHE D 53 TRP 0.028 0.002 TRP B 454 HIS 0.026 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00518 (20286) covalent geometry : angle 0.61890 (28338) hydrogen bonds : bond 0.04418 ( 1053) hydrogen bonds : angle 3.70890 ( 2783) metal coordination : bond 0.00400 ( 16) metal coordination : angle 3.01593 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 400 time to evaluate : 0.572 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 85 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6596 (mmm-85) REVERT: A 135 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6746 (tm-30) REVERT: A 157 SER cc_start: 0.7423 (p) cc_final: 0.7213 (p) REVERT: A 163 TYR cc_start: 0.8222 (m-80) cc_final: 0.7843 (m-80) REVERT: A 182 GLU cc_start: 0.7924 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 186 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: A 235 LEU cc_start: 0.8720 (mt) cc_final: 0.8034 (mt) REVERT: A 239 MET cc_start: 0.7547 (mmm) cc_final: 0.7043 (mmm) REVERT: A 250 LEU cc_start: 0.7437 (tp) cc_final: 0.7120 (mt) REVERT: A 276 GLU cc_start: 0.7438 (mp0) cc_final: 0.7129 (mp0) REVERT: A 279 ARG cc_start: 0.8414 (tmm-80) cc_final: 0.8195 (tmm-80) REVERT: A 342 MET cc_start: 0.6214 (ttp) cc_final: 0.5814 (ttp) REVERT: A 419 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 423 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6253 (mm) REVERT: B 17 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7617 (p) REVERT: B 27 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7879 (mm110) REVERT: B 40 VAL cc_start: 0.8645 (t) cc_final: 0.8307 (m) REVERT: B 45 ASP cc_start: 0.6843 (t0) cc_final: 0.6594 (t0) REVERT: B 88 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7002 (mtp85) REVERT: B 98 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7054 (mt-10) REVERT: B 137 ILE cc_start: 0.8112 (pt) cc_final: 0.7728 (mt) REVERT: B 139 GLU cc_start: 0.7691 (tp30) cc_final: 0.6725 (tp30) REVERT: B 142 ARG cc_start: 0.7029 (ttp-110) cc_final: 0.6603 (ttp-110) REVERT: B 181 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.7243 (ttp-110) REVERT: B 182 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 215 ASP cc_start: 0.7530 (m-30) cc_final: 0.7321 (t0) REVERT: B 219 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 251 ASN cc_start: 0.8584 (m-40) cc_final: 0.8351 (m-40) REVERT: B 352 GLN cc_start: 0.8643 (mm110) cc_final: 0.8186 (mm-40) REVERT: B 466 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6993 (m) REVERT: C 20 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 22 GLN cc_start: 0.7940 (mt0) cc_final: 0.7303 (mt0) REVERT: C 26 CYS cc_start: 0.8132 (m) cc_final: 0.7814 (m) REVERT: C 28 GLN cc_start: 0.7874 (tt0) cc_final: 0.7603 (mt0) REVERT: C 54 ASP cc_start: 0.7484 (t0) cc_final: 0.6842 (t0) REVERT: C 57 ARG cc_start: 0.7015 (mpp80) cc_final: 0.6640 (mpp80) REVERT: C 68 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 69 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7294 (tp30) REVERT: C 118 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7143 (t80) REVERT: C 139 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7263 (tp30) REVERT: C 181 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8147 (mtp85) REVERT: C 186 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 226 GLN cc_start: 0.7347 (mp10) cc_final: 0.6896 (mp10) REVERT: C 231 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8182 (t) REVERT: C 241 SER cc_start: 0.8488 (m) cc_final: 0.8053 (p) REVERT: C 267 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 9 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7697 (mt) REVERT: D 17 THR cc_start: 0.7538 (p) cc_final: 0.7242 (p) REVERT: D 18 SER cc_start: 0.8683 (t) cc_final: 0.8200 (p) REVERT: D 20 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: D 25 SER cc_start: 0.7904 (p) cc_final: 0.7596 (t) REVERT: D 68 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7259 (mt-10) REVERT: D 73 ASP cc_start: 0.7118 (m-30) cc_final: 0.6550 (p0) REVERT: D 79 ARG cc_start: 0.7467 (mtp180) cc_final: 0.6964 (ttm110) REVERT: D 86 SER cc_start: 0.8446 (t) cc_final: 0.8058 (m) REVERT: D 101 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7876 (mmtt) REVERT: D 102 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7502 (mmtm) REVERT: D 109 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6321 (mt-10) REVERT: D 132 MET cc_start: 0.7318 (mmm) cc_final: 0.6907 (mmm) REVERT: D 139 GLU cc_start: 0.7259 (tp30) cc_final: 0.6852 (tp30) REVERT: D 142 ARG cc_start: 0.7826 (ttt90) cc_final: 0.7577 (ptm-80) REVERT: D 182 GLU cc_start: 0.8153 (tt0) cc_final: 0.7841 (tt0) REVERT: D 183 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7191 (mtm-85) REVERT: D 199 HIS cc_start: 0.6918 (t70) cc_final: 0.6174 (t70) REVERT: D 229 GLU cc_start: 0.7650 (pt0) cc_final: 0.7358 (pt0) REVERT: D 230 TRP cc_start: 0.7413 (m100) cc_final: 0.6963 (m100) REVERT: D 244 MET cc_start: 0.7606 (mmt) cc_final: 0.7064 (mmt) REVERT: D 276 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6547 (mm-30) REVERT: D 279 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7324 (ptp-110) REVERT: D 281 GLU cc_start: 0.7585 (tp30) cc_final: 0.7157 (tt0) REVERT: D 329 MET cc_start: 0.7231 (tpp) cc_final: 0.6894 (tpp) REVERT: D 331 PHE cc_start: 0.7266 (m-10) cc_final: 0.7027 (m-10) REVERT: D 333 LYS cc_start: 0.6559 (tttp) cc_final: 0.6337 (tttp) REVERT: D 345 TRP cc_start: 0.6875 (m100) cc_final: 0.6522 (m100) REVERT: D 348 PHE cc_start: 0.7479 (t80) cc_final: 0.6766 (t80) REVERT: D 351 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: D 403 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7635 (tpp80) REVERT: D 409 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7920 (tpp-160) outliers start: 47 outliers final: 33 residues processed: 417 average time/residue: 0.1777 time to fit residues: 103.5284 Evaluate side-chains 435 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 392 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 43 optimal weight: 40.0000 chunk 177 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 95 HIS B 32 GLN B 131 GLN B 226 GLN B 274 GLN C 27 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.189395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142838 restraints weight = 35913.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141178 restraints weight = 17452.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141760 restraints weight = 13405.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142914 restraints weight = 10899.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142877 restraints weight = 9421.069| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20302 Z= 0.174 Angle : 0.596 17.587 28362 Z= 0.321 Chirality : 0.038 0.158 3108 Planarity : 0.004 0.054 3020 Dihedral : 22.816 79.740 4287 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.68 % Allowed : 21.76 % Favored : 75.56 % 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: 2.08 (0.19), residues: 1936 helix: 2.42 (0.16), residues: 913 sheet: 0.05 (0.29), residues: 291 loop : 0.75 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 208 TYR 0.014 0.002 TYR C 216 PHE 0.021 0.001 PHE C 314 TRP 0.029 0.001 TRP B 454 HIS 0.026 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00378 (20286) covalent geometry : angle 0.59070 (28338) hydrogen bonds : bond 0.03839 ( 1053) hydrogen bonds : angle 3.59969 ( 2783) metal coordination : bond 0.00279 ( 16) metal coordination : angle 2.90312 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 403 time to evaluate : 0.357 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 25 SER cc_start: 0.8420 (m) cc_final: 0.8055 (p) REVERT: A 33 ARG cc_start: 0.7671 (mmt180) cc_final: 0.7320 (tpp80) REVERT: A 70 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 85 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6721 (mmm-85) REVERT: A 135 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6704 (tm-30) REVERT: A 182 GLU cc_start: 0.7907 (tt0) cc_final: 0.7337 (tm-30) REVERT: A 186 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: A 235 LEU cc_start: 0.8702 (mt) cc_final: 0.7995 (mt) REVERT: A 239 MET cc_start: 0.7530 (mmm) cc_final: 0.7062 (mmm) REVERT: A 250 LEU cc_start: 0.7400 (tp) cc_final: 0.7069 (mt) REVERT: A 342 MET cc_start: 0.6337 (ttp) cc_final: 0.5963 (ttp) REVERT: A 419 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 423 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6276 (mm) REVERT: B 17 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7420 (p) REVERT: B 40 VAL cc_start: 0.8653 (t) cc_final: 0.8311 (m) REVERT: B 69 GLU cc_start: 0.8128 (tp30) cc_final: 0.7397 (tp30) REVERT: B 88 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7115 (mtp85) REVERT: B 98 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 137 ILE cc_start: 0.7995 (pt) cc_final: 0.7642 (mt) REVERT: B 142 ARG cc_start: 0.7042 (ttp-110) cc_final: 0.6446 (ttp-110) REVERT: B 182 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 219 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 251 ASN cc_start: 0.8553 (m-40) cc_final: 0.8273 (m-40) REVERT: B 276 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7210 (mp0) REVERT: B 352 GLN cc_start: 0.8687 (mm110) cc_final: 0.8239 (mm-40) REVERT: B 466 VAL cc_start: 0.7245 (OUTLIER) cc_final: 0.7022 (m) REVERT: C 20 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 26 CYS cc_start: 0.8126 (m) cc_final: 0.7756 (m) REVERT: C 28 GLN cc_start: 0.7866 (tt0) cc_final: 0.7613 (mt0) REVERT: C 54 ASP cc_start: 0.7506 (t0) cc_final: 0.6852 (t0) REVERT: C 57 ARG cc_start: 0.7019 (mpp80) cc_final: 0.6637 (mpp80) REVERT: C 69 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7612 (tp30) REVERT: C 98 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6702 (tp30) REVERT: C 118 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 139 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7369 (tp30) REVERT: C 175 VAL cc_start: 0.7493 (p) cc_final: 0.7101 (m) REVERT: C 181 ARG cc_start: 0.8427 (mtp85) cc_final: 0.8129 (mtp85) REVERT: C 186 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 226 GLN cc_start: 0.7351 (mp10) cc_final: 0.6983 (mp10) REVERT: C 231 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8121 (t) REVERT: C 241 SER cc_start: 0.8442 (m) cc_final: 0.8027 (p) REVERT: C 267 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 344 GLU cc_start: 0.7613 (pm20) cc_final: 0.7240 (pm20) REVERT: C 355 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7211 (p0) REVERT: C 367 TRP cc_start: 0.7242 (t-100) cc_final: 0.6879 (t-100) REVERT: D 9 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7666 (mt) REVERT: D 17 THR cc_start: 0.7493 (p) cc_final: 0.7197 (p) REVERT: D 18 SER cc_start: 0.8717 (t) cc_final: 0.8392 (p) REVERT: D 25 SER cc_start: 0.7893 (p) cc_final: 0.7582 (t) REVERT: D 68 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7269 (mt-10) REVERT: D 73 ASP cc_start: 0.7044 (m-30) cc_final: 0.6534 (p0) REVERT: D 86 SER cc_start: 0.8422 (t) cc_final: 0.8045 (m) REVERT: D 101 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7906 (mmtt) REVERT: D 102 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7491 (mmtm) REVERT: D 109 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6571 (mt-10) REVERT: D 132 MET cc_start: 0.7315 (mmm) cc_final: 0.6877 (mmm) REVERT: D 139 GLU cc_start: 0.7268 (tp30) cc_final: 0.6839 (tp30) REVERT: D 142 ARG cc_start: 0.7794 (ttt90) cc_final: 0.7554 (ptm-80) REVERT: D 182 GLU cc_start: 0.8122 (tt0) cc_final: 0.7790 (tt0) REVERT: D 183 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7137 (mtm-85) REVERT: D 199 HIS cc_start: 0.6940 (t70) cc_final: 0.6180 (t70) REVERT: D 229 GLU cc_start: 0.7661 (pt0) cc_final: 0.7365 (pt0) REVERT: D 230 TRP cc_start: 0.7487 (m100) cc_final: 0.7098 (m100) REVERT: D 244 MET cc_start: 0.7604 (mmt) cc_final: 0.7048 (mmt) REVERT: D 276 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6564 (mm-30) REVERT: D 279 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7277 (ptp-110) REVERT: D 281 GLU cc_start: 0.7582 (tp30) cc_final: 0.7154 (tt0) REVERT: D 329 MET cc_start: 0.7010 (tpp) cc_final: 0.6678 (tpp) REVERT: D 333 LYS cc_start: 0.6564 (tttp) cc_final: 0.6348 (tttp) REVERT: D 345 TRP cc_start: 0.6922 (m100) cc_final: 0.6518 (m100) REVERT: D 348 PHE cc_start: 0.7413 (t80) cc_final: 0.6680 (t80) REVERT: D 351 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: D 409 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7919 (tpp-160) outliers start: 43 outliers final: 27 residues processed: 418 average time/residue: 0.1723 time to fit residues: 101.1340 Evaluate side-chains 434 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS B 32 GLN B 226 GLN B 274 GLN C 27 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.190884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144028 restraints weight = 36112.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143281 restraints weight = 18300.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143714 restraints weight = 13049.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145029 restraints weight = 10299.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144952 restraints weight = 8696.206| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20302 Z= 0.137 Angle : 0.583 17.769 28362 Z= 0.312 Chirality : 0.037 0.154 3108 Planarity : 0.004 0.052 3020 Dihedral : 22.808 79.797 4287 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.43 % Allowed : 21.95 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1936 helix: 2.52 (0.17), residues: 909 sheet: 0.11 (0.29), residues: 291 loop : 0.77 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.013 0.001 TYR C 216 PHE 0.021 0.001 PHE C 314 TRP 0.028 0.001 TRP B 454 HIS 0.028 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00290 (20286) covalent geometry : angle 0.57764 (28338) hydrogen bonds : bond 0.03524 ( 1053) hydrogen bonds : angle 3.55563 ( 2783) metal coordination : bond 0.00204 ( 16) metal coordination : angle 2.70299 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3721.20 seconds wall clock time: 64 minutes 31.52 seconds (3871.52 seconds total)