Starting phenix.real_space_refine on Mon Apr 6 15:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu3_60888/04_2026/9iu3_60888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu3_60888/04_2026/9iu3_60888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iu3_60888/04_2026/9iu3_60888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu3_60888/04_2026/9iu3_60888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu3_60888/04_2026/9iu3_60888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu3_60888/04_2026/9iu3_60888.map" } resolution = 3.97 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= 0.001 sd= 0.025 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 11581 2.51 5 N 3618 2.21 5 O 4023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 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: 19482 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: 3871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Conformer: "B" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} bond proxies already assigned to first conformer: 3938 Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "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: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 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 304 102.884 146.482 33.303 1.00390.12 S ATOM 2447 SG CYS A 307 100.414 144.911 35.548 1.00390.03 S ATOM 2598 SG CYS A 326 99.526 145.211 32.471 1.00390.10 S ATOM 2670 SG CYS A 335 99.913 148.571 34.334 1.00390.38 S ATOM 6300 SG CYS B 304 62.651 34.148 120.764 1.00195.29 S ATOM 6318 SG CYS B 307 62.714 35.404 117.306 1.00195.14 S ATOM 6469 SG CYS B 326 59.848 35.365 118.696 1.00195.40 S ATOM 6541 SG CYS B 335 61.291 31.864 118.031 1.00195.71 S ATOM 10163 SG CYS C 304 46.799 148.184 86.167 1.00265.55 S ATOM 10181 SG CYS C 307 45.953 145.157 88.073 1.00265.49 S ATOM 10332 SG CYS C 326 44.176 145.613 85.449 1.00264.90 S ATOM 10404 SG CYS C 335 43.535 148.201 88.125 1.00264.74 S ATOM 14026 SG CYS D 304 54.087 25.727 46.129 1.00170.47 S ATOM 14044 SG CYS D 307 55.021 28.203 43.606 1.00170.17 S ATOM 14195 SG CYS D 326 52.013 28.435 44.623 1.00168.50 S ATOM 14267 SG CYS D 335 52.706 25.247 42.600 1.00168.83 S Time building chain proxies: 5.06, per 1000 atoms: 0.26 Number of scatterers: 19482 At special positions: 0 Unit cell: (136.396, 178.726, 157.561, 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 4023 8.00 N 3618 7.00 C 11581 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: 1.50 Conformation dependent library (CDL) restraints added in 962.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 307 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " Number of angles added : 24 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.6% alpha, 13.7% beta 93 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.631A 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 removed outlier: 3.540A pdb=" N THR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.169A 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: 3.801A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.675A 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 removed outlier: 3.531A pdb=" N GLN A 446 " --> pdb=" O TRP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 18 through 34 removed outlier: 4.064A pdb=" N GLN B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.619A 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: 4.083A 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: 3.827A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.654A 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 removed outlier: 3.527A pdb=" N GLN B 446 " --> pdb=" O TRP B 442 " (cutoff:3.500A) 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: 3.632A 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: 3.704A 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 removed outlier: 3.525A pdb=" N GLN C 446 " --> pdb=" O TRP C 442 " (cutoff:3.500A) 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: 3.639A 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: 3.692A 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 removed outlier: 3.530A pdb=" N GLN D 446 " --> pdb=" O TRP D 442 " (cutoff:3.500A) 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 37 through 44 removed outlier: 6.807A pdb=" N ALA A 3 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 41 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 5 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP A 43 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 7 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 6.200A 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: 7.091A 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: 7.520A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.210A 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: 7.095A 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: 7.535A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.220A 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: 7.503A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.217A 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: 7.125A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2276 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: 4.08 Time building geometry restraints manager: 1.94 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: 3603 1.33 - 1.45: 5895 1.45 - 1.57: 10303 1.57 - 1.69: 403 1.69 - 1.81: 92 Bond restraints: 20296 Sorted by residual: bond pdb=" C LYS A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.22e-02 6.72e+03 1.10e+01 bond pdb=" C VAL A 175 " pdb=" N PRO A 176 " ideal model delta sigma weight residual 1.330 1.369 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" C THR A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 1.329 1.368 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" C HIS C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.22e-02 6.72e+03 1.06e+01 bond pdb=" C ALA B 261 " pdb=" N PRO B 262 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.20e-02 6.94e+03 9.98e+00 ... (remaining 20291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 26079 3.49 - 6.97: 2115 6.97 - 10.46: 145 10.46 - 13.95: 10 13.95 - 17.43: 5 Bond angle restraints: 28354 Sorted by residual: angle pdb=" O3' DGF1 32 " pdb=" P DTF1 33 " pdb=" O5' DTF1 33 " ideal model delta sigma weight residual 104.00 86.57 17.43 1.50e+00 4.44e-01 1.35e+02 angle pdb=" O3' DGE2 32 " pdb=" P DTE2 33 " pdb=" O5' DTE2 33 " ideal model delta sigma weight residual 104.00 88.92 15.08 1.50e+00 4.44e-01 1.01e+02 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.34 14.66 1.50e+00 4.44e-01 9.55e+01 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 89.41 14.59 1.50e+00 4.44e-01 9.46e+01 angle pdb=" O3' DAF2 20 " pdb=" P DCF2 21 " pdb=" O5' DCF2 21 " ideal model delta sigma weight residual 104.00 89.49 14.51 1.50e+00 4.44e-01 9.35e+01 ... (remaining 28349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 9467 17.79 - 35.59: 1055 35.59 - 53.38: 858 53.38 - 71.17: 211 71.17 - 88.97: 26 Dihedral angle restraints: 11617 sinusoidal: 6001 harmonic: 5616 Sorted by residual: dihedral pdb=" CA LEU D 423 " pdb=" C LEU D 423 " pdb=" N GLU D 424 " pdb=" CA GLU D 424 " ideal model delta harmonic sigma weight residual 180.00 148.66 31.34 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA SER B 18 " pdb=" C SER B 18 " pdb=" N PRO B 19 " pdb=" CA PRO B 19 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE A 118 " pdb=" C PHE A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 11614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2679 0.128 - 0.257: 398 0.257 - 0.385: 27 0.385 - 0.513: 1 0.513 - 0.642: 4 Chirality restraints: 3109 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 -0.64 2.00e-01 2.50e+01 1.03e+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 1.03e+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 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 3106 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 35 " -0.042 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP D 35 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 35 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 35 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP D 35 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 35 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 35 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 35 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 35 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 35 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCE2 30 " 0.035 2.00e-02 2.50e+03 2.03e-02 9.26e+00 pdb=" N1 DCE2 30 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DCE2 30 " -0.022 2.00e-02 2.50e+03 pdb=" O2 DCE2 30 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DCE2 30 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DCE2 30 " 0.009 2.00e-02 2.50e+03 pdb=" N4 DCE2 30 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DCE2 30 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DCE2 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.026 2.00e-02 2.50e+03 1.84e-02 8.45e+00 pdb=" CG TRP A 432 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " -0.028 2.00e-02 2.50e+03 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 4 2.27 - 2.92: 6633 2.92 - 3.58: 28260 3.58 - 4.24: 47260 4.24 - 4.90: 76983 Nonbonded interactions: 159140 Sorted by model distance: nonbonded pdb=" OG SER B 10 " pdb=" P DCE2 28 " model vdw 1.608 3.400 nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.609 3.400 nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.611 3.400 nonbonded pdb=" OG SER A 10 " pdb=" P DCF1 28 " model vdw 1.612 3.400 nonbonded pdb=" NH1 ARG B 58 " pdb=" O LEU B 83 " model vdw 2.280 3.120 ... (remaining 159135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'B' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'C' and (resid 1 through 141 or resid 143 through 1000)) selection = (chain 'D' and (resid 1 through 141 or resid 143 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 22.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 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 : 0.011 0.076 20312 Z= 0.657 Angle : 2.004 20.916 28378 Z= 1.288 Chirality : 0.091 0.642 3109 Planarity : 0.007 0.078 3022 Dihedral : 21.344 88.967 7983 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.93 % Rotamer: Outliers : 4.11 % Allowed : 6.48 % Favored : 89.41 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.13 (0.17), residues: 1937 helix: 0.00 (0.14), residues: 916 sheet: 0.10 (0.29), residues: 263 loop : -0.02 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.005 ARG B 8 TYR 0.030 0.005 TYR B 482 PHE 0.035 0.005 PHE C 118 TRP 0.042 0.005 TRP D 35 HIS 0.019 0.003 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.01085 (20296) covalent geometry : angle 1.98498 (28354) hydrogen bonds : bond 0.15671 ( 1046) hydrogen bonds : angle 5.92849 ( 2758) metal coordination : bond 0.06085 ( 16) metal coordination : angle 9.63146 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 523 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 GLN cc_start: 0.8280 (mt0) cc_final: 0.8076 (mt0) REVERT: A 25 SER cc_start: 0.6924 (m) cc_final: 0.6683 (p) REVERT: A 28 GLN cc_start: 0.8844 (mt0) cc_final: 0.8493 (mt0) REVERT: A 40 VAL cc_start: 0.7999 (t) cc_final: 0.7085 (p) REVERT: A 43 ASP cc_start: 0.5033 (m-30) cc_final: 0.4570 (m-30) REVERT: A 55 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7380 (ttm-80) REVERT: A 74 VAL cc_start: 0.5692 (p) cc_final: 0.5311 (t) REVERT: A 88 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8169 (mmp-170) REVERT: A 100 HIS cc_start: 0.8641 (m90) cc_final: 0.8372 (m90) REVERT: A 104 VAL cc_start: 0.6368 (t) cc_final: 0.6089 (p) REVERT: A 109 GLU cc_start: 0.4985 (mt-10) cc_final: 0.4685 (mp0) REVERT: A 125 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 126 MET cc_start: 0.8815 (mmm) cc_final: 0.8236 (mmm) REVERT: A 133 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7725 (tp30) REVERT: A 134 LEU cc_start: 0.9058 (tp) cc_final: 0.8740 (tt) REVERT: A 135 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 238 SER cc_start: 0.7514 (m) cc_final: 0.6942 (p) REVERT: A 239 MET cc_start: 0.7448 (mmm) cc_final: 0.6948 (mmm) REVERT: A 275 LEU cc_start: 0.7044 (tp) cc_final: 0.6836 (mp) REVERT: A 379 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7268 (tm-30) REVERT: B 8 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5414 (ttp-170) REVERT: B 21 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7293 (ttm-80) REVERT: B 23 LEU cc_start: 0.8648 (tp) cc_final: 0.7963 (pp) REVERT: B 33 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7450 (mmt90) REVERT: B 35 TRP cc_start: 0.7020 (m-10) cc_final: 0.6614 (m-10) REVERT: B 88 ARG cc_start: 0.7672 (ttt90) cc_final: 0.6821 (tpt-90) REVERT: B 92 GLN cc_start: 0.8365 (mt0) cc_final: 0.8070 (mm-40) REVERT: B 95 HIS cc_start: 0.8287 (m90) cc_final: 0.7288 (m170) REVERT: B 100 HIS cc_start: 0.8031 (m90) cc_final: 0.7608 (m90) REVERT: B 132 MET cc_start: 0.8104 (mtp) cc_final: 0.7819 (mtp) REVERT: B 135 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 146 HIS cc_start: 0.7976 (m170) cc_final: 0.7442 (m170) REVERT: B 153 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7455 (mtmp) REVERT: B 181 ARG cc_start: 0.7293 (ttt180) cc_final: 0.6748 (ttp-110) REVERT: B 183 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7208 (mmt180) REVERT: B 186 GLU cc_start: 0.8020 (tt0) cc_final: 0.7105 (tt0) REVERT: B 204 ASP cc_start: 0.7895 (t70) cc_final: 0.7584 (t0) REVERT: B 207 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7383 (tpp80) REVERT: B 226 GLN cc_start: 0.8015 (mt0) cc_final: 0.7213 (mt0) REVERT: B 228 ARG cc_start: 0.6520 (mtm-85) cc_final: 0.6162 (mtt90) REVERT: B 229 GLU cc_start: 0.7601 (pt0) cc_final: 0.7110 (pt0) REVERT: B 235 LEU cc_start: 0.7642 (mt) cc_final: 0.7159 (mp) REVERT: B 239 MET cc_start: 0.7510 (mmm) cc_final: 0.6860 (mmm) REVERT: B 242 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7096 (mt-10) REVERT: B 257 ASP cc_start: 0.7654 (t70) cc_final: 0.7449 (t0) REVERT: B 265 ARG cc_start: 0.7641 (ptt180) cc_final: 0.7317 (ptm160) REVERT: B 281 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: B 299 LEU cc_start: 0.8485 (tp) cc_final: 0.8035 (tp) REVERT: B 350 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7676 (tp30) REVERT: B 376 GLU cc_start: 0.8525 (tt0) cc_final: 0.7721 (tt0) REVERT: B 452 ASN cc_start: 0.8027 (t0) cc_final: 0.7362 (t0) REVERT: B 463 THR cc_start: 0.7334 (m) cc_final: 0.7118 (t) REVERT: B 464 PHE cc_start: 0.7444 (p90) cc_final: 0.6816 (p90) REVERT: C 2 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7053 (ptm160) REVERT: C 33 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7972 (tpp80) REVERT: C 60 ASN cc_start: 0.7531 (m-40) cc_final: 0.7066 (t0) REVERT: C 69 GLU cc_start: 0.6949 (mp0) cc_final: 0.6661 (mp0) REVERT: C 73 ASP cc_start: 0.6570 (m-30) cc_final: 0.6059 (m-30) REVERT: C 84 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8130 (m) REVERT: C 88 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7522 (mmm160) REVERT: C 100 HIS cc_start: 0.7386 (m90) cc_final: 0.6893 (m90) REVERT: C 129 VAL cc_start: 0.8304 (t) cc_final: 0.7814 (m) REVERT: C 133 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 140 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7602 (mpt-90) REVERT: C 150 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8297 (mtt-85) REVERT: C 183 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8318 (mmp-170) REVERT: C 186 GLU cc_start: 0.8781 (tp30) cc_final: 0.7902 (tp30) REVERT: C 199 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7158 (p-80) REVERT: C 208 ARG cc_start: 0.8270 (mpp80) cc_final: 0.7993 (mtm110) REVERT: C 214 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7900 (ttmt) REVERT: C 230 TRP cc_start: 0.6770 (m100) cc_final: 0.6563 (m100) REVERT: C 233 THR cc_start: 0.8530 (m) cc_final: 0.8080 (p) REVERT: C 237 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.7870 (mtp180) REVERT: C 244 MET cc_start: 0.8718 (mmt) cc_final: 0.8449 (mmt) REVERT: C 250 LEU cc_start: 0.8825 (tp) cc_final: 0.8620 (tt) REVERT: C 274 GLN cc_start: 0.8206 (mt0) cc_final: 0.7919 (mt0) REVERT: C 331 PHE cc_start: 0.8332 (m-80) cc_final: 0.8011 (m-80) REVERT: C 452 ASN cc_start: 0.8078 (t0) cc_final: 0.7556 (t0) REVERT: C 475 ASP cc_start: 0.6588 (t0) cc_final: 0.6361 (t0) REVERT: D 9 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6845 (mt) REVERT: D 22 GLN cc_start: 0.7764 (mt0) cc_final: 0.7422 (mt0) REVERT: D 33 ARG cc_start: 0.7683 (mtp180) cc_final: 0.6930 (mtp180) REVERT: D 56 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7879 (ttmt) REVERT: D 67 PHE cc_start: 0.6951 (m-80) cc_final: 0.6040 (m-80) REVERT: D 70 GLN cc_start: 0.7409 (tt0) cc_final: 0.7097 (tm-30) REVERT: D 88 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7569 (ttm110) REVERT: D 95 HIS cc_start: 0.7428 (m-70) cc_final: 0.6764 (m90) REVERT: D 96 TRP cc_start: 0.7310 (t60) cc_final: 0.6501 (t60) REVERT: D 99 ASP cc_start: 0.7134 (m-30) cc_final: 0.6852 (m-30) REVERT: D 100 HIS cc_start: 0.7506 (m-70) cc_final: 0.7090 (m170) REVERT: D 102 LYS cc_start: 0.7320 (mmtt) cc_final: 0.7028 (mmmt) REVERT: D 114 THR cc_start: 0.8745 (p) cc_final: 0.8360 (m) REVERT: D 134 LEU cc_start: 0.8092 (tp) cc_final: 0.7831 (tt) REVERT: D 135 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7287 (mm-30) REVERT: D 138 LYS cc_start: 0.7921 (mttt) cc_final: 0.7282 (mtpp) REVERT: D 146 HIS cc_start: 0.8060 (m170) cc_final: 0.7695 (m-70) REVERT: D 149 ILE cc_start: 0.8119 (mm) cc_final: 0.7850 (mm) REVERT: D 177 ASP cc_start: 0.7006 (t0) cc_final: 0.6261 (t0) REVERT: D 235 LEU cc_start: 0.8049 (mt) cc_final: 0.7688 (mt) REVERT: D 238 SER cc_start: 0.7179 (m) cc_final: 0.6893 (p) REVERT: D 239 MET cc_start: 0.7686 (mmm) cc_final: 0.7405 (mmp) REVERT: D 247 TYR cc_start: 0.6494 (m-10) cc_final: 0.6223 (m-10) REVERT: D 265 ARG cc_start: 0.7227 (ptt180) cc_final: 0.6906 (ttp80) REVERT: D 269 ILE cc_start: 0.8196 (mm) cc_final: 0.7930 (mm) REVERT: D 272 ARG cc_start: 0.8212 (tpt170) cc_final: 0.7868 (mmm-85) REVERT: D 278 LEU cc_start: 0.8693 (mt) cc_final: 0.8421 (mt) REVERT: D 327 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8211 (tmt-80) REVERT: D 329 MET cc_start: 0.7900 (tpp) cc_final: 0.7413 (tpp) REVERT: D 339 THR cc_start: 0.7417 (p) cc_final: 0.6655 (m) REVERT: D 340 VAL cc_start: 0.7120 (m) cc_final: 0.6874 (m) REVERT: D 345 TRP cc_start: 0.8377 (m100) cc_final: 0.7881 (m100) REVERT: D 458 MET cc_start: 0.7537 (mmt) cc_final: 0.6914 (mmt) REVERT: D 459 ASN cc_start: 0.7753 (m110) cc_final: 0.7446 (m110) outliers start: 66 outliers final: 18 residues processed: 561 average time/residue: 0.1830 time to fit residues: 144.4294 Evaluate side-chains 478 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 450 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 180 GLN B 180 GLN C 334 HIS C 480 GLN D 180 GLN D 189 HIS D 446 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.215805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.164982 restraints weight = 53475.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167758 restraints weight = 24547.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169209 restraints weight = 15757.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.170671 restraints weight = 12551.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.170445 restraints weight = 11107.729| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20312 Z= 0.172 Angle : 0.628 8.984 28378 Z= 0.355 Chirality : 0.040 0.283 3109 Planarity : 0.005 0.038 3022 Dihedral : 22.915 82.305 4334 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % Rotamer: Outliers : 3.12 % Allowed : 12.34 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 1937 helix: 2.17 (0.16), residues: 922 sheet: 0.04 (0.27), residues: 291 loop : 0.84 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 181 TYR 0.018 0.002 TYR D 78 PHE 0.027 0.002 PHE D 217 TRP 0.021 0.002 TRP C 35 HIS 0.008 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00363 (20296) covalent geometry : angle 0.62129 (28354) hydrogen bonds : bond 0.04644 ( 1046) hydrogen bonds : angle 3.87299 ( 2758) metal coordination : bond 0.00351 ( 16) metal coordination : angle 3.16718 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 465 time to evaluate : 0.606 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7039 (t) cc_final: 0.6488 (m) REVERT: A 8 ARG cc_start: 0.6916 (ttt-90) cc_final: 0.5792 (ttp80) REVERT: A 28 GLN cc_start: 0.8804 (mt0) cc_final: 0.8421 (tm-30) REVERT: A 60 ASN cc_start: 0.6396 (m110) cc_final: 0.6133 (m110) REVERT: A 79 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6924 (mtp180) REVERT: A 90 LEU cc_start: 0.8583 (tp) cc_final: 0.8330 (pp) REVERT: A 126 MET cc_start: 0.7904 (mmm) cc_final: 0.7409 (mmm) REVERT: A 133 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7630 (tm-30) REVERT: A 134 LEU cc_start: 0.8947 (tp) cc_final: 0.7702 (tp) REVERT: A 135 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 138 LYS cc_start: 0.8207 (mttm) cc_final: 0.8000 (mttm) REVERT: A 139 GLU cc_start: 0.8138 (tp30) cc_final: 0.7872 (tp30) REVERT: A 180 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6411 (mm-40) REVERT: A 219 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6789 (mm110) REVERT: A 237 ARG cc_start: 0.8411 (ttt-90) cc_final: 0.8007 (ttt-90) REVERT: A 238 SER cc_start: 0.8296 (m) cc_final: 0.7670 (p) REVERT: A 239 MET cc_start: 0.7680 (mmm) cc_final: 0.6950 (mmm) REVERT: A 244 MET cc_start: 0.5763 (mmp) cc_final: 0.5227 (ppp) REVERT: A 275 LEU cc_start: 0.7373 (tp) cc_final: 0.7131 (tp) REVERT: A 416 ARG cc_start: 0.7667 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: B 8 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.5438 (tmm160) REVERT: B 20 GLU cc_start: 0.7750 (mp0) cc_final: 0.7233 (mp0) REVERT: B 21 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7492 (ttp-170) REVERT: B 24 GLU cc_start: 0.7632 (tt0) cc_final: 0.7076 (tt0) REVERT: B 38 VAL cc_start: 0.6415 (OUTLIER) cc_final: 0.5990 (m) REVERT: B 95 HIS cc_start: 0.7887 (m90) cc_final: 0.7632 (m90) REVERT: B 135 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 141 ASN cc_start: 0.8430 (m-40) cc_final: 0.8210 (m110) REVERT: B 146 HIS cc_start: 0.7624 (m170) cc_final: 0.7305 (m-70) REVERT: B 181 ARG cc_start: 0.7135 (ttt180) cc_final: 0.6646 (ttp-110) REVERT: B 183 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7119 (mmt180) REVERT: B 191 VAL cc_start: 0.8093 (t) cc_final: 0.7856 (p) REVERT: B 196 GLU cc_start: 0.7554 (tt0) cc_final: 0.7347 (tt0) REVERT: B 200 LEU cc_start: 0.7358 (mt) cc_final: 0.6788 (mt) REVERT: B 204 ASP cc_start: 0.7506 (t70) cc_final: 0.7298 (t0) REVERT: B 205 LEU cc_start: 0.8376 (mt) cc_final: 0.8105 (mp) REVERT: B 207 ARG cc_start: 0.7466 (mtm110) cc_final: 0.7211 (tpp80) REVERT: B 212 SER cc_start: 0.7106 (t) cc_final: 0.6674 (p) REVERT: B 226 GLN cc_start: 0.7962 (mt0) cc_final: 0.7632 (mt0) REVERT: B 228 ARG cc_start: 0.6139 (mtm-85) cc_final: 0.5920 (mtm-85) REVERT: B 239 MET cc_start: 0.7712 (mmm) cc_final: 0.7378 (mmm) REVERT: B 242 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 254 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7063 (t) REVERT: B 265 ARG cc_start: 0.8316 (ptt180) cc_final: 0.7950 (ptt180) REVERT: B 272 ARG cc_start: 0.7563 (ttp80) cc_final: 0.6629 (ttp80) REVERT: B 275 LEU cc_start: 0.8278 (tp) cc_final: 0.7996 (tp) REVERT: B 281 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6252 (mm-30) REVERT: B 299 LEU cc_start: 0.8526 (tp) cc_final: 0.8319 (tt) REVERT: B 329 MET cc_start: 0.6712 (mmt) cc_final: 0.6432 (mmt) REVERT: B 376 GLU cc_start: 0.8248 (tt0) cc_final: 0.7987 (tt0) REVERT: B 383 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 413 LEU cc_start: 0.9066 (mm) cc_final: 0.8615 (pp) REVERT: B 451 LYS cc_start: 0.8385 (mttt) cc_final: 0.8181 (mttm) REVERT: B 464 PHE cc_start: 0.7176 (p90) cc_final: 0.6754 (p90) REVERT: B 475 ASP cc_start: 0.7461 (t70) cc_final: 0.7183 (t70) REVERT: C 29 LEU cc_start: 0.8319 (tp) cc_final: 0.7899 (tt) REVERT: C 68 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6289 (mt-10) REVERT: C 76 VAL cc_start: 0.6982 (t) cc_final: 0.6461 (p) REVERT: C 83 LEU cc_start: 0.7477 (mt) cc_final: 0.7226 (mp) REVERT: C 100 HIS cc_start: 0.7775 (m90) cc_final: 0.7330 (m90) REVERT: C 121 VAL cc_start: 0.8642 (t) cc_final: 0.8184 (t) REVERT: C 133 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 140 ARG cc_start: 0.7387 (mpt-90) cc_final: 0.7060 (mpt-90) REVERT: C 150 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8051 (mtt-85) REVERT: C 182 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7717 (tm-30) REVERT: C 183 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8311 (mmp-170) REVERT: C 187 VAL cc_start: 0.8466 (t) cc_final: 0.8164 (p) REVERT: C 204 ASP cc_start: 0.7811 (t70) cc_final: 0.7355 (t70) REVERT: C 208 ARG cc_start: 0.8015 (mpp80) cc_final: 0.7320 (mtm180) REVERT: C 214 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7524 (ttmt) REVERT: C 224 GLU cc_start: 0.7432 (tt0) cc_final: 0.7182 (pp20) REVERT: C 237 ARG cc_start: 0.8698 (ttp-170) cc_final: 0.8074 (mtp180) REVERT: C 242 GLU cc_start: 0.7051 (pm20) cc_final: 0.6625 (pm20) REVERT: C 244 MET cc_start: 0.8538 (mmt) cc_final: 0.8277 (mmt) REVERT: C 274 GLN cc_start: 0.8339 (mt0) cc_final: 0.7746 (mt0) REVERT: C 276 GLU cc_start: 0.8277 (pt0) cc_final: 0.8014 (pt0) REVERT: C 331 PHE cc_start: 0.8301 (m-80) cc_final: 0.8093 (m-80) REVERT: C 350 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 452 ASN cc_start: 0.8214 (t0) cc_final: 0.7696 (t0) REVERT: C 454 TRP cc_start: 0.8270 (t-100) cc_final: 0.7971 (t-100) REVERT: C 455 LEU cc_start: 0.9004 (mt) cc_final: 0.8751 (tp) REVERT: D 22 GLN cc_start: 0.7855 (mt0) cc_final: 0.7403 (mt0) REVERT: D 33 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7287 (mmm160) REVERT: D 51 ASP cc_start: 0.7977 (t0) cc_final: 0.7497 (t0) REVERT: D 56 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7880 (ttmt) REVERT: D 65 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7648 (mm) REVERT: D 67 PHE cc_start: 0.7149 (m-80) cc_final: 0.6638 (m-80) REVERT: D 99 ASP cc_start: 0.6973 (m-30) cc_final: 0.6674 (m-30) REVERT: D 114 THR cc_start: 0.8446 (p) cc_final: 0.8238 (m) REVERT: D 135 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6961 (mm-30) REVERT: D 138 LYS cc_start: 0.8378 (mttt) cc_final: 0.7900 (mtpp) REVERT: D 140 ARG cc_start: 0.7361 (tpt170) cc_final: 0.6721 (tpt170) REVERT: D 149 ILE cc_start: 0.8258 (mm) cc_final: 0.8015 (mm) REVERT: D 215 ASP cc_start: 0.7437 (m-30) cc_final: 0.6963 (t0) REVERT: D 235 LEU cc_start: 0.8436 (mt) cc_final: 0.7836 (mm) REVERT: D 239 MET cc_start: 0.7811 (mmm) cc_final: 0.7456 (mmm) REVERT: D 329 MET cc_start: 0.7615 (tpp) cc_final: 0.7037 (tpp) REVERT: D 337 ASN cc_start: 0.7722 (t0) cc_final: 0.6876 (t0) REVERT: D 345 TRP cc_start: 0.7914 (m100) cc_final: 0.7612 (m100) REVERT: D 350 GLU cc_start: 0.8427 (tp30) cc_final: 0.7782 (tp30) REVERT: D 351 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: D 452 ASN cc_start: 0.8036 (t0) cc_final: 0.7727 (t0) REVERT: D 459 ASN cc_start: 0.7911 (m110) cc_final: 0.7603 (m110) REVERT: D 461 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.6901 (ttm-80) REVERT: D 464 PHE cc_start: 0.6643 (p90) cc_final: 0.5403 (p90) outliers start: 50 outliers final: 26 residues processed: 496 average time/residue: 0.1923 time to fit residues: 132.3700 Evaluate side-chains 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 439 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 3 optimal weight: 0.0020 chunk 179 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 131 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.207070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150993 restraints weight = 47650.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156334 restraints weight = 21723.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159551 restraints weight = 13396.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161511 restraints weight = 9875.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.162566 restraints weight = 8219.064| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 20312 Z= 0.314 Angle : 0.688 10.947 28378 Z= 0.390 Chirality : 0.045 0.225 3109 Planarity : 0.006 0.051 3022 Dihedral : 22.852 87.797 4287 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.86 % Allowed : 14.83 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1937 helix: 1.78 (0.16), residues: 916 sheet: -0.02 (0.28), residues: 279 loop : 0.76 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 208 TYR 0.025 0.002 TYR B 324 PHE 0.025 0.002 PHE C 118 TRP 0.036 0.002 TRP C 35 HIS 0.022 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00650 (20296) covalent geometry : angle 0.67483 (28354) hydrogen bonds : bond 0.05288 ( 1046) hydrogen bonds : angle 4.10231 ( 2758) metal coordination : bond 0.00855 ( 16) metal coordination : angle 4.58262 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 439 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5654 (tmm) cc_final: 0.5120 (tmm) REVERT: A 8 ARG cc_start: 0.7400 (ttt-90) cc_final: 0.6493 (ttt-90) REVERT: A 28 GLN cc_start: 0.8743 (mt0) cc_final: 0.8344 (tm-30) REVERT: A 29 LEU cc_start: 0.8553 (tp) cc_final: 0.8119 (tp) REVERT: A 38 VAL cc_start: 0.5170 (OUTLIER) cc_final: 0.4200 (t) REVERT: A 50 VAL cc_start: 0.7680 (t) cc_final: 0.7242 (p) REVERT: A 63 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.6873 (mtm110) REVERT: A 79 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7015 (mtp180) REVERT: A 109 GLU cc_start: 0.6378 (mt-10) cc_final: 0.5637 (mp0) REVERT: A 126 MET cc_start: 0.7952 (mmm) cc_final: 0.7453 (mmm) REVERT: A 133 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7500 (tp30) REVERT: A 134 LEU cc_start: 0.8906 (tp) cc_final: 0.7661 (tp) REVERT: A 135 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7216 (mm-30) REVERT: A 219 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6844 (mm110) REVERT: A 235 LEU cc_start: 0.8810 (mt) cc_final: 0.8198 (mt) REVERT: A 238 SER cc_start: 0.8596 (m) cc_final: 0.8005 (p) REVERT: A 239 MET cc_start: 0.7937 (mmm) cc_final: 0.7137 (mmm) REVERT: A 275 LEU cc_start: 0.7641 (tp) cc_final: 0.7378 (mp) REVERT: A 281 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6767 (mm-30) REVERT: B 8 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.6075 (ttt-90) REVERT: B 9 LEU cc_start: 0.8120 (mt) cc_final: 0.7796 (tp) REVERT: B 21 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7763 (ttm170) REVERT: B 22 GLN cc_start: 0.8085 (mt0) cc_final: 0.7810 (mt0) REVERT: B 28 GLN cc_start: 0.8288 (mt0) cc_final: 0.8015 (mt0) REVERT: B 60 ASN cc_start: 0.7919 (m110) cc_final: 0.7305 (p0) REVERT: B 95 HIS cc_start: 0.7798 (m90) cc_final: 0.7253 (m-70) REVERT: B 109 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7221 (mp0) REVERT: B 146 HIS cc_start: 0.7516 (m170) cc_final: 0.7266 (m-70) REVERT: B 149 ILE cc_start: 0.8224 (mt) cc_final: 0.7893 (tt) REVERT: B 153 LYS cc_start: 0.7872 (mtmp) cc_final: 0.7391 (mtmp) REVERT: B 180 GLN cc_start: 0.7232 (mm-40) cc_final: 0.7002 (mm-40) REVERT: B 181 ARG cc_start: 0.6791 (ttt180) cc_final: 0.6396 (ttp-110) REVERT: B 183 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.6775 (mmt180) REVERT: B 200 LEU cc_start: 0.7701 (mt) cc_final: 0.7455 (mt) REVERT: B 205 LEU cc_start: 0.8353 (mt) cc_final: 0.8075 (mp) REVERT: B 226 GLN cc_start: 0.8035 (mt0) cc_final: 0.7513 (mt0) REVERT: B 228 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.6149 (mtm-85) REVERT: B 242 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7823 (mt-10) REVERT: B 244 MET cc_start: 0.6976 (mmp) cc_final: 0.6745 (mmp) REVERT: B 265 ARG cc_start: 0.8467 (ptt180) cc_final: 0.8094 (ptt180) REVERT: B 274 GLN cc_start: 0.8001 (mt0) cc_final: 0.7222 (mt0) REVERT: B 275 LEU cc_start: 0.8422 (tp) cc_final: 0.8089 (tp) REVERT: B 281 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6842 (mm-30) REVERT: B 284 LYS cc_start: 0.7231 (mtmt) cc_final: 0.6961 (mtmm) REVERT: B 294 THR cc_start: 0.8454 (p) cc_final: 0.8221 (p) REVERT: B 299 LEU cc_start: 0.8530 (tp) cc_final: 0.7920 (tp) REVERT: B 348 PHE cc_start: 0.8445 (t80) cc_final: 0.8167 (t80) REVERT: B 377 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 383 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8055 (mm-30) REVERT: B 419 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: B 445 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6761 (pp20) REVERT: B 446 GLN cc_start: 0.7922 (mm-40) cc_final: 0.6840 (mm-40) REVERT: B 451 LYS cc_start: 0.8524 (mttt) cc_final: 0.8117 (mttm) REVERT: B 461 ARG cc_start: 0.7767 (tpt170) cc_final: 0.7539 (tpp80) REVERT: B 464 PHE cc_start: 0.6885 (p90) cc_final: 0.6598 (p90) REVERT: B 475 ASP cc_start: 0.7648 (t70) cc_final: 0.7224 (t70) REVERT: C 29 LEU cc_start: 0.8392 (tp) cc_final: 0.8178 (tt) REVERT: C 68 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6573 (mt-10) REVERT: C 181 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7163 (tpp-160) REVERT: C 182 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 183 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.8215 (mmp80) REVERT: C 204 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7731 (t70) REVERT: C 208 ARG cc_start: 0.8169 (mpp80) cc_final: 0.7709 (mtm180) REVERT: C 214 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7695 (ttmt) REVERT: C 224 GLU cc_start: 0.7482 (tt0) cc_final: 0.7272 (pp20) REVERT: C 237 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.8238 (mtp180) REVERT: C 239 MET cc_start: 0.7819 (mmm) cc_final: 0.7261 (mmm) REVERT: C 242 GLU cc_start: 0.7442 (pm20) cc_final: 0.6978 (pm20) REVERT: C 244 MET cc_start: 0.8648 (mmt) cc_final: 0.8111 (mtt) REVERT: C 251 ASN cc_start: 0.8652 (p0) cc_final: 0.8437 (p0) REVERT: C 276 GLU cc_start: 0.8218 (pt0) cc_final: 0.7958 (pt0) REVERT: C 331 PHE cc_start: 0.8439 (m-80) cc_final: 0.8099 (m-80) REVERT: C 350 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8183 (mt-10) REVERT: C 452 ASN cc_start: 0.8187 (t0) cc_final: 0.7507 (t0) REVERT: D 9 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7841 (mt) REVERT: D 22 GLN cc_start: 0.8153 (mt0) cc_final: 0.7883 (mt0) REVERT: D 51 ASP cc_start: 0.8467 (t0) cc_final: 0.8114 (t0) REVERT: D 56 LYS cc_start: 0.8248 (ttmt) cc_final: 0.8024 (ttmt) REVERT: D 70 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7391 (tm-30) REVERT: D 99 ASP cc_start: 0.7155 (m-30) cc_final: 0.6861 (m-30) REVERT: D 109 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6811 (mt-10) REVERT: D 114 THR cc_start: 0.8493 (p) cc_final: 0.8245 (m) REVERT: D 138 LYS cc_start: 0.8459 (mttt) cc_final: 0.7922 (mtpp) REVERT: D 139 GLU cc_start: 0.7738 (tp30) cc_final: 0.7128 (tp30) REVERT: D 140 ARG cc_start: 0.7738 (tpt170) cc_final: 0.7010 (tpt170) REVERT: D 149 ILE cc_start: 0.8387 (mm) cc_final: 0.8142 (tp) REVERT: D 199 HIS cc_start: 0.7636 (t-90) cc_final: 0.7377 (t-170) REVERT: D 215 ASP cc_start: 0.7460 (m-30) cc_final: 0.7072 (t70) REVERT: D 235 LEU cc_start: 0.8374 (mt) cc_final: 0.8135 (mt) REVERT: D 239 MET cc_start: 0.7969 (mmm) cc_final: 0.7267 (mpp) REVERT: D 272 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7924 (mmm160) REVERT: D 329 MET cc_start: 0.8081 (tpp) cc_final: 0.7628 (tpp) REVERT: D 333 LYS cc_start: 0.7014 (tttp) cc_final: 0.6805 (tttp) REVERT: D 337 ASN cc_start: 0.7760 (t0) cc_final: 0.7311 (t0) REVERT: D 348 PHE cc_start: 0.8026 (t80) cc_final: 0.7724 (t80) REVERT: D 350 GLU cc_start: 0.8212 (tp30) cc_final: 0.7530 (tp30) REVERT: D 351 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: D 452 ASN cc_start: 0.8200 (t0) cc_final: 0.7656 (t0) REVERT: D 455 LEU cc_start: 0.8660 (mt) cc_final: 0.8459 (mt) REVERT: D 459 ASN cc_start: 0.8172 (m110) cc_final: 0.7951 (m110) REVERT: D 461 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6908 (ttm-80) outliers start: 62 outliers final: 41 residues processed: 472 average time/residue: 0.1928 time to fit residues: 126.1305 Evaluate side-chains 470 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 420 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 36 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS A 131 GLN A 146 HIS A 180 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS B 141 ASN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.210042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158370 restraints weight = 60668.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163456 restraints weight = 26765.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163390 restraints weight = 16832.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.165102 restraints weight = 13010.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164991 restraints weight = 11592.391| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20312 Z= 0.167 Angle : 0.594 10.877 28378 Z= 0.328 Chirality : 0.038 0.178 3109 Planarity : 0.005 0.048 3022 Dihedral : 22.777 81.817 4285 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.24 % Allowed : 17.13 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1937 helix: 2.07 (0.16), residues: 919 sheet: -0.04 (0.28), residues: 290 loop : 0.92 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 444 TYR 0.020 0.002 TYR B 324 PHE 0.070 0.002 PHE C 118 TRP 0.041 0.002 TRP C 35 HIS 0.008 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00344 (20296) covalent geometry : angle 0.58364 (28354) hydrogen bonds : bond 0.03817 ( 1046) hydrogen bonds : angle 3.72841 ( 2758) metal coordination : bond 0.00423 ( 16) metal coordination : angle 3.79435 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 437 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5490 (tmm) cc_final: 0.4823 (tmm) REVERT: A 6 VAL cc_start: 0.7246 (t) cc_final: 0.6801 (m) REVERT: A 8 ARG cc_start: 0.7286 (ttt-90) cc_final: 0.6475 (ttt-90) REVERT: A 9 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7474 (tt) REVERT: A 28 GLN cc_start: 0.8693 (mt0) cc_final: 0.8312 (tm-30) REVERT: A 29 LEU cc_start: 0.8569 (tp) cc_final: 0.8229 (tp) REVERT: A 63 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7385 (mtm110) REVERT: A 82 ARG cc_start: 0.8377 (mmt180) cc_final: 0.7871 (mmp80) REVERT: A 96 TRP cc_start: 0.7836 (t60) cc_final: 0.7378 (t60) REVERT: A 101 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7997 (mmtt) REVERT: A 109 GLU cc_start: 0.6433 (mt-10) cc_final: 0.5799 (mp0) REVERT: A 131 GLN cc_start: 0.8126 (tp-100) cc_final: 0.6954 (tp-100) REVERT: A 134 LEU cc_start: 0.8681 (tp) cc_final: 0.7579 (tp) REVERT: A 135 GLU cc_start: 0.7931 (mm-30) cc_final: 0.6444 (mm-30) REVERT: A 138 LYS cc_start: 0.8447 (mttm) cc_final: 0.7564 (mttm) REVERT: A 219 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6840 (mm110) REVERT: A 235 LEU cc_start: 0.8819 (mt) cc_final: 0.8329 (mt) REVERT: A 237 ARG cc_start: 0.8387 (ttt-90) cc_final: 0.7918 (ttt-90) REVERT: A 239 MET cc_start: 0.7853 (mmm) cc_final: 0.7016 (mmm) REVERT: A 244 MET cc_start: 0.5622 (mmt) cc_final: 0.5036 (ppp) REVERT: A 275 LEU cc_start: 0.7547 (tp) cc_final: 0.7195 (tp) REVERT: A 409 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7327 (tpm170) REVERT: B 8 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.5873 (ttt-90) REVERT: B 9 LEU cc_start: 0.7895 (mt) cc_final: 0.7611 (tp) REVERT: B 21 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7628 (ttm170) REVERT: B 82 ARG cc_start: 0.7448 (mmp-170) cc_final: 0.7166 (mmp-170) REVERT: B 88 ARG cc_start: 0.8009 (tpp80) cc_final: 0.6275 (tpt-90) REVERT: B 91 GLN cc_start: 0.8102 (mt0) cc_final: 0.7801 (mt0) REVERT: B 95 HIS cc_start: 0.7710 (m-70) cc_final: 0.6471 (m-70) REVERT: B 109 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7095 (mp0) REVERT: B 146 HIS cc_start: 0.7591 (m170) cc_final: 0.7361 (m-70) REVERT: B 149 ILE cc_start: 0.8122 (mt) cc_final: 0.7841 (tt) REVERT: B 153 LYS cc_start: 0.7932 (mtmp) cc_final: 0.7483 (mtmp) REVERT: B 181 ARG cc_start: 0.6810 (ttt180) cc_final: 0.6315 (ttp-110) REVERT: B 183 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.6721 (mmt180) REVERT: B 191 VAL cc_start: 0.8240 (t) cc_final: 0.7508 (p) REVERT: B 200 LEU cc_start: 0.7527 (mt) cc_final: 0.7200 (mt) REVERT: B 203 HIS cc_start: 0.7724 (m-70) cc_final: 0.6854 (t-90) REVERT: B 205 LEU cc_start: 0.8290 (mt) cc_final: 0.8071 (mp) REVERT: B 207 ARG cc_start: 0.7581 (tpp80) cc_final: 0.6881 (tpp80) REVERT: B 242 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 247 TYR cc_start: 0.7994 (m-10) cc_final: 0.7466 (m-10) REVERT: B 265 ARG cc_start: 0.8442 (ptt180) cc_final: 0.7924 (ptt180) REVERT: B 274 GLN cc_start: 0.7963 (mt0) cc_final: 0.7057 (mt0) REVERT: B 275 LEU cc_start: 0.8475 (tp) cc_final: 0.8123 (tp) REVERT: B 294 THR cc_start: 0.8479 (p) cc_final: 0.8221 (p) REVERT: B 348 PHE cc_start: 0.8295 (t80) cc_final: 0.7932 (t80) REVERT: B 377 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7876 (mt) REVERT: B 379 GLU cc_start: 0.8470 (pt0) cc_final: 0.8184 (mt-10) REVERT: B 383 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8042 (mm-30) REVERT: B 409 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6867 (ptt90) REVERT: B 444 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8164 (mmm-85) REVERT: B 451 LYS cc_start: 0.8411 (mttt) cc_final: 0.8079 (mttm) REVERT: B 464 PHE cc_start: 0.6917 (p90) cc_final: 0.6504 (p90) REVERT: B 475 ASP cc_start: 0.7453 (t70) cc_final: 0.6989 (t70) REVERT: C 2 ARG cc_start: 0.6826 (ptm160) cc_final: 0.6511 (mtp180) REVERT: C 68 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6446 (mt-10) REVERT: C 95 HIS cc_start: 0.7532 (t-170) cc_final: 0.7166 (t-170) REVERT: C 96 TRP cc_start: 0.8744 (t60) cc_final: 0.7499 (t60) REVERT: C 98 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6432 (pp20) REVERT: C 181 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7143 (tpp-160) REVERT: C 182 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7346 (tm-30) REVERT: C 183 ARG cc_start: 0.8586 (mmt-90) cc_final: 0.8065 (mmp-170) REVERT: C 190 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7575 (mmm-85) REVERT: C 204 ASP cc_start: 0.8103 (t70) cc_final: 0.7644 (t70) REVERT: C 208 ARG cc_start: 0.8093 (mpp80) cc_final: 0.7844 (mtm-85) REVERT: C 237 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8070 (mtp180) REVERT: C 242 GLU cc_start: 0.7283 (pm20) cc_final: 0.6846 (pm20) REVERT: C 276 GLU cc_start: 0.8238 (pt0) cc_final: 0.7975 (pt0) REVERT: C 331 PHE cc_start: 0.8402 (m-80) cc_final: 0.8160 (m-80) REVERT: C 350 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 452 ASN cc_start: 0.8191 (t0) cc_final: 0.7629 (t0) REVERT: C 454 TRP cc_start: 0.8153 (t-100) cc_final: 0.7806 (t-100) REVERT: D 9 LEU cc_start: 0.8251 (tt) cc_final: 0.7763 (mp) REVERT: D 22 GLN cc_start: 0.8055 (mt0) cc_final: 0.7689 (mt0) REVERT: D 43 ASP cc_start: 0.6945 (t0) cc_final: 0.6579 (t0) REVERT: D 51 ASP cc_start: 0.8336 (t0) cc_final: 0.7919 (t0) REVERT: D 60 ASN cc_start: 0.8130 (m110) cc_final: 0.7739 (t0) REVERT: D 70 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7188 (tm-30) REVERT: D 95 HIS cc_start: 0.7447 (m-70) cc_final: 0.7190 (m-70) REVERT: D 109 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6552 (mt-10) REVERT: D 114 THR cc_start: 0.8476 (p) cc_final: 0.8269 (m) REVERT: D 140 ARG cc_start: 0.7675 (tpt170) cc_final: 0.6566 (tpt170) REVERT: D 215 ASP cc_start: 0.7249 (m-30) cc_final: 0.6677 (t70) REVERT: D 229 GLU cc_start: 0.7088 (pt0) cc_final: 0.6758 (pt0) REVERT: D 329 MET cc_start: 0.7858 (tpp) cc_final: 0.7464 (mpp) REVERT: D 333 LYS cc_start: 0.7041 (tttp) cc_final: 0.6778 (tttp) REVERT: D 337 ASN cc_start: 0.7745 (t0) cc_final: 0.7161 (t0) REVERT: D 348 PHE cc_start: 0.7932 (t80) cc_final: 0.7632 (t80) REVERT: D 351 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: D 452 ASN cc_start: 0.8209 (t0) cc_final: 0.7684 (t0) REVERT: D 455 LEU cc_start: 0.8615 (mt) cc_final: 0.8414 (mt) REVERT: D 459 ASN cc_start: 0.8090 (m110) cc_final: 0.7869 (m110) REVERT: D 461 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6920 (ttm-80) REVERT: D 472 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.6906 (ttm-80) outliers start: 52 outliers final: 31 residues processed: 464 average time/residue: 0.1984 time to fit residues: 126.8120 Evaluate side-chains 464 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 427 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 22 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 50.0000 chunk 173 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.204446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148350 restraints weight = 47091.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.153763 restraints weight = 21227.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157072 restraints weight = 12984.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159041 restraints weight = 9527.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.160052 restraints weight = 7883.343| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 20312 Z= 0.352 Angle : 0.714 10.393 28378 Z= 0.401 Chirality : 0.046 0.234 3109 Planarity : 0.006 0.051 3022 Dihedral : 22.998 89.185 4275 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.24 % Allowed : 17.32 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1937 helix: 1.35 (0.16), residues: 918 sheet: -0.17 (0.29), residues: 275 loop : 0.63 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 155 TYR 0.023 0.002 TYR B 324 PHE 0.038 0.002 PHE D 217 TRP 0.046 0.003 TRP C 35 HIS 0.016 0.002 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00732 (20296) covalent geometry : angle 0.70111 (28354) hydrogen bonds : bond 0.05585 ( 1046) hydrogen bonds : angle 4.28259 ( 2758) metal coordination : bond 0.00859 ( 16) metal coordination : angle 4.70115 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 454 time to evaluate : 0.588 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5806 (tmm) cc_final: 0.5013 (tmm) REVERT: A 8 ARG cc_start: 0.7089 (ttt-90) cc_final: 0.6500 (ttt-90) REVERT: A 9 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7904 (tt) REVERT: A 21 ARG cc_start: 0.7060 (tpt90) cc_final: 0.6577 (mmm160) REVERT: A 22 GLN cc_start: 0.8432 (mp10) cc_final: 0.8046 (pm20) REVERT: A 28 GLN cc_start: 0.8635 (mt0) cc_final: 0.8371 (tm-30) REVERT: A 63 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.7254 (mtm110) REVERT: A 65 LEU cc_start: 0.8226 (mt) cc_final: 0.7151 (mm) REVERT: A 69 GLU cc_start: 0.5801 (mm-30) cc_final: 0.2303 (pm20) REVERT: A 82 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8137 (mmp80) REVERT: A 94 VAL cc_start: 0.8998 (m) cc_final: 0.8759 (p) REVERT: A 96 TRP cc_start: 0.7968 (t60) cc_final: 0.7276 (t60) REVERT: A 109 GLU cc_start: 0.5923 (mt-10) cc_final: 0.5632 (mp0) REVERT: A 126 MET cc_start: 0.7991 (mmm) cc_final: 0.7524 (mmm) REVERT: A 129 VAL cc_start: 0.8808 (m) cc_final: 0.8576 (p) REVERT: A 131 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7329 (tp-100) REVERT: A 134 LEU cc_start: 0.8596 (tp) cc_final: 0.8351 (tp) REVERT: A 135 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 235 LEU cc_start: 0.9076 (mt) cc_final: 0.8720 (mt) REVERT: A 238 SER cc_start: 0.8983 (m) cc_final: 0.8573 (p) REVERT: A 239 MET cc_start: 0.8093 (mmm) cc_final: 0.7465 (mmm) REVERT: A 257 ASP cc_start: 0.7703 (p0) cc_final: 0.7461 (p0) REVERT: A 275 LEU cc_start: 0.7785 (tp) cc_final: 0.7554 (mp) REVERT: A 409 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7761 (tpp-160) REVERT: B 8 ARG cc_start: 0.7441 (ttt-90) cc_final: 0.6111 (tmm160) REVERT: B 9 LEU cc_start: 0.8130 (mt) cc_final: 0.7550 (tt) REVERT: B 21 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7813 (ttm170) REVERT: B 22 GLN cc_start: 0.8110 (mt0) cc_final: 0.7660 (mt0) REVERT: B 44 LEU cc_start: 0.8306 (mp) cc_final: 0.8075 (mm) REVERT: B 56 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7651 (ptpp) REVERT: B 79 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7522 (mtp85) REVERT: B 88 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7837 (tpp80) REVERT: B 109 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7093 (mp0) REVERT: B 135 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 149 ILE cc_start: 0.8214 (mt) cc_final: 0.7935 (tt) REVERT: B 153 LYS cc_start: 0.7993 (mtmp) cc_final: 0.7583 (mtmp) REVERT: B 164 LEU cc_start: 0.8113 (tp) cc_final: 0.7620 (mt) REVERT: B 183 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6734 (mmt180) REVERT: B 196 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 200 LEU cc_start: 0.7746 (mt) cc_final: 0.7528 (mt) REVERT: B 203 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7086 (t-90) REVERT: B 207 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7066 (tpp80) REVERT: B 226 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: B 242 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 265 ARG cc_start: 0.8463 (ptt180) cc_final: 0.7876 (ptt90) REVERT: B 274 GLN cc_start: 0.7927 (mt0) cc_final: 0.7170 (mt0) REVERT: B 275 LEU cc_start: 0.8370 (tp) cc_final: 0.8029 (tp) REVERT: B 281 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7477 (tt0) REVERT: B 294 THR cc_start: 0.8448 (p) cc_final: 0.8209 (p) REVERT: B 348 PHE cc_start: 0.8402 (t80) cc_final: 0.8039 (t80) REVERT: B 377 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B 379 GLU cc_start: 0.8727 (pt0) cc_final: 0.8449 (mt-10) REVERT: B 383 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8379 (mt-10) REVERT: B 451 LYS cc_start: 0.8547 (mttt) cc_final: 0.8188 (mttm) REVERT: B 459 ASN cc_start: 0.8396 (m-40) cc_final: 0.8108 (m-40) REVERT: B 464 PHE cc_start: 0.6781 (p90) cc_final: 0.6443 (p90) REVERT: B 475 ASP cc_start: 0.7947 (t70) cc_final: 0.7572 (t70) REVERT: C 63 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7338 (ttm-80) REVERT: C 68 GLU cc_start: 0.6820 (mt-10) cc_final: 0.5930 (mt-10) REVERT: C 74 VAL cc_start: 0.6995 (OUTLIER) cc_final: 0.6618 (t) REVERT: C 95 HIS cc_start: 0.7701 (t-170) cc_final: 0.6873 (t-170) REVERT: C 98 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6478 (pp20) REVERT: C 99 ASP cc_start: 0.7821 (m-30) cc_final: 0.7348 (m-30) REVERT: C 113 ASP cc_start: 0.7843 (t0) cc_final: 0.7622 (t0) REVERT: C 138 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8173 (mmmt) REVERT: C 155 ARG cc_start: 0.7286 (ptm-80) cc_final: 0.6977 (ttp80) REVERT: C 182 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 183 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.8152 (mmp80) REVERT: C 204 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7619 (t70) REVERT: C 237 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8376 (mtp180) REVERT: C 239 MET cc_start: 0.7845 (mmm) cc_final: 0.7401 (mmm) REVERT: C 242 GLU cc_start: 0.7555 (pm20) cc_final: 0.7304 (pm20) REVERT: C 244 MET cc_start: 0.8597 (mmt) cc_final: 0.8185 (mtt) REVERT: C 276 GLU cc_start: 0.8289 (pt0) cc_final: 0.8016 (pt0) REVERT: C 329 MET cc_start: 0.8666 (ttm) cc_final: 0.8215 (tmm) REVERT: C 331 PHE cc_start: 0.8605 (m-80) cc_final: 0.8256 (m-80) REVERT: C 350 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8240 (mt-10) REVERT: C 452 ASN cc_start: 0.8074 (t0) cc_final: 0.7389 (t0) REVERT: D 9 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7774 (mm) REVERT: D 21 ARG cc_start: 0.7476 (mtp-110) cc_final: 0.7180 (mtp-110) REVERT: D 22 GLN cc_start: 0.8273 (mt0) cc_final: 0.7998 (mt0) REVERT: D 51 ASP cc_start: 0.8433 (t0) cc_final: 0.8070 (t0) REVERT: D 55 ARG cc_start: 0.6755 (mmm-85) cc_final: 0.6553 (tpp80) REVERT: D 57 ARG cc_start: 0.7349 (mmm160) cc_final: 0.7079 (mmm160) REVERT: D 60 ASN cc_start: 0.8112 (m110) cc_final: 0.7574 (t0) REVERT: D 70 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7274 (tm-30) REVERT: D 109 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6883 (pm20) REVERT: D 114 THR cc_start: 0.8562 (p) cc_final: 0.8333 (m) REVERT: D 133 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8007 (mt-10) REVERT: D 138 LYS cc_start: 0.8435 (mttt) cc_final: 0.7816 (mtpp) REVERT: D 139 GLU cc_start: 0.7794 (tp30) cc_final: 0.7174 (tp30) REVERT: D 140 ARG cc_start: 0.7709 (tpt170) cc_final: 0.6933 (tpt170) REVERT: D 215 ASP cc_start: 0.7418 (m-30) cc_final: 0.6731 (t0) REVERT: D 229 GLU cc_start: 0.7097 (pt0) cc_final: 0.6897 (pt0) REVERT: D 274 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: D 281 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: D 287 ARG cc_start: 0.4654 (OUTLIER) cc_final: 0.4404 (ptm160) REVERT: D 329 MET cc_start: 0.8060 (tpp) cc_final: 0.7827 (tpp) REVERT: D 333 LYS cc_start: 0.7383 (tttp) cc_final: 0.7118 (tttp) REVERT: D 337 ASN cc_start: 0.7780 (t0) cc_final: 0.7180 (t0) REVERT: D 350 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7722 (tp30) REVERT: D 351 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: D 452 ASN cc_start: 0.8346 (t0) cc_final: 0.7770 (t0) REVERT: D 455 LEU cc_start: 0.8814 (mt) cc_final: 0.8585 (mt) REVERT: D 458 MET cc_start: 0.8119 (mmt) cc_final: 0.7364 (mmt) REVERT: D 461 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6888 (ttm-80) outliers start: 68 outliers final: 44 residues processed: 478 average time/residue: 0.1850 time to fit residues: 124.1976 Evaluate side-chains 498 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 440 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 185 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 137 optimal weight: 50.0000 chunk 199 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 177 optimal weight: 0.4980 chunk 47 optimal weight: 50.0000 chunk 146 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.207003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151992 restraints weight = 49780.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.157584 restraints weight = 21920.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.160952 restraints weight = 13235.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163001 restraints weight = 9621.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164153 restraints weight = 7895.586| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20312 Z= 0.212 Angle : 0.637 12.999 28378 Z= 0.351 Chirality : 0.040 0.204 3109 Planarity : 0.005 0.054 3022 Dihedral : 22.869 83.473 4272 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.61 % Allowed : 19.50 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 1937 helix: 1.59 (0.17), residues: 917 sheet: -0.24 (0.29), residues: 276 loop : 0.71 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 150 TYR 0.020 0.002 TYR D 216 PHE 0.043 0.002 PHE D 217 TRP 0.050 0.002 TRP D 96 HIS 0.010 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00445 (20296) covalent geometry : angle 0.62720 (28354) hydrogen bonds : bond 0.04242 ( 1046) hydrogen bonds : angle 3.98318 ( 2758) metal coordination : bond 0.00517 ( 16) metal coordination : angle 3.97293 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 443 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6020 (tmm) cc_final: 0.5604 (tmm) REVERT: A 8 ARG cc_start: 0.7020 (ttt-90) cc_final: 0.6337 (tmt170) REVERT: A 9 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 21 ARG cc_start: 0.6964 (tpt90) cc_final: 0.6655 (mmm160) REVERT: A 27 GLN cc_start: 0.8414 (mt0) cc_final: 0.8090 (mm-40) REVERT: A 63 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.6700 (mtm110) REVERT: A 65 LEU cc_start: 0.8032 (mt) cc_final: 0.6850 (mm) REVERT: A 69 GLU cc_start: 0.5380 (mm-30) cc_final: 0.2784 (pm20) REVERT: A 82 ARG cc_start: 0.8519 (mmt180) cc_final: 0.8116 (mmp80) REVERT: A 94 VAL cc_start: 0.8921 (m) cc_final: 0.8700 (p) REVERT: A 96 TRP cc_start: 0.7899 (t60) cc_final: 0.7172 (t60) REVERT: A 109 GLU cc_start: 0.5775 (mt-10) cc_final: 0.5469 (mp0) REVERT: A 126 MET cc_start: 0.7945 (mmm) cc_final: 0.7477 (mmm) REVERT: A 131 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7064 (tp-100) REVERT: A 132 MET cc_start: 0.7510 (mpm) cc_final: 0.7211 (mpm) REVERT: A 134 LEU cc_start: 0.8553 (tp) cc_final: 0.7980 (tp) REVERT: A 135 GLU cc_start: 0.8077 (mm-30) cc_final: 0.6611 (mm-30) REVERT: A 138 LYS cc_start: 0.8560 (mttm) cc_final: 0.7569 (mttm) REVERT: A 235 LEU cc_start: 0.9096 (mt) cc_final: 0.8474 (mt) REVERT: A 236 LYS cc_start: 0.8871 (tptp) cc_final: 0.8412 (mmmt) REVERT: A 237 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.7277 (ttm110) REVERT: A 238 SER cc_start: 0.9132 (m) cc_final: 0.8552 (p) REVERT: A 239 MET cc_start: 0.8030 (mmm) cc_final: 0.7457 (mmm) REVERT: A 257 ASP cc_start: 0.7584 (p0) cc_final: 0.7222 (p0) REVERT: A 275 LEU cc_start: 0.7650 (tp) cc_final: 0.7446 (mp) REVERT: B 8 ARG cc_start: 0.7278 (ttt-90) cc_final: 0.6169 (tmm160) REVERT: B 9 LEU cc_start: 0.7903 (mt) cc_final: 0.7506 (tt) REVERT: B 21 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7855 (ttm170) REVERT: B 23 LEU cc_start: 0.8647 (tp) cc_final: 0.8334 (pp) REVERT: B 26 CYS cc_start: 0.8052 (m) cc_final: 0.7563 (p) REVERT: B 56 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7643 (ptpp) REVERT: B 79 ARG cc_start: 0.7735 (mtp85) cc_final: 0.6971 (mtp85) REVERT: B 88 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7395 (tpt-90) REVERT: B 109 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7199 (mp0) REVERT: B 121 VAL cc_start: 0.8680 (m) cc_final: 0.8339 (p) REVERT: B 135 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 149 ILE cc_start: 0.8107 (mt) cc_final: 0.7888 (tt) REVERT: B 153 LYS cc_start: 0.7947 (mtmp) cc_final: 0.7558 (mtmp) REVERT: B 164 LEU cc_start: 0.8097 (tp) cc_final: 0.7880 (tp) REVERT: B 183 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6640 (mmt180) REVERT: B 196 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6989 (mp0) REVERT: B 200 LEU cc_start: 0.7605 (mt) cc_final: 0.7384 (mt) REVERT: B 203 HIS cc_start: 0.7843 (m-70) cc_final: 0.6800 (t-90) REVERT: B 207 ARG cc_start: 0.7612 (tpp80) cc_final: 0.6808 (tpp80) REVERT: B 226 GLN cc_start: 0.7566 (mt0) cc_final: 0.7200 (tp40) REVERT: B 265 ARG cc_start: 0.8503 (ptt180) cc_final: 0.7898 (ptt90) REVERT: B 272 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7628 (tpp80) REVERT: B 274 GLN cc_start: 0.7929 (mt0) cc_final: 0.7151 (mt0) REVERT: B 275 LEU cc_start: 0.8402 (tp) cc_final: 0.8072 (tp) REVERT: B 281 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7327 (tt0) REVERT: B 294 THR cc_start: 0.8339 (p) cc_final: 0.8095 (p) REVERT: B 348 PHE cc_start: 0.8382 (t80) cc_final: 0.8082 (t80) REVERT: B 377 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8109 (mt) REVERT: B 379 GLU cc_start: 0.8710 (pt0) cc_final: 0.8424 (mt-10) REVERT: B 383 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 419 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6243 (tm-30) REVERT: B 444 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8144 (mmm-85) REVERT: B 451 LYS cc_start: 0.8503 (mttt) cc_final: 0.8021 (mttm) REVERT: B 459 ASN cc_start: 0.8313 (m-40) cc_final: 0.8024 (m-40) REVERT: B 464 PHE cc_start: 0.6715 (p90) cc_final: 0.6402 (p90) REVERT: B 475 ASP cc_start: 0.7827 (t70) cc_final: 0.7422 (t70) REVERT: C 63 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7363 (ttm-80) REVERT: C 68 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5950 (mt-10) REVERT: C 95 HIS cc_start: 0.7615 (t-170) cc_final: 0.7047 (t-170) REVERT: C 96 TRP cc_start: 0.8852 (t60) cc_final: 0.8525 (t60) REVERT: C 99 ASP cc_start: 0.7739 (m-30) cc_final: 0.7466 (m-30) REVERT: C 138 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8128 (mmmt) REVERT: C 155 ARG cc_start: 0.7359 (ptm-80) cc_final: 0.7114 (ttp80) REVERT: C 164 LEU cc_start: 0.8032 (tp) cc_final: 0.7795 (mm) REVERT: C 181 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7150 (tpp-160) REVERT: C 182 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7021 (tm-30) REVERT: C 183 ARG cc_start: 0.8695 (mmt-90) cc_final: 0.8086 (mmp-170) REVERT: C 237 ARG cc_start: 0.8687 (ttp-170) cc_final: 0.8307 (mtp180) REVERT: C 242 GLU cc_start: 0.7431 (pm20) cc_final: 0.7186 (pm20) REVERT: C 274 GLN cc_start: 0.8430 (mt0) cc_final: 0.7990 (mt0) REVERT: C 276 GLU cc_start: 0.8222 (pt0) cc_final: 0.7955 (pt0) REVERT: C 329 MET cc_start: 0.8652 (ttm) cc_final: 0.8160 (tmm) REVERT: C 331 PHE cc_start: 0.8644 (m-80) cc_final: 0.8274 (m-80) REVERT: C 350 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8232 (mt-10) REVERT: C 452 ASN cc_start: 0.8022 (t0) cc_final: 0.7423 (t0) REVERT: D 9 LEU cc_start: 0.8203 (tt) cc_final: 0.7717 (mm) REVERT: D 21 ARG cc_start: 0.7476 (mtp-110) cc_final: 0.7124 (mtp-110) REVERT: D 57 ARG cc_start: 0.7319 (mmm160) cc_final: 0.7053 (mmm160) REVERT: D 60 ASN cc_start: 0.8067 (m110) cc_final: 0.7602 (t0) REVERT: D 64 TRP cc_start: 0.7956 (m100) cc_final: 0.7517 (m100) REVERT: D 70 GLN cc_start: 0.7838 (tm-30) cc_final: 0.6819 (tm-30) REVERT: D 138 LYS cc_start: 0.8403 (mttt) cc_final: 0.7741 (ttmm) REVERT: D 139 GLU cc_start: 0.7802 (tp30) cc_final: 0.7144 (tp30) REVERT: D 140 ARG cc_start: 0.7733 (tpt170) cc_final: 0.6871 (tpt170) REVERT: D 215 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6826 (t70) REVERT: D 229 GLU cc_start: 0.7205 (pt0) cc_final: 0.6972 (pt0) REVERT: D 265 ARG cc_start: 0.7517 (ptt180) cc_final: 0.7250 (ptp-170) REVERT: D 272 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.6874 (mmm-85) REVERT: D 276 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8078 (mm-30) REVERT: D 281 GLU cc_start: 0.7895 (tp30) cc_final: 0.7487 (tp30) REVERT: D 287 ARG cc_start: 0.4711 (OUTLIER) cc_final: 0.4495 (ptm160) REVERT: D 329 MET cc_start: 0.8030 (tpp) cc_final: 0.7784 (tpp) REVERT: D 333 LYS cc_start: 0.7419 (tttp) cc_final: 0.7137 (tttp) REVERT: D 337 ASN cc_start: 0.7923 (t0) cc_final: 0.7395 (t0) REVERT: D 351 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: D 386 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6489 (t70) REVERT: D 452 ASN cc_start: 0.8293 (t0) cc_final: 0.7736 (t0) REVERT: D 455 LEU cc_start: 0.8819 (mt) cc_final: 0.8609 (mt) REVERT: D 461 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.6870 (ttm-80) outliers start: 58 outliers final: 39 residues processed: 469 average time/residue: 0.1835 time to fit residues: 121.1475 Evaluate side-chains 487 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 163 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 133 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.206881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152946 restraints weight = 42440.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.158127 restraints weight = 20000.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.161249 restraints weight = 12496.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163145 restraints weight = 9317.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164266 restraints weight = 7756.032| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20312 Z= 0.220 Angle : 0.645 11.674 28378 Z= 0.356 Chirality : 0.042 0.392 3109 Planarity : 0.005 0.053 3022 Dihedral : 22.830 86.049 4269 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.49 % Allowed : 19.88 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 1937 helix: 1.49 (0.17), residues: 923 sheet: -0.24 (0.29), residues: 275 loop : 0.65 (0.25), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 150 TYR 0.028 0.002 TYR D 216 PHE 0.039 0.002 PHE D 217 TRP 0.045 0.002 TRP C 35 HIS 0.012 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00463 (20296) covalent geometry : angle 0.63459 (28354) hydrogen bonds : bond 0.04439 ( 1046) hydrogen bonds : angle 4.02832 ( 2758) metal coordination : bond 0.00588 ( 16) metal coordination : angle 4.09693 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 441 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6024 (tmm) cc_final: 0.5710 (tmm) REVERT: A 8 ARG cc_start: 0.6912 (ttt-90) cc_final: 0.5862 (tmt170) REVERT: A 9 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7994 (tt) REVERT: A 21 ARG cc_start: 0.6847 (tpt90) cc_final: 0.6610 (mmm160) REVERT: A 22 GLN cc_start: 0.8410 (mp10) cc_final: 0.8195 (pm20) REVERT: A 27 GLN cc_start: 0.8319 (mt0) cc_final: 0.7975 (mm-40) REVERT: A 28 GLN cc_start: 0.8704 (mt0) cc_final: 0.8489 (mt0) REVERT: A 63 ARG cc_start: 0.7488 (mtp-110) cc_final: 0.6906 (mtm110) REVERT: A 65 LEU cc_start: 0.8151 (mt) cc_final: 0.6971 (mm) REVERT: A 69 GLU cc_start: 0.5512 (mm-30) cc_final: 0.2627 (pm20) REVERT: A 82 ARG cc_start: 0.8437 (mmt180) cc_final: 0.7855 (mmp-170) REVERT: A 94 VAL cc_start: 0.8942 (m) cc_final: 0.8705 (p) REVERT: A 96 TRP cc_start: 0.7832 (t60) cc_final: 0.7116 (t60) REVERT: A 126 MET cc_start: 0.8086 (mmm) cc_final: 0.7807 (mmm) REVERT: A 129 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8580 (m) REVERT: A 132 MET cc_start: 0.7509 (mpm) cc_final: 0.7297 (mpm) REVERT: A 134 LEU cc_start: 0.8609 (tp) cc_final: 0.8053 (tp) REVERT: A 135 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7010 (mm-30) REVERT: A 138 LYS cc_start: 0.8536 (mttm) cc_final: 0.7578 (mttm) REVERT: A 235 LEU cc_start: 0.8993 (mt) cc_final: 0.8410 (mt) REVERT: A 236 LYS cc_start: 0.8914 (tptp) cc_final: 0.8589 (mmmm) REVERT: A 237 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.6997 (ttm110) REVERT: A 238 SER cc_start: 0.9273 (m) cc_final: 0.8870 (p) REVERT: A 239 MET cc_start: 0.8123 (mmm) cc_final: 0.7494 (mmm) REVERT: A 275 LEU cc_start: 0.7675 (tp) cc_final: 0.7195 (mp) REVERT: A 278 LEU cc_start: 0.8109 (tp) cc_final: 0.7768 (pp) REVERT: B 8 ARG cc_start: 0.7106 (ttt-90) cc_final: 0.6119 (tmm160) REVERT: B 9 LEU cc_start: 0.7693 (mt) cc_final: 0.7433 (tp) REVERT: B 21 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7722 (ttm-80) REVERT: B 23 LEU cc_start: 0.8640 (tp) cc_final: 0.8410 (pp) REVERT: B 26 CYS cc_start: 0.8066 (m) cc_final: 0.7550 (p) REVERT: B 56 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7561 (ptpp) REVERT: B 88 ARG cc_start: 0.7984 (tpp80) cc_final: 0.6893 (tpp80) REVERT: B 91 GLN cc_start: 0.8198 (mt0) cc_final: 0.7903 (mt0) REVERT: B 121 VAL cc_start: 0.8634 (m) cc_final: 0.8353 (p) REVERT: B 135 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7041 (mm-30) REVERT: B 149 ILE cc_start: 0.8135 (mt) cc_final: 0.7901 (tt) REVERT: B 153 LYS cc_start: 0.7957 (mtmp) cc_final: 0.7581 (mtmp) REVERT: B 164 LEU cc_start: 0.8115 (tp) cc_final: 0.7885 (tp) REVERT: B 183 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.6593 (tpt90) REVERT: B 196 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7089 (mp0) REVERT: B 200 LEU cc_start: 0.7590 (mt) cc_final: 0.7364 (mt) REVERT: B 203 HIS cc_start: 0.7872 (m-70) cc_final: 0.6880 (t-90) REVERT: B 207 ARG cc_start: 0.7583 (tpp80) cc_final: 0.6794 (tpp80) REVERT: B 226 GLN cc_start: 0.7565 (mt0) cc_final: 0.7327 (mt0) REVERT: B 244 MET cc_start: 0.7132 (mmp) cc_final: 0.6842 (mmm) REVERT: B 265 ARG cc_start: 0.8493 (ptt180) cc_final: 0.7912 (ptt90) REVERT: B 272 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7640 (tpp80) REVERT: B 274 GLN cc_start: 0.7985 (mt0) cc_final: 0.7222 (mt0) REVERT: B 275 LEU cc_start: 0.8381 (tp) cc_final: 0.8071 (tp) REVERT: B 281 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7369 (tt0) REVERT: B 348 PHE cc_start: 0.8422 (t80) cc_final: 0.8143 (t80) REVERT: B 350 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8371 (pp20) REVERT: B 377 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8143 (mt) REVERT: B 379 GLU cc_start: 0.8729 (pt0) cc_final: 0.8459 (mt-10) REVERT: B 383 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 409 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7110 (ptt90) REVERT: B 419 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: B 444 ARG cc_start: 0.8451 (mmm160) cc_final: 0.8102 (mmm-85) REVERT: B 451 LYS cc_start: 0.8538 (mttt) cc_final: 0.7950 (mttm) REVERT: B 459 ASN cc_start: 0.8365 (m-40) cc_final: 0.8117 (m-40) REVERT: B 464 PHE cc_start: 0.6752 (p90) cc_final: 0.6512 (p90) REVERT: B 475 ASP cc_start: 0.7848 (t70) cc_final: 0.7444 (t70) REVERT: C 63 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7342 (ttm-80) REVERT: C 95 HIS cc_start: 0.7574 (t-170) cc_final: 0.6378 (t-170) REVERT: C 96 TRP cc_start: 0.8835 (t60) cc_final: 0.8459 (t60) REVERT: C 98 GLU cc_start: 0.6748 (pp20) cc_final: 0.6526 (pp20) REVERT: C 133 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 138 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8252 (mmmt) REVERT: C 155 ARG cc_start: 0.7264 (ptm-80) cc_final: 0.7023 (ptm-80) REVERT: C 164 LEU cc_start: 0.7994 (tp) cc_final: 0.7773 (mm) REVERT: C 182 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6765 (tm-30) REVERT: C 183 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.7933 (mmp-170) REVERT: C 237 ARG cc_start: 0.8714 (ttp-170) cc_final: 0.8319 (mtp180) REVERT: C 242 GLU cc_start: 0.7421 (pm20) cc_final: 0.7183 (pm20) REVERT: C 270 LEU cc_start: 0.8197 (tp) cc_final: 0.7864 (tp) REVERT: C 274 GLN cc_start: 0.8415 (mt0) cc_final: 0.8189 (tt0) REVERT: C 275 LEU cc_start: 0.8125 (tp) cc_final: 0.7780 (tp) REVERT: C 276 GLU cc_start: 0.8243 (pt0) cc_final: 0.7920 (pt0) REVERT: C 329 MET cc_start: 0.8723 (ttm) cc_final: 0.8235 (tmm) REVERT: C 331 PHE cc_start: 0.8586 (m-80) cc_final: 0.8241 (m-80) REVERT: C 345 TRP cc_start: 0.7115 (m100) cc_final: 0.6776 (m100) REVERT: C 350 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8289 (mt-10) REVERT: C 452 ASN cc_start: 0.8019 (t0) cc_final: 0.7419 (t0) REVERT: D 9 LEU cc_start: 0.8218 (tt) cc_final: 0.7718 (mm) REVERT: D 21 ARG cc_start: 0.7304 (mtp-110) cc_final: 0.6944 (mtp-110) REVERT: D 43 ASP cc_start: 0.7267 (t0) cc_final: 0.7037 (t0) REVERT: D 51 ASP cc_start: 0.8226 (t0) cc_final: 0.7859 (t0) REVERT: D 60 ASN cc_start: 0.8054 (m110) cc_final: 0.7650 (t0) REVERT: D 64 TRP cc_start: 0.7864 (m100) cc_final: 0.7472 (m100) REVERT: D 70 GLN cc_start: 0.7783 (tm-30) cc_final: 0.6815 (tm-30) REVERT: D 95 HIS cc_start: 0.7776 (m-70) cc_final: 0.7070 (m-70) REVERT: D 102 LYS cc_start: 0.8105 (mttm) cc_final: 0.7734 (mttm) REVERT: D 138 LYS cc_start: 0.8326 (mttt) cc_final: 0.7656 (ttmm) REVERT: D 139 GLU cc_start: 0.7794 (tp30) cc_final: 0.7137 (tp30) REVERT: D 140 ARG cc_start: 0.7663 (tpt170) cc_final: 0.7126 (tpt170) REVERT: D 215 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.6932 (t70) REVERT: D 224 GLU cc_start: 0.6981 (tp30) cc_final: 0.6730 (tp30) REVERT: D 229 GLU cc_start: 0.7197 (pt0) cc_final: 0.6969 (pt0) REVERT: D 265 ARG cc_start: 0.7504 (ptt180) cc_final: 0.7097 (ptp-170) REVERT: D 272 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7029 (mmm160) REVERT: D 276 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8168 (mm-30) REVERT: D 281 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: D 287 ARG cc_start: 0.4805 (OUTLIER) cc_final: 0.4556 (ptm160) REVERT: D 329 MET cc_start: 0.7994 (tpp) cc_final: 0.7588 (mpp) REVERT: D 333 LYS cc_start: 0.7447 (tttp) cc_final: 0.7158 (tttp) REVERT: D 337 ASN cc_start: 0.7856 (t0) cc_final: 0.7415 (t0) REVERT: D 350 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: D 351 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: D 452 ASN cc_start: 0.8346 (t0) cc_final: 0.7797 (t0) REVERT: D 455 LEU cc_start: 0.8806 (mt) cc_final: 0.8600 (mt) REVERT: D 461 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.6895 (ttm-80) outliers start: 56 outliers final: 40 residues processed: 465 average time/residue: 0.1925 time to fit residues: 124.4725 Evaluate side-chains 480 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 430 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 200 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 53 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN B 22 GLN B 27 GLN B 28 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 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 = 0.4557 r_free = 0.4557 target = 0.209055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.161912 restraints weight = 60785.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163084 restraints weight = 27115.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164780 restraints weight = 16378.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164580 restraints weight = 13415.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164752 restraints weight = 12444.456| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20312 Z= 0.157 Angle : 0.621 12.089 28378 Z= 0.339 Chirality : 0.039 0.318 3109 Planarity : 0.005 0.060 3022 Dihedral : 22.810 81.138 4269 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.12 % Allowed : 20.50 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1937 helix: 1.65 (0.17), residues: 923 sheet: -0.27 (0.29), residues: 283 loop : 0.77 (0.26), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 467 TYR 0.032 0.002 TYR D 216 PHE 0.032 0.002 PHE D 217 TRP 0.038 0.002 TRP D 96 HIS 0.012 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00333 (20296) covalent geometry : angle 0.61209 (28354) hydrogen bonds : bond 0.03837 ( 1046) hydrogen bonds : angle 3.88248 ( 2758) metal coordination : bond 0.00415 ( 16) metal coordination : angle 3.72647 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 431 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7931 (tt) REVERT: A 21 ARG cc_start: 0.6831 (tpt90) cc_final: 0.6623 (mmm160) REVERT: A 27 GLN cc_start: 0.8239 (mt0) cc_final: 0.7930 (mm-40) REVERT: A 28 GLN cc_start: 0.8658 (mt0) cc_final: 0.8381 (mt0) REVERT: A 63 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.6293 (mtm110) REVERT: A 69 GLU cc_start: 0.5229 (mm-30) cc_final: 0.2453 (pm20) REVERT: A 82 ARG cc_start: 0.8460 (mmt180) cc_final: 0.7973 (mmp80) REVERT: A 96 TRP cc_start: 0.7713 (t60) cc_final: 0.7325 (t60) REVERT: A 129 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8547 (m) REVERT: A 131 GLN cc_start: 0.8272 (tp40) cc_final: 0.7140 (tp40) REVERT: A 132 MET cc_start: 0.7399 (mpm) cc_final: 0.7137 (mpm) REVERT: A 134 LEU cc_start: 0.8612 (tp) cc_final: 0.7995 (tp) REVERT: A 135 GLU cc_start: 0.8079 (mm-30) cc_final: 0.6611 (mm-30) REVERT: A 138 LYS cc_start: 0.8539 (mttm) cc_final: 0.7673 (mttm) REVERT: A 235 LEU cc_start: 0.9000 (mt) cc_final: 0.8411 (mt) REVERT: A 236 LYS cc_start: 0.8849 (tptp) cc_final: 0.8547 (mmmm) REVERT: A 237 ARG cc_start: 0.8432 (ttt-90) cc_final: 0.6737 (ttm110) REVERT: A 238 SER cc_start: 0.9238 (m) cc_final: 0.8671 (p) REVERT: A 239 MET cc_start: 0.7879 (mmm) cc_final: 0.7364 (mmm) REVERT: B 8 ARG cc_start: 0.7119 (ttt-90) cc_final: 0.5933 (tmm160) REVERT: B 9 LEU cc_start: 0.7817 (mt) cc_final: 0.7343 (tt) REVERT: B 21 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7481 (ttm-80) REVERT: B 56 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7725 (ptpp) REVERT: B 88 ARG cc_start: 0.7951 (tpp80) cc_final: 0.6921 (tpp80) REVERT: B 121 VAL cc_start: 0.8632 (m) cc_final: 0.8309 (p) REVERT: B 135 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 149 ILE cc_start: 0.8151 (mt) cc_final: 0.7905 (tt) REVERT: B 153 LYS cc_start: 0.7960 (mtmp) cc_final: 0.7591 (mtmp) REVERT: B 164 LEU cc_start: 0.8141 (tp) cc_final: 0.7899 (tp) REVERT: B 183 ARG cc_start: 0.7317 (ttm-80) cc_final: 0.6613 (tpt90) REVERT: B 191 VAL cc_start: 0.8344 (t) cc_final: 0.7681 (t) REVERT: B 196 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6926 (mp0) REVERT: B 200 LEU cc_start: 0.7676 (mt) cc_final: 0.7441 (mt) REVERT: B 203 HIS cc_start: 0.7857 (m-70) cc_final: 0.6752 (t-90) REVERT: B 207 ARG cc_start: 0.7582 (tpp80) cc_final: 0.6714 (tpp80) REVERT: B 265 ARG cc_start: 0.8547 (ptt180) cc_final: 0.7991 (ptt90) REVERT: B 272 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7593 (tpp80) REVERT: B 274 GLN cc_start: 0.7934 (mt0) cc_final: 0.7420 (mt0) REVERT: B 281 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7387 (tt0) REVERT: B 348 PHE cc_start: 0.8225 (t80) cc_final: 0.7965 (t80) REVERT: B 350 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8276 (pp20) REVERT: B 377 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 379 GLU cc_start: 0.8530 (pt0) cc_final: 0.8299 (mt-10) REVERT: B 383 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 409 ARG cc_start: 0.7422 (mtm110) cc_final: 0.7096 (ptt90) REVERT: B 419 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: B 444 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8090 (mmm-85) REVERT: B 451 LYS cc_start: 0.8340 (mttt) cc_final: 0.7891 (mttm) REVERT: B 459 ASN cc_start: 0.8278 (m-40) cc_final: 0.8041 (m-40) REVERT: B 464 PHE cc_start: 0.6805 (p90) cc_final: 0.6550 (p90) REVERT: B 475 ASP cc_start: 0.7722 (t70) cc_final: 0.7314 (t70) REVERT: C 21 ARG cc_start: 0.9003 (mmt180) cc_final: 0.8296 (mmm160) REVERT: C 63 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7630 (ptp90) REVERT: C 95 HIS cc_start: 0.7524 (t-170) cc_final: 0.6331 (t-170) REVERT: C 96 TRP cc_start: 0.8716 (t60) cc_final: 0.8291 (t60) REVERT: C 98 GLU cc_start: 0.6649 (pp20) cc_final: 0.6410 (pp20) REVERT: C 133 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7476 (mt-10) REVERT: C 138 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8247 (mmmt) REVERT: C 182 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 183 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.7842 (mmp-170) REVERT: C 229 GLU cc_start: 0.7651 (pt0) cc_final: 0.7416 (pt0) REVERT: C 237 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8171 (ptp-110) REVERT: C 270 LEU cc_start: 0.8066 (tp) cc_final: 0.7844 (tp) REVERT: C 275 LEU cc_start: 0.8067 (tp) cc_final: 0.7722 (tp) REVERT: C 276 GLU cc_start: 0.8089 (pt0) cc_final: 0.7783 (pt0) REVERT: C 329 MET cc_start: 0.8679 (ttm) cc_final: 0.8154 (tmm) REVERT: C 331 PHE cc_start: 0.8514 (m-80) cc_final: 0.8203 (m-80) REVERT: C 350 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8130 (mt-10) REVERT: C 452 ASN cc_start: 0.7981 (t0) cc_final: 0.7415 (t0) REVERT: C 458 MET cc_start: 0.8215 (mmm) cc_final: 0.7230 (mpp) REVERT: D 9 LEU cc_start: 0.8176 (tt) cc_final: 0.7697 (mm) REVERT: D 21 ARG cc_start: 0.7245 (mtp-110) cc_final: 0.6838 (mtp-110) REVERT: D 22 GLN cc_start: 0.8102 (mt0) cc_final: 0.7877 (mt0) REVERT: D 43 ASP cc_start: 0.7195 (t0) cc_final: 0.6974 (t0) REVERT: D 51 ASP cc_start: 0.8148 (t0) cc_final: 0.7765 (t0) REVERT: D 60 ASN cc_start: 0.8027 (m110) cc_final: 0.7592 (t0) REVERT: D 64 TRP cc_start: 0.7818 (m100) cc_final: 0.7532 (m100) REVERT: D 70 GLN cc_start: 0.7773 (tm-30) cc_final: 0.6720 (tm-30) REVERT: D 95 HIS cc_start: 0.7768 (m-70) cc_final: 0.7083 (m-70) REVERT: D 102 LYS cc_start: 0.8098 (mttm) cc_final: 0.7714 (mttm) REVERT: D 109 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6997 (mp0) REVERT: D 138 LYS cc_start: 0.8222 (mttt) cc_final: 0.7429 (ttmm) REVERT: D 140 ARG cc_start: 0.7658 (tpt170) cc_final: 0.7089 (tpt170) REVERT: D 215 ASP cc_start: 0.7594 (m-30) cc_final: 0.6968 (t70) REVERT: D 229 GLU cc_start: 0.7068 (pt0) cc_final: 0.6751 (pt0) REVERT: D 265 ARG cc_start: 0.7488 (ptt180) cc_final: 0.7285 (ptp-170) REVERT: D 272 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7297 (mmm160) REVERT: D 274 GLN cc_start: 0.7731 (pt0) cc_final: 0.7519 (pt0) REVERT: D 276 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8135 (mm-30) REVERT: D 281 GLU cc_start: 0.7829 (tp30) cc_final: 0.7445 (tp30) REVERT: D 287 ARG cc_start: 0.5295 (OUTLIER) cc_final: 0.4958 (ptm160) REVERT: D 329 MET cc_start: 0.7838 (tpp) cc_final: 0.7504 (mpp) REVERT: D 333 LYS cc_start: 0.7451 (tttp) cc_final: 0.7159 (tttp) REVERT: D 337 ASN cc_start: 0.7807 (t0) cc_final: 0.7413 (t0) REVERT: D 350 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7710 (tp30) REVERT: D 351 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: D 452 ASN cc_start: 0.8303 (t0) cc_final: 0.7760 (t0) REVERT: D 455 LEU cc_start: 0.8773 (mt) cc_final: 0.8545 (mt) REVERT: D 461 ARG cc_start: 0.7326 (ttm-80) cc_final: 0.6861 (ttm-80) outliers start: 50 outliers final: 37 residues processed: 453 average time/residue: 0.1872 time to fit residues: 119.5110 Evaluate side-chains 477 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 432 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 183 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 99 optimal weight: 0.0010 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 133 optimal weight: 0.0030 chunk 22 optimal weight: 0.4980 chunk 202 optimal weight: 0.9990 chunk 186 optimal weight: 50.0000 chunk 126 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 352 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.210534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160999 restraints weight = 48265.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163238 restraints weight = 22669.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164741 restraints weight = 15469.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166918 restraints weight = 12247.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166678 restraints weight = 11656.797| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20312 Z= 0.139 Angle : 0.644 13.625 28378 Z= 0.347 Chirality : 0.039 0.232 3109 Planarity : 0.005 0.051 3022 Dihedral : 22.732 81.978 4269 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.55 % Allowed : 20.87 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1937 helix: 1.73 (0.17), residues: 918 sheet: -0.13 (0.29), residues: 279 loop : 0.84 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 467 TYR 0.027 0.002 TYR D 216 PHE 0.024 0.001 PHE D 217 TRP 0.042 0.002 TRP C 35 HIS 0.011 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00297 (20296) covalent geometry : angle 0.63696 (28354) hydrogen bonds : bond 0.03694 ( 1046) hydrogen bonds : angle 3.87611 ( 2758) metal coordination : bond 0.00323 ( 16) metal coordination : angle 3.36972 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 436 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 28 GLN cc_start: 0.8591 (mt0) cc_final: 0.8334 (mt0) REVERT: A 63 ARG cc_start: 0.7445 (mtp-110) cc_final: 0.6192 (mtm110) REVERT: A 65 LEU cc_start: 0.8058 (mt) cc_final: 0.7289 (mm) REVERT: A 69 GLU cc_start: 0.5091 (mm-30) cc_final: 0.2994 (pm20) REVERT: A 82 ARG cc_start: 0.8491 (mmt180) cc_final: 0.7985 (mmp80) REVERT: A 96 TRP cc_start: 0.7789 (t60) cc_final: 0.7161 (t60) REVERT: A 126 MET cc_start: 0.7575 (mmm) cc_final: 0.7272 (mmm) REVERT: A 129 VAL cc_start: 0.8838 (p) cc_final: 0.8546 (m) REVERT: A 131 GLN cc_start: 0.8215 (tp40) cc_final: 0.7223 (tp40) REVERT: A 132 MET cc_start: 0.7433 (mpm) cc_final: 0.7155 (mpm) REVERT: A 134 LEU cc_start: 0.8683 (tp) cc_final: 0.8028 (tp) REVERT: A 135 GLU cc_start: 0.8107 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 138 LYS cc_start: 0.8501 (mttm) cc_final: 0.7650 (mttm) REVERT: A 235 LEU cc_start: 0.9016 (mt) cc_final: 0.8443 (mt) REVERT: A 236 LYS cc_start: 0.8936 (tptp) cc_final: 0.8718 (mmmm) REVERT: A 237 ARG cc_start: 0.8461 (ttt-90) cc_final: 0.6963 (ttm110) REVERT: A 239 MET cc_start: 0.8132 (mmm) cc_final: 0.7627 (mmm) REVERT: A 244 MET cc_start: 0.6465 (mpp) cc_final: 0.5973 (mpp) REVERT: A 409 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7534 (tpm170) REVERT: A 416 ARG cc_start: 0.7422 (ptm160) cc_final: 0.7158 (ptm160) REVERT: B 8 ARG cc_start: 0.7087 (ttt-90) cc_final: 0.5881 (tmm160) REVERT: B 9 LEU cc_start: 0.7733 (mt) cc_final: 0.7233 (tt) REVERT: B 45 ASP cc_start: 0.7431 (m-30) cc_final: 0.7161 (m-30) REVERT: B 56 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7728 (ptpp) REVERT: B 88 ARG cc_start: 0.8020 (tpp80) cc_final: 0.6600 (tpt-90) REVERT: B 121 VAL cc_start: 0.8583 (m) cc_final: 0.8268 (p) REVERT: B 135 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7019 (mm-30) REVERT: B 138 LYS cc_start: 0.8329 (mttt) cc_final: 0.7946 (mtpp) REVERT: B 149 ILE cc_start: 0.8144 (mt) cc_final: 0.7873 (tt) REVERT: B 164 LEU cc_start: 0.8150 (tp) cc_final: 0.7909 (tp) REVERT: B 183 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.7059 (mmt180) REVERT: B 196 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6748 (mp0) REVERT: B 200 LEU cc_start: 0.7593 (mt) cc_final: 0.7376 (mt) REVERT: B 203 HIS cc_start: 0.7771 (m-70) cc_final: 0.6716 (t-90) REVERT: B 207 ARG cc_start: 0.7485 (tpp80) cc_final: 0.6964 (tpp80) REVERT: B 265 ARG cc_start: 0.8533 (ptt180) cc_final: 0.7938 (ptt90) REVERT: B 272 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7588 (tpp80) REVERT: B 274 GLN cc_start: 0.7874 (mt0) cc_final: 0.7323 (mt0) REVERT: B 339 THR cc_start: 0.8166 (p) cc_final: 0.7918 (t) REVERT: B 348 PHE cc_start: 0.8302 (t80) cc_final: 0.8084 (t80) REVERT: B 350 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8441 (pp20) REVERT: B 377 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7969 (mt) REVERT: B 379 GLU cc_start: 0.8598 (pt0) cc_final: 0.8374 (mt-10) REVERT: B 383 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 386 ASP cc_start: 0.8514 (m-30) cc_final: 0.8022 (p0) REVERT: B 409 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7204 (ptt90) REVERT: B 418 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 421 GLU cc_start: 0.7935 (pt0) cc_final: 0.7493 (pt0) REVERT: B 444 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8189 (mmm-85) REVERT: B 451 LYS cc_start: 0.8461 (mttt) cc_final: 0.7943 (mttm) REVERT: B 459 ASN cc_start: 0.8351 (m-40) cc_final: 0.8121 (m-40) REVERT: B 464 PHE cc_start: 0.6997 (p90) cc_final: 0.6727 (p90) REVERT: B 475 ASP cc_start: 0.7804 (t70) cc_final: 0.7399 (t70) REVERT: B 476 PHE cc_start: 0.6795 (m-10) cc_final: 0.6558 (m-80) REVERT: C 21 ARG cc_start: 0.9054 (mmt180) cc_final: 0.8334 (mmm160) REVERT: C 63 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7637 (ptp90) REVERT: C 95 HIS cc_start: 0.7558 (t-170) cc_final: 0.6337 (t-170) REVERT: C 96 TRP cc_start: 0.8707 (t60) cc_final: 0.8216 (t60) REVERT: C 98 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6357 (pp20) REVERT: C 133 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 138 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8188 (mmmt) REVERT: C 150 ARG cc_start: 0.8553 (mmt180) cc_final: 0.7666 (tpp80) REVERT: C 182 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 183 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.7900 (mmp-170) REVERT: C 214 LYS cc_start: 0.8008 (ptmm) cc_final: 0.7484 (pptt) REVERT: C 229 GLU cc_start: 0.7629 (pt0) cc_final: 0.7379 (pt0) REVERT: C 237 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8241 (ptp-110) REVERT: C 275 LEU cc_start: 0.8192 (tp) cc_final: 0.7906 (tp) REVERT: C 276 GLU cc_start: 0.8175 (pt0) cc_final: 0.7877 (pt0) REVERT: C 329 MET cc_start: 0.8780 (ttm) cc_final: 0.8286 (tmm) REVERT: C 331 PHE cc_start: 0.8538 (m-80) cc_final: 0.8261 (m-80) REVERT: C 350 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8247 (mt-10) REVERT: C 452 ASN cc_start: 0.8029 (t0) cc_final: 0.7448 (t0) REVERT: C 454 TRP cc_start: 0.8105 (t-100) cc_final: 0.7697 (t-100) REVERT: C 458 MET cc_start: 0.8142 (mmm) cc_final: 0.7176 (mpp) REVERT: D 9 LEU cc_start: 0.8024 (tt) cc_final: 0.7437 (mm) REVERT: D 22 GLN cc_start: 0.8036 (mt0) cc_final: 0.7771 (mt0) REVERT: D 43 ASP cc_start: 0.7160 (t0) cc_final: 0.6929 (t0) REVERT: D 51 ASP cc_start: 0.7787 (t0) cc_final: 0.7532 (t0) REVERT: D 60 ASN cc_start: 0.7965 (m110) cc_final: 0.7521 (t0) REVERT: D 64 TRP cc_start: 0.7743 (m100) cc_final: 0.7484 (m100) REVERT: D 70 GLN cc_start: 0.7779 (tm-30) cc_final: 0.6800 (tm-30) REVERT: D 88 ARG cc_start: 0.7315 (ttm110) cc_final: 0.6894 (ttm170) REVERT: D 95 HIS cc_start: 0.7782 (m-70) cc_final: 0.7217 (m-70) REVERT: D 101 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8534 (mmmt) REVERT: D 102 LYS cc_start: 0.8091 (mttm) cc_final: 0.7754 (mttm) REVERT: D 109 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6934 (mp0) REVERT: D 138 LYS cc_start: 0.8330 (mttt) cc_final: 0.7727 (ttmm) REVERT: D 139 GLU cc_start: 0.7750 (tp30) cc_final: 0.7124 (tp30) REVERT: D 140 ARG cc_start: 0.7526 (tpt170) cc_final: 0.6914 (tpt170) REVERT: D 190 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7657 (mtp85) REVERT: D 215 ASP cc_start: 0.7566 (m-30) cc_final: 0.6820 (t70) REVERT: D 229 GLU cc_start: 0.7060 (pt0) cc_final: 0.6751 (pt0) REVERT: D 250 LEU cc_start: 0.8776 (tp) cc_final: 0.8463 (mp) REVERT: D 265 ARG cc_start: 0.7413 (ptt180) cc_final: 0.7069 (ptp-170) REVERT: D 272 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7006 (mmm160) REVERT: D 276 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7997 (mm-30) REVERT: D 281 GLU cc_start: 0.7825 (tp30) cc_final: 0.7385 (tp30) REVERT: D 287 ARG cc_start: 0.5273 (OUTLIER) cc_final: 0.4963 (ptm160) REVERT: D 329 MET cc_start: 0.7790 (tpp) cc_final: 0.7444 (mpp) REVERT: D 333 LYS cc_start: 0.7482 (tttp) cc_final: 0.7277 (tttp) REVERT: D 337 ASN cc_start: 0.7823 (t0) cc_final: 0.7478 (t0) REVERT: D 350 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: D 351 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: D 452 ASN cc_start: 0.8209 (t0) cc_final: 0.7728 (t0) REVERT: D 455 LEU cc_start: 0.8785 (mt) cc_final: 0.8544 (mt) REVERT: D 461 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.6865 (ttm-80) REVERT: D 467 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7057 (mtm110) outliers start: 41 outliers final: 29 residues processed: 453 average time/residue: 0.1831 time to fit residues: 116.4652 Evaluate side-chains 464 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 428 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 35 TRP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 350 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 113 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 92 optimal weight: 0.0970 chunk 45 optimal weight: 0.0270 chunk 89 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 95 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.210802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162209 restraints weight = 47445.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163648 restraints weight = 22944.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.165350 restraints weight = 17628.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167957 restraints weight = 12360.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167841 restraints weight = 10960.602| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20312 Z= 0.142 Angle : 0.652 13.053 28378 Z= 0.352 Chirality : 0.039 0.238 3109 Planarity : 0.005 0.051 3022 Dihedral : 22.702 83.517 4269 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 21.43 % Favored : 76.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1937 helix: 1.66 (0.17), residues: 920 sheet: -0.10 (0.30), residues: 275 loop : 0.81 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 467 TYR 0.040 0.002 TYR D 216 PHE 0.027 0.001 PHE D 217 TRP 0.043 0.001 TRP D 96 HIS 0.009 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00305 (20296) covalent geometry : angle 0.64533 (28354) hydrogen bonds : bond 0.03806 ( 1046) hydrogen bonds : angle 3.93848 ( 2758) metal coordination : bond 0.00326 ( 16) metal coordination : angle 3.29021 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3874 Ramachandran restraints generated. 1937 Oldfield, 0 Emsley, 1937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 432 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5762 (tmm) cc_final: 0.5384 (tpp) REVERT: A 2 ARG cc_start: 0.7132 (mtp85) cc_final: 0.6362 (tpp80) REVERT: A 9 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7855 (tt) REVERT: A 21 ARG cc_start: 0.6904 (tpt90) cc_final: 0.6580 (mmm160) REVERT: A 63 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.6423 (mtm110) REVERT: A 65 LEU cc_start: 0.8085 (mt) cc_final: 0.7145 (mm) REVERT: A 69 GLU cc_start: 0.5065 (mm-30) cc_final: 0.2591 (pm20) REVERT: A 82 ARG cc_start: 0.8479 (mmt180) cc_final: 0.7977 (mmp80) REVERT: A 96 TRP cc_start: 0.7789 (t60) cc_final: 0.7099 (t60) REVERT: A 126 MET cc_start: 0.7595 (mmm) cc_final: 0.7297 (mmm) REVERT: A 129 VAL cc_start: 0.8827 (p) cc_final: 0.8529 (m) REVERT: A 131 GLN cc_start: 0.8227 (tp40) cc_final: 0.7202 (tp40) REVERT: A 132 MET cc_start: 0.7392 (mpm) cc_final: 0.7120 (mpm) REVERT: A 134 LEU cc_start: 0.8651 (tp) cc_final: 0.8060 (tp) REVERT: A 135 GLU cc_start: 0.8049 (mm-30) cc_final: 0.6657 (mm-30) REVERT: A 138 LYS cc_start: 0.8489 (mttm) cc_final: 0.7666 (mttm) REVERT: A 235 LEU cc_start: 0.8986 (mt) cc_final: 0.8430 (mt) REVERT: A 236 LYS cc_start: 0.8929 (tptp) cc_final: 0.8711 (mmmm) REVERT: A 237 ARG cc_start: 0.8456 (ttt-90) cc_final: 0.6977 (ttm110) REVERT: A 239 MET cc_start: 0.8130 (mmm) cc_final: 0.7495 (mmm) REVERT: A 244 MET cc_start: 0.6526 (mpp) cc_final: 0.6086 (mpp) REVERT: A 409 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7526 (tpm170) REVERT: B 8 ARG cc_start: 0.7094 (ttt-90) cc_final: 0.5845 (tmm160) REVERT: B 9 LEU cc_start: 0.7738 (mt) cc_final: 0.7261 (tt) REVERT: B 45 ASP cc_start: 0.7334 (m-30) cc_final: 0.7087 (m-30) REVERT: B 56 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7731 (ptpp) REVERT: B 88 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7037 (tpt-90) REVERT: B 121 VAL cc_start: 0.8573 (m) cc_final: 0.8266 (p) REVERT: B 131 GLN cc_start: 0.8320 (tt0) cc_final: 0.7905 (tt0) REVERT: B 135 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 138 LYS cc_start: 0.8347 (mttt) cc_final: 0.7962 (mtpp) REVERT: B 149 ILE cc_start: 0.8224 (mt) cc_final: 0.7883 (tt) REVERT: B 164 LEU cc_start: 0.8151 (tp) cc_final: 0.7905 (tp) REVERT: B 183 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6930 (tpt90) REVERT: B 196 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6777 (mp0) REVERT: B 200 LEU cc_start: 0.7540 (mt) cc_final: 0.7271 (mt) REVERT: B 203 HIS cc_start: 0.7787 (m-70) cc_final: 0.6716 (t-90) REVERT: B 207 ARG cc_start: 0.7673 (tpp80) cc_final: 0.6872 (tpp80) REVERT: B 244 MET cc_start: 0.7145 (mmp) cc_final: 0.6847 (mmm) REVERT: B 265 ARG cc_start: 0.8511 (ptt180) cc_final: 0.7764 (ptt90) REVERT: B 272 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7579 (tpp80) REVERT: B 274 GLN cc_start: 0.7861 (mt0) cc_final: 0.7305 (mt0) REVERT: B 323 ARG cc_start: 0.6560 (mmm160) cc_final: 0.6177 (tpt170) REVERT: B 348 PHE cc_start: 0.8143 (t80) cc_final: 0.7907 (t80) REVERT: B 377 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 379 GLU cc_start: 0.8536 (pt0) cc_final: 0.8332 (mt-10) REVERT: B 383 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 386 ASP cc_start: 0.8519 (m-30) cc_final: 0.8061 (p0) REVERT: B 409 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7090 (ptt90) REVERT: B 418 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 421 GLU cc_start: 0.7950 (pt0) cc_final: 0.7519 (pt0) REVERT: B 444 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8172 (mmm-85) REVERT: B 451 LYS cc_start: 0.8419 (mttt) cc_final: 0.7988 (mttm) REVERT: B 459 ASN cc_start: 0.8307 (m-40) cc_final: 0.8101 (m-40) REVERT: B 464 PHE cc_start: 0.6935 (p90) cc_final: 0.6658 (p90) REVERT: B 475 ASP cc_start: 0.7719 (t70) cc_final: 0.7292 (t70) REVERT: B 476 PHE cc_start: 0.6704 (m-10) cc_final: 0.6500 (m-80) REVERT: C 21 ARG cc_start: 0.9046 (mmt180) cc_final: 0.8141 (mmm-85) REVERT: C 61 LEU cc_start: 0.8173 (tp) cc_final: 0.7848 (tp) REVERT: C 63 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7609 (ptp90) REVERT: C 95 HIS cc_start: 0.7526 (t-170) cc_final: 0.6289 (t-170) REVERT: C 98 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6305 (pp20) REVERT: C 133 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 138 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8180 (mmmt) REVERT: C 150 ARG cc_start: 0.8552 (mmt180) cc_final: 0.7652 (tpp80) REVERT: C 164 LEU cc_start: 0.8067 (tp) cc_final: 0.7829 (mm) REVERT: C 174 LEU cc_start: 0.8231 (mt) cc_final: 0.7937 (mm) REVERT: C 183 ARG cc_start: 0.8659 (mmt-90) cc_final: 0.7980 (mmp-170) REVERT: C 229 GLU cc_start: 0.7654 (pt0) cc_final: 0.7395 (pt0) REVERT: C 237 ARG cc_start: 0.8556 (ttp-170) cc_final: 0.8217 (ptp-110) REVERT: C 244 MET cc_start: 0.8531 (mmt) cc_final: 0.7897 (mtp) REVERT: C 275 LEU cc_start: 0.8092 (tp) cc_final: 0.7851 (tp) REVERT: C 276 GLU cc_start: 0.8133 (pt0) cc_final: 0.7840 (pt0) REVERT: C 329 MET cc_start: 0.8787 (ttm) cc_final: 0.8229 (tmm) REVERT: C 331 PHE cc_start: 0.8500 (m-80) cc_final: 0.8249 (m-80) REVERT: C 350 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8260 (mt-10) REVERT: C 452 ASN cc_start: 0.8022 (t0) cc_final: 0.7439 (t0) REVERT: D 9 LEU cc_start: 0.7954 (tt) cc_final: 0.7349 (mm) REVERT: D 20 GLU cc_start: 0.7744 (pm20) cc_final: 0.7377 (pm20) REVERT: D 22 GLN cc_start: 0.8094 (mt0) cc_final: 0.7741 (mt0) REVERT: D 27 GLN cc_start: 0.8481 (pt0) cc_final: 0.8065 (pm20) REVERT: D 43 ASP cc_start: 0.7145 (t0) cc_final: 0.6931 (t0) REVERT: D 60 ASN cc_start: 0.7898 (m110) cc_final: 0.7533 (t0) REVERT: D 64 TRP cc_start: 0.7735 (m100) cc_final: 0.7507 (m100) REVERT: D 70 GLN cc_start: 0.7786 (tm-30) cc_final: 0.6830 (tm-30) REVERT: D 79 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.6885 (mtm-85) REVERT: D 88 ARG cc_start: 0.7299 (ttm110) cc_final: 0.6870 (ttm170) REVERT: D 95 HIS cc_start: 0.7796 (m-70) cc_final: 0.7146 (m-70) REVERT: D 101 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8510 (mmmt) REVERT: D 109 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6783 (mt-10) REVERT: D 140 ARG cc_start: 0.7539 (tpt170) cc_final: 0.6915 (tpt170) REVERT: D 190 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7699 (mtp85) REVERT: D 215 ASP cc_start: 0.7529 (m-30) cc_final: 0.6991 (t70) REVERT: D 229 GLU cc_start: 0.7053 (pt0) cc_final: 0.6781 (pt0) REVERT: D 250 LEU cc_start: 0.8777 (tp) cc_final: 0.8519 (mp) REVERT: D 265 ARG cc_start: 0.7411 (ptt180) cc_final: 0.7180 (ptp-170) REVERT: D 272 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.6999 (mmm160) REVERT: D 276 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7979 (mm-30) REVERT: D 281 GLU cc_start: 0.7819 (tp30) cc_final: 0.7467 (tp30) REVERT: D 287 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.4922 (ptm160) REVERT: D 329 MET cc_start: 0.7741 (tpp) cc_final: 0.7418 (mpp) REVERT: D 337 ASN cc_start: 0.7810 (t0) cc_final: 0.7465 (t0) REVERT: D 348 PHE cc_start: 0.7423 (t80) cc_final: 0.7113 (t80) REVERT: D 351 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7039 (pt0) REVERT: D 452 ASN cc_start: 0.8179 (t0) cc_final: 0.7708 (t0) REVERT: D 455 LEU cc_start: 0.8765 (mt) cc_final: 0.8519 (mt) REVERT: D 456 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8215 (mmm-85) REVERT: D 461 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6821 (ttm-80) REVERT: D 467 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7145 (mtm110) outliers start: 36 outliers final: 26 residues processed: 449 average time/residue: 0.1796 time to fit residues: 113.8917 Evaluate side-chains 455 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 423 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 47 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.204855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149148 restraints weight = 46607.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154572 restraints weight = 21114.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157857 restraints weight = 12954.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159831 restraints weight = 9570.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161001 restraints weight = 7916.820| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20312 Z= 0.308 Angle : 0.734 12.546 28378 Z= 0.407 Chirality : 0.045 0.302 3109 Planarity : 0.006 0.057 3022 Dihedral : 22.691 85.607 4269 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.49 % Allowed : 22.06 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1937 helix: 1.30 (0.17), residues: 915 sheet: -0.29 (0.29), residues: 279 loop : 0.60 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 467 TYR 0.041 0.002 TYR D 216 PHE 0.034 0.002 PHE D 217 TRP 0.043 0.002 TRP C 64 HIS 0.014 0.002 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00646 (20296) covalent geometry : angle 0.72538 (28354) hydrogen bonds : bond 0.05114 ( 1046) hydrogen bonds : angle 4.31128 ( 2758) metal coordination : bond 0.00730 ( 16) metal coordination : angle 3.97987 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4981.25 seconds wall clock time: 85 minutes 52.61 seconds (5152.61 seconds total)