Starting phenix.real_space_refine on Fri Aug 7 07:01:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu3_60888/08_2026/9iu3_60888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu3_60888/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu3_60888/08_2026/9iu3_60888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu3_60888/08_2026/9iu3_60888.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu3_60888/08_2026/9iu3_60888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu3_60888/08_2026/9iu3_60888.cif" } 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-2.2rc3-6140/lib/python3.11/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: 3.64, per 1000 atoms: 0.19 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: 1.23 Conformation dependent library (CDL) restraints added in 610.1 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: 2.53 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: 2.88 Time building geometry restraints manager: 1.52 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: 26180 3.49 - 6.97: 2017 6.97 - 10.46: 142 10.46 - 13.95: 10 13.95 - 17.43: 5 Bond angle restraints: 28354 Sorted by residual: angle pdb=" O4' DGG2 36 " pdb=" C1' DGG2 36 " pdb=" N9 DGG2 36 " ideal model delta sigma weight residual 108.00 115.43 -7.43 7.00e-01 2.04e+00 1.13e+02 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 1.90e+00 2.77e-01 8.42e+01 angle pdb=" CA ASP C 355 " pdb=" CB ASP C 355 " pdb=" CG ASP C 355 " ideal model delta sigma weight residual 112.60 120.76 -8.16 1.00e+00 1.00e+00 6.66e+01 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 1.90e+00 2.77e-01 6.30e+01 angle pdb=" N VAL D 255 " pdb=" CA VAL D 255 " pdb=" CB VAL D 255 " ideal model delta sigma weight residual 110.95 119.80 -8.85 1.12e+00 7.97e-01 6.24e+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 - 0.130: 2687 0.130 - 0.261: 392 0.261 - 0.391: 25 0.391 - 0.521: 1 0.521 - 0.652: 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 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+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 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.990 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 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= 0.730 Angle : 1.983 20.916 28378 Z= 1.361 Chirality : 0.091 0.652 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/Z covalent geometry : bond 0.01118 / 0.73 (20296) covalent geometry : angle 1.96432 / 1.36 (28354) hydrogen bonds : bond 0.15671 / 10.69 ( 1046) hydrogen bonds : angle 5.92849 / 4.28 ( 2758) metal coordination : bond 0.06085 / 3.66 ( 16) metal coordination : angle 9.63146 / 6.41 ( 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 : 0.479 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: 0.6685 (p) REVERT: A 28 GLN cc_start: 0.8844 (mt0) cc_final: 0.8494 (mt0) REVERT: A 40 VAL cc_start: 0.7999 (t) cc_final: 0.7086 (p) REVERT: A 43 ASP cc_start: 0.5033 (m-30) cc_final: 0.4568 (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: 0.5310 (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: 0.4689 (mp0) REVERT: A 125 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 126 MET cc_start: 0.8815 (mmm) cc_final: 0.8235 (mmm) REVERT: A 133 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7726 (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: 0.6966 (p) REVERT: A 239 MET cc_start: 0.7448 (mmm) cc_final: 0.6939 (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: 0.5415 (ttp-170) REVERT: B 21 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7343 (ttm-80) REVERT: B 23 LEU cc_start: 0.8648 (tp) cc_final: 0.7964 (pp) REVERT: B 33 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7449 (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: 0.6822 (tpt-90) REVERT: B 92 GLN cc_start: 0.8365 (mt0) cc_final: 0.8071 (mm-40) REVERT: B 95 HIS cc_start: 0.8287 (m90) cc_final: 0.7291 (m170) REVERT: B 100 HIS cc_start: 0.8031 (m90) cc_final: 0.7609 (m90) REVERT: B 132 MET cc_start: 0.8104 (mtp) cc_final: 0.7818 (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: 0.7443 (m170) REVERT: B 153 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7457 (mtmp) REVERT: B 181 ARG cc_start: 0.7293 (ttt180) cc_final: 0.6749 (ttp-110) REVERT: B 183 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7207 (mmt180) REVERT: B 186 GLU cc_start: 0.8020 (tt0) cc_final: 0.7106 (tt0) REVERT: B 204 ASP cc_start: 0.7895 (t70) cc_final: 0.7587 (t0) REVERT: B 207 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7382 (tpp80) REVERT: B 226 GLN cc_start: 0.8015 (mt0) cc_final: 0.7207 (mt0) REVERT: B 228 ARG cc_start: 0.6520 (mtm-85) cc_final: 0.6033 (mtt90) REVERT: B 229 GLU cc_start: 0.7601 (pt0) cc_final: 0.7123 (pt0) REVERT: B 235 LEU cc_start: 0.7642 (mt) cc_final: 0.7163 (mp) REVERT: B 239 MET cc_start: 0.7510 (mmm) cc_final: 0.6857 (mmm) REVERT: B 242 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7092 (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: 0.7316 (ptm160) REVERT: B 281 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: B 350 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7677 (tp30) REVERT: B 376 GLU cc_start: 0.8525 (tt0) cc_final: 0.7720 (tt0) REVERT: B 452 ASN cc_start: 0.8027 (t0) cc_final: 0.7380 (t0) REVERT: B 463 THR cc_start: 0.7334 (m) cc_final: 0.7117 (t) REVERT: B 464 PHE cc_start: 0.7444 (p90) cc_final: 0.6812 (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: 0.7971 (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: 0.7523 (mmm160) REVERT: C 100 HIS cc_start: 0.7386 (m90) cc_final: 0.6892 (m90) REVERT: C 129 VAL cc_start: 0.8304 (t) cc_final: 0.7816 (m) REVERT: C 133 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 140 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7606 (mpt-90) REVERT: C 150 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8295 (mtt-85) REVERT: C 183 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8319 (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: 0.7901 (ttmt) REVERT: C 230 TRP cc_start: 0.6770 (m100) cc_final: 0.6562 (m100) REVERT: C 233 THR cc_start: 0.8530 (m) cc_final: 0.8081 (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: 0.8448 (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: 0.8010 (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: 0.6847 (mt) REVERT: D 22 GLN cc_start: 0.7764 (mt0) cc_final: 0.7421 (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: 0.6043 (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: 0.7573 (ttm110) REVERT: D 95 HIS cc_start: 0.7428 (m-70) cc_final: 0.6761 (m90) REVERT: D 96 TRP cc_start: 0.7310 (t60) cc_final: 0.6498 (t60) REVERT: D 99 ASP cc_start: 0.7134 (m-30) cc_final: 0.6853 (m-30) REVERT: D 100 HIS cc_start: 0.7506 (m-70) cc_final: 0.7093 (m170) REVERT: D 102 LYS cc_start: 0.7320 (mmtt) cc_final: 0.7029 (mmmt) REVERT: D 114 THR cc_start: 0.8745 (p) cc_final: 0.8358 (m) REVERT: D 134 LEU cc_start: 0.8092 (tp) cc_final: 0.7839 (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: 0.7542 (mttt) REVERT: D 146 HIS cc_start: 0.8060 (m170) cc_final: 0.7706 (m-70) REVERT: D 149 ILE cc_start: 0.8119 (mm) cc_final: 0.7847 (mm) REVERT: D 177 ASP cc_start: 0.7006 (t0) cc_final: 0.6259 (t0) REVERT: D 235 LEU cc_start: 0.8049 (mt) cc_final: 0.7687 (mt) REVERT: D 238 SER cc_start: 0.7179 (m) cc_final: 0.6892 (p) REVERT: D 239 MET cc_start: 0.7686 (mmm) cc_final: 0.7403 (mmp) REVERT: D 247 TYR cc_start: 0.6494 (m-10) cc_final: 0.6221 (m-10) REVERT: D 265 ARG cc_start: 0.7227 (ptt180) cc_final: 0.6905 (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: 0.7869 (mmm-85) REVERT: D 278 LEU cc_start: 0.8693 (mt) cc_final: 0.8420 (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: 0.7411 (tpp) REVERT: D 339 THR cc_start: 0.7417 (p) cc_final: 0.6654 (m) REVERT: D 340 VAL cc_start: 0.7120 (m) cc_final: 0.6875 (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: 0.6915 (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: 0.1489 time to fit residues: 118.3257 Evaluate side-chains 476 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 448 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 1.9990 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: 50.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 146 HIS A 417 GLN B 180 GLN C 480 GLN D 180 GLN D 189 HIS ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.216338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159743 restraints weight = 53239.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.165651 restraints weight = 23496.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169181 restraints weight = 14099.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.171368 restraints weight = 10208.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.172620 restraints weight = 8361.081| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20312 Z= 0.180 Angle : 0.796 12.063 28378 Z= 0.444 Chirality : 0.056 0.259 3109 Planarity : 0.005 0.063 3022 Dihedral : 23.605 87.371 4334 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.55 % Favored : 98.40 % Rotamer: Outliers : 3.36 % Allowed : 12.09 % 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: 1.58 (0.18), residues: 1937 helix: 1.85 (0.16), residues: 919 sheet: -0.04 (0.28), residues: 277 loop : 0.63 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 181 TYR 0.025 0.002 TYR B 216 PHE 0.029 0.002 PHE D 217 TRP 0.016 0.002 TRP B 454 HIS 0.007 0.001 HIS D 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (20296) covalent geometry : angle 0.78448 / 0.44 (28354) hydrogen bonds : bond 0.05691 / 3.89 ( 1046) hydrogen bonds : angle 4.10186 / 3.00 ( 2758) metal coordination : bond 0.00406 / 0.25 ( 16) metal coordination : angle 4.77506 / 3.02 ( 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 509 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 455 time to evaluate : 0.542 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: A 6 VAL cc_start: 0.7059 (t) cc_final: 0.6516 (m) REVERT: A 8 ARG cc_start: 0.6473 (ttt-90) cc_final: 0.6099 (tmt170) REVERT: A 28 GLN cc_start: 0.8773 (mt0) cc_final: 0.8382 (tm-30) REVERT: A 43 ASP cc_start: 0.3837 (m-30) cc_final: 0.3332 (m-30) REVERT: A 60 ASN cc_start: 0.6217 (m-40) cc_final: 0.5843 (m-40) REVERT: A 63 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7080 (mtm110) REVERT: A 90 LEU cc_start: 0.8591 (tp) cc_final: 0.8301 (pp) REVERT: A 104 VAL cc_start: 0.6672 (t) cc_final: 0.6296 (p) REVERT: A 109 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5432 (mp0) REVERT: A 126 MET cc_start: 0.7982 (mmm) cc_final: 0.7584 (mmm) REVERT: A 134 LEU cc_start: 0.8943 (tp) cc_final: 0.7511 (tp) REVERT: A 135 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 138 LYS cc_start: 0.8320 (mttm) cc_final: 0.8008 (mttm) REVERT: A 180 GLN cc_start: 0.7291 (mm110) cc_final: 0.6667 (mm-40) REVERT: A 219 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6783 (mm110) REVERT: A 239 MET cc_start: 0.7685 (mmm) cc_final: 0.6767 (mmm) REVERT: A 379 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7412 (tm-30) REVERT: B 8 ARG cc_start: 0.7216 (ttt-90) cc_final: 0.5575 (ttp-170) REVERT: B 21 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7598 (ptm160) REVERT: B 23 LEU cc_start: 0.8512 (tp) cc_final: 0.8249 (pp) REVERT: B 56 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7533 (ptmm) REVERT: B 88 ARG cc_start: 0.7320 (ttt90) cc_final: 0.6581 (tpt-90) REVERT: B 95 HIS cc_start: 0.7833 (m90) cc_final: 0.7589 (m90) REVERT: B 100 HIS cc_start: 0.7908 (m90) cc_final: 0.7700 (m-70) REVERT: B 135 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 146 HIS cc_start: 0.7448 (m170) cc_final: 0.7191 (m-70) REVERT: B 153 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7353 (mtmp) REVERT: B 181 ARG cc_start: 0.7155 (ttt180) cc_final: 0.6642 (ttp-110) REVERT: B 183 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.6989 (mmt180) REVERT: B 186 GLU cc_start: 0.7044 (tt0) cc_final: 0.6753 (tt0) REVERT: B 191 VAL cc_start: 0.7926 (t) cc_final: 0.7707 (p) REVERT: B 196 GLU cc_start: 0.7546 (tt0) cc_final: 0.7188 (tt0) REVERT: B 200 LEU cc_start: 0.7244 (mt) cc_final: 0.6595 (mt) REVERT: B 204 ASP cc_start: 0.7412 (t70) cc_final: 0.7184 (t0) REVERT: B 205 LEU cc_start: 0.8375 (mt) cc_final: 0.8132 (mp) REVERT: B 215 ASP cc_start: 0.7581 (m-30) cc_final: 0.6547 (m-30) REVERT: B 228 ARG cc_start: 0.5979 (mtm-85) cc_final: 0.5718 (mtm-85) REVERT: B 239 MET cc_start: 0.7699 (mmm) cc_final: 0.7456 (mmm) REVERT: B 242 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 265 ARG cc_start: 0.8130 (ptt180) cc_final: 0.7840 (ptt180) REVERT: B 272 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7144 (ttp80) REVERT: B 275 LEU cc_start: 0.8253 (tp) cc_final: 0.7978 (tp) REVERT: B 276 GLU cc_start: 0.7927 (mt-10) cc_final: 0.6635 (mt-10) REVERT: B 281 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6373 (mm-30) REVERT: B 299 LEU cc_start: 0.8593 (tt) cc_final: 0.8385 (tt) REVERT: B 329 MET cc_start: 0.6643 (mmt) cc_final: 0.6375 (mmt) REVERT: B 376 GLU cc_start: 0.8350 (tt0) cc_final: 0.7686 (tt0) REVERT: B 383 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7817 (mp0) REVERT: B 413 LEU cc_start: 0.9138 (mm) cc_final: 0.8618 (pp) REVERT: B 463 THR cc_start: 0.7491 (m) cc_final: 0.7290 (t) REVERT: B 464 PHE cc_start: 0.6935 (p90) cc_final: 0.6513 (p90) REVERT: C 29 LEU cc_start: 0.8224 (tp) cc_final: 0.7748 (tt) REVERT: C 63 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7433 (mtp-110) REVERT: C 76 VAL cc_start: 0.6930 (t) cc_final: 0.6678 (p) REVERT: C 83 LEU cc_start: 0.7266 (mt) cc_final: 0.6713 (tt) REVERT: C 84 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7827 (m) REVERT: C 92 GLN cc_start: 0.8260 (mt0) cc_final: 0.7653 (mt0) REVERT: C 100 HIS cc_start: 0.7739 (m90) cc_final: 0.7297 (m90) REVERT: C 129 VAL cc_start: 0.8337 (t) cc_final: 0.7809 (m) REVERT: C 133 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 150 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7947 (mtt-85) REVERT: C 182 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 183 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.8286 (mmp80) REVERT: C 199 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6918 (p-80) REVERT: C 208 ARG cc_start: 0.8016 (mpp80) cc_final: 0.7424 (ttm170) REVERT: C 214 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7568 (ttmt) REVERT: C 237 ARG cc_start: 0.8747 (ttp-170) cc_final: 0.8032 (mtp180) REVERT: C 242 GLU cc_start: 0.7190 (pm20) cc_final: 0.6626 (pm20) REVERT: C 244 MET cc_start: 0.8562 (mmt) cc_final: 0.8286 (mmt) REVERT: C 276 GLU cc_start: 0.8308 (pt0) cc_final: 0.8000 (pt0) REVERT: C 331 PHE cc_start: 0.8246 (m-80) cc_final: 0.7958 (m-80) REVERT: C 452 ASN cc_start: 0.8242 (t0) cc_final: 0.7686 (t0) REVERT: D 22 GLN cc_start: 0.7959 (mt0) cc_final: 0.7384 (mt0) REVERT: D 51 ASP cc_start: 0.7923 (t0) cc_final: 0.7432 (t0) REVERT: D 56 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7885 (ttmt) REVERT: D 57 ARG cc_start: 0.6884 (mmm160) cc_final: 0.6656 (mmm160) REVERT: D 65 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7437 (mm) REVERT: D 67 PHE cc_start: 0.7104 (m-80) cc_final: 0.6479 (m-80) REVERT: D 70 GLN cc_start: 0.7497 (tt0) cc_final: 0.7279 (tm-30) REVERT: D 92 GLN cc_start: 0.8094 (tt0) cc_final: 0.7834 (mt0) REVERT: D 95 HIS cc_start: 0.7439 (m-70) cc_final: 0.6760 (m90) REVERT: D 99 ASP cc_start: 0.6994 (m-30) cc_final: 0.6647 (m-30) REVERT: D 114 THR cc_start: 0.8550 (p) cc_final: 0.8325 (m) REVERT: D 135 GLU cc_start: 0.7202 (mm-30) cc_final: 0.7002 (mm-30) REVERT: D 164 LEU cc_start: 0.7340 (tp) cc_final: 0.7137 (tt) REVERT: D 215 ASP cc_start: 0.7481 (m-30) cc_final: 0.7077 (t70) REVERT: D 235 LEU cc_start: 0.8404 (mt) cc_final: 0.7719 (mm) REVERT: D 236 LYS cc_start: 0.8532 (tttt) cc_final: 0.8264 (ttmt) REVERT: D 239 MET cc_start: 0.7807 (mmm) cc_final: 0.6987 (mpp) REVERT: D 247 TYR cc_start: 0.6610 (m-10) cc_final: 0.6225 (m-10) REVERT: D 265 ARG cc_start: 0.7426 (ptt180) cc_final: 0.6792 (ttp-110) REVERT: D 278 LEU cc_start: 0.8617 (mt) cc_final: 0.8358 (mt) REVERT: D 327 ARG cc_start: 0.8465 (ttt180) cc_final: 0.7950 (ttt-90) REVERT: D 329 MET cc_start: 0.7649 (tpp) cc_final: 0.7022 (tpp) REVERT: D 337 ASN cc_start: 0.7751 (t0) cc_final: 0.6862 (t0) REVERT: D 351 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: D 458 MET cc_start: 0.7644 (mmt) cc_final: 0.7128 (mmt) REVERT: D 459 ASN cc_start: 0.7833 (m110) cc_final: 0.7502 (m110) REVERT: D 461 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6797 (ttm-80) REVERT: D 464 PHE cc_start: 0.6659 (p90) cc_final: 0.5384 (p90) outliers start: 54 outliers final: 30 residues processed: 487 average time/residue: 0.1418 time to fit residues: 98.4348 Evaluate side-chains 454 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 135 GLU 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 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 116 THR 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 240 ILE Chi-restraints excluded: chain D residue 287 ARG 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 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 195 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS C 60 ASN C 89 HIS ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.203323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148873 restraints weight = 43863.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153933 restraints weight = 20673.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156966 restraints weight = 12907.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.158907 restraints weight = 9587.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160048 restraints weight = 7959.289| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 20312 Z= 0.491 Angle : 1.014 13.867 28378 Z= 0.561 Chirality : 0.061 0.343 3109 Planarity : 0.008 0.087 3022 Dihedral : 23.357 88.793 4299 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.55 % Allowed : 13.71 % Favored : 81.74 % 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: 0.09 (0.18), residues: 1937 helix: 0.39 (0.16), residues: 912 sheet: -0.28 (0.29), residues: 258 loop : 0.01 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG A 183 TYR 0.032 0.003 TYR D 324 PHE 0.042 0.003 PHE C 118 TRP 0.054 0.004 TRP B 161 HIS 0.033 0.003 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.49 (20296) covalent geometry : angle 1.00152 / 0.56 (28354) hydrogen bonds : bond 0.08660 / 6.05 ( 1046) hydrogen bonds : angle 5.15453 / 3.76 ( 2758) metal coordination : bond 0.01468 / 0.91 ( 16) metal coordination : angle 5.46686 / 3.59 ( 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 533 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 460 time to evaluate : 0.427 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: A 1 MET cc_start: 0.5607 (tmm) cc_final: 0.5239 (tmm) REVERT: A 8 ARG cc_start: 0.7556 (ttt-90) cc_final: 0.6558 (tmt170) REVERT: A 27 GLN cc_start: 0.8627 (mt0) cc_final: 0.8252 (mt0) REVERT: A 28 GLN cc_start: 0.8707 (mt0) cc_final: 0.8375 (tm-30) REVERT: A 29 LEU cc_start: 0.8578 (tp) cc_final: 0.8331 (tp) REVERT: A 50 VAL cc_start: 0.7574 (t) cc_final: 0.7146 (p) REVERT: A 55 ARG cc_start: 0.6867 (mmt90) cc_final: 0.6536 (tpt170) REVERT: A 79 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7184 (mtp180) REVERT: A 96 TRP cc_start: 0.8093 (t60) cc_final: 0.7329 (t60) REVERT: A 104 VAL cc_start: 0.7488 (t) cc_final: 0.7226 (p) REVERT: A 109 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6271 (mt-10) REVERT: A 118 PHE cc_start: 0.5367 (m-80) cc_final: 0.5090 (m-10) REVERT: A 133 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 134 LEU cc_start: 0.8786 (tp) cc_final: 0.8475 (tt) REVERT: A 135 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 180 GLN cc_start: 0.7145 (mm110) cc_final: 0.6928 (mm110) REVERT: A 184 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (mt) REVERT: A 219 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6852 (mm110) REVERT: A 235 LEU cc_start: 0.8857 (mt) cc_final: 0.8523 (mt) REVERT: A 239 MET cc_start: 0.7751 (mmm) cc_final: 0.7044 (mmm) REVERT: A 281 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6743 (mm-30) REVERT: B 8 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.6007 (tmm160) REVERT: B 20 GLU cc_start: 0.7923 (mp0) cc_final: 0.7619 (pm20) REVERT: B 21 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7654 (ttm-80) REVERT: B 22 GLN cc_start: 0.8105 (mt0) cc_final: 0.7863 (mt0) REVERT: B 88 ARG cc_start: 0.8197 (ttt90) cc_final: 0.7154 (tpp80) REVERT: B 92 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 95 HIS cc_start: 0.7951 (m90) cc_final: 0.7343 (m-70) REVERT: B 109 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7008 (mp0) REVERT: B 121 VAL cc_start: 0.8617 (t) cc_final: 0.8337 (p) REVERT: B 135 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 146 HIS cc_start: 0.7677 (m170) cc_final: 0.7402 (m-70) REVERT: B 157 SER cc_start: 0.7144 (t) cc_final: 0.6880 (p) REVERT: B 181 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6722 (ttp-110) REVERT: B 183 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7037 (mmt180) REVERT: B 200 LEU cc_start: 0.7908 (mt) cc_final: 0.7654 (mt) REVERT: B 207 ARG cc_start: 0.7762 (tpp80) cc_final: 0.7503 (tpp80) REVERT: B 215 ASP cc_start: 0.8062 (m-30) cc_final: 0.7237 (m-30) REVERT: B 226 GLN cc_start: 0.7844 (mt0) cc_final: 0.7360 (mt0) REVERT: B 228 ARG cc_start: 0.6538 (mtm-85) cc_final: 0.5880 (mtm-85) REVERT: B 265 ARG cc_start: 0.8520 (ptt180) cc_final: 0.8003 (ptt180) REVERT: B 272 ARG cc_start: 0.7785 (ttp80) cc_final: 0.6764 (ttp80) REVERT: B 274 GLN cc_start: 0.8257 (mt0) cc_final: 0.7883 (mt0) REVERT: B 299 LEU cc_start: 0.8720 (tt) cc_final: 0.8437 (tt) REVERT: B 323 ARG cc_start: 0.7000 (mmm-85) cc_final: 0.6590 (mmm-85) REVERT: B 348 PHE cc_start: 0.8568 (t80) cc_final: 0.8200 (t80) REVERT: B 351 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: B 377 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 383 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8165 (mm-30) REVERT: B 459 ASN cc_start: 0.8362 (m-40) cc_final: 0.8152 (m-40) REVERT: B 464 PHE cc_start: 0.6752 (p90) cc_final: 0.6533 (p90) REVERT: C 42 GLU cc_start: 0.7518 (tp30) cc_final: 0.7312 (tp30) REVERT: C 63 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7699 (mtp-110) REVERT: C 64 TRP cc_start: 0.8408 (m100) cc_final: 0.8127 (m100) REVERT: C 68 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6653 (mt-10) REVERT: C 74 VAL cc_start: 0.7315 (OUTLIER) cc_final: 0.6937 (t) REVERT: C 76 VAL cc_start: 0.7987 (t) cc_final: 0.7574 (p) REVERT: C 83 LEU cc_start: 0.7888 (mt) cc_final: 0.7312 (tp) REVERT: C 92 GLN cc_start: 0.8554 (mt0) cc_final: 0.7979 (mt0) REVERT: C 113 ASP cc_start: 0.7826 (t0) cc_final: 0.7494 (t0) REVERT: C 131 GLN cc_start: 0.7898 (tt0) cc_final: 0.6707 (tp-100) REVERT: C 183 ARG cc_start: 0.8726 (mmt-90) cc_final: 0.8271 (mmp80) REVERT: C 199 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6849 (p-80) REVERT: C 208 ARG cc_start: 0.8334 (mpp80) cc_final: 0.7644 (mtm180) REVERT: C 214 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7778 (ttmt) REVERT: C 237 ARG cc_start: 0.8877 (ttp-170) cc_final: 0.8353 (mtp180) REVERT: C 242 GLU cc_start: 0.7834 (pm20) cc_final: 0.7263 (pm20) REVERT: C 270 LEU cc_start: 0.8535 (tp) cc_final: 0.8309 (tp) REVERT: C 274 GLN cc_start: 0.8540 (mt0) cc_final: 0.8168 (mt0) REVERT: C 276 GLU cc_start: 0.8383 (pt0) cc_final: 0.8082 (pt0) REVERT: C 329 MET cc_start: 0.8392 (ttm) cc_final: 0.8178 (ttm) REVERT: C 331 PHE cc_start: 0.8431 (m-80) cc_final: 0.8117 (m-80) REVERT: C 345 TRP cc_start: 0.7290 (m100) cc_final: 0.7063 (m100) REVERT: C 452 ASN cc_start: 0.8223 (t0) cc_final: 0.7673 (t0) REVERT: D 9 LEU cc_start: 0.8338 (tt) cc_final: 0.8121 (tt) REVERT: D 21 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.7181 (ttp-110) REVERT: D 22 GLN cc_start: 0.8234 (mt0) cc_final: 0.7878 (mt0) REVERT: D 60 ASN cc_start: 0.8392 (m110) cc_final: 0.7675 (t0) REVERT: D 95 HIS cc_start: 0.7857 (m-70) cc_final: 0.7476 (m-70) REVERT: D 112 PHE cc_start: 0.7837 (t80) cc_final: 0.7535 (t80) REVERT: D 114 THR cc_start: 0.8510 (p) cc_final: 0.8247 (m) REVERT: D 138 LYS cc_start: 0.8673 (mttt) cc_final: 0.8376 (tttp) REVERT: D 139 GLU cc_start: 0.7762 (tp30) cc_final: 0.7212 (tp30) REVERT: D 140 ARG cc_start: 0.7786 (tpt170) cc_final: 0.6914 (tpt90) REVERT: D 215 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7013 (t0) REVERT: D 235 LEU cc_start: 0.8409 (mt) cc_final: 0.8055 (mm) REVERT: D 239 MET cc_start: 0.8116 (mmm) cc_final: 0.7393 (mpp) REVERT: D 245 LEU cc_start: 0.7612 (mt) cc_final: 0.6984 (mt) REVERT: D 247 TYR cc_start: 0.7147 (m-10) cc_final: 0.6436 (m-10) REVERT: D 278 LEU cc_start: 0.8609 (mt) cc_final: 0.8389 (mt) REVERT: D 329 MET cc_start: 0.8202 (tpp) cc_final: 0.7665 (tpp) REVERT: D 333 LYS cc_start: 0.7021 (tttp) cc_final: 0.6779 (tttp) REVERT: D 337 ASN cc_start: 0.7794 (t0) cc_final: 0.7328 (t0) REVERT: D 351 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: D 452 ASN cc_start: 0.8173 (t0) cc_final: 0.7819 (t0) REVERT: D 459 ASN cc_start: 0.8218 (m110) cc_final: 0.7940 (m110) REVERT: D 461 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6964 (ttm-80) outliers start: 73 outliers final: 46 residues processed: 498 average time/residue: 0.1518 time to fit residues: 108.2721 Evaluate side-chains 508 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 454 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 ASP 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 74 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 233 THR 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 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 472 ARG 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: 0.0370 chunk 133 optimal weight: 40.0000 chunk 76 optimal weight: 0.0270 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 22 GLN B 95 HIS B 446 GLN C 194 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.210476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154144 restraints weight = 61332.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162000 restraints weight = 26767.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163049 restraints weight = 15488.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165162 restraints weight = 11043.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165581 restraints weight = 9088.487| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20312 Z= 0.163 Angle : 0.707 12.271 28378 Z= 0.396 Chirality : 0.046 0.291 3109 Planarity : 0.006 0.081 3022 Dihedral : 23.341 89.905 4290 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.68 % Allowed : 16.88 % Favored : 79.44 % 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: 0.95 (0.19), residues: 1937 helix: 1.24 (0.16), residues: 919 sheet: -0.20 (0.29), residues: 260 loop : 0.37 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 181 TYR 0.028 0.002 TYR D 154 PHE 0.041 0.002 PHE D 217 TRP 0.038 0.002 TRP C 35 HIS 0.013 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (20296) covalent geometry : angle 0.69495 / 0.40 (28354) hydrogen bonds : bond 0.05067 / 3.50 ( 1046) hydrogen bonds : angle 4.20891 / 3.03 ( 2758) metal coordination : bond 0.00497 / 0.28 ( 16) metal coordination : angle 4.43155 / 2.69 ( 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 510 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 451 time to evaluate : 0.391 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 1 MET cc_start: 0.5603 (tmm) cc_final: 0.5340 (tmm) REVERT: A 6 VAL cc_start: 0.7168 (t) cc_final: 0.6693 (m) REVERT: A 8 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.6960 (tmt170) REVERT: A 27 GLN cc_start: 0.8504 (mt0) cc_final: 0.8102 (mt0) REVERT: A 28 GLN cc_start: 0.8722 (mt0) cc_final: 0.8324 (tm-30) REVERT: A 29 LEU cc_start: 0.8503 (tp) cc_final: 0.8116 (tp) REVERT: A 50 VAL cc_start: 0.7428 (t) cc_final: 0.6929 (p) REVERT: A 60 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6745 (t0) REVERT: A 79 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6878 (mtp180) REVERT: A 87 ILE cc_start: 0.8422 (tp) cc_final: 0.7454 (mp) REVERT: A 101 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7743 (mmtm) REVERT: A 104 VAL cc_start: 0.7443 (t) cc_final: 0.7054 (p) REVERT: A 132 MET cc_start: 0.7476 (mpm) cc_final: 0.7123 (mpm) REVERT: A 133 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 134 LEU cc_start: 0.8753 (tp) cc_final: 0.8542 (tt) REVERT: A 135 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 180 GLN cc_start: 0.7293 (mm110) cc_final: 0.7018 (mm-40) REVERT: A 184 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 219 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6926 (mm110) REVERT: A 235 LEU cc_start: 0.8792 (mt) cc_final: 0.8346 (mt) REVERT: A 239 MET cc_start: 0.7816 (mmm) cc_final: 0.7092 (mmm) REVERT: B 8 ARG cc_start: 0.7375 (ttt-90) cc_final: 0.5804 (tmm160) REVERT: B 21 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7488 (ttm-80) REVERT: B 60 ASN cc_start: 0.8020 (m-40) cc_final: 0.7803 (m-40) REVERT: B 88 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7449 (tpt-90) REVERT: B 95 HIS cc_start: 0.7573 (m-70) cc_final: 0.7024 (m-70) REVERT: B 135 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 146 HIS cc_start: 0.7763 (m170) cc_final: 0.7032 (m-70) REVERT: B 149 ILE cc_start: 0.8160 (mt) cc_final: 0.7873 (tt) REVERT: B 183 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7100 (mmt180) REVERT: B 215 ASP cc_start: 0.7772 (m-30) cc_final: 0.7207 (m-30) REVERT: B 226 GLN cc_start: 0.7820 (mt0) cc_final: 0.7006 (mt0) REVERT: B 228 ARG cc_start: 0.6491 (mtm-85) cc_final: 0.5743 (mtm-85) REVERT: B 247 TYR cc_start: 0.7892 (m-10) cc_final: 0.7689 (m-10) REVERT: B 265 ARG cc_start: 0.8454 (ptt180) cc_final: 0.7977 (ptt180) REVERT: B 272 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7028 (ttp80) REVERT: B 274 GLN cc_start: 0.8041 (mt0) cc_final: 0.7810 (mt0) REVERT: B 275 LEU cc_start: 0.8327 (tp) cc_final: 0.8038 (tp) REVERT: B 276 GLU cc_start: 0.7998 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 299 LEU cc_start: 0.8691 (tt) cc_final: 0.8478 (tt) REVERT: B 329 MET cc_start: 0.6961 (mmt) cc_final: 0.6755 (mmt) REVERT: B 348 PHE cc_start: 0.8509 (t80) cc_final: 0.8120 (t80) REVERT: B 377 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 419 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 464 PHE cc_start: 0.6873 (p90) cc_final: 0.6518 (p90) REVERT: B 475 ASP cc_start: 0.7370 (t70) cc_final: 0.7126 (t0) REVERT: C 1 MET cc_start: 0.5740 (tpp) cc_final: 0.5520 (tpp) REVERT: C 27 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7629 (mm-40) REVERT: C 29 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8075 (tt) REVERT: C 42 GLU cc_start: 0.7287 (tp30) cc_final: 0.6990 (tp30) REVERT: C 55 ARG cc_start: 0.6460 (mmm-85) cc_final: 0.6184 (mmm-85) REVERT: C 68 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6569 (mt-10) REVERT: C 76 VAL cc_start: 0.7746 (t) cc_final: 0.7429 (p) REVERT: C 83 LEU cc_start: 0.7844 (mt) cc_final: 0.7339 (tt) REVERT: C 92 GLN cc_start: 0.8350 (mt0) cc_final: 0.7937 (mt0) REVERT: C 96 TRP cc_start: 0.8729 (t60) cc_final: 0.8272 (t60) REVERT: C 100 HIS cc_start: 0.8228 (m90) cc_final: 0.7671 (m90) REVERT: C 131 GLN cc_start: 0.7816 (tt0) cc_final: 0.6534 (tp-100) REVERT: C 140 ARG cc_start: 0.7228 (mpt-90) cc_final: 0.6803 (mpt-90) REVERT: C 183 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8073 (mmp-170) REVERT: C 190 ARG cc_start: 0.7909 (mmm-85) cc_final: 0.7695 (mmm-85) REVERT: C 199 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6706 (p-80) REVERT: C 208 ARG cc_start: 0.8224 (mpp80) cc_final: 0.7655 (mtm-85) REVERT: C 214 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7778 (ttmt) REVERT: C 237 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8170 (mtp180) REVERT: C 242 GLU cc_start: 0.7513 (pm20) cc_final: 0.6885 (pm20) REVERT: C 276 GLU cc_start: 0.8293 (pt0) cc_final: 0.8034 (pt0) REVERT: C 331 PHE cc_start: 0.8411 (m-80) cc_final: 0.8080 (m-80) REVERT: C 345 TRP cc_start: 0.7426 (m100) cc_final: 0.7226 (m100) REVERT: C 350 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8080 (mt-10) REVERT: C 452 ASN cc_start: 0.8145 (t0) cc_final: 0.7612 (t0) REVERT: C 455 LEU cc_start: 0.8967 (mt) cc_final: 0.8753 (tp) REVERT: D 9 LEU cc_start: 0.8257 (tt) cc_final: 0.7644 (mt) REVERT: D 22 GLN cc_start: 0.7952 (mt0) cc_final: 0.7648 (mt0) REVERT: D 28 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7917 (tm-30) REVERT: D 51 ASP cc_start: 0.8343 (t0) cc_final: 0.7967 (t0) REVERT: D 57 ARG cc_start: 0.7158 (mmm160) cc_final: 0.6911 (mmm160) REVERT: D 60 ASN cc_start: 0.8255 (m110) cc_final: 0.7572 (t0) REVERT: D 70 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6912 (tm-30) REVERT: D 101 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8514 (mmmt) REVERT: D 102 LYS cc_start: 0.8043 (mttm) cc_final: 0.7822 (mttm) REVERT: D 112 PHE cc_start: 0.7773 (t80) cc_final: 0.7562 (t80) REVERT: D 114 THR cc_start: 0.8443 (p) cc_final: 0.8212 (m) REVERT: D 133 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7999 (mt-10) REVERT: D 134 LEU cc_start: 0.7904 (tp) cc_final: 0.7644 (tp) REVERT: D 138 LYS cc_start: 0.8587 (mttt) cc_final: 0.8282 (tttp) REVERT: D 140 ARG cc_start: 0.7673 (tpt170) cc_final: 0.6796 (tpt170) REVERT: D 215 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6785 (t0) REVERT: D 239 MET cc_start: 0.8015 (mmm) cc_final: 0.7334 (mpp) REVERT: D 247 TYR cc_start: 0.7039 (m-10) cc_final: 0.6192 (m-10) REVERT: D 250 LEU cc_start: 0.8427 (tp) cc_final: 0.8136 (tp) REVERT: D 265 ARG cc_start: 0.7566 (ptt180) cc_final: 0.7208 (ptt180) REVERT: D 272 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7934 (mmm160) REVERT: D 278 LEU cc_start: 0.8627 (mt) cc_final: 0.8395 (mt) REVERT: D 329 MET cc_start: 0.7886 (tpp) cc_final: 0.7426 (tpp) REVERT: D 333 LYS cc_start: 0.6997 (tttp) cc_final: 0.6737 (tttp) REVERT: D 337 ASN cc_start: 0.7653 (t0) cc_final: 0.7233 (t0) REVERT: D 351 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: D 452 ASN cc_start: 0.7967 (t0) cc_final: 0.7736 (t0) REVERT: D 459 ASN cc_start: 0.8075 (m110) cc_final: 0.7804 (m110) REVERT: D 461 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6871 (ttm-80) outliers start: 59 outliers final: 38 residues processed: 479 average time/residue: 0.1516 time to fit residues: 104.2022 Evaluate side-chains 487 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 441 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 29 LEU 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 175 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER 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 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 92 GLN Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 149 ILE 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 351 GLU Chi-restraints excluded: chain D residue 361 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: 0.9980 chunk 191 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 173 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 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** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.207544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151300 restraints weight = 47674.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156902 restraints weight = 21329.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160274 restraints weight = 12973.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162253 restraints weight = 9526.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.163546 restraints weight = 7908.651| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20312 Z= 0.231 Angle : 0.704 11.408 28378 Z= 0.396 Chirality : 0.046 0.242 3109 Planarity : 0.005 0.060 3022 Dihedral : 23.239 87.691 4285 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.68 % Allowed : 17.57 % Favored : 78.75 % 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: 0.86 (0.19), residues: 1937 helix: 1.14 (0.16), residues: 916 sheet: -0.28 (0.29), residues: 283 loop : 0.39 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 409 TYR 0.022 0.002 TYR C 216 PHE 0.032 0.002 PHE D 217 TRP 0.038 0.002 TRP C 64 HIS 0.010 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.23 (20296) covalent geometry : angle 0.69102 / 0.40 (28354) hydrogen bonds : bond 0.05373 / 3.74 ( 1046) hydrogen bonds : angle 4.28786 / 3.09 ( 2758) metal coordination : bond 0.00679 / 0.39 ( 16) metal coordination : angle 4.68237 / 2.89 ( 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 503 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 444 time to evaluate : 0.462 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: A 6 VAL cc_start: 0.7263 (t) cc_final: 0.6846 (m) REVERT: A 27 GLN cc_start: 0.8440 (mt0) cc_final: 0.8036 (mt0) REVERT: A 28 GLN cc_start: 0.8661 (mt0) cc_final: 0.8323 (tm-30) REVERT: A 29 LEU cc_start: 0.8489 (tp) cc_final: 0.8176 (tp) REVERT: A 79 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7160 (mtp180) REVERT: A 87 ILE cc_start: 0.8477 (tp) cc_final: 0.8088 (mp) REVERT: A 104 VAL cc_start: 0.7506 (t) cc_final: 0.7152 (p) REVERT: A 109 GLU cc_start: 0.6526 (mt-10) cc_final: 0.5805 (mp0) REVERT: A 132 MET cc_start: 0.7403 (mpm) cc_final: 0.6984 (mpm) REVERT: A 134 LEU cc_start: 0.8782 (tp) cc_final: 0.7776 (tp) REVERT: A 135 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 138 LYS cc_start: 0.8207 (mttm) cc_final: 0.7936 (mttm) REVERT: A 180 GLN cc_start: 0.7171 (mm110) cc_final: 0.6702 (mm-40) REVERT: A 219 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6872 (mm110) REVERT: A 235 LEU cc_start: 0.8847 (mt) cc_final: 0.8461 (mt) REVERT: A 239 MET cc_start: 0.7912 (mmm) cc_final: 0.7137 (mmm) REVERT: B 8 ARG cc_start: 0.7435 (ttt-90) cc_final: 0.5815 (tmm160) REVERT: B 21 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7565 (ttm170) REVERT: B 51 ASP cc_start: 0.7266 (t0) cc_final: 0.6781 (t0) REVERT: B 88 ARG cc_start: 0.7876 (ttt90) cc_final: 0.7401 (tpt-90) REVERT: B 95 HIS cc_start: 0.7548 (m-70) cc_final: 0.7123 (m-70) REVERT: B 116 THR cc_start: 0.7279 (m) cc_final: 0.6990 (m) REVERT: B 149 ILE cc_start: 0.8159 (mt) cc_final: 0.7818 (tt) REVERT: B 153 LYS cc_start: 0.7869 (mtmp) cc_final: 0.7316 (mtmp) REVERT: B 164 LEU cc_start: 0.8068 (tp) cc_final: 0.7616 (mt) REVERT: B 183 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.6841 (mmt180) REVERT: B 203 HIS cc_start: 0.7777 (m-70) cc_final: 0.6963 (t-90) REVERT: B 205 LEU cc_start: 0.8279 (mp) cc_final: 0.7925 (mm) REVERT: B 207 ARG cc_start: 0.7503 (tpp80) cc_final: 0.7017 (tpp80) REVERT: B 215 ASP cc_start: 0.7905 (m-30) cc_final: 0.7317 (m-30) REVERT: B 226 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: B 228 ARG cc_start: 0.6474 (mtm-85) cc_final: 0.6018 (mtm-85) REVERT: B 244 MET cc_start: 0.6918 (mmp) cc_final: 0.6694 (mmm) REVERT: B 265 ARG cc_start: 0.8469 (ptt180) cc_final: 0.7953 (ptt180) REVERT: B 272 ARG cc_start: 0.7707 (ttp80) cc_final: 0.6902 (ttp80) REVERT: B 274 GLN cc_start: 0.8049 (mt0) cc_final: 0.7086 (mt0) REVERT: B 275 LEU cc_start: 0.8369 (tp) cc_final: 0.8075 (tp) REVERT: B 281 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7478 (mt-10) REVERT: B 348 PHE cc_start: 0.8300 (t80) cc_final: 0.7910 (t80) REVERT: B 351 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8375 (tm-30) REVERT: B 377 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7699 (mt) REVERT: B 383 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 421 GLU cc_start: 0.8277 (tt0) cc_final: 0.8053 (mt-10) REVERT: B 459 ASN cc_start: 0.8280 (m-40) cc_final: 0.8049 (m-40) REVERT: B 464 PHE cc_start: 0.6637 (p90) cc_final: 0.6347 (p90) REVERT: B 475 ASP cc_start: 0.7383 (t70) cc_final: 0.7082 (t0) REVERT: C 8 ARG cc_start: 0.4697 (ttp80) cc_final: 0.3585 (ttp-170) REVERT: C 29 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7937 (pp) REVERT: C 76 VAL cc_start: 0.7797 (t) cc_final: 0.7550 (p) REVERT: C 96 TRP cc_start: 0.8773 (t60) cc_final: 0.7679 (t60) REVERT: C 114 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7656 (p) REVERT: C 131 GLN cc_start: 0.7883 (tt0) cc_final: 0.6633 (tp-100) REVERT: C 133 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 208 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7057 (ttp-110) REVERT: C 214 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7765 (ttmt) REVERT: C 237 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8165 (mtp180) REVERT: C 244 MET cc_start: 0.8692 (mmt) cc_final: 0.8139 (mtt) REVERT: C 272 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7560 (tpp80) REVERT: C 276 GLU cc_start: 0.8318 (pt0) cc_final: 0.7498 (mm-30) REVERT: C 331 PHE cc_start: 0.8427 (m-80) cc_final: 0.8089 (m-80) REVERT: C 452 ASN cc_start: 0.8132 (t0) cc_final: 0.7506 (t0) REVERT: C 455 LEU cc_start: 0.8999 (mt) cc_final: 0.8763 (tp) REVERT: D 9 LEU cc_start: 0.8254 (tt) cc_final: 0.7622 (mt) REVERT: D 22 GLN cc_start: 0.7950 (mt0) cc_final: 0.7639 (mt0) REVERT: D 51 ASP cc_start: 0.8355 (t0) cc_final: 0.8016 (t0) REVERT: D 57 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6953 (mmm160) REVERT: D 60 ASN cc_start: 0.8280 (m110) cc_final: 0.7840 (t0) REVERT: D 64 TRP cc_start: 0.8035 (m100) cc_final: 0.7319 (m100) REVERT: D 70 GLN cc_start: 0.7569 (tm-30) cc_final: 0.6301 (tm-30) REVERT: D 102 LYS cc_start: 0.8138 (mttm) cc_final: 0.7732 (mttm) REVERT: D 134 LEU cc_start: 0.7938 (tp) cc_final: 0.7705 (tp) REVERT: D 138 LYS cc_start: 0.8606 (mttt) cc_final: 0.8282 (tttp) REVERT: D 140 ARG cc_start: 0.7758 (tpt170) cc_final: 0.6995 (tpt170) REVERT: D 199 HIS cc_start: 0.7652 (t-90) cc_final: 0.7418 (t70) REVERT: D 215 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6709 (t0) REVERT: D 226 GLN cc_start: 0.7573 (mp-120) cc_final: 0.7277 (mp10) REVERT: D 239 MET cc_start: 0.8037 (mmm) cc_final: 0.7316 (mpp) REVERT: D 265 ARG cc_start: 0.7532 (ptt180) cc_final: 0.7130 (ptt180) REVERT: D 278 LEU cc_start: 0.8611 (mt) cc_final: 0.8373 (mt) REVERT: D 281 GLU cc_start: 0.7930 (tp30) cc_final: 0.7534 (tp30) REVERT: D 329 MET cc_start: 0.7955 (tpp) cc_final: 0.7503 (tpp) REVERT: D 333 LYS cc_start: 0.7010 (tttp) cc_final: 0.6747 (tttp) REVERT: D 337 ASN cc_start: 0.7825 (t0) cc_final: 0.7321 (t0) REVERT: D 351 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: D 459 ASN cc_start: 0.8143 (m110) cc_final: 0.7913 (m110) REVERT: D 461 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.6877 (ttm-80) outliers start: 59 outliers final: 37 residues processed: 468 average time/residue: 0.1530 time to fit residues: 101.8995 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 : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER 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 35 TRP Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 342 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 0.0770 chunk 137 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 446 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.203608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146774 restraints weight = 50089.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153382 restraints weight = 23550.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154847 restraints weight = 14610.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156435 restraints weight = 11045.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157052 restraints weight = 9426.854| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 20312 Z= 0.363 Angle : 0.816 10.483 28378 Z= 0.457 Chirality : 0.050 0.248 3109 Planarity : 0.007 0.067 3022 Dihedral : 23.340 87.075 4282 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.42 % Allowed : 18.50 % Favored : 77.07 % 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: 0.17 (0.19), residues: 1937 helix: 0.57 (0.16), residues: 914 sheet: -0.46 (0.29), residues: 285 loop : -0.01 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 208 TYR 0.035 0.003 TYR D 154 PHE 0.071 0.002 PHE C 118 TRP 0.051 0.003 TRP D 96 HIS 0.020 0.002 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.36 (20296) covalent geometry : angle 0.80576 / 0.46 (28354) hydrogen bonds : bond 0.06444 / 4.48 ( 1046) hydrogen bonds : angle 4.71146 / 3.39 ( 2758) metal coordination : bond 0.01134 / 0.66 ( 16) metal coordination : angle 4.51328 / 3.01 ( 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: 71 poor density : 430 time to evaluate : 0.527 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: A 28 GLN cc_start: 0.8675 (mt0) cc_final: 0.8392 (tm-30) REVERT: A 29 LEU cc_start: 0.8614 (tp) cc_final: 0.8341 (tp) REVERT: A 79 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7143 (mtp180) REVERT: A 109 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5880 (mp0) REVERT: A 118 PHE cc_start: 0.5664 (m-80) cc_final: 0.5346 (m-80) REVERT: A 131 GLN cc_start: 0.8085 (tp40) cc_final: 0.7000 (tp40) REVERT: A 132 MET cc_start: 0.7499 (mpm) cc_final: 0.6901 (mpm) REVERT: A 134 LEU cc_start: 0.8790 (tp) cc_final: 0.7816 (tp) REVERT: A 135 GLU cc_start: 0.8238 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 138 LYS cc_start: 0.8215 (mttm) cc_final: 0.7791 (mttm) REVERT: A 180 GLN cc_start: 0.7412 (mm110) cc_final: 0.7081 (mm-40) REVERT: A 219 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6995 (mm110) REVERT: A 235 LEU cc_start: 0.8935 (mt) cc_final: 0.8566 (mt) REVERT: A 239 MET cc_start: 0.8003 (mmm) cc_final: 0.7247 (mmm) REVERT: B 8 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.6149 (tmm160) REVERT: B 21 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7848 (ttm170) REVERT: B 88 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7540 (tpt-90) REVERT: B 95 HIS cc_start: 0.7582 (m-70) cc_final: 0.6189 (m-70) REVERT: B 149 ILE cc_start: 0.8218 (mt) cc_final: 0.7915 (tt) REVERT: B 153 LYS cc_start: 0.8066 (mtmp) cc_final: 0.7539 (mtmp) REVERT: B 164 LEU cc_start: 0.8093 (tp) cc_final: 0.7692 (mt) REVERT: B 183 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6834 (mmt180) REVERT: B 203 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7063 (t-90) REVERT: B 205 LEU cc_start: 0.8362 (mp) cc_final: 0.8031 (mm) REVERT: B 207 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7133 (tpp80) REVERT: B 226 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.6524 (mt0) REVERT: B 228 ARG cc_start: 0.6526 (mtm-85) cc_final: 0.5804 (mtt90) REVERT: B 244 MET cc_start: 0.6944 (mmp) cc_final: 0.6636 (mmm) REVERT: B 265 ARG cc_start: 0.8557 (ptt180) cc_final: 0.8351 (ptt90) REVERT: B 274 GLN cc_start: 0.8084 (mt0) cc_final: 0.7358 (mt0) REVERT: B 275 LEU cc_start: 0.8327 (tp) cc_final: 0.8011 (tp) REVERT: B 348 PHE cc_start: 0.8536 (t80) cc_final: 0.8034 (t80) REVERT: B 377 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 419 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7928 (tt0) REVERT: B 459 ASN cc_start: 0.8382 (m-40) cc_final: 0.8122 (m-40) REVERT: B 464 PHE cc_start: 0.6790 (p90) cc_final: 0.6487 (p90) REVERT: B 475 ASP cc_start: 0.7593 (t70) cc_final: 0.7221 (t0) REVERT: C 24 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: C 29 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8120 (tt) REVERT: C 55 ARG cc_start: 0.6802 (mmm-85) cc_final: 0.6510 (mmm-85) REVERT: C 63 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7648 (ttm-80) REVERT: C 68 GLU cc_start: 0.6629 (mt-10) cc_final: 0.5673 (mm-30) REVERT: C 76 VAL cc_start: 0.7860 (t) cc_final: 0.7536 (p) REVERT: C 92 GLN cc_start: 0.8426 (mt0) cc_final: 0.8124 (mt0) REVERT: C 113 ASP cc_start: 0.7935 (t0) cc_final: 0.7667 (t0) REVERT: C 131 GLN cc_start: 0.8003 (tt0) cc_final: 0.6776 (tp-100) REVERT: C 132 MET cc_start: 0.7680 (mmm) cc_final: 0.7429 (mmm) REVERT: C 133 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C 168 VAL cc_start: 0.5725 (OUTLIER) cc_final: 0.4858 (m) REVERT: C 204 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7782 (t70) REVERT: C 208 ARG cc_start: 0.8290 (mpp80) cc_final: 0.7411 (mtm110) REVERT: C 228 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6253 (mtm-85) REVERT: C 237 ARG cc_start: 0.8836 (ttp-170) cc_final: 0.8347 (mtp180) REVERT: C 276 GLU cc_start: 0.8334 (pt0) cc_final: 0.7572 (mm-30) REVERT: C 331 PHE cc_start: 0.8500 (m-80) cc_final: 0.8148 (m-80) REVERT: C 452 ASN cc_start: 0.8029 (t0) cc_final: 0.7411 (t0) REVERT: D 9 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7693 (mt) REVERT: D 21 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.7127 (ttp-110) REVERT: D 57 ARG cc_start: 0.7379 (mmm160) cc_final: 0.7078 (mmm160) REVERT: D 60 ASN cc_start: 0.8282 (m110) cc_final: 0.7900 (t0) REVERT: D 64 TRP cc_start: 0.8043 (m100) cc_final: 0.7270 (m100) REVERT: D 70 GLN cc_start: 0.7681 (tm-30) cc_final: 0.6565 (tm-30) REVERT: D 102 LYS cc_start: 0.8261 (mttm) cc_final: 0.7986 (mttm) REVERT: D 133 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7952 (mt-10) REVERT: D 138 LYS cc_start: 0.8696 (mttt) cc_final: 0.8460 (tttp) REVERT: D 139 GLU cc_start: 0.7766 (tp30) cc_final: 0.7143 (tp30) REVERT: D 140 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7071 (tpt170) REVERT: D 215 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7097 (t70) REVERT: D 239 MET cc_start: 0.8066 (mmm) cc_final: 0.7408 (mpp) REVERT: D 250 LEU cc_start: 0.8585 (tp) cc_final: 0.8332 (mm) REVERT: D 265 ARG cc_start: 0.7463 (ptt180) cc_final: 0.7024 (ptt180) REVERT: D 278 LEU cc_start: 0.8633 (mt) cc_final: 0.8417 (mt) REVERT: D 329 MET cc_start: 0.8072 (tpp) cc_final: 0.7684 (mpp) REVERT: D 333 LYS cc_start: 0.7017 (tttp) cc_final: 0.6754 (tttp) REVERT: D 337 ASN cc_start: 0.7747 (t0) cc_final: 0.7268 (t0) REVERT: D 351 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: D 386 ASP cc_start: 0.5078 (OUTLIER) cc_final: 0.4779 (t70) REVERT: D 459 ASN cc_start: 0.8238 (m110) cc_final: 0.8027 (m110) REVERT: D 461 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6938 (ttm-80) outliers start: 71 outliers final: 48 residues processed: 460 average time/residue: 0.1589 time to fit residues: 103.6083 Evaluate side-chains 479 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 418 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 129 VAL 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 236 LYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE 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 253 LYS Chi-restraints excluded: chain B residue 375 VAL 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 29 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 456 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 56 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL 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 473 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 163 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 133 optimal weight: 50.0000 chunk 138 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 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** D 226 GLN D 274 GLN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.205540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149498 restraints weight = 43178.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154746 restraints weight = 20088.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157933 restraints weight = 12495.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159824 restraints weight = 9316.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.160852 restraints weight = 7820.299| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20312 Z= 0.259 Angle : 0.734 11.670 28378 Z= 0.412 Chirality : 0.046 0.249 3109 Planarity : 0.006 0.073 3022 Dihedral : 23.413 89.442 4280 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.24 % Allowed : 19.31 % Favored : 76.45 % 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: 0.30 (0.19), residues: 1937 helix: 0.69 (0.16), residues: 917 sheet: -0.40 (0.29), residues: 282 loop : 0.03 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 88 TYR 0.033 0.002 TYR D 154 PHE 0.031 0.002 PHE D 217 TRP 0.044 0.002 TRP C 35 HIS 0.014 0.002 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.26 (20296) covalent geometry : angle 0.72235 / 0.41 (28354) hydrogen bonds : bond 0.05427 / 3.78 ( 1046) hydrogen bonds : angle 4.47879 / 3.22 ( 2758) metal coordination : bond 0.00749 / 0.45 ( 16) metal coordination : angle 4.46987 / 2.80 ( 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 503 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 435 time to evaluate : 0.512 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: A 8 ARG cc_start: 0.6982 (ttp80) cc_final: 0.5594 (ptt90) REVERT: A 27 GLN cc_start: 0.8425 (mt0) cc_final: 0.7992 (mt0) REVERT: A 28 GLN cc_start: 0.8654 (mt0) cc_final: 0.8352 (tm-30) REVERT: A 29 LEU cc_start: 0.8604 (tp) cc_final: 0.8323 (tp) REVERT: A 79 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7132 (mtp180) REVERT: A 82 ARG cc_start: 0.8497 (mmt180) cc_final: 0.7796 (mmp-170) REVERT: A 109 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6177 (mt-10) REVERT: A 131 GLN cc_start: 0.8073 (tp40) cc_final: 0.6941 (tp40) REVERT: A 132 MET cc_start: 0.7627 (mpm) cc_final: 0.7113 (mpm) REVERT: A 134 LEU cc_start: 0.8764 (tp) cc_final: 0.7793 (tp) REVERT: A 135 GLU cc_start: 0.8280 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 138 LYS cc_start: 0.8174 (mttm) cc_final: 0.7752 (mttm) REVERT: A 180 GLN cc_start: 0.7357 (mm110) cc_final: 0.6911 (mm-40) REVERT: A 219 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6818 (mm110) REVERT: A 235 LEU cc_start: 0.8948 (mt) cc_final: 0.8586 (mt) REVERT: A 239 MET cc_start: 0.7983 (mmm) cc_final: 0.7212 (mmm) REVERT: B 21 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7871 (ttm170) REVERT: B 79 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7267 (mtp85) REVERT: B 88 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7541 (tpt-90) REVERT: B 95 HIS cc_start: 0.7615 (m-70) cc_final: 0.7162 (m-70) REVERT: B 149 ILE cc_start: 0.8151 (mt) cc_final: 0.7884 (tt) REVERT: B 150 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7786 (ttm110) REVERT: B 153 LYS cc_start: 0.7984 (mtmp) cc_final: 0.7441 (mtmp) REVERT: B 164 LEU cc_start: 0.8042 (tp) cc_final: 0.7675 (mt) REVERT: B 183 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.6785 (mmt180) REVERT: B 203 HIS cc_start: 0.7788 (m-70) cc_final: 0.6996 (t-90) REVERT: B 205 LEU cc_start: 0.8347 (mp) cc_final: 0.7882 (mm) REVERT: B 207 ARG cc_start: 0.7585 (tpp80) cc_final: 0.7064 (tpp80) REVERT: B 226 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6699 (mt0) REVERT: B 228 ARG cc_start: 0.6446 (mtm-85) cc_final: 0.5771 (mtt90) REVERT: B 244 MET cc_start: 0.6921 (mmp) cc_final: 0.6616 (mmm) REVERT: B 265 ARG cc_start: 0.8514 (ptt180) cc_final: 0.7905 (ptt90) REVERT: B 272 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7778 (mmm160) REVERT: B 274 GLN cc_start: 0.8030 (mt0) cc_final: 0.7314 (mt0) REVERT: B 275 LEU cc_start: 0.8309 (tp) cc_final: 0.7978 (tp) REVERT: B 348 PHE cc_start: 0.8220 (t80) cc_final: 0.7833 (t80) REVERT: B 377 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 379 GLU cc_start: 0.8610 (pt0) cc_final: 0.8370 (mp0) REVERT: B 418 GLU cc_start: 0.8442 (mp0) cc_final: 0.7470 (mm-30) REVERT: B 421 GLU cc_start: 0.8230 (tt0) cc_final: 0.8002 (mt-10) REVERT: B 459 ASN cc_start: 0.8321 (m-40) cc_final: 0.8062 (m-40) REVERT: B 464 PHE cc_start: 0.6584 (p90) cc_final: 0.6324 (p90) REVERT: B 475 ASP cc_start: 0.7645 (t70) cc_final: 0.7303 (t0) REVERT: C 29 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8089 (tt) REVERT: C 55 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6521 (mmm-85) REVERT: C 63 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7390 (ttm-80) REVERT: C 68 GLU cc_start: 0.6369 (mt-10) cc_final: 0.5957 (mt-10) REVERT: C 76 VAL cc_start: 0.7851 (t) cc_final: 0.7487 (p) REVERT: C 92 GLN cc_start: 0.8411 (mt0) cc_final: 0.8077 (mt0) REVERT: C 95 HIS cc_start: 0.7338 (t-170) cc_final: 0.6433 (t-170) REVERT: C 98 GLU cc_start: 0.6798 (pp20) cc_final: 0.6549 (pp20) REVERT: C 99 ASP cc_start: 0.7651 (m-30) cc_final: 0.7423 (m-30) REVERT: C 113 ASP cc_start: 0.7945 (t0) cc_final: 0.7667 (t0) REVERT: C 131 GLN cc_start: 0.8102 (tt0) cc_final: 0.6841 (tp-100) REVERT: C 132 MET cc_start: 0.7741 (mmm) cc_final: 0.7355 (mmm) REVERT: C 133 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 182 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 183 ARG cc_start: 0.8662 (mmt-90) cc_final: 0.8135 (mmp80) REVERT: C 204 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7634 (t70) REVERT: C 208 ARG cc_start: 0.8168 (mpp80) cc_final: 0.7877 (mtm-85) REVERT: C 228 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6155 (mtm-85) REVERT: C 236 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8693 (pttt) REVERT: C 237 ARG cc_start: 0.8801 (ttp-170) cc_final: 0.8391 (mtp180) REVERT: C 244 MET cc_start: 0.8754 (mmt) cc_final: 0.8186 (mtt) REVERT: C 276 GLU cc_start: 0.8300 (pt0) cc_final: 0.8012 (pt0) REVERT: C 331 PHE cc_start: 0.8486 (m-80) cc_final: 0.8151 (m-80) REVERT: C 452 ASN cc_start: 0.8048 (t0) cc_final: 0.7426 (t0) REVERT: D 9 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7692 (mt) REVERT: D 20 GLU cc_start: 0.7782 (pm20) cc_final: 0.7475 (pm20) REVERT: D 21 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.7022 (ttp-110) REVERT: D 57 ARG cc_start: 0.7366 (mmm160) cc_final: 0.7063 (mmm160) REVERT: D 60 ASN cc_start: 0.8209 (m110) cc_final: 0.7822 (t0) REVERT: D 64 TRP cc_start: 0.8055 (m100) cc_final: 0.7329 (m100) REVERT: D 70 GLN cc_start: 0.7746 (tm-30) cc_final: 0.6612 (tm-30) REVERT: D 102 LYS cc_start: 0.8274 (mttm) cc_final: 0.7992 (mttm) REVERT: D 133 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 138 LYS cc_start: 0.8626 (mttt) cc_final: 0.8384 (tttp) REVERT: D 140 ARG cc_start: 0.7779 (tpt170) cc_final: 0.7239 (tpt170) REVERT: D 215 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6845 (t70) REVERT: D 239 MET cc_start: 0.8050 (mmm) cc_final: 0.7393 (mpp) REVERT: D 250 LEU cc_start: 0.8573 (tp) cc_final: 0.8265 (tp) REVERT: D 265 ARG cc_start: 0.7476 (ptt180) cc_final: 0.7033 (ptt180) REVERT: D 278 LEU cc_start: 0.8604 (mt) cc_final: 0.8378 (mt) REVERT: D 329 MET cc_start: 0.8031 (tpp) cc_final: 0.7739 (tpp) REVERT: D 333 LYS cc_start: 0.7207 (tttp) cc_final: 0.6891 (tttp) REVERT: D 337 ASN cc_start: 0.7690 (t0) cc_final: 0.7138 (t0) REVERT: D 351 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: D 386 ASP cc_start: 0.5071 (OUTLIER) cc_final: 0.4721 (t70) REVERT: D 461 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.6911 (ttm-80) outliers start: 68 outliers final: 47 residues processed: 460 average time/residue: 0.1631 time to fit residues: 106.7683 Evaluate side-chains 486 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 428 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 350 GLU 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 29 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 456 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 56 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 MET 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: 50.0000 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 127 optimal weight: 40.0000 chunk 53 optimal weight: 0.0970 chunk 207 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 146 HIS C 352 GLN ** D 27 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** D 274 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.208293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152279 restraints weight = 60314.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159988 restraints weight = 26572.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160193 restraints weight = 16060.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162661 restraints weight = 11691.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163145 restraints weight = 9295.131| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20312 Z= 0.165 Angle : 0.681 11.036 28378 Z= 0.381 Chirality : 0.043 0.266 3109 Planarity : 0.006 0.081 3022 Dihedral : 23.392 87.696 4273 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.43 % Allowed : 21.18 % Favored : 75.39 % 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: 0.64 (0.19), residues: 1937 helix: 1.04 (0.17), residues: 917 sheet: -0.41 (0.29), residues: 284 loop : 0.18 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 467 TYR 0.033 0.002 TYR D 154 PHE 0.064 0.002 PHE C 118 TRP 0.060 0.002 TRP C 64 HIS 0.017 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (20296) covalent geometry : angle 0.66989 / 0.38 (28354) hydrogen bonds : bond 0.04644 / 3.23 ( 1046) hydrogen bonds : angle 4.21181 / 3.03 ( 2758) metal coordination : bond 0.00380 / 0.22 ( 16) metal coordination : angle 4.19874 / 2.54 ( 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 489 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 434 time to evaluate : 0.507 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 6 VAL cc_start: 0.7151 (t) cc_final: 0.6705 (m) REVERT: A 8 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6562 (ttp80) REVERT: A 27 GLN cc_start: 0.8355 (mt0) cc_final: 0.7920 (mt0) REVERT: A 28 GLN cc_start: 0.8652 (mt0) cc_final: 0.8375 (tm-30) REVERT: A 29 LEU cc_start: 0.8592 (tp) cc_final: 0.8292 (tp) REVERT: A 79 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7163 (mtp180) REVERT: A 109 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6107 (mt-10) REVERT: A 131 GLN cc_start: 0.7982 (tp40) cc_final: 0.6787 (tp40) REVERT: A 132 MET cc_start: 0.7443 (mpm) cc_final: 0.7088 (mpm) REVERT: A 134 LEU cc_start: 0.8676 (tp) cc_final: 0.7733 (tp) REVERT: A 135 GLU cc_start: 0.8162 (mm-30) cc_final: 0.6887 (mm-30) REVERT: A 138 LYS cc_start: 0.8122 (mttm) cc_final: 0.7710 (mttm) REVERT: A 180 GLN cc_start: 0.7389 (mm110) cc_final: 0.6931 (mm-40) REVERT: A 219 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6923 (mm110) REVERT: A 235 LEU cc_start: 0.8982 (mt) cc_final: 0.8605 (mt) REVERT: A 239 MET cc_start: 0.7960 (mmm) cc_final: 0.7214 (mmm) REVERT: B 8 ARG cc_start: 0.7259 (ttt-90) cc_final: 0.5874 (tmm160) REVERT: B 9 LEU cc_start: 0.8113 (tp) cc_final: 0.7689 (tt) REVERT: B 21 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7783 (ttm170) REVERT: B 26 CYS cc_start: 0.7705 (m) cc_final: 0.7231 (p) REVERT: B 88 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7454 (tpt-90) REVERT: B 109 GLU cc_start: 0.6997 (mp0) cc_final: 0.6636 (mp0) REVERT: B 121 VAL cc_start: 0.8678 (m) cc_final: 0.8369 (p) REVERT: B 149 ILE cc_start: 0.8102 (mt) cc_final: 0.7873 (tt) REVERT: B 150 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7622 (ttm110) REVERT: B 153 LYS cc_start: 0.8022 (mtmp) cc_final: 0.7473 (mtmp) REVERT: B 164 LEU cc_start: 0.8089 (tp) cc_final: 0.7865 (mt) REVERT: B 183 ARG cc_start: 0.7181 (ttm-80) cc_final: 0.6693 (mmt180) REVERT: B 203 HIS cc_start: 0.7758 (m-70) cc_final: 0.6913 (t-90) REVERT: B 205 LEU cc_start: 0.8313 (mp) cc_final: 0.7806 (mm) REVERT: B 207 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7011 (tpp80) REVERT: B 215 ASP cc_start: 0.7806 (m-30) cc_final: 0.6798 (m-30) REVERT: B 226 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7202 (mt0) REVERT: B 228 ARG cc_start: 0.6405 (mtm-85) cc_final: 0.5733 (mtm-85) REVERT: B 265 ARG cc_start: 0.8539 (ptt180) cc_final: 0.7829 (ptt90) REVERT: B 272 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7693 (mmm160) REVERT: B 274 GLN cc_start: 0.7930 (mt0) cc_final: 0.7144 (mt0) REVERT: B 275 LEU cc_start: 0.8346 (tp) cc_final: 0.7998 (tp) REVERT: B 377 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (mt) REVERT: B 379 GLU cc_start: 0.8588 (pt0) cc_final: 0.8204 (mp0) REVERT: B 386 ASP cc_start: 0.8660 (m-30) cc_final: 0.8304 (p0) REVERT: B 418 GLU cc_start: 0.8430 (mp0) cc_final: 0.7410 (mm-30) REVERT: B 421 GLU cc_start: 0.8251 (tt0) cc_final: 0.7968 (mt-10) REVERT: B 459 ASN cc_start: 0.8346 (m-40) cc_final: 0.8077 (m-40) REVERT: B 464 PHE cc_start: 0.6628 (p90) cc_final: 0.6386 (p90) REVERT: B 475 ASP cc_start: 0.7570 (t70) cc_final: 0.7203 (t0) REVERT: C 74 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6931 (t) REVERT: C 76 VAL cc_start: 0.7780 (t) cc_final: 0.7389 (p) REVERT: C 92 GLN cc_start: 0.8222 (mt0) cc_final: 0.7833 (mt0) REVERT: C 95 HIS cc_start: 0.7346 (t-170) cc_final: 0.6369 (t-170) REVERT: C 98 GLU cc_start: 0.6585 (pp20) cc_final: 0.6385 (pp20) REVERT: C 99 ASP cc_start: 0.7593 (m-30) cc_final: 0.7316 (m-30) REVERT: C 113 ASP cc_start: 0.7924 (t0) cc_final: 0.7673 (t0) REVERT: C 131 GLN cc_start: 0.7980 (tt0) cc_final: 0.6711 (tp-100) REVERT: C 132 MET cc_start: 0.7483 (mmm) cc_final: 0.7117 (mmm) REVERT: C 133 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7559 (mt-10) REVERT: C 181 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7110 (tpp-160) REVERT: C 182 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 183 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.7992 (mmp-170) REVERT: C 204 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7788 (t70) REVERT: C 208 ARG cc_start: 0.8139 (mpp80) cc_final: 0.7506 (mtm180) REVERT: C 228 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6157 (mtm-85) REVERT: C 236 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8611 (pttt) REVERT: C 237 ARG cc_start: 0.8743 (ttp-170) cc_final: 0.8278 (mtp180) REVERT: C 274 GLN cc_start: 0.8424 (mt0) cc_final: 0.7950 (mp10) REVERT: C 276 GLU cc_start: 0.8247 (pt0) cc_final: 0.7935 (pt0) REVERT: C 329 MET cc_start: 0.8573 (ttm) cc_final: 0.8097 (tmm) REVERT: C 331 PHE cc_start: 0.8523 (m-80) cc_final: 0.8163 (m-80) REVERT: C 452 ASN cc_start: 0.8025 (t0) cc_final: 0.7442 (t0) REVERT: D 9 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7639 (mt) REVERT: D 20 GLU cc_start: 0.7798 (pm20) cc_final: 0.7505 (pm20) REVERT: D 21 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6861 (ttp-110) REVERT: D 51 ASP cc_start: 0.8398 (t0) cc_final: 0.8018 (t0) REVERT: D 57 ARG cc_start: 0.7227 (mmm160) cc_final: 0.6926 (mmm160) REVERT: D 60 ASN cc_start: 0.8236 (m110) cc_final: 0.7753 (t0) REVERT: D 64 TRP cc_start: 0.7919 (m100) cc_final: 0.7284 (m100) REVERT: D 70 GLN cc_start: 0.7745 (tm-30) cc_final: 0.6667 (tm-30) REVERT: D 88 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7274 (tpp80) REVERT: D 102 LYS cc_start: 0.8217 (mttm) cc_final: 0.7957 (mttm) REVERT: D 138 LYS cc_start: 0.8618 (mttt) cc_final: 0.8400 (tttp) REVERT: D 140 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7020 (tpt170) REVERT: D 208 ARG cc_start: 0.7460 (mmp80) cc_final: 0.7171 (mmp80) REVERT: D 215 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6792 (t70) REVERT: D 239 MET cc_start: 0.8076 (mmm) cc_final: 0.7862 (mmp) REVERT: D 250 LEU cc_start: 0.8674 (tp) cc_final: 0.8380 (tp) REVERT: D 265 ARG cc_start: 0.7479 (ptt180) cc_final: 0.7022 (ptt180) REVERT: D 274 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: D 278 LEU cc_start: 0.8566 (mt) cc_final: 0.8279 (mt) REVERT: D 281 GLU cc_start: 0.7823 (tp30) cc_final: 0.7469 (tp30) REVERT: D 329 MET cc_start: 0.7923 (tpp) cc_final: 0.7559 (mpp) REVERT: D 333 LYS cc_start: 0.7222 (tttp) cc_final: 0.6911 (tttp) REVERT: D 337 ASN cc_start: 0.7765 (t0) cc_final: 0.7176 (t0) REVERT: D 345 TRP cc_start: 0.8200 (m100) cc_final: 0.7930 (m-10) REVERT: D 351 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: D 461 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6903 (ttm-80) outliers start: 55 outliers final: 35 residues processed: 457 average time/residue: 0.1559 time to fit residues: 100.6920 Evaluate side-chains 475 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 428 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 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 60 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 456 ARG 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 94 VAL 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 274 GLN Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU 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: 0.0010 chunk 16 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 29 optimal weight: 0.0060 chunk 133 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 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** D 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.209237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154240 restraints weight = 50339.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159949 restraints weight = 21988.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163404 restraints weight = 13164.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165473 restraints weight = 9539.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166685 restraints weight = 7839.381| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20312 Z= 0.150 Angle : 0.665 12.293 28378 Z= 0.371 Chirality : 0.042 0.268 3109 Planarity : 0.005 0.058 3022 Dihedral : 23.372 83.974 4272 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.12 % Allowed : 21.56 % Favored : 75.33 % 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: 0.84 (0.19), residues: 1937 helix: 1.23 (0.17), residues: 916 sheet: -0.41 (0.29), residues: 284 loop : 0.29 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 272 TYR 0.031 0.002 TYR D 216 PHE 0.034 0.002 PHE C 118 TRP 0.059 0.002 TRP C 64 HIS 0.008 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (20296) covalent geometry : angle 0.65523 / 0.37 (28354) hydrogen bonds : bond 0.04431 / 3.07 ( 1046) hydrogen bonds : angle 4.11075 / 2.96 ( 2758) metal coordination : bond 0.00329 / 0.20 ( 16) metal coordination : angle 3.88557 / 2.33 ( 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 485 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 435 time to evaluate : 0.586 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: A 6 VAL cc_start: 0.7154 (t) cc_final: 0.6739 (m) REVERT: A 8 ARG cc_start: 0.6895 (ttp80) cc_final: 0.6376 (ttp80) REVERT: A 27 GLN cc_start: 0.8344 (mt0) cc_final: 0.7855 (mt0) REVERT: A 28 GLN cc_start: 0.8605 (mt0) cc_final: 0.8341 (tm-30) REVERT: A 29 LEU cc_start: 0.8564 (tp) cc_final: 0.8265 (tp) REVERT: A 63 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7067 (ttp-110) REVERT: A 79 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7142 (mtp180) REVERT: A 96 TRP cc_start: 0.7869 (t60) cc_final: 0.7622 (t60) REVERT: A 109 GLU cc_start: 0.6443 (mt-10) cc_final: 0.6020 (mt-10) REVERT: A 131 GLN cc_start: 0.8011 (tp40) cc_final: 0.6785 (tp40) REVERT: A 132 MET cc_start: 0.7566 (mpm) cc_final: 0.7155 (mpm) REVERT: A 134 LEU cc_start: 0.8677 (tp) cc_final: 0.7728 (tp) REVERT: A 135 GLU cc_start: 0.8168 (mm-30) cc_final: 0.6882 (mm-30) REVERT: A 138 LYS cc_start: 0.8122 (mttm) cc_final: 0.7704 (mttm) REVERT: A 180 GLN cc_start: 0.7190 (mm110) cc_final: 0.6744 (mm-40) REVERT: A 235 LEU cc_start: 0.8960 (mt) cc_final: 0.8573 (mt) REVERT: A 239 MET cc_start: 0.7908 (mmm) cc_final: 0.7181 (mmm) REVERT: A 409 ARG cc_start: 0.7996 (tpm170) cc_final: 0.7752 (tpm170) REVERT: A 418 GLU cc_start: 0.6268 (mm-30) cc_final: 0.5548 (mm-30) REVERT: B 8 ARG cc_start: 0.7220 (ttt-90) cc_final: 0.5760 (tmm160) REVERT: B 9 LEU cc_start: 0.8083 (tp) cc_final: 0.7616 (tt) REVERT: B 21 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7785 (ttm170) REVERT: B 26 CYS cc_start: 0.7653 (m) cc_final: 0.7197 (p) REVERT: B 79 ARG cc_start: 0.7439 (mtp180) cc_final: 0.6420 (mtp85) REVERT: B 88 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7447 (tpt-90) REVERT: B 121 VAL cc_start: 0.8666 (m) cc_final: 0.8375 (p) REVERT: B 135 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7012 (mm-30) REVERT: B 149 ILE cc_start: 0.8027 (mt) cc_final: 0.7799 (tt) REVERT: B 150 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7537 (ttm110) REVERT: B 153 LYS cc_start: 0.7936 (mtmp) cc_final: 0.7464 (mtmp) REVERT: B 164 LEU cc_start: 0.8049 (tp) cc_final: 0.7821 (mt) REVERT: B 183 ARG cc_start: 0.7156 (ttm-80) cc_final: 0.6661 (mmt180) REVERT: B 203 HIS cc_start: 0.7777 (m-70) cc_final: 0.6907 (t-90) REVERT: B 205 LEU cc_start: 0.8328 (mp) cc_final: 0.7855 (mm) REVERT: B 207 ARG cc_start: 0.7536 (tpp80) cc_final: 0.7007 (tpp80) REVERT: B 215 ASP cc_start: 0.7707 (m-30) cc_final: 0.6764 (m-30) REVERT: B 226 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: B 228 ARG cc_start: 0.6303 (mtm-85) cc_final: 0.5681 (mtm-85) REVERT: B 265 ARG cc_start: 0.8517 (ptt180) cc_final: 0.7778 (ptt90) REVERT: B 272 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7729 (mmm-85) REVERT: B 274 GLN cc_start: 0.7888 (mt0) cc_final: 0.7046 (mt0) REVERT: B 275 LEU cc_start: 0.8361 (tp) cc_final: 0.8023 (tp) REVERT: B 377 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 379 GLU cc_start: 0.8571 (pt0) cc_final: 0.8184 (mp0) REVERT: B 386 ASP cc_start: 0.8628 (m-30) cc_final: 0.8263 (p0) REVERT: B 421 GLU cc_start: 0.8226 (tt0) cc_final: 0.8004 (mt-10) REVERT: B 459 ASN cc_start: 0.8282 (m-40) cc_final: 0.8036 (m-40) REVERT: B 475 ASP cc_start: 0.7597 (t70) cc_final: 0.7213 (t0) REVERT: C 63 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7475 (ttm-80) REVERT: C 65 LEU cc_start: 0.8331 (mp) cc_final: 0.8069 (mm) REVERT: C 76 VAL cc_start: 0.7743 (t) cc_final: 0.7410 (p) REVERT: C 92 GLN cc_start: 0.8106 (mt0) cc_final: 0.7829 (mt0) REVERT: C 95 HIS cc_start: 0.7392 (t-170) cc_final: 0.6545 (t-170) REVERT: C 113 ASP cc_start: 0.7889 (t0) cc_final: 0.7614 (t0) REVERT: C 131 GLN cc_start: 0.7913 (tt0) cc_final: 0.6690 (tp-100) REVERT: C 132 MET cc_start: 0.7518 (mmm) cc_final: 0.7146 (mmm) REVERT: C 133 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 181 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7085 (tpp-160) REVERT: C 182 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7423 (tm-30) REVERT: C 183 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.8053 (mmp80) REVERT: C 204 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7767 (t70) REVERT: C 208 ARG cc_start: 0.7976 (mpp80) cc_final: 0.7574 (mtm180) REVERT: C 228 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6189 (mtm-85) REVERT: C 236 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8578 (pttt) REVERT: C 237 ARG cc_start: 0.8738 (ttp-170) cc_final: 0.8249 (mtp180) REVERT: C 272 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7477 (tpp80) REVERT: C 274 GLN cc_start: 0.8383 (mt0) cc_final: 0.7824 (mp10) REVERT: C 276 GLU cc_start: 0.8261 (pt0) cc_final: 0.7496 (mm-30) REVERT: C 329 MET cc_start: 0.8468 (ttm) cc_final: 0.7974 (tmm) REVERT: C 331 PHE cc_start: 0.8437 (m-80) cc_final: 0.8098 (m-80) REVERT: C 452 ASN cc_start: 0.7992 (t0) cc_final: 0.7427 (t0) REVERT: D 9 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7551 (mp) REVERT: D 21 ARG cc_start: 0.7140 (ttp-170) cc_final: 0.6853 (ttp-110) REVERT: D 51 ASP cc_start: 0.8301 (t0) cc_final: 0.7943 (t0) REVERT: D 57 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6712 (mmm160) REVERT: D 60 ASN cc_start: 0.8091 (m110) cc_final: 0.7658 (t0) REVERT: D 64 TRP cc_start: 0.7909 (m100) cc_final: 0.7292 (m100) REVERT: D 70 GLN cc_start: 0.7793 (tm-30) cc_final: 0.6760 (tm-30) REVERT: D 102 LYS cc_start: 0.8179 (mttm) cc_final: 0.7688 (mttm) REVERT: D 134 LEU cc_start: 0.7893 (tp) cc_final: 0.7639 (tp) REVERT: D 138 LYS cc_start: 0.8580 (mttt) cc_final: 0.8359 (tttp) REVERT: D 140 ARG cc_start: 0.7639 (tpt170) cc_final: 0.7116 (tpt170) REVERT: D 208 ARG cc_start: 0.7371 (mmp80) cc_final: 0.7055 (mmp80) REVERT: D 215 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6678 (t0) REVERT: D 239 MET cc_start: 0.7892 (mmm) cc_final: 0.7226 (mpp) REVERT: D 265 ARG cc_start: 0.7465 (ptt180) cc_final: 0.6996 (ptt180) REVERT: D 274 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: D 278 LEU cc_start: 0.8561 (mt) cc_final: 0.8316 (mt) REVERT: D 281 GLU cc_start: 0.7807 (tp30) cc_final: 0.7426 (tp30) REVERT: D 329 MET cc_start: 0.7917 (tpp) cc_final: 0.7525 (mpp) REVERT: D 333 LYS cc_start: 0.7238 (tttp) cc_final: 0.6936 (tttp) REVERT: D 337 ASN cc_start: 0.7858 (t0) cc_final: 0.7232 (t0) REVERT: D 351 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: D 461 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.6867 (ttm-80) outliers start: 50 outliers final: 33 residues processed: 454 average time/residue: 0.1540 time to fit residues: 99.1471 Evaluate side-chains 465 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 421 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 350 GLU 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 60 ASN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 456 ARG 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 67 PHE Chi-restraints excluded: chain D residue 92 GLN 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 274 GLN 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 473 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 77 optimal weight: 0.0070 chunk 127 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS A 131 GLN B 28 GLN B 91 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 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** ** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.204732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.148963 restraints weight = 46811.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154429 restraints weight = 20952.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157699 restraints weight = 12803.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159705 restraints weight = 9439.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160753 restraints weight = 7801.620| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20312 Z= 0.295 Angle : 0.763 10.915 28378 Z= 0.427 Chirality : 0.046 0.243 3109 Planarity : 0.006 0.061 3022 Dihedral : 23.370 87.737 4269 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 21.87 % Favored : 75.08 % 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: 0.41 (0.19), residues: 1937 helix: 0.86 (0.16), residues: 916 sheet: -0.51 (0.29), residues: 284 loop : 0.05 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 323 TYR 0.043 0.002 TYR D 216 PHE 0.057 0.002 PHE C 118 TRP 0.066 0.003 TRP C 64 HIS 0.016 0.002 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.30 (20296) covalent geometry : angle 0.75445 / 0.43 (28354) hydrogen bonds : bond 0.05730 / 3.98 ( 1046) hydrogen bonds : angle 4.40220 / 3.16 ( 2758) metal coordination : bond 0.00831 / 0.49 ( 16) metal coordination : angle 4.01334 / 2.63 ( 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 493 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 444 time to evaluate : 0.426 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: A 27 GLN cc_start: 0.8383 (mt0) cc_final: 0.7888 (mt0) REVERT: A 28 GLN cc_start: 0.8637 (mt0) cc_final: 0.8386 (tm-30) REVERT: A 29 LEU cc_start: 0.8594 (tp) cc_final: 0.8309 (tp) REVERT: A 109 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6167 (mt-10) REVERT: A 131 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7168 (tp-100) REVERT: A 132 MET cc_start: 0.7682 (mpm) cc_final: 0.7261 (mpm) REVERT: A 134 LEU cc_start: 0.8727 (tp) cc_final: 0.7837 (tp) REVERT: A 135 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 138 LYS cc_start: 0.8210 (mttm) cc_final: 0.7799 (mttm) REVERT: A 180 GLN cc_start: 0.7247 (mm110) cc_final: 0.6795 (mm-40) REVERT: A 200 LEU cc_start: 0.8781 (mt) cc_final: 0.8464 (mp) REVERT: A 235 LEU cc_start: 0.8936 (mt) cc_final: 0.8541 (mt) REVERT: A 238 SER cc_start: 0.8956 (m) cc_final: 0.8697 (p) REVERT: A 239 MET cc_start: 0.8006 (mmm) cc_final: 0.7234 (mmm) REVERT: A 257 ASP cc_start: 0.7730 (p0) cc_final: 0.7412 (p0) REVERT: A 273 GLU cc_start: 0.8782 (mp0) cc_final: 0.8315 (pm20) REVERT: B 8 ARG cc_start: 0.7237 (ttt-90) cc_final: 0.5551 (tmm160) REVERT: B 21 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7911 (ttm170) REVERT: B 79 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7245 (mtp85) REVERT: B 88 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7472 (tpt-90) REVERT: B 91 GLN cc_start: 0.8212 (mt0) cc_final: 0.7964 (mt0) REVERT: B 133 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 135 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7157 (mm-30) REVERT: B 149 ILE cc_start: 0.8162 (mt) cc_final: 0.7881 (tt) REVERT: B 150 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7782 (ttm110) REVERT: B 153 LYS cc_start: 0.8039 (mtmp) cc_final: 0.7550 (mtmp) REVERT: B 164 LEU cc_start: 0.8084 (tp) cc_final: 0.7687 (mt) REVERT: B 183 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6735 (mmt180) REVERT: B 203 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7036 (t-90) REVERT: B 205 LEU cc_start: 0.8348 (mp) cc_final: 0.7876 (mm) REVERT: B 207 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7224 (tpp80) REVERT: B 215 ASP cc_start: 0.7998 (m-30) cc_final: 0.7587 (m-30) REVERT: B 226 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7164 (tp40) REVERT: B 265 ARG cc_start: 0.8535 (ptt180) cc_final: 0.7949 (ptt90) REVERT: B 272 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7799 (mmm-85) REVERT: B 274 GLN cc_start: 0.8038 (mt0) cc_final: 0.7302 (mt0) REVERT: B 275 LEU cc_start: 0.8363 (tp) cc_final: 0.8028 (tp) REVERT: B 344 GLU cc_start: 0.7691 (mp0) cc_final: 0.7491 (tm-30) REVERT: B 379 GLU cc_start: 0.8658 (pt0) cc_final: 0.8303 (mp0) REVERT: B 419 GLU cc_start: 0.8182 (tm-30) cc_final: 0.6943 (tm-30) REVERT: B 459 ASN cc_start: 0.8355 (m-40) cc_final: 0.8070 (m-40) REVERT: B 475 ASP cc_start: 0.7761 (t70) cc_final: 0.7290 (t0) REVERT: C 63 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7586 (ttm-80) REVERT: C 76 VAL cc_start: 0.7842 (t) cc_final: 0.7500 (p) REVERT: C 92 GLN cc_start: 0.8435 (mt0) cc_final: 0.7997 (mt0) REVERT: C 95 HIS cc_start: 0.7199 (t-170) cc_final: 0.6975 (t-170) REVERT: C 113 ASP cc_start: 0.8041 (t0) cc_final: 0.7687 (t0) REVERT: C 131 GLN cc_start: 0.8001 (tt0) cc_final: 0.6797 (tp-100) REVERT: C 132 MET cc_start: 0.7726 (mmm) cc_final: 0.7366 (mmm) REVERT: C 133 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 181 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7157 (tpp-160) REVERT: C 182 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 183 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8238 (mmp-170) REVERT: C 208 ARG cc_start: 0.8087 (mpp80) cc_final: 0.7630 (mtm180) REVERT: C 228 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6289 (mtm180) REVERT: C 236 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8684 (pttt) REVERT: C 237 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.8419 (mtp180) REVERT: C 272 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7435 (tpp80) REVERT: C 275 LEU cc_start: 0.7880 (tp) cc_final: 0.7495 (tp) REVERT: C 276 GLU cc_start: 0.8283 (pt0) cc_final: 0.7819 (pp20) REVERT: C 329 MET cc_start: 0.8653 (ttm) cc_final: 0.8145 (tmm) REVERT: C 331 PHE cc_start: 0.8544 (m-80) cc_final: 0.8201 (m-80) REVERT: C 452 ASN cc_start: 0.7992 (t0) cc_final: 0.7403 (t0) REVERT: D 9 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7589 (mt) REVERT: D 21 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.7050 (ttp-110) REVERT: D 51 ASP cc_start: 0.8397 (t0) cc_final: 0.8082 (t0) REVERT: D 57 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6981 (mmm160) REVERT: D 60 ASN cc_start: 0.8230 (m110) cc_final: 0.7798 (t0) REVERT: D 64 TRP cc_start: 0.8035 (m100) cc_final: 0.7344 (m100) REVERT: D 70 GLN cc_start: 0.7790 (tm-30) cc_final: 0.6687 (tm-30) REVERT: D 102 LYS cc_start: 0.8260 (mttm) cc_final: 0.7969 (mttm) REVERT: D 133 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 138 LYS cc_start: 0.8661 (mttt) cc_final: 0.8442 (tttp) REVERT: D 139 GLU cc_start: 0.7802 (tp30) cc_final: 0.7171 (tp30) REVERT: D 140 ARG cc_start: 0.7813 (tpt170) cc_final: 0.7228 (tpt170) REVERT: D 208 ARG cc_start: 0.7571 (mmp80) cc_final: 0.7269 (mmp80) REVERT: D 215 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7038 (t0) REVERT: D 216 TYR cc_start: 0.7905 (t80) cc_final: 0.7616 (t80) REVERT: D 250 LEU cc_start: 0.8679 (tp) cc_final: 0.8348 (tp) REVERT: D 265 ARG cc_start: 0.7437 (ptt180) cc_final: 0.6964 (ptt180) REVERT: D 272 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7798 (mmm160) REVERT: D 274 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: D 278 LEU cc_start: 0.8584 (mt) cc_final: 0.8298 (mt) REVERT: D 329 MET cc_start: 0.8080 (tpp) cc_final: 0.7807 (tpp) REVERT: D 333 LYS cc_start: 0.7330 (tttp) cc_final: 0.7032 (tttp) REVERT: D 337 ASN cc_start: 0.7676 (t0) cc_final: 0.6157 (t0) REVERT: D 351 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: D 461 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6914 (ttm-80) REVERT: D 464 PHE cc_start: 0.6719 (p90) cc_final: 0.5031 (p90) outliers start: 49 outliers final: 36 residues processed: 461 average time/residue: 0.1488 time to fit residues: 97.8757 Evaluate side-chains 475 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 431 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 196 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 253 LYS 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 84 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 456 ARG 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 67 PHE 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 195 HIS Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 472 ARG 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: 0.7980 chunk 98 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN B 28 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 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** D 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.206018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151421 restraints weight = 47118.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156893 restraints weight = 20947.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160273 restraints weight = 12711.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162340 restraints weight = 9215.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163500 restraints weight = 7550.716| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20312 Z= 0.222 Angle : 0.726 11.267 28378 Z= 0.404 Chirality : 0.044 0.220 3109 Planarity : 0.006 0.071 3022 Dihedral : 23.393 86.879 4267 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.68 % Allowed : 22.24 % Favored : 75.08 % 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: 0.45 (0.19), residues: 1937 helix: 0.90 (0.16), residues: 916 sheet: -0.52 (0.29), residues: 284 loop : 0.08 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 167 TYR 0.040 0.002 TYR D 216 PHE 0.060 0.002 PHE C 118 TRP 0.055 0.003 TRP C 64 HIS 0.010 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.22 (20296) covalent geometry : angle 0.71772 / 0.40 (28354) hydrogen bonds : bond 0.05094 / 3.54 ( 1046) hydrogen bonds : angle 4.27480 / 3.07 ( 2758) metal coordination : bond 0.00618 / 0.37 ( 16) metal coordination : angle 3.85241 / 2.48 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.94 seconds wall clock time: 73 minutes 6.97 seconds (4386.97 seconds total)