Starting phenix.real_space_refine on Sat Jul 4 10:11:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu3_60888/07_2026/9iu3_60888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu3_60888/07_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_60888/07_2026/9iu3_60888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu3_60888/07_2026/9iu3_60888.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu3_60888/07_2026/9iu3_60888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu3_60888/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.84, per 1000 atoms: 0.25 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: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.631A pdb=" N TRP A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 118 through 151 removed outlier: 3.540A pdb=" N THR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.169A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.801A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.531A pdb=" N GLN A 446 " --> pdb=" O TRP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 18 through 34 removed outlier: 4.064A pdb=" N GLN B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.619A pdb=" N TRP B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 118 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.083A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.827A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.527A pdb=" N GLN B 446 " --> pdb=" O TRP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.632A pdb=" N TRP C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 118 through 151 Processing helix chain 'C' and resid 177 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.704A pdb=" N LEU C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.525A pdb=" N GLN C 446 " --> pdb=" O TRP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 478 through 486 Processing helix chain 'D' and resid 18 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.639A pdb=" N TRP D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'D' and resid 118 through 151 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.692A pdb=" N LEU D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.530A pdb=" N GLN D 446 " --> pdb=" O TRP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.807A pdb=" N ALA A 3 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 41 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 5 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP A 43 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 7 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 4 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 368 removed outlier: 7.091A pdb=" N ARG A 362 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 44 removed outlier: 7.520A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 4 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 368 removed outlier: 7.095A pdb=" N ARG B 362 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 44 removed outlier: 7.535A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU C 4 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 249 through 250 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB8, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 368 removed outlier: 7.105A pdb=" N ARG C 362 " --> pdb=" O THR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 44 removed outlier: 7.503A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU D 4 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AC3, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'D' and resid 302 through 304 Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'D' and resid 361 through 368 removed outlier: 7.125A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 241 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 2.14 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: 26200 3.49 - 6.97: 1997 6.97 - 10.46: 142 10.46 - 13.95: 10 13.95 - 17.43: 5 Bond angle restraints: 28354 Sorted by residual: angle pdb=" O3' DGF1 32 " pdb=" P DTF1 33 " pdb=" O5' DTF1 33 " ideal model delta sigma weight residual 104.00 86.57 17.43 1.50e+00 4.44e-01 1.35e+02 angle pdb=" 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' DGE2 32 " pdb=" P DTE2 33 " pdb=" O5' DTE2 33 " ideal model delta sigma weight residual 104.00 88.92 15.08 1.50e+00 4.44e-01 1.01e+02 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.34 14.66 1.50e+00 4.44e-01 9.55e+01 angle pdb=" O3' DCH1 25 " pdb=" P DGH1 26 " pdb=" O5' DGH1 26 " ideal model delta sigma weight residual 104.00 89.41 14.59 1.50e+00 4.44e-01 9.46e+01 ... (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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.700 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- 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 : 1.980 20.916 28378 Z= 1.368 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 1.96109 / 1.37 (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 : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8280 (mt0) cc_final: 0.8076 (mt0) REVERT: A 25 SER cc_start: 0.6924 (m) cc_final: 0.6683 (p) REVERT: A 28 GLN cc_start: 0.8844 (mt0) cc_final: 0.8493 (mt0) REVERT: A 40 VAL cc_start: 0.7999 (t) cc_final: 0.7085 (p) REVERT: A 43 ASP cc_start: 0.5033 (m-30) cc_final: 0.4570 (m-30) REVERT: A 55 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7380 (ttm-80) REVERT: A 74 VAL cc_start: 0.5692 (p) cc_final: 0.5311 (t) REVERT: A 88 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8169 (mmp-170) REVERT: A 100 HIS cc_start: 0.8641 (m90) cc_final: 0.8372 (m90) REVERT: A 104 VAL cc_start: 0.6368 (t) cc_final: 0.6089 (p) REVERT: A 109 GLU cc_start: 0.4985 (mt-10) cc_final: 0.4685 (mp0) REVERT: A 125 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 126 MET cc_start: 0.8815 (mmm) cc_final: 0.8236 (mmm) REVERT: A 133 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7725 (tp30) REVERT: A 134 LEU cc_start: 0.9058 (tp) cc_final: 0.8740 (tt) REVERT: A 135 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 238 SER cc_start: 0.7514 (m) cc_final: 0.6942 (p) REVERT: A 239 MET cc_start: 0.7448 (mmm) cc_final: 0.6948 (mmm) REVERT: A 275 LEU cc_start: 0.7044 (tp) cc_final: 0.6836 (mp) REVERT: A 379 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7268 (tm-30) REVERT: B 8 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5414 (ttp-170) REVERT: B 21 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7293 (ttm-80) REVERT: B 23 LEU cc_start: 0.8648 (tp) cc_final: 0.7963 (pp) REVERT: B 33 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7450 (mmt90) REVERT: B 35 TRP cc_start: 0.7020 (m-10) cc_final: 0.6614 (m-10) REVERT: B 88 ARG cc_start: 0.7672 (ttt90) cc_final: 0.6821 (tpt-90) REVERT: B 92 GLN cc_start: 0.8365 (mt0) cc_final: 0.8070 (mm-40) REVERT: B 95 HIS cc_start: 0.8287 (m90) cc_final: 0.7288 (m170) REVERT: B 100 HIS cc_start: 0.8031 (m90) cc_final: 0.7608 (m90) REVERT: B 132 MET cc_start: 0.8104 (mtp) cc_final: 0.7819 (mtp) REVERT: B 135 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 146 HIS cc_start: 0.7976 (m170) cc_final: 0.7442 (m170) REVERT: B 153 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7455 (mtmp) REVERT: B 181 ARG cc_start: 0.7293 (ttt180) cc_final: 0.6748 (ttp-110) REVERT: B 183 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7208 (mmt180) REVERT: B 186 GLU cc_start: 0.8020 (tt0) cc_final: 0.7105 (tt0) REVERT: B 204 ASP cc_start: 0.7895 (t70) cc_final: 0.7584 (t0) REVERT: B 207 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7383 (tpp80) REVERT: B 226 GLN cc_start: 0.8015 (mt0) cc_final: 0.7213 (mt0) REVERT: B 228 ARG cc_start: 0.6520 (mtm-85) cc_final: 0.6162 (mtt90) REVERT: B 229 GLU cc_start: 0.7601 (pt0) cc_final: 0.7110 (pt0) REVERT: B 235 LEU cc_start: 0.7642 (mt) cc_final: 0.7159 (mp) REVERT: B 239 MET cc_start: 0.7510 (mmm) cc_final: 0.6860 (mmm) REVERT: B 242 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7096 (mt-10) REVERT: B 257 ASP cc_start: 0.7654 (t70) cc_final: 0.7449 (t0) REVERT: B 265 ARG cc_start: 0.7641 (ptt180) cc_final: 0.7317 (ptm160) REVERT: B 281 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: B 299 LEU cc_start: 0.8485 (tp) cc_final: 0.8035 (tp) REVERT: B 350 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7676 (tp30) REVERT: B 376 GLU cc_start: 0.8525 (tt0) cc_final: 0.7721 (tt0) REVERT: B 452 ASN cc_start: 0.8027 (t0) cc_final: 0.7362 (t0) REVERT: B 463 THR cc_start: 0.7334 (m) cc_final: 0.7118 (t) REVERT: B 464 PHE cc_start: 0.7444 (p90) cc_final: 0.6816 (p90) REVERT: C 2 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7053 (ptm160) REVERT: C 33 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7972 (tpp80) REVERT: C 60 ASN cc_start: 0.7531 (m-40) cc_final: 0.7066 (t0) REVERT: C 69 GLU cc_start: 0.6949 (mp0) cc_final: 0.6661 (mp0) REVERT: C 73 ASP cc_start: 0.6570 (m-30) cc_final: 0.6059 (m-30) REVERT: C 84 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8130 (m) REVERT: C 88 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7522 (mmm160) REVERT: C 100 HIS cc_start: 0.7386 (m90) cc_final: 0.6893 (m90) REVERT: C 129 VAL cc_start: 0.8304 (t) cc_final: 0.7814 (m) REVERT: C 133 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 140 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7602 (mpt-90) REVERT: C 150 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8297 (mtt-85) REVERT: C 183 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8318 (mmp-170) REVERT: C 186 GLU cc_start: 0.8781 (tp30) cc_final: 0.7902 (tp30) REVERT: C 199 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7158 (p-80) REVERT: C 208 ARG cc_start: 0.8270 (mpp80) cc_final: 0.7993 (mtm110) REVERT: C 214 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7900 (ttmt) REVERT: C 230 TRP cc_start: 0.6770 (m100) cc_final: 0.6563 (m100) REVERT: C 233 THR cc_start: 0.8530 (m) cc_final: 0.8080 (p) REVERT: C 237 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.7870 (mtp180) REVERT: C 244 MET cc_start: 0.8718 (mmt) cc_final: 0.8449 (mmt) REVERT: C 250 LEU cc_start: 0.8825 (tp) cc_final: 0.8620 (tt) REVERT: C 274 GLN cc_start: 0.8206 (mt0) cc_final: 0.7919 (mt0) REVERT: C 331 PHE cc_start: 0.8332 (m-80) cc_final: 0.8011 (m-80) REVERT: C 452 ASN cc_start: 0.8078 (t0) cc_final: 0.7556 (t0) REVERT: C 475 ASP cc_start: 0.6588 (t0) cc_final: 0.6361 (t0) REVERT: D 9 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6845 (mt) REVERT: D 22 GLN cc_start: 0.7764 (mt0) cc_final: 0.7422 (mt0) REVERT: D 33 ARG cc_start: 0.7683 (mtp180) cc_final: 0.6930 (mtp180) REVERT: D 56 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7879 (ttmt) REVERT: D 67 PHE cc_start: 0.6951 (m-80) cc_final: 0.6040 (m-80) REVERT: D 70 GLN cc_start: 0.7409 (tt0) cc_final: 0.7097 (tm-30) REVERT: D 88 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7569 (ttm110) REVERT: D 95 HIS cc_start: 0.7428 (m-70) cc_final: 0.6764 (m90) REVERT: D 96 TRP cc_start: 0.7310 (t60) cc_final: 0.6501 (t60) REVERT: D 99 ASP cc_start: 0.7134 (m-30) cc_final: 0.6852 (m-30) REVERT: D 100 HIS cc_start: 0.7506 (m-70) cc_final: 0.7090 (m170) REVERT: D 102 LYS cc_start: 0.7320 (mmtt) cc_final: 0.7028 (mmmt) REVERT: D 114 THR cc_start: 0.8745 (p) cc_final: 0.8360 (m) REVERT: D 134 LEU cc_start: 0.8092 (tp) cc_final: 0.7831 (tt) REVERT: D 135 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7287 (mm-30) REVERT: D 138 LYS cc_start: 0.7921 (mttt) cc_final: 0.7282 (mtpp) REVERT: D 146 HIS cc_start: 0.8060 (m170) cc_final: 0.7695 (m-70) REVERT: D 149 ILE cc_start: 0.8119 (mm) cc_final: 0.7850 (mm) REVERT: D 177 ASP cc_start: 0.7006 (t0) cc_final: 0.6261 (t0) REVERT: D 235 LEU cc_start: 0.8049 (mt) cc_final: 0.7688 (mt) REVERT: D 238 SER cc_start: 0.7179 (m) cc_final: 0.6893 (p) REVERT: D 239 MET cc_start: 0.7686 (mmm) cc_final: 0.7405 (mmp) REVERT: D 247 TYR cc_start: 0.6494 (m-10) cc_final: 0.6223 (m-10) REVERT: D 265 ARG cc_start: 0.7227 (ptt180) cc_final: 0.6906 (ttp80) REVERT: D 269 ILE cc_start: 0.8196 (mm) cc_final: 0.7930 (mm) REVERT: D 272 ARG cc_start: 0.8212 (tpt170) cc_final: 0.7868 (mmm-85) REVERT: D 278 LEU cc_start: 0.8693 (mt) cc_final: 0.8421 (mt) REVERT: D 327 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8211 (tmt-80) REVERT: D 329 MET cc_start: 0.7900 (tpp) cc_final: 0.7413 (tpp) REVERT: D 339 THR cc_start: 0.7417 (p) cc_final: 0.6655 (m) REVERT: D 340 VAL cc_start: 0.7120 (m) cc_final: 0.6874 (m) REVERT: D 345 TRP cc_start: 0.8377 (m100) cc_final: 0.7881 (m100) REVERT: D 458 MET cc_start: 0.7537 (mmt) cc_final: 0.6914 (mmt) REVERT: D 459 ASN cc_start: 0.7753 (m110) cc_final: 0.7446 (m110) outliers start: 66 outliers final: 18 residues processed: 561 average time/residue: 0.1629 time to fit residues: 130.0777 Evaluate side-chains 478 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 450 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 1.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 146 HIS A 180 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.215399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159463 restraints weight = 53163.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165346 restraints weight = 23406.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.168908 restraints weight = 14068.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171041 restraints weight = 10145.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172410 restraints weight = 8299.887| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20312 Z= 0.183 Angle : 0.791 12.028 28378 Z= 0.444 Chirality : 0.056 0.248 3109 Planarity : 0.005 0.069 3022 Dihedral : 23.610 88.232 4334 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.04 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: 1.54 (0.18), residues: 1937 helix: 1.82 (0.16), residues: 919 sheet: -0.05 (0.28), residues: 277 loop : 0.61 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 181 TYR 0.024 0.002 TYR B 216 PHE 0.030 0.002 PHE D 217 TRP 0.015 0.002 TRP B 454 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (20296) covalent geometry : angle 0.77947 / 0.44 (28354) hydrogen bonds : bond 0.05781 / 3.95 ( 1046) hydrogen bonds : angle 4.11078 / 3.00 ( 2758) metal coordination : bond 0.00407 / 0.22 ( 16) metal coordination : angle 4.75224 / 2.99 ( 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 518 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 464 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7102 (t) cc_final: 0.6591 (m) REVERT: A 8 ARG cc_start: 0.6538 (ttt-90) cc_final: 0.5802 (ttp80) REVERT: A 28 GLN cc_start: 0.8763 (mt0) cc_final: 0.8393 (tm-30) REVERT: A 38 VAL cc_start: 0.4309 (OUTLIER) cc_final: 0.3355 (t) REVERT: A 43 ASP cc_start: 0.3887 (m-30) cc_final: 0.3457 (m-30) REVERT: A 60 ASN cc_start: 0.6214 (m-40) cc_final: 0.5821 (m-40) REVERT: A 88 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7402 (tpm170) REVERT: A 90 LEU cc_start: 0.8599 (tp) cc_final: 0.8338 (pp) REVERT: A 92 GLN cc_start: 0.8361 (tt0) cc_final: 0.7660 (mt0) REVERT: A 104 VAL cc_start: 0.6705 (t) cc_final: 0.6314 (p) REVERT: A 109 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5437 (mp0) REVERT: A 125 LEU cc_start: 0.8360 (mp) cc_final: 0.8132 (tt) REVERT: A 126 MET cc_start: 0.7970 (mmm) cc_final: 0.7590 (mmm) REVERT: A 134 LEU cc_start: 0.8935 (tp) cc_final: 0.7496 (tp) REVERT: A 135 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 138 LYS cc_start: 0.8321 (mttm) cc_final: 0.8023 (mttm) REVERT: A 180 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6254 (mm-40) REVERT: A 219 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6773 (mm110) REVERT: A 237 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8134 (ttt-90) REVERT: A 239 MET cc_start: 0.7694 (mmm) cc_final: 0.6778 (mmm) REVERT: A 379 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7414 (tm-30) REVERT: B 8 ARG cc_start: 0.7285 (ttt-90) cc_final: 0.5338 (ttp80) REVERT: B 21 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7547 (ttp-170) REVERT: B 23 LEU cc_start: 0.8515 (tp) cc_final: 0.8222 (pp) REVERT: B 30 CYS cc_start: 0.8076 (m) cc_final: 0.7668 (p) REVERT: B 56 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7541 (ptmm) REVERT: B 95 HIS cc_start: 0.7850 (m90) cc_final: 0.7641 (m90) REVERT: B 131 GLN cc_start: 0.8095 (mt0) cc_final: 0.7786 (mt0) REVERT: B 132 MET cc_start: 0.7621 (mtp) cc_final: 0.7378 (mtp) REVERT: B 135 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 146 HIS cc_start: 0.7460 (m170) cc_final: 0.6851 (m-70) REVERT: B 153 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7400 (mtmp) REVERT: B 181 ARG cc_start: 0.7157 (ttt180) cc_final: 0.6604 (ttp-110) REVERT: B 183 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7000 (mmt180) REVERT: B 186 GLU cc_start: 0.7130 (tt0) cc_final: 0.6832 (tt0) REVERT: B 191 VAL cc_start: 0.7932 (t) cc_final: 0.7710 (p) REVERT: B 196 GLU cc_start: 0.7604 (tt0) cc_final: 0.7247 (tt0) REVERT: B 200 LEU cc_start: 0.7253 (mt) cc_final: 0.6601 (mt) REVERT: B 204 ASP cc_start: 0.7402 (t70) cc_final: 0.7175 (t0) REVERT: B 205 LEU cc_start: 0.8395 (mt) cc_final: 0.8157 (mp) REVERT: B 207 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7156 (tpp80) REVERT: B 212 SER cc_start: 0.7224 (t) cc_final: 0.6897 (p) REVERT: B 214 LYS cc_start: 0.7885 (tppt) cc_final: 0.7416 (tppt) REVERT: B 215 ASP cc_start: 0.7684 (m-30) cc_final: 0.6787 (m-30) REVERT: B 228 ARG cc_start: 0.6163 (mtm-85) cc_final: 0.5731 (mtm-85) REVERT: B 239 MET cc_start: 0.7714 (mmm) cc_final: 0.7444 (mmm) REVERT: B 242 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 265 ARG cc_start: 0.8155 (ptt180) cc_final: 0.7789 (ptt180) REVERT: B 272 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7154 (ttp80) REVERT: B 275 LEU cc_start: 0.8258 (tp) cc_final: 0.7982 (tp) REVERT: B 276 GLU cc_start: 0.7913 (mt-10) cc_final: 0.6640 (mt-10) REVERT: B 281 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: B 299 LEU cc_start: 0.8558 (tp) cc_final: 0.8059 (tp) REVERT: B 329 MET cc_start: 0.6646 (mmt) cc_final: 0.6389 (mmt) REVERT: B 376 GLU cc_start: 0.8342 (tt0) cc_final: 0.7284 (tt0) REVERT: B 383 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7725 (mp0) REVERT: B 463 THR cc_start: 0.7498 (m) cc_final: 0.7295 (t) REVERT: B 464 PHE cc_start: 0.6868 (p90) cc_final: 0.6543 (p90) REVERT: C 29 LEU cc_start: 0.8232 (tp) cc_final: 0.7820 (tt) REVERT: C 63 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7319 (mtp-110) REVERT: C 68 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6126 (mt-10) REVERT: C 76 VAL cc_start: 0.6986 (t) cc_final: 0.6724 (p) REVERT: C 83 LEU cc_start: 0.7279 (mt) cc_final: 0.6716 (tt) REVERT: C 84 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7837 (m) REVERT: C 92 GLN cc_start: 0.8258 (mt0) cc_final: 0.7664 (mt0) REVERT: C 100 HIS cc_start: 0.7750 (m90) cc_final: 0.7308 (m90) REVERT: C 129 VAL cc_start: 0.8331 (t) cc_final: 0.7830 (m) REVERT: C 133 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 150 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: C 182 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 183 ARG cc_start: 0.8584 (mmt-90) cc_final: 0.8232 (mmp80) REVERT: C 199 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6892 (p-80) REVERT: C 208 ARG cc_start: 0.7976 (mpp80) cc_final: 0.7321 (ttm170) REVERT: C 214 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7536 (ttmt) REVERT: C 237 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8077 (mtp180) REVERT: C 242 GLU cc_start: 0.7175 (pm20) cc_final: 0.6620 (pm20) REVERT: C 244 MET cc_start: 0.8565 (mmt) cc_final: 0.8285 (mmt) REVERT: C 274 GLN cc_start: 0.8353 (mt0) cc_final: 0.8001 (mt0) REVERT: C 276 GLU cc_start: 0.8295 (pt0) cc_final: 0.7983 (pt0) REVERT: C 331 PHE cc_start: 0.8223 (m-80) cc_final: 0.7950 (m-80) REVERT: C 352 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8959 (mm-40) REVERT: C 452 ASN cc_start: 0.8242 (t0) cc_final: 0.7699 (t0) REVERT: D 22 GLN cc_start: 0.7963 (mt0) cc_final: 0.7389 (mt0) REVERT: D 51 ASP cc_start: 0.7940 (t0) cc_final: 0.7447 (t0) REVERT: D 56 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7905 (ttmt) REVERT: D 57 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6683 (mmm160) REVERT: D 65 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7442 (mm) REVERT: D 67 PHE cc_start: 0.7126 (m-80) cc_final: 0.6511 (m-80) REVERT: D 70 GLN cc_start: 0.7497 (tt0) cc_final: 0.7292 (tm-30) REVERT: D 92 GLN cc_start: 0.8073 (tt0) cc_final: 0.7797 (mt0) REVERT: D 99 ASP cc_start: 0.7006 (m-30) cc_final: 0.6690 (m-30) REVERT: D 114 THR cc_start: 0.8548 (p) cc_final: 0.8321 (m) REVERT: D 215 ASP cc_start: 0.7498 (m-30) cc_final: 0.7107 (t70) REVERT: D 235 LEU cc_start: 0.8413 (mt) cc_final: 0.7738 (mm) REVERT: D 239 MET cc_start: 0.7798 (mmm) cc_final: 0.7006 (mpp) REVERT: D 247 TYR cc_start: 0.6639 (m-10) cc_final: 0.6272 (m-10) REVERT: D 265 ARG cc_start: 0.7433 (ptt180) cc_final: 0.6793 (ttp-110) REVERT: D 278 LEU cc_start: 0.8684 (mt) cc_final: 0.8414 (mt) REVERT: D 327 ARG cc_start: 0.8470 (ttt180) cc_final: 0.7962 (ttt-90) REVERT: D 329 MET cc_start: 0.7669 (tpp) cc_final: 0.7037 (tpp) REVERT: D 337 ASN cc_start: 0.7751 (t0) cc_final: 0.6866 (t0) REVERT: D 351 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: D 458 MET cc_start: 0.7674 (mmt) cc_final: 0.7152 (mmt) REVERT: D 459 ASN cc_start: 0.7844 (m110) cc_final: 0.7516 (m110) REVERT: D 461 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.6806 (ttm-80) REVERT: D 464 PHE cc_start: 0.6643 (p90) cc_final: 0.5280 (p90) outliers start: 54 outliers final: 30 residues processed: 495 average time/residue: 0.1801 time to fit residues: 125.4601 Evaluate side-chains 473 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 434 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 88 ARG 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 184 ILE 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 47 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 VAL 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: 10.0000 chunk 201 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 150 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS B 22 GLN B 89 HIS B 100 HIS ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 89 HIS ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.203838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148768 restraints weight = 43530.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153825 restraints weight = 20525.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156892 restraints weight = 12833.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158736 restraints weight = 9578.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159868 restraints weight = 8014.634| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 20312 Z= 0.481 Angle : 1.003 14.219 28378 Z= 0.560 Chirality : 0.060 0.350 3109 Planarity : 0.008 0.085 3022 Dihedral : 23.373 89.213 4303 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.67 % Allowed : 13.33 % Favored : 81.99 % 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: 0.06 (0.19), residues: 1937 helix: 0.37 (0.16), residues: 912 sheet: -0.31 (0.29), residues: 258 loop : -0.01 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 33 TYR 0.033 0.003 TYR D 324 PHE 0.042 0.003 PHE D 53 TRP 0.053 0.004 TRP B 161 HIS 0.032 0.003 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00864 / 0.48 (20296) covalent geometry : angle 0.99000 / 0.56 (28354) hydrogen bonds : bond 0.08796 / 6.15 ( 1046) hydrogen bonds : angle 5.21279 / 3.79 ( 2758) metal coordination : bond 0.01427 / 0.86 ( 16) metal coordination : angle 5.53290 / 3.67 ( 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 536 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 461 time to evaluate : 0.603 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: A 1 MET cc_start: 0.5190 (tmm) cc_final: 0.4950 (tmm) REVERT: A 8 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.6377 (tmt170) REVERT: A 27 GLN cc_start: 0.8611 (mt0) cc_final: 0.8252 (mt0) REVERT: A 28 GLN cc_start: 0.8754 (mt0) cc_final: 0.8406 (tm-30) REVERT: A 45 ASP cc_start: 0.8128 (m-30) cc_final: 0.7897 (t70) REVERT: A 50 VAL cc_start: 0.7660 (t) cc_final: 0.7234 (p) REVERT: A 53 PHE cc_start: 0.7187 (m-80) cc_final: 0.6956 (m-80) REVERT: A 55 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: A 79 ARG cc_start: 0.7569 (mtp180) cc_final: 0.7068 (mtp180) REVERT: A 96 TRP cc_start: 0.8112 (t60) cc_final: 0.7323 (t60) REVERT: A 109 GLU cc_start: 0.6599 (mt-10) cc_final: 0.5803 (mp0) REVERT: A 118 PHE cc_start: 0.5385 (m-80) cc_final: 0.5081 (m-10) REVERT: A 125 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8157 (tp) REVERT: A 133 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 134 LEU cc_start: 0.8777 (tp) cc_final: 0.8471 (tt) REVERT: A 135 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 219 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6864 (mm110) REVERT: A 235 LEU cc_start: 0.8837 (mt) cc_final: 0.8541 (mt) REVERT: A 239 MET cc_start: 0.7788 (mmm) cc_final: 0.6984 (mmm) REVERT: A 278 LEU cc_start: 0.8223 (tp) cc_final: 0.7801 (pp) REVERT: A 281 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6785 (mm-30) REVERT: B 8 ARG cc_start: 0.7323 (ttt-90) cc_final: 0.5907 (ttt-90) REVERT: B 9 LEU cc_start: 0.8006 (mt) cc_final: 0.7599 (tp) REVERT: B 20 GLU cc_start: 0.7910 (mp0) cc_final: 0.7614 (pm20) REVERT: B 21 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7811 (ttm170) REVERT: B 50 VAL cc_start: 0.7662 (p) cc_final: 0.7457 (m) REVERT: B 79 ARG cc_start: 0.7939 (mtp85) cc_final: 0.6920 (mtp85) REVERT: B 92 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8182 (mm-40) REVERT: B 95 HIS cc_start: 0.7915 (m90) cc_final: 0.7514 (m90) REVERT: B 96 TRP cc_start: 0.8160 (t60) cc_final: 0.7870 (t60) REVERT: B 109 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7006 (mp0) REVERT: B 132 MET cc_start: 0.8299 (mtp) cc_final: 0.8038 (mtp) REVERT: B 135 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 141 ASN cc_start: 0.8366 (m110) cc_final: 0.8160 (m110) REVERT: B 146 HIS cc_start: 0.7659 (m170) cc_final: 0.7382 (m-70) REVERT: B 149 ILE cc_start: 0.8289 (mt) cc_final: 0.7914 (tt) REVERT: B 157 SER cc_start: 0.7137 (t) cc_final: 0.6893 (p) REVERT: B 181 ARG cc_start: 0.7009 (ttt180) cc_final: 0.6731 (ttp-110) REVERT: B 183 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.6884 (mmt180) REVERT: B 199 HIS cc_start: 0.7724 (p-80) cc_final: 0.7360 (p-80) REVERT: B 200 LEU cc_start: 0.7845 (mt) cc_final: 0.7555 (mt) REVERT: B 226 GLN cc_start: 0.7874 (mt0) cc_final: 0.7303 (mt0) REVERT: B 228 ARG cc_start: 0.6640 (mtm-85) cc_final: 0.6219 (mtm-85) REVERT: B 265 ARG cc_start: 0.8527 (ptt180) cc_final: 0.8131 (ptt180) REVERT: B 270 LEU cc_start: 0.8163 (mt) cc_final: 0.7942 (mt) REVERT: B 272 ARG cc_start: 0.7779 (ttp80) cc_final: 0.6759 (ttp80) REVERT: B 274 GLN cc_start: 0.8243 (mt0) cc_final: 0.7871 (mt0) REVERT: B 284 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7437 (mtmm) REVERT: B 323 ARG cc_start: 0.6992 (mmm-85) cc_final: 0.6620 (mmm-85) REVERT: B 348 PHE cc_start: 0.8567 (t80) cc_final: 0.8227 (t80) REVERT: B 351 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: B 377 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 383 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8130 (mm-30) REVERT: B 419 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 464 PHE cc_start: 0.6754 (p90) cc_final: 0.6542 (p90) REVERT: C 63 ARG cc_start: 0.8080 (mtp-110) cc_final: 0.7660 (mtp-110) REVERT: C 64 TRP cc_start: 0.8432 (m100) cc_final: 0.8016 (m100) REVERT: C 68 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6612 (mt-10) REVERT: C 74 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7155 (t) REVERT: C 76 VAL cc_start: 0.7956 (t) cc_final: 0.7635 (p) REVERT: C 83 LEU cc_start: 0.7900 (mt) cc_final: 0.7343 (tp) REVERT: C 92 GLN cc_start: 0.8543 (mt0) cc_final: 0.7864 (mp10) REVERT: C 95 HIS cc_start: 0.7523 (t-170) cc_final: 0.5613 (t-170) REVERT: C 113 ASP cc_start: 0.7876 (t0) cc_final: 0.7522 (t0) REVERT: C 121 VAL cc_start: 0.8676 (t) cc_final: 0.8439 (t) REVERT: C 171 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 199 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6764 (p-80) REVERT: C 208 ARG cc_start: 0.8339 (mpp80) cc_final: 0.7685 (mtt90) REVERT: C 214 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7760 (ttmt) REVERT: C 242 GLU cc_start: 0.7838 (pm20) cc_final: 0.7296 (pm20) REVERT: C 276 GLU cc_start: 0.8364 (pt0) cc_final: 0.8094 (pt0) REVERT: C 329 MET cc_start: 0.8433 (ttm) cc_final: 0.8194 (ttm) REVERT: C 331 PHE cc_start: 0.8441 (m-80) cc_final: 0.8116 (m-80) REVERT: C 345 TRP cc_start: 0.7293 (m100) cc_final: 0.7082 (m100) REVERT: C 452 ASN cc_start: 0.8215 (t0) cc_final: 0.7395 (t0) REVERT: C 456 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8560 (mmt90) REVERT: D 9 LEU cc_start: 0.8357 (tt) cc_final: 0.8085 (tt) REVERT: D 21 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.7187 (ttp-110) REVERT: D 22 GLN cc_start: 0.8261 (mt0) cc_final: 0.7900 (mt0) REVERT: D 60 ASN cc_start: 0.8386 (m110) cc_final: 0.7666 (t0) REVERT: D 101 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8532 (mmmt) REVERT: D 112 PHE cc_start: 0.7837 (t80) cc_final: 0.7518 (t80) REVERT: D 114 THR cc_start: 0.8522 (p) cc_final: 0.8247 (m) REVERT: D 138 LYS cc_start: 0.8716 (mttt) cc_final: 0.8296 (mttp) REVERT: D 139 GLU cc_start: 0.7736 (tp30) cc_final: 0.7212 (tp30) REVERT: D 140 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7063 (tpt170) REVERT: D 215 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7082 (t0) REVERT: D 235 LEU cc_start: 0.8415 (mt) cc_final: 0.8073 (mm) REVERT: D 239 MET cc_start: 0.8119 (mmm) cc_final: 0.7423 (mpp) REVERT: D 245 LEU cc_start: 0.7593 (mt) cc_final: 0.6948 (mt) REVERT: D 247 TYR cc_start: 0.7160 (m-10) cc_final: 0.6454 (m-10) REVERT: D 272 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7809 (mmm160) REVERT: D 278 LEU cc_start: 0.8605 (mt) cc_final: 0.8370 (mt) REVERT: D 281 GLU cc_start: 0.8028 (tp30) cc_final: 0.7767 (tp30) REVERT: D 329 MET cc_start: 0.8185 (tpp) cc_final: 0.7696 (tpp) REVERT: D 333 LYS cc_start: 0.7029 (tttp) cc_final: 0.6783 (tttp) REVERT: D 337 ASN cc_start: 0.7746 (t0) cc_final: 0.7287 (t0) REVERT: D 351 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: D 452 ASN cc_start: 0.8074 (t0) cc_final: 0.7779 (t0) REVERT: D 459 ASN cc_start: 0.8221 (m110) cc_final: 0.7962 (m110) REVERT: D 461 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6965 (ttm-80) outliers start: 75 outliers final: 46 residues processed: 499 average time/residue: 0.1756 time to fit residues: 123.9944 Evaluate side-chains 500 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 446 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 147 PHE 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 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 B residue 451 LYS 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 231 SER 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 125 LEU 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 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 36 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 446 GLN C 28 GLN C 91 GLN ** C 194 ASN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.208694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152398 restraints weight = 60436.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160048 restraints weight = 26482.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161223 restraints weight = 15280.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.163425 restraints weight = 11363.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164330 restraints weight = 9260.738| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20312 Z= 0.209 Angle : 0.707 12.195 28378 Z= 0.401 Chirality : 0.047 0.294 3109 Planarity : 0.006 0.057 3022 Dihedral : 23.370 88.802 4290 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.86 % Allowed : 15.89 % Favored : 80.25 % 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: 0.77 (0.19), residues: 1937 helix: 1.10 (0.16), residues: 917 sheet: -0.20 (0.29), residues: 265 loop : 0.22 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 265 TYR 0.032 0.002 TYR D 154 PHE 0.045 0.002 PHE D 217 TRP 0.042 0.002 TRP C 35 HIS 0.011 0.002 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.21 (20296) covalent geometry : angle 0.69340 / 0.40 (28354) hydrogen bonds : bond 0.05235 / 3.62 ( 1046) hydrogen bonds : angle 4.33672 / 3.11 ( 2758) metal coordination : bond 0.00680 / 0.40 ( 16) metal coordination : angle 4.72679 / 2.91 ( 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 508 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 446 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7484 (ttt-90) cc_final: 0.6551 (ptm-80) REVERT: A 27 GLN cc_start: 0.8457 (mt0) cc_final: 0.8068 (mt0) REVERT: A 28 GLN cc_start: 0.8751 (mt0) cc_final: 0.8358 (tm-30) REVERT: A 38 VAL cc_start: 0.5469 (OUTLIER) cc_final: 0.4724 (t) REVERT: A 43 ASP cc_start: 0.5355 (m-30) cc_final: 0.4805 (m-30) REVERT: A 53 PHE cc_start: 0.7142 (m-80) cc_final: 0.6882 (m-10) REVERT: A 55 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7683 (ptp90) REVERT: A 69 GLU cc_start: 0.5210 (mm-30) cc_final: 0.1945 (mt-10) REVERT: A 79 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7093 (mtp180) REVERT: A 87 ILE cc_start: 0.8573 (tp) cc_final: 0.8166 (mp) REVERT: A 109 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5457 (mp0) REVERT: A 125 LEU cc_start: 0.8358 (mp) cc_final: 0.8068 (tp) REVERT: A 132 MET cc_start: 0.7452 (mpm) cc_final: 0.7119 (mpm) REVERT: A 133 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7186 (tm-30) REVERT: A 134 LEU cc_start: 0.8755 (tp) cc_final: 0.8334 (tt) REVERT: A 135 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 219 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6947 (mm110) REVERT: A 235 LEU cc_start: 0.8815 (mt) cc_final: 0.8466 (mt) REVERT: A 239 MET cc_start: 0.7963 (mmm) cc_final: 0.7216 (mmm) REVERT: A 409 ARG cc_start: 0.7973 (tpp-160) cc_final: 0.7768 (tpp-160) REVERT: B 8 ARG cc_start: 0.7452 (ttt-90) cc_final: 0.6249 (tmm-80) REVERT: B 20 GLU cc_start: 0.7651 (mp0) cc_final: 0.7424 (pm20) REVERT: B 109 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7020 (mp0) REVERT: B 116 THR cc_start: 0.7265 (m) cc_final: 0.6998 (m) REVERT: B 146 HIS cc_start: 0.7739 (m170) cc_final: 0.7468 (m-70) REVERT: B 149 ILE cc_start: 0.8077 (mt) cc_final: 0.7756 (tt) REVERT: B 164 LEU cc_start: 0.8109 (tp) cc_final: 0.7895 (tp) REVERT: B 183 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.6983 (mmt180) REVERT: B 186 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7168 (mt-10) REVERT: B 199 HIS cc_start: 0.7397 (p-80) cc_final: 0.7138 (p-80) REVERT: B 200 LEU cc_start: 0.7626 (mt) cc_final: 0.7325 (mt) REVERT: B 223 ARG cc_start: 0.6194 (mtm-85) cc_final: 0.5853 (mtp-110) REVERT: B 226 GLN cc_start: 0.7978 (mt0) cc_final: 0.6883 (mt0) REVERT: B 228 ARG cc_start: 0.6677 (mtm-85) cc_final: 0.6169 (mtm-85) REVERT: B 265 ARG cc_start: 0.8488 (ptt180) cc_final: 0.7994 (ptt180) REVERT: B 272 ARG cc_start: 0.7641 (ttp80) cc_final: 0.6650 (ttp80) REVERT: B 275 LEU cc_start: 0.8333 (tp) cc_final: 0.8035 (tp) REVERT: B 299 LEU cc_start: 0.8561 (tt) cc_final: 0.7900 (mt) REVERT: B 348 PHE cc_start: 0.8527 (t80) cc_final: 0.8112 (t80) REVERT: B 377 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8013 (mt) REVERT: B 419 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 464 PHE cc_start: 0.6831 (p90) cc_final: 0.6496 (p90) REVERT: B 475 ASP cc_start: 0.7375 (t70) cc_final: 0.7130 (t70) REVERT: C 63 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7314 (ttm-80) REVERT: C 65 LEU cc_start: 0.8363 (mp) cc_final: 0.8158 (mm) REVERT: C 68 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6465 (mt-10) REVERT: C 74 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6969 (t) REVERT: C 76 VAL cc_start: 0.7833 (t) cc_final: 0.7504 (p) REVERT: C 95 HIS cc_start: 0.6783 (t-170) cc_final: 0.6364 (t-90) REVERT: C 114 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7602 (p) REVERT: C 133 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 140 ARG cc_start: 0.7146 (mpt-90) cc_final: 0.6824 (mpt-90) REVERT: C 182 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 183 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8095 (mmp-170) REVERT: C 199 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6689 (p-80) REVERT: C 208 ARG cc_start: 0.8207 (mpp80) cc_final: 0.7831 (mtt90) REVERT: C 242 GLU cc_start: 0.7571 (pm20) cc_final: 0.7022 (pm20) REVERT: C 244 MET cc_start: 0.8471 (mmt) cc_final: 0.8087 (mtt) REVERT: C 276 GLU cc_start: 0.8288 (pt0) cc_final: 0.8031 (pt0) REVERT: C 331 PHE cc_start: 0.8449 (m-80) cc_final: 0.8080 (m-80) REVERT: C 350 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 452 ASN cc_start: 0.8131 (t0) cc_final: 0.7598 (t0) REVERT: C 455 LEU cc_start: 0.8975 (mt) cc_final: 0.8763 (tp) REVERT: D 9 LEU cc_start: 0.8392 (tt) cc_final: 0.7771 (mp) REVERT: D 22 GLN cc_start: 0.7994 (mt0) cc_final: 0.7618 (mt0) REVERT: D 28 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 51 ASP cc_start: 0.8465 (t0) cc_final: 0.8158 (t0) REVERT: D 57 ARG cc_start: 0.7351 (mmm160) cc_final: 0.7098 (mmm160) REVERT: D 60 ASN cc_start: 0.8298 (m110) cc_final: 0.7642 (t0) REVERT: D 64 TRP cc_start: 0.7963 (m100) cc_final: 0.7349 (m100) REVERT: D 65 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7408 (mp) REVERT: D 70 GLN cc_start: 0.7617 (tm-30) cc_final: 0.6497 (tm-30) REVERT: D 101 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8549 (mmmt) REVERT: D 114 THR cc_start: 0.8442 (p) cc_final: 0.8224 (m) REVERT: D 133 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 138 LYS cc_start: 0.8613 (mttt) cc_final: 0.8093 (ttmm) REVERT: D 139 GLU cc_start: 0.7800 (tp30) cc_final: 0.7152 (tp30) REVERT: D 140 ARG cc_start: 0.7800 (tpt170) cc_final: 0.7109 (tpt170) REVERT: D 215 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6853 (t0) REVERT: D 221 GLN cc_start: 0.8034 (mm110) cc_final: 0.7817 (mm110) REVERT: D 239 MET cc_start: 0.8053 (mmm) cc_final: 0.7374 (mpp) REVERT: D 247 TYR cc_start: 0.7093 (m-10) cc_final: 0.6204 (m-10) REVERT: D 250 LEU cc_start: 0.8358 (tp) cc_final: 0.8065 (tp) REVERT: D 265 ARG cc_start: 0.7546 (ptt180) cc_final: 0.7128 (ptt180) REVERT: D 272 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7959 (mmm160) REVERT: D 278 LEU cc_start: 0.8630 (mt) cc_final: 0.8383 (mt) REVERT: D 281 GLU cc_start: 0.7918 (tp30) cc_final: 0.7533 (tp30) REVERT: D 329 MET cc_start: 0.7953 (tpp) cc_final: 0.7537 (mpp) REVERT: D 333 LYS cc_start: 0.7010 (tttp) cc_final: 0.6750 (tttp) REVERT: D 337 ASN cc_start: 0.7763 (t0) cc_final: 0.7225 (t0) REVERT: D 351 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: D 459 ASN cc_start: 0.8175 (m110) cc_final: 0.7930 (m110) REVERT: D 461 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.6894 (ttm-80) outliers start: 62 outliers final: 36 residues processed: 477 average time/residue: 0.1791 time to fit residues: 121.0908 Evaluate side-chains 480 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 435 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 12 VAL 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 253 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 28 GLN 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 114 THR Chi-restraints excluded: chain C residue 175 VAL 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 283 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 351 GLU 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 65 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 211 LEU 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 473 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8366 > 50: distance: 104 - 110: 27.215 distance: 110 - 111: 28.990 distance: 111 - 112: 27.518 distance: 112 - 113: 8.862 distance: 112 - 114: 7.896 distance: 114 - 115: 12.708 distance: 115 - 116: 9.155 distance: 115 - 118: 12.812 distance: 116 - 117: 10.477 distance: 116 - 119: 20.685 distance: 119 - 120: 16.046 distance: 119 - 125: 13.973 distance: 120 - 121: 39.751 distance: 120 - 123: 34.326 distance: 121 - 122: 20.332 distance: 121 - 126: 30.403 distance: 123 - 124: 19.854 distance: 124 - 125: 13.709 distance: 126 - 127: 13.169 distance: 127 - 128: 19.153 distance: 127 - 130: 22.397 distance: 128 - 129: 26.836 distance: 128 - 134: 41.112 distance: 130 - 131: 30.374 distance: 131 - 132: 15.936 distance: 131 - 133: 14.680 distance: 134 - 135: 40.299 distance: 135 - 136: 43.434 distance: 135 - 138: 45.927 distance: 136 - 137: 21.142 distance: 136 - 141: 45.576 distance: 138 - 139: 30.945 distance: 138 - 140: 34.322 distance: 141 - 142: 31.430 distance: 142 - 143: 18.468 distance: 142 - 145: 21.147 distance: 143 - 144: 23.824 distance: 143 - 152: 40.052 distance: 145 - 146: 15.767 distance: 146 - 147: 7.014 distance: 147 - 148: 4.378 distance: 148 - 149: 5.246 distance: 149 - 151: 8.558 distance: 152 - 153: 33.513 distance: 153 - 154: 25.344 distance: 153 - 156: 16.468 distance: 154 - 155: 17.511 distance: 154 - 157: 29.857 distance: 157 - 158: 23.663 distance: 158 - 159: 24.842 distance: 158 - 161: 19.725 distance: 159 - 160: 29.055 distance: 159 - 166: 17.571 distance: 161 - 162: 21.212 distance: 162 - 163: 9.722 distance: 163 - 165: 4.003 distance: 166 - 167: 17.899 distance: 166 - 172: 29.998 distance: 167 - 168: 33.017 distance: 167 - 170: 31.706 distance: 168 - 169: 26.971 distance: 168 - 173: 24.712 distance: 170 - 171: 22.927 distance: 171 - 172: 25.723 distance: 173 - 174: 3.165 distance: 174 - 175: 3.604 distance: 174 - 177: 12.790 distance: 175 - 176: 4.690 distance: 175 - 181: 4.076 distance: 177 - 178: 9.033 distance: 177 - 179: 8.303 distance: 178 - 180: 5.467