Starting phenix.real_space_refine on Sat Jul 4 10:02:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu5_60890/07_2026/9iu5_60890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu5_60890/07_2026/9iu5_60890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu5_60890/07_2026/9iu5_60890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu5_60890/07_2026/9iu5_60890.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu5_60890/07_2026/9iu5_60890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu5_60890/07_2026/9iu5_60890.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 196 5.49 5 S 60 5.16 5 C 11574 2.51 5 N 3620 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s 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: 19472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "D" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3863 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 23, 'TRANS': 462} Chain: "E1" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E2" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F1" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F2" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 495 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 304 100.701 146.761 33.299 1.00365.26 S ATOM 2447 SG CYS A 307 98.291 145.285 35.705 1.00365.18 S ATOM 2598 SG CYS A 326 97.388 145.304 32.599 1.00365.36 S ATOM 2670 SG CYS A 335 97.660 148.814 34.160 1.00366.12 S ATOM 6292 SG CYS B 304 61.272 33.418 128.399 1.00287.61 S ATOM 6310 SG CYS B 307 61.341 34.617 124.898 1.00287.11 S ATOM 6461 SG CYS B 326 58.498 34.765 126.377 1.00287.63 S ATOM 6533 SG CYS B 335 59.718 31.166 125.753 1.00289.25 S ATOM 10155 SG CYS C 304 42.887 149.001 86.057 1.00250.96 S ATOM 10173 SG CYS C 307 42.551 146.234 88.478 1.00249.47 S ATOM 10324 SG CYS C 326 40.509 146.113 85.992 1.00243.67 S ATOM 10396 SG CYS C 335 39.815 149.032 88.302 1.00243.88 S ATOM 14018 SG CYS D 304 54.254 24.971 51.138 1.00300.38 S ATOM 14036 SG CYS D 307 55.235 27.485 48.640 1.00299.96 S ATOM 14187 SG CYS D 326 52.212 27.723 49.674 1.00298.18 S ATOM 14259 SG CYS D 335 52.858 24.559 47.608 1.00298.54 S Time building chain proxies: 4.69, per 1000 atoms: 0.24 Number of scatterers: 19472 At special positions: 0 Unit cell: (135.22, 175.199, 164.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 60 16.00 P 196 15.00 O 4018 8.00 N 3620 7.00 C 11574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 692.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 307 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " Number of angles added : 24 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 24 sheets defined 49.6% alpha, 13.9% beta 93 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.630A pdb=" N TRP A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 118 through 151 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 284 removed outlier: 4.121A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.819A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.626A pdb=" N TRP B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 118 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.095A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.812A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.625A pdb=" N TRP C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 118 through 151 Processing helix chain 'C' and resid 177 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.693A pdb=" N LEU C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 478 through 486 Processing helix chain 'D' and resid 18 through 34 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.630A pdb=" N TRP D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'D' and resid 118 through 151 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.678A pdb=" N LEU D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 44 removed outlier: 7.520A pdb=" N VAL A 5 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 40 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 7 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 42 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 9 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 44 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 2 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 76 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 4 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 368 removed outlier: 7.087A pdb=" N ARG A 362 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 44 removed outlier: 7.507A pdb=" N VAL B 5 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 40 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 7 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 42 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 9 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 44 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG B 2 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL B 76 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 4 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 368 removed outlier: 7.089A pdb=" N ARG B 362 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 44 removed outlier: 7.513A pdb=" N VAL C 5 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 40 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 7 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 42 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C 9 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU C 44 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 2 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL C 76 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 4 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 249 through 250 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB8, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 368 removed outlier: 7.105A pdb=" N ARG C 362 " --> pdb=" O THR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 44 removed outlier: 7.482A pdb=" N VAL D 5 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 40 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D 7 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU D 42 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU D 9 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU D 44 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG D 2 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 76 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU D 4 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AC3, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'D' and resid 302 through 304 Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'D' and resid 361 through 368 removed outlier: 7.109A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 241 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3730 1.33 - 1.45: 6023 1.45 - 1.57: 10057 1.57 - 1.70: 384 1.70 - 1.82: 92 Bond restraints: 20286 Sorted by residual: bond pdb=" N1 DTE2 29 " pdb=" C2 DTE2 29 " ideal model delta sigma weight residual 1.376 1.405 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" N1 DCG1 23 " pdb=" C6 DCG1 23 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.14e+01 bond pdb=" C4' DTE2 33 " pdb=" C3' DTE2 33 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.00e-02 1.00e+04 1.14e+01 bond pdb=" N1 DCE2 30 " pdb=" C6 DCE2 30 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.13e+01 bond pdb=" N1 DCF2 21 " pdb=" C6 DCF2 21 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 1.02e+01 ... (remaining 20281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 26416 3.45 - 6.89: 1766 6.89 - 10.34: 134 10.34 - 13.79: 15 13.79 - 17.23: 7 Bond angle restraints: 28338 Sorted by residual: angle pdb=" O3' DGF1 32 " pdb=" P DTF1 33 " pdb=" O5' DTF1 33 " ideal model delta sigma weight residual 104.00 86.77 17.23 1.50e+00 4.44e-01 1.32e+02 angle pdb=" O3' DGE2 32 " pdb=" P DTE2 33 " pdb=" O5' DTE2 33 " ideal model delta sigma weight residual 104.00 88.81 15.19 1.50e+00 4.44e-01 1.03e+02 angle pdb=" C ARG C 140 " pdb=" CA ARG C 140 " pdb=" CB ARG C 140 " ideal model delta sigma weight residual 110.88 95.26 15.62 1.57e+00 4.06e-01 9.90e+01 angle pdb=" O3' DAE1 20 " pdb=" P DCE1 21 " pdb=" O5' DCE1 21 " ideal model delta sigma weight residual 104.00 89.49 14.51 1.50e+00 4.44e-01 9.36e+01 angle pdb=" O4' DCE2 28 " pdb=" C4' DCE2 28 " pdb=" C3' DCE2 28 " ideal model delta sigma weight residual 106.00 100.21 5.79 6.00e-01 2.78e+00 9.32e+01 ... (remaining 28333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9457 17.91 - 35.82: 1062 35.82 - 53.73: 871 53.73 - 71.64: 198 71.64 - 89.55: 28 Dihedral angle restraints: 11616 sinusoidal: 6004 harmonic: 5612 Sorted by residual: dihedral pdb=" N LEU D 125 " pdb=" C LEU D 125 " pdb=" CA LEU D 125 " pdb=" CB LEU D 125 " ideal model delta harmonic sigma weight residual 122.80 139.10 -16.30 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" C ASP B 359 " pdb=" N ASP B 359 " pdb=" CA ASP B 359 " pdb=" CB ASP B 359 " ideal model delta harmonic sigma weight residual -122.60 -137.71 15.11 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" C ASP D 407 " pdb=" N ASP D 407 " pdb=" CA ASP D 407 " pdb=" CB ASP D 407 " ideal model delta harmonic sigma weight residual -122.60 -136.44 13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2709 0.132 - 0.264: 370 0.264 - 0.396: 22 0.396 - 0.528: 2 0.528 - 0.660: 5 Chirality restraints: 3108 Sorted by residual: chirality pdb=" P DTF2 1 " pdb=" OP1 DTF2 1 " pdb=" OP2 DTF2 1 " pdb=" O5' DTF2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P 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 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 3105 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCF2 27 " -0.112 2.00e-02 2.50e+03 5.23e-02 6.16e+01 pdb=" N1 DCF2 27 " 0.073 2.00e-02 2.50e+03 pdb=" C2 DCF2 27 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DCF2 27 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DCF2 27 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DCF2 27 " -0.020 2.00e-02 2.50e+03 pdb=" N4 DCF2 27 " -0.046 2.00e-02 2.50e+03 pdb=" C5 DCF2 27 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DCF2 27 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 35 " -0.053 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP D 35 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 35 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 35 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP D 35 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 35 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 35 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 35 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 35 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DAF2 24 " -0.025 2.00e-02 2.50e+03 2.38e-02 1.56e+01 pdb=" N9 DAF2 24 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DAF2 24 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DAF2 24 " 0.042 2.00e-02 2.50e+03 pdb=" C5 DAF2 24 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DAF2 24 " -0.030 2.00e-02 2.50e+03 pdb=" N6 DAF2 24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DAF2 24 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DAF2 24 " 0.025 2.00e-02 2.50e+03 pdb=" N3 DAF2 24 " 0.027 2.00e-02 2.50e+03 pdb=" C4 DAF2 24 " -0.005 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 6 2.26 - 2.92: 6804 2.92 - 3.58: 28325 3.58 - 4.24: 47767 4.24 - 4.90: 77603 Nonbonded interactions: 160505 Sorted by model distance: nonbonded pdb=" OG SER A 10 " pdb=" P DCF1 28 " model vdw 1.603 3.400 nonbonded pdb=" OG SER D 10 " pdb=" P DCG2 25 " model vdw 1.605 3.400 nonbonded pdb=" OG SER B 10 " pdb=" P DCE2 28 " model vdw 1.608 3.400 nonbonded pdb=" OG SER C 10 " pdb=" P DCH1 25 " model vdw 1.618 3.400 nonbonded pdb=" OP1 DCE2 28 " pdb=" O3' DAG1 24 " model vdw 2.144 3.040 ... (remaining 160500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.320 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 20302 Z= 0.666 Angle : 1.861 20.416 28362 Z= 1.284 Chirality : 0.090 0.660 3108 Planarity : 0.007 0.078 3020 Dihedral : 21.338 89.554 7984 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 4.18 % Allowed : 6.67 % Favored : 89.15 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 1936 helix: 0.55 (0.14), residues: 920 sheet: 0.12 (0.28), residues: 261 loop : 0.24 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.005 ARG C 287 TYR 0.028 0.006 TYR A 482 PHE 0.036 0.006 PHE C 118 TRP 0.053 0.005 TRP D 35 HIS 0.019 0.004 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.01007 / 0.66 (20286) covalent geometry : angle 1.84124 / 1.28 (28338) hydrogen bonds : bond 0.16284 / 11.17 ( 1053) hydrogen bonds : angle 6.00215 / 4.34 ( 2783) metal coordination : bond 0.05536 / 3.40 ( 16) metal coordination : angle 9.43780 / 6.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 475 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8103 (tpt-90) cc_final: 0.7856 (mmt180) REVERT: A 24 GLU cc_start: 0.7652 (tp30) cc_final: 0.7073 (tp30) REVERT: A 25 SER cc_start: 0.7362 (m) cc_final: 0.7022 (p) REVERT: A 33 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7675 (tpp80) REVERT: A 46 VAL cc_start: 0.7465 (t) cc_final: 0.7056 (p) REVERT: A 54 ASP cc_start: 0.5719 (t0) cc_final: 0.5363 (t0) REVERT: A 63 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.6764 (mtm-85) REVERT: A 68 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 72 PHE cc_start: 0.7278 (p90) cc_final: 0.6836 (p90) REVERT: A 73 ASP cc_start: 0.7420 (m-30) cc_final: 0.7164 (m-30) REVERT: A 102 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7040 (mmtp) REVERT: A 135 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 137 ILE cc_start: 0.6951 (mt) cc_final: 0.6736 (mm) REVERT: A 161 TRP cc_start: 0.6828 (t60) cc_final: 0.5861 (t60) REVERT: A 163 TYR cc_start: 0.4922 (m-80) cc_final: 0.4636 (m-80) REVERT: A 181 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7869 (ptp90) REVERT: A 182 GLU cc_start: 0.8804 (tt0) cc_final: 0.8492 (tt0) REVERT: A 199 HIS cc_start: 0.7480 (p-80) cc_final: 0.7035 (p-80) REVERT: A 204 ASP cc_start: 0.8450 (t0) cc_final: 0.8074 (t0) REVERT: A 216 TYR cc_start: 0.8035 (t80) cc_final: 0.7677 (t80) REVERT: A 220 LEU cc_start: 0.8186 (mt) cc_final: 0.7945 (mt) REVERT: A 270 LEU cc_start: 0.7856 (mt) cc_final: 0.7606 (mt) REVERT: A 276 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7829 (tp30) REVERT: A 342 MET cc_start: 0.5621 (ttp) cc_final: 0.5404 (ttp) REVERT: A 397 ARG cc_start: 0.0965 (OUTLIER) cc_final: 0.0058 (ttm170) REVERT: B 17 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7609 (p) REVERT: B 20 GLU cc_start: 0.7673 (mp0) cc_final: 0.7105 (mp0) REVERT: B 42 GLU cc_start: 0.7524 (tt0) cc_final: 0.7158 (tt0) REVERT: B 68 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7326 (tt0) REVERT: B 73 ASP cc_start: 0.7326 (m-30) cc_final: 0.7083 (m-30) REVERT: B 74 VAL cc_start: 0.7817 (t) cc_final: 0.7423 (p) REVERT: B 98 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 125 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6700 (tp) REVERT: B 128 THR cc_start: 0.7529 (m) cc_final: 0.7028 (p) REVERT: B 153 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7783 (mtmp) REVERT: B 155 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: B 175 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7437 (p) REVERT: B 250 LEU cc_start: 0.7709 (tp) cc_final: 0.7467 (tt) REVERT: B 255 VAL cc_start: 0.7312 (t) cc_final: 0.7067 (p) REVERT: B 269 ILE cc_start: 0.7641 (mm) cc_final: 0.7352 (mm) REVERT: B 281 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: B 351 GLU cc_start: 0.9427 (tt0) cc_final: 0.9185 (tp30) REVERT: B 376 GLU cc_start: 0.8762 (tt0) cc_final: 0.8460 (tt0) REVERT: B 379 GLU cc_start: 0.8520 (pt0) cc_final: 0.8291 (pt0) REVERT: B 454 TRP cc_start: 0.8935 (t60) cc_final: 0.8482 (t60) REVERT: B 466 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6808 (m) REVERT: B 480 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6322 (mp10) REVERT: C 1 MET cc_start: 0.5801 (tpp) cc_final: 0.5592 (tpp) REVERT: C 24 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 26 CYS cc_start: 0.7871 (m) cc_final: 0.7583 (m) REVERT: C 28 GLN cc_start: 0.7920 (tt0) cc_final: 0.7656 (tt0) REVERT: C 57 ARG cc_start: 0.7539 (mmt90) cc_final: 0.7248 (mpp-170) REVERT: C 79 ARG cc_start: 0.7292 (mtp85) cc_final: 0.7020 (mtp85) REVERT: C 96 TRP cc_start: 0.7403 (t60) cc_final: 0.7115 (t60) REVERT: C 109 GLU cc_start: 0.6387 (mt-10) cc_final: 0.5559 (mt-10) REVERT: C 140 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7339 (ttm170) REVERT: C 142 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6905 (ttp80) REVERT: C 149 ILE cc_start: 0.8029 (mm) cc_final: 0.7601 (mt) REVERT: C 183 ARG cc_start: 0.7589 (mmt-90) cc_final: 0.7384 (tpp80) REVERT: C 186 GLU cc_start: 0.8068 (tp30) cc_final: 0.7628 (tp30) REVERT: C 196 GLU cc_start: 0.5204 (tt0) cc_final: 0.4784 (tt0) REVERT: C 200 LEU cc_start: 0.7846 (mt) cc_final: 0.7473 (mt) REVERT: C 267 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6661 (tm-30) REVERT: C 272 ARG cc_start: 0.6736 (tpt90) cc_final: 0.6215 (tpt90) REVERT: C 274 GLN cc_start: 0.7712 (mt0) cc_final: 0.7491 (mt0) REVERT: C 275 LEU cc_start: 0.7606 (tp) cc_final: 0.7332 (tp) REVERT: C 300 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7727 (ttm-80) REVERT: C 314 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4673 (p90) REVERT: C 325 ARG cc_start: 0.6742 (ptt180) cc_final: 0.6303 (ttp80) REVERT: C 344 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 351 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 355 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7120 (p0) REVERT: D 9 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6834 (mt) REVERT: D 11 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6360 (mmm-85) REVERT: D 20 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: D 22 GLN cc_start: 0.7480 (mt0) cc_final: 0.6866 (mt0) REVERT: D 32 GLN cc_start: 0.8244 (tp40) cc_final: 0.8001 (tp40) REVERT: D 56 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7820 (ttmt) REVERT: D 68 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6604 (mt-10) REVERT: D 73 ASP cc_start: 0.7134 (m-30) cc_final: 0.6651 (m-30) REVERT: D 81 ASP cc_start: 0.7355 (p0) cc_final: 0.7097 (p0) REVERT: D 88 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7094 (ttm-80) REVERT: D 98 GLU cc_start: 0.7593 (pt0) cc_final: 0.7172 (pt0) REVERT: D 101 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7602 (mmtt) REVERT: D 135 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 155 ARG cc_start: 0.4818 (ptt180) cc_final: 0.3882 (tmm-80) REVERT: D 199 HIS cc_start: 0.7652 (t-90) cc_final: 0.7067 (t-90) REVERT: D 204 ASP cc_start: 0.7925 (t70) cc_final: 0.7650 (t0) REVERT: D 214 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7561 (ttmm) REVERT: D 228 ARG cc_start: 0.6952 (mtt-85) cc_final: 0.6609 (mtm180) REVERT: D 235 LEU cc_start: 0.8257 (mt) cc_final: 0.7924 (mt) REVERT: D 238 SER cc_start: 0.6439 (m) cc_final: 0.6103 (t) REVERT: D 241 SER cc_start: 0.6905 (t) cc_final: 0.5593 (p) REVERT: D 242 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7918 (mt-10) REVERT: D 244 MET cc_start: 0.7745 (mmt) cc_final: 0.7382 (mmp) REVERT: D 276 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6231 (mm-30) REVERT: D 279 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7469 (ptp90) REVERT: D 339 THR cc_start: 0.6942 (p) cc_final: 0.5278 (m) REVERT: D 348 PHE cc_start: 0.8216 (t80) cc_final: 0.7856 (t80) REVERT: D 457 SER cc_start: 0.8606 (p) cc_final: 0.8312 (p) outliers start: 67 outliers final: 21 residues processed: 521 average time/residue: 0.1951 time to fit residues: 142.1520 Evaluate side-chains 457 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 421 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 32 GLN A 95 HIS A 417 GLN B 22 GLN B 131 GLN C 95 HIS C 251 ASN C 480 GLN D 141 ASN D 189 HIS D 199 HIS D 251 ASN D 352 GLN D 452 ASN D 459 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.192595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146298 restraints weight = 37022.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144831 restraints weight = 17009.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145572 restraints weight = 12570.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146143 restraints weight = 10521.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146315 restraints weight = 9200.845| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20302 Z= 0.217 Angle : 0.787 13.684 28362 Z= 0.436 Chirality : 0.055 0.249 3108 Planarity : 0.006 0.060 3020 Dihedral : 23.665 86.238 4358 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % Rotamer: Outliers : 3.87 % Allowed : 12.47 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1936 helix: 2.21 (0.16), residues: 909 sheet: -0.20 (0.28), residues: 266 loop : 0.77 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 472 TYR 0.023 0.003 TYR D 324 PHE 0.017 0.002 PHE D 217 TRP 0.037 0.002 TRP D 454 HIS 0.018 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 (20286) covalent geometry : angle 0.77122 / 0.44 (28338) hydrogen bonds : bond 0.05799 / 3.97 ( 1053) hydrogen bonds : angle 4.09577 / 2.99 ( 2783) metal coordination : bond 0.00432 / 0.27 ( 16) metal coordination : angle 5.40950 / 3.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 433 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7122 (tp30) cc_final: 0.6588 (tp30) REVERT: A 33 ARG cc_start: 0.7787 (mmt90) cc_final: 0.7505 (tpp80) REVERT: A 46 VAL cc_start: 0.8396 (t) cc_final: 0.8158 (p) REVERT: A 70 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 88 ARG cc_start: 0.6876 (tpp-160) cc_final: 0.6472 (tpp-160) REVERT: A 140 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7317 (ttp80) REVERT: A 155 ARG cc_start: 0.5267 (ptt180) cc_final: 0.4825 (ttp-170) REVERT: A 161 TRP cc_start: 0.7400 (t60) cc_final: 0.5618 (t60) REVERT: A 164 LEU cc_start: 0.8011 (mt) cc_final: 0.7747 (mm) REVERT: A 182 GLU cc_start: 0.8008 (tt0) cc_final: 0.7628 (tt0) REVERT: A 190 ARG cc_start: 0.8920 (mtm180) cc_final: 0.8624 (mtp180) REVERT: A 208 ARG cc_start: 0.7338 (ptp-170) cc_final: 0.7100 (ptp-170) REVERT: A 220 LEU cc_start: 0.8413 (mt) cc_final: 0.8204 (mt) REVERT: A 235 LEU cc_start: 0.8278 (mt) cc_final: 0.7690 (mt) REVERT: A 239 MET cc_start: 0.7689 (mmm) cc_final: 0.6711 (mmm) REVERT: A 250 LEU cc_start: 0.7107 (tp) cc_final: 0.6739 (mt) REVERT: A 342 MET cc_start: 0.6086 (ttp) cc_final: 0.5812 (ttp) REVERT: A 397 ARG cc_start: 0.0269 (OUTLIER) cc_final: -0.0984 (ttm170) REVERT: B 17 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7285 (p) REVERT: B 26 CYS cc_start: 0.7953 (m) cc_final: 0.7498 (m) REVERT: B 68 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 74 VAL cc_start: 0.8371 (t) cc_final: 0.8099 (p) REVERT: B 128 THR cc_start: 0.8019 (m) cc_final: 0.7463 (p) REVERT: B 153 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7694 (mtmp) REVERT: B 175 VAL cc_start: 0.8623 (t) cc_final: 0.8325 (p) REVERT: B 196 GLU cc_start: 0.7304 (tt0) cc_final: 0.6967 (tt0) REVERT: B 250 LEU cc_start: 0.8025 (tp) cc_final: 0.7813 (tt) REVERT: B 281 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: B 289 LYS cc_start: 0.7774 (mttp) cc_final: 0.7542 (mttp) REVERT: B 299 LEU cc_start: 0.8198 (tp) cc_final: 0.7904 (tp) REVERT: B 342 MET cc_start: 0.5454 (ttp) cc_final: 0.5053 (ttp) REVERT: B 351 GLU cc_start: 0.8844 (tt0) cc_final: 0.8539 (tp30) REVERT: B 376 GLU cc_start: 0.8158 (tt0) cc_final: 0.7926 (tt0) REVERT: B 466 VAL cc_start: 0.6764 (OUTLIER) cc_final: 0.6485 (m) REVERT: C 1 MET cc_start: 0.6880 (tpp) cc_final: 0.6474 (tpt) REVERT: C 22 GLN cc_start: 0.7784 (mt0) cc_final: 0.7041 (mt0) REVERT: C 26 CYS cc_start: 0.7971 (m) cc_final: 0.7600 (m) REVERT: C 43 ASP cc_start: 0.7635 (m-30) cc_final: 0.7368 (m-30) REVERT: C 109 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6614 (mt-10) REVERT: C 118 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7498 (t80) REVERT: C 142 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7292 (ttp80) REVERT: C 186 GLU cc_start: 0.7750 (tp30) cc_final: 0.7459 (tp30) REVERT: C 194 ASN cc_start: 0.8627 (m-40) cc_final: 0.8265 (m-40) REVERT: C 196 GLU cc_start: 0.6230 (tt0) cc_final: 0.6022 (tt0) REVERT: C 241 SER cc_start: 0.8303 (m) cc_final: 0.8101 (t) REVERT: C 272 ARG cc_start: 0.7048 (tpt90) cc_final: 0.6684 (tpt90) REVERT: C 300 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7836 (tpp80) REVERT: C 314 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6294 (p90) REVERT: C 325 ARG cc_start: 0.6854 (ptt180) cc_final: 0.6353 (ttp80) REVERT: C 344 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 351 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7229 (tm-30) REVERT: C 433 ARG cc_start: 0.6894 (mmp80) cc_final: 0.6609 (mmp80) REVERT: D 9 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7817 (mt) REVERT: D 11 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7670 (mtp85) REVERT: D 20 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7220 (mp0) REVERT: D 25 SER cc_start: 0.7817 (m) cc_final: 0.7582 (p) REVERT: D 32 GLN cc_start: 0.7976 (tp40) cc_final: 0.7648 (tp40) REVERT: D 42 GLU cc_start: 0.6753 (tt0) cc_final: 0.6278 (tt0) REVERT: D 51 ASP cc_start: 0.7916 (t0) cc_final: 0.7451 (t70) REVERT: D 72 PHE cc_start: 0.7823 (p90) cc_final: 0.7515 (p90) REVERT: D 73 ASP cc_start: 0.7286 (m-30) cc_final: 0.6861 (m-30) REVERT: D 86 SER cc_start: 0.8321 (t) cc_final: 0.7890 (m) REVERT: D 101 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8084 (mmtt) REVERT: D 102 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7137 (mmtm) REVERT: D 109 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6413 (mp0) REVERT: D 125 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8089 (mp) REVERT: D 155 ARG cc_start: 0.6627 (ptt180) cc_final: 0.5616 (tmm-80) REVERT: D 164 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7712 (mt) REVERT: D 182 GLU cc_start: 0.8230 (tt0) cc_final: 0.7930 (tt0) REVERT: D 214 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7608 (ttmm) REVERT: D 235 LEU cc_start: 0.8528 (mt) cc_final: 0.8266 (mt) REVERT: D 271 THR cc_start: 0.7988 (p) cc_final: 0.7588 (p) REVERT: D 276 GLU cc_start: 0.6553 (mm-30) cc_final: 0.5940 (mm-30) REVERT: D 329 MET cc_start: 0.7404 (tpp) cc_final: 0.6944 (tpp) REVERT: D 346 ASP cc_start: 0.6811 (m-30) cc_final: 0.6546 (m-30) REVERT: D 348 PHE cc_start: 0.7851 (t80) cc_final: 0.7374 (t80) REVERT: D 351 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: D 454 TRP cc_start: 0.7742 (t60) cc_final: 0.7394 (t60) REVERT: D 458 MET cc_start: 0.7185 (mmt) cc_final: 0.6696 (mmt) outliers start: 62 outliers final: 27 residues processed: 468 average time/residue: 0.1743 time to fit residues: 114.1768 Evaluate side-chains 442 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 403 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 129 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 0.0000 chunk 111 optimal weight: 1.9990 chunk 181 optimal weight: 50.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 95 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 334 HIS B 352 GLN C 27 GLN C 131 GLN D 189 HIS D 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.190267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144146 restraints weight = 36932.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141531 restraints weight = 18630.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142151 restraints weight = 14369.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142714 restraints weight = 12068.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144149 restraints weight = 9703.588| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20302 Z= 0.232 Angle : 0.688 10.810 28362 Z= 0.392 Chirality : 0.048 0.195 3108 Planarity : 0.005 0.062 3020 Dihedral : 23.469 87.864 4322 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % Rotamer: Outliers : 3.93 % Allowed : 14.34 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1936 helix: 2.16 (0.16), residues: 913 sheet: -0.26 (0.29), residues: 265 loop : 0.75 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 272 TYR 0.025 0.003 TYR B 154 PHE 0.030 0.002 PHE D 217 TRP 0.022 0.002 TRP C 430 HIS 0.017 0.002 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 (20286) covalent geometry : angle 0.67746 / 0.39 (28338) hydrogen bonds : bond 0.05490 / 3.76 ( 1053) hydrogen bonds : angle 3.99185 / 2.91 ( 2783) metal coordination : bond 0.00588 / 0.29 ( 16) metal coordination : angle 4.25423 / 2.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 429 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7140 (tp30) cc_final: 0.6703 (tp30) REVERT: A 33 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7506 (tpp80) REVERT: A 46 VAL cc_start: 0.8382 (t) cc_final: 0.8149 (p) REVERT: A 63 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7175 (mtm-85) REVERT: A 70 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 138 LYS cc_start: 0.8365 (mttm) cc_final: 0.8091 (mttm) REVERT: A 140 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.7232 (ttp-170) REVERT: A 150 ARG cc_start: 0.7234 (ttm170) cc_final: 0.6970 (mmm-85) REVERT: A 182 GLU cc_start: 0.7936 (tt0) cc_final: 0.7383 (tp30) REVERT: A 233 THR cc_start: 0.8519 (m) cc_final: 0.8299 (p) REVERT: A 235 LEU cc_start: 0.8439 (mt) cc_final: 0.7929 (mt) REVERT: A 239 MET cc_start: 0.7689 (mmm) cc_final: 0.7048 (mmm) REVERT: A 250 LEU cc_start: 0.7192 (tp) cc_final: 0.6936 (tp) REVERT: A 276 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 279 ARG cc_start: 0.8361 (ptt90) cc_final: 0.8125 (ptp90) REVERT: A 342 MET cc_start: 0.6281 (ttp) cc_final: 0.5919 (ttp) REVERT: A 383 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 397 ARG cc_start: 0.0337 (OUTLIER) cc_final: -0.0912 (ttm170) REVERT: A 419 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 423 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.5738 (mm) REVERT: B 17 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7346 (p) REVERT: B 26 CYS cc_start: 0.7983 (m) cc_final: 0.7508 (m) REVERT: B 74 VAL cc_start: 0.8395 (t) cc_final: 0.8155 (p) REVERT: B 88 ARG cc_start: 0.7549 (mtp85) cc_final: 0.6742 (mmt180) REVERT: B 175 VAL cc_start: 0.8654 (t) cc_final: 0.8326 (p) REVERT: B 215 ASP cc_start: 0.7368 (m-30) cc_final: 0.7125 (t0) REVERT: B 250 LEU cc_start: 0.8072 (tp) cc_final: 0.7836 (tt) REVERT: B 251 ASN cc_start: 0.8539 (m-40) cc_final: 0.8309 (m-40) REVERT: B 299 LEU cc_start: 0.8306 (tp) cc_final: 0.8071 (tp) REVERT: B 355 ASP cc_start: 0.8236 (m-30) cc_final: 0.7127 (m-30) REVERT: B 376 GLU cc_start: 0.8189 (tt0) cc_final: 0.7681 (tt0) REVERT: B 466 VAL cc_start: 0.6803 (OUTLIER) cc_final: 0.6538 (m) REVERT: C 1 MET cc_start: 0.7063 (tpp) cc_final: 0.6774 (tpt) REVERT: C 22 GLN cc_start: 0.7860 (mt0) cc_final: 0.7109 (mt0) REVERT: C 26 CYS cc_start: 0.7990 (m) cc_final: 0.7676 (m) REVERT: C 28 GLN cc_start: 0.7801 (tt0) cc_final: 0.7295 (mt0) REVERT: C 57 ARG cc_start: 0.6928 (mpp80) cc_final: 0.6612 (mpp80) REVERT: C 81 ASP cc_start: 0.6818 (p0) cc_final: 0.6530 (p0) REVERT: C 108 THR cc_start: 0.8251 (m) cc_final: 0.7959 (t) REVERT: C 109 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6758 (mt-10) REVERT: C 118 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7463 (t80) REVERT: C 186 GLU cc_start: 0.7727 (tp30) cc_final: 0.7421 (tp30) REVERT: C 241 SER cc_start: 0.8391 (m) cc_final: 0.8150 (t) REVERT: C 267 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6933 (tm-30) REVERT: C 300 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7812 (tpp80) REVERT: C 314 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6536 (p90) REVERT: C 325 ARG cc_start: 0.7052 (ptt180) cc_final: 0.6481 (ttp-170) REVERT: C 342 MET cc_start: 0.6290 (tpp) cc_final: 0.5769 (tpp) REVERT: C 344 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 351 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 365 LYS cc_start: 0.8427 (tttm) cc_final: 0.8166 (tttm) REVERT: C 367 TRP cc_start: 0.7749 (t-100) cc_final: 0.7161 (t-100) REVERT: D 9 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7919 (mt) REVERT: D 11 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7714 (tpp80) REVERT: D 20 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: D 21 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6737 (tpp80) REVERT: D 32 GLN cc_start: 0.7962 (tp40) cc_final: 0.7615 (tp40) REVERT: D 42 GLU cc_start: 0.6775 (tt0) cc_final: 0.6333 (tm-30) REVERT: D 44 LEU cc_start: 0.8555 (mp) cc_final: 0.7964 (mp) REVERT: D 51 ASP cc_start: 0.7841 (t0) cc_final: 0.7428 (t70) REVERT: D 73 ASP cc_start: 0.7247 (m-30) cc_final: 0.7031 (m-30) REVERT: D 79 ARG cc_start: 0.7517 (mtp180) cc_final: 0.6900 (ttm-80) REVERT: D 95 HIS cc_start: 0.7296 (m170) cc_final: 0.7068 (m90) REVERT: D 98 GLU cc_start: 0.7052 (pt0) cc_final: 0.6645 (pt0) REVERT: D 109 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6115 (mt-10) REVERT: D 132 MET cc_start: 0.7187 (mmm) cc_final: 0.6961 (mmm) REVERT: D 138 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7749 (mtpp) REVERT: D 139 GLU cc_start: 0.7344 (tp30) cc_final: 0.7045 (tp30) REVERT: D 142 ARG cc_start: 0.7740 (ttt90) cc_final: 0.7414 (ptm-80) REVERT: D 164 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7807 (mt) REVERT: D 199 HIS cc_start: 0.7236 (t70) cc_final: 0.6693 (t70) REVERT: D 214 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7928 (ttmm) REVERT: D 217 PHE cc_start: 0.7911 (t80) cc_final: 0.7663 (t80) REVERT: D 220 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8062 (mm) REVERT: D 221 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8307 (mm110) REVERT: D 235 LEU cc_start: 0.8556 (mt) cc_final: 0.8278 (mt) REVERT: D 240 ILE cc_start: 0.8272 (pt) cc_final: 0.8053 (mp) REVERT: D 276 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6322 (mm-30) REVERT: D 279 ARG cc_start: 0.7415 (ptp-110) cc_final: 0.7144 (ptp90) REVERT: D 348 PHE cc_start: 0.7941 (t80) cc_final: 0.7565 (t80) REVERT: D 350 GLU cc_start: 0.8489 (tp30) cc_final: 0.8103 (mm-30) REVERT: D 351 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: D 454 TRP cc_start: 0.7703 (t60) cc_final: 0.7193 (t60) REVERT: D 458 MET cc_start: 0.7323 (mmt) cc_final: 0.6542 (mmt) outliers start: 63 outliers final: 30 residues processed: 460 average time/residue: 0.1746 time to fit residues: 112.6742 Evaluate side-chains 454 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 411 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 95 HIS A 417 GLN B 131 GLN B 194 ASN B 352 GLN C 27 GLN C 480 GLN D 131 GLN D 226 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.191538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142940 restraints weight = 36764.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142539 restraints weight = 20897.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142872 restraints weight = 12462.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143634 restraints weight = 11950.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144024 restraints weight = 9581.390| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20302 Z= 0.152 Angle : 0.613 12.808 28362 Z= 0.350 Chirality : 0.043 0.193 3108 Planarity : 0.005 0.062 3020 Dihedral : 23.455 85.241 4314 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.87 % Allowed : 15.77 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.19), residues: 1936 helix: 2.29 (0.17), residues: 913 sheet: -0.20 (0.29), residues: 262 loop : 0.84 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 88 TYR 0.015 0.002 TYR C 216 PHE 0.017 0.001 PHE D 217 TRP 0.017 0.001 TRP B 454 HIS 0.017 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (20286) covalent geometry : angle 0.60423 / 0.35 (28338) hydrogen bonds : bond 0.04675 / 3.21 ( 1053) hydrogen bonds : angle 3.80828 / 2.77 ( 2783) metal coordination : bond 0.00339 / 0.19 ( 16) metal coordination : angle 3.69629 / 2.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7724 (mmt90) cc_final: 0.7492 (tpp80) REVERT: A 46 VAL cc_start: 0.8328 (t) cc_final: 0.8109 (p) REVERT: A 63 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.7038 (ttm-80) REVERT: A 70 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 88 ARG cc_start: 0.6837 (tpp-160) cc_final: 0.6538 (tpp-160) REVERT: A 131 GLN cc_start: 0.7699 (tp40) cc_final: 0.7343 (tt0) REVERT: A 135 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6582 (tm-30) REVERT: A 138 LYS cc_start: 0.8389 (mttm) cc_final: 0.8021 (mttp) REVERT: A 140 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7304 (ttp80) REVERT: A 150 ARG cc_start: 0.7290 (ttm170) cc_final: 0.6986 (mmm-85) REVERT: A 181 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7431 (ptp-170) REVERT: A 233 THR cc_start: 0.8527 (m) cc_final: 0.8250 (p) REVERT: A 235 LEU cc_start: 0.8449 (mt) cc_final: 0.7984 (mt) REVERT: A 239 MET cc_start: 0.7836 (mmm) cc_final: 0.7150 (mmm) REVERT: A 250 LEU cc_start: 0.7151 (tp) cc_final: 0.6796 (tp) REVERT: A 276 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6486 (mt-10) REVERT: A 342 MET cc_start: 0.6318 (ttp) cc_final: 0.5911 (ttp) REVERT: A 383 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7970 (mt-10) REVERT: A 397 ARG cc_start: 0.0369 (OUTLIER) cc_final: -0.0876 (ttm170) REVERT: A 423 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5954 (mm) REVERT: B 26 CYS cc_start: 0.8011 (m) cc_final: 0.7682 (m) REVERT: B 68 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 69 GLU cc_start: 0.7397 (tp30) cc_final: 0.6877 (tp30) REVERT: B 74 VAL cc_start: 0.8446 (t) cc_final: 0.8242 (p) REVERT: B 135 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7236 (mm-30) REVERT: B 215 ASP cc_start: 0.7382 (m-30) cc_final: 0.7175 (t0) REVERT: B 251 ASN cc_start: 0.8494 (m-40) cc_final: 0.8239 (m-40) REVERT: B 281 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: B 299 LEU cc_start: 0.8280 (tp) cc_final: 0.7958 (tp) REVERT: B 342 MET cc_start: 0.5729 (ttp) cc_final: 0.5245 (ttp) REVERT: B 350 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7606 (pp20) REVERT: B 379 GLU cc_start: 0.7763 (pp20) cc_final: 0.7557 (tm-30) REVERT: B 466 VAL cc_start: 0.6854 (OUTLIER) cc_final: 0.6574 (m) REVERT: C 22 GLN cc_start: 0.7817 (mt0) cc_final: 0.7140 (mt0) REVERT: C 26 CYS cc_start: 0.8015 (m) cc_final: 0.7659 (m) REVERT: C 28 GLN cc_start: 0.7793 (tt0) cc_final: 0.7329 (mt0) REVERT: C 81 ASP cc_start: 0.6783 (p0) cc_final: 0.6527 (p0) REVERT: C 108 THR cc_start: 0.8291 (m) cc_final: 0.8015 (t) REVERT: C 109 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6719 (mt-10) REVERT: C 118 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7172 (t80) REVERT: C 181 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7735 (mtp85) REVERT: C 182 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6651 (tm-30) REVERT: C 186 GLU cc_start: 0.7709 (tp30) cc_final: 0.7439 (tm-30) REVERT: C 240 ILE cc_start: 0.8302 (mt) cc_final: 0.7929 (tt) REVERT: C 241 SER cc_start: 0.8323 (m) cc_final: 0.7976 (t) REVERT: C 267 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: C 300 ARG cc_start: 0.8171 (mmt180) cc_final: 0.7601 (tpp80) REVERT: C 314 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6546 (p90) REVERT: C 342 MET cc_start: 0.6161 (tpp) cc_final: 0.5643 (tpp) REVERT: C 351 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 355 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6701 (p0) REVERT: C 365 LYS cc_start: 0.8414 (tttm) cc_final: 0.8168 (tttm) REVERT: C 367 TRP cc_start: 0.7723 (t-100) cc_final: 0.7107 (t-100) REVERT: D 9 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7797 (mt) REVERT: D 20 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: D 21 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6817 (tpp80) REVERT: D 32 GLN cc_start: 0.7974 (tp40) cc_final: 0.7599 (tp40) REVERT: D 44 LEU cc_start: 0.8535 (mp) cc_final: 0.7991 (mt) REVERT: D 73 ASP cc_start: 0.7199 (m-30) cc_final: 0.6937 (m-30) REVERT: D 86 SER cc_start: 0.8481 (t) cc_final: 0.8049 (m) REVERT: D 101 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8082 (mmtt) REVERT: D 102 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7310 (mmtp) REVERT: D 109 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6550 (mt-10) REVERT: D 132 MET cc_start: 0.7197 (mmm) cc_final: 0.6910 (mmm) REVERT: D 138 LYS cc_start: 0.8080 (mttp) cc_final: 0.7816 (mtpp) REVERT: D 164 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7821 (mt) REVERT: D 199 HIS cc_start: 0.7175 (t70) cc_final: 0.6574 (t70) REVERT: D 214 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7757 (ttmm) REVERT: D 217 PHE cc_start: 0.7868 (t80) cc_final: 0.7654 (t80) REVERT: D 221 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8316 (mm110) REVERT: D 226 GLN cc_start: 0.7504 (mt0) cc_final: 0.7180 (mt0) REVERT: D 235 LEU cc_start: 0.8525 (mt) cc_final: 0.8233 (mt) REVERT: D 276 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6492 (mm-30) REVERT: D 279 ARG cc_start: 0.7517 (ptp-110) cc_final: 0.7204 (ptp90) REVERT: D 331 PHE cc_start: 0.7235 (m-10) cc_final: 0.6983 (m-10) REVERT: D 348 PHE cc_start: 0.7940 (t80) cc_final: 0.7720 (t80) REVERT: D 350 GLU cc_start: 0.8553 (tp30) cc_final: 0.8133 (mm-30) REVERT: D 351 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: D 404 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7572 (mp0) REVERT: D 454 TRP cc_start: 0.7775 (t60) cc_final: 0.7204 (t60) REVERT: D 458 MET cc_start: 0.7244 (mmt) cc_final: 0.6515 (mmt) outliers start: 62 outliers final: 32 residues processed: 439 average time/residue: 0.1918 time to fit residues: 117.9131 Evaluate side-chains 440 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 394 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 95 HIS B 194 ASN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN D 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.188499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138756 restraints weight = 36401.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138859 restraints weight = 19777.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139151 restraints weight = 11765.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139718 restraints weight = 11292.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140279 restraints weight = 9590.650| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20302 Z= 0.253 Angle : 0.670 11.460 28362 Z= 0.376 Chirality : 0.045 0.200 3108 Planarity : 0.005 0.062 3020 Dihedral : 23.497 83.009 4308 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.86 % Allowed : 15.27 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 1936 helix: 2.11 (0.17), residues: 914 sheet: -0.29 (0.30), residues: 259 loop : 0.66 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 444 TYR 0.022 0.002 TYR B 154 PHE 0.019 0.002 PHE C 147 TRP 0.021 0.002 TRP B 454 HIS 0.019 0.002 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.25 (20286) covalent geometry : angle 0.66235 / 0.38 (28338) hydrogen bonds : bond 0.05253 / 3.58 ( 1053) hydrogen bonds : angle 3.95756 / 2.89 ( 2783) metal coordination : bond 0.00488 / 0.28 ( 16) metal coordination : angle 3.42527 / 2.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 404 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7179 (tp30) cc_final: 0.6915 (tp30) REVERT: A 46 VAL cc_start: 0.8326 (t) cc_final: 0.8113 (p) REVERT: A 135 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6733 (tm-30) REVERT: A 138 LYS cc_start: 0.8424 (mttm) cc_final: 0.7938 (mttp) REVERT: A 140 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.7401 (tmm-80) REVERT: A 150 ARG cc_start: 0.7381 (ttm170) cc_final: 0.7093 (mtp85) REVERT: A 181 ARG cc_start: 0.7865 (ptp90) cc_final: 0.7522 (ptp-170) REVERT: A 233 THR cc_start: 0.8588 (m) cc_final: 0.8374 (p) REVERT: A 235 LEU cc_start: 0.8575 (mt) cc_final: 0.8062 (mt) REVERT: A 239 MET cc_start: 0.7719 (mmm) cc_final: 0.7073 (mmm) REVERT: A 250 LEU cc_start: 0.7200 (tp) cc_final: 0.6875 (tp) REVERT: A 253 LYS cc_start: 0.7818 (mptt) cc_final: 0.7487 (mptt) REVERT: A 342 MET cc_start: 0.6317 (ttp) cc_final: 0.5922 (ttp) REVERT: A 383 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 397 ARG cc_start: 0.0303 (OUTLIER) cc_final: -0.0915 (ttm170) REVERT: A 423 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6053 (mm) REVERT: B 68 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 69 GLU cc_start: 0.7729 (tp30) cc_final: 0.7025 (tp30) REVERT: B 135 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 139 GLU cc_start: 0.7632 (tp30) cc_final: 0.6776 (tp30) REVERT: B 142 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6639 (ttp-110) REVERT: B 175 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 244 MET cc_start: 0.8306 (mmt) cc_final: 0.7932 (mmt) REVERT: B 273 GLU cc_start: 0.7800 (tt0) cc_final: 0.7267 (tp30) REVERT: B 350 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: B 466 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6660 (m) REVERT: C 22 GLN cc_start: 0.7866 (mt0) cc_final: 0.7216 (mt0) REVERT: C 26 CYS cc_start: 0.8085 (m) cc_final: 0.7752 (m) REVERT: C 28 GLN cc_start: 0.7909 (tt0) cc_final: 0.7443 (mt0) REVERT: C 57 ARG cc_start: 0.7010 (mpp80) cc_final: 0.6774 (mpp80) REVERT: C 81 ASP cc_start: 0.6797 (p0) cc_final: 0.6480 (p0) REVERT: C 109 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6946 (mt-10) REVERT: C 118 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7244 (t80) REVERT: C 153 LYS cc_start: 0.8582 (mttt) cc_final: 0.8292 (mttt) REVERT: C 182 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6737 (tm-30) REVERT: C 241 SER cc_start: 0.8457 (m) cc_final: 0.7975 (p) REVERT: C 242 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 263 LEU cc_start: 0.8513 (tp) cc_final: 0.8259 (tt) REVERT: C 267 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: C 300 ARG cc_start: 0.8229 (mmt180) cc_final: 0.7699 (tpp80) REVERT: C 314 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6773 (p90) REVERT: C 342 MET cc_start: 0.6248 (tpp) cc_final: 0.5772 (tpp) REVERT: C 351 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 365 LYS cc_start: 0.8446 (tttm) cc_final: 0.7823 (tttm) REVERT: C 367 TRP cc_start: 0.7677 (t-100) cc_final: 0.7359 (t-100) REVERT: C 430 TRP cc_start: 0.7319 (m100) cc_final: 0.6006 (m100) REVERT: D 9 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7782 (mt) REVERT: D 20 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: D 21 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6766 (tpp80) REVERT: D 25 SER cc_start: 0.7922 (p) cc_final: 0.7694 (t) REVERT: D 32 GLN cc_start: 0.7998 (tp40) cc_final: 0.7633 (tp40) REVERT: D 42 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6350 (tm-30) REVERT: D 44 LEU cc_start: 0.8456 (mp) cc_final: 0.7882 (mt) REVERT: D 73 ASP cc_start: 0.7196 (m-30) cc_final: 0.6965 (m-30) REVERT: D 79 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7081 (ttm110) REVERT: D 101 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7979 (mmtt) REVERT: D 109 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6371 (mt-10) REVERT: D 132 MET cc_start: 0.7327 (mmm) cc_final: 0.7058 (mmm) REVERT: D 138 LYS cc_start: 0.8119 (mttp) cc_final: 0.7771 (mtpp) REVERT: D 142 ARG cc_start: 0.7764 (ttt90) cc_final: 0.7502 (ptm-80) REVERT: D 164 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7848 (mt) REVERT: D 183 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7211 (mmp80) REVERT: D 199 HIS cc_start: 0.7048 (t70) cc_final: 0.6322 (t70) REVERT: D 214 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7910 (ttmm) REVERT: D 220 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7964 (mm) REVERT: D 226 GLN cc_start: 0.7583 (mt0) cc_final: 0.7275 (mt0) REVERT: D 229 GLU cc_start: 0.7631 (pt0) cc_final: 0.7302 (pt0) REVERT: D 235 LEU cc_start: 0.8530 (mt) cc_final: 0.8277 (mt) REVERT: D 276 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6496 (mm-30) REVERT: D 279 ARG cc_start: 0.7486 (ptp-110) cc_final: 0.7241 (ptp90) REVERT: D 281 GLU cc_start: 0.7323 (pp20) cc_final: 0.6927 (pp20) REVERT: D 301 VAL cc_start: 0.5741 (OUTLIER) cc_final: 0.5510 (m) REVERT: D 329 MET cc_start: 0.7348 (ttp) cc_final: 0.6913 (ttp) REVERT: D 331 PHE cc_start: 0.7340 (m-10) cc_final: 0.7050 (m-10) REVERT: D 348 PHE cc_start: 0.7904 (t80) cc_final: 0.7557 (t80) REVERT: D 350 GLU cc_start: 0.8543 (tp30) cc_final: 0.8206 (mm-30) REVERT: D 351 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: D 409 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.7923 (tpp-160) REVERT: D 454 TRP cc_start: 0.7802 (t60) cc_final: 0.7199 (t60) REVERT: D 458 MET cc_start: 0.7411 (mmt) cc_final: 0.6649 (mmt) outliers start: 78 outliers final: 45 residues processed: 441 average time/residue: 0.1882 time to fit residues: 116.8654 Evaluate side-chains 450 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 99 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 95 HIS ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN D 95 HIS D 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.189038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139864 restraints weight = 36383.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139217 restraints weight = 20307.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140405 restraints weight = 11986.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141003 restraints weight = 10458.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141218 restraints weight = 9218.487| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20302 Z= 0.174 Angle : 0.628 13.356 28362 Z= 0.355 Chirality : 0.043 0.227 3108 Planarity : 0.005 0.059 3020 Dihedral : 23.501 82.024 4305 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.74 % Allowed : 16.52 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1936 helix: 2.15 (0.17), residues: 915 sheet: -0.16 (0.31), residues: 252 loop : 0.65 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 444 TYR 0.022 0.002 TYR D 216 PHE 0.014 0.001 PHE D 67 TRP 0.023 0.001 TRP B 454 HIS 0.019 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (20286) covalent geometry : angle 0.62079 / 0.35 (28338) hydrogen bonds : bond 0.04705 / 3.23 ( 1053) hydrogen bonds : angle 3.86504 / 2.82 ( 2783) metal coordination : bond 0.00365 / 0.22 ( 16) metal coordination : angle 3.36484 / 2.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 396 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 135 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6688 (tm-30) REVERT: A 140 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7431 (tmm-80) REVERT: A 150 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7162 (ttm170) REVERT: A 182 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 233 THR cc_start: 0.8605 (m) cc_final: 0.8382 (p) REVERT: A 235 LEU cc_start: 0.8576 (mt) cc_final: 0.8053 (mt) REVERT: A 239 MET cc_start: 0.7681 (mmm) cc_final: 0.7026 (mmm) REVERT: A 250 LEU cc_start: 0.7170 (tp) cc_final: 0.6876 (tt) REVERT: A 253 LYS cc_start: 0.7780 (mptt) cc_final: 0.7450 (mptt) REVERT: A 342 MET cc_start: 0.6300 (ttp) cc_final: 0.5911 (ttp) REVERT: A 383 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 397 ARG cc_start: 0.0324 (OUTLIER) cc_final: -0.0908 (ttm170) REVERT: A 423 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5975 (mm) REVERT: B 69 GLU cc_start: 0.7777 (tp30) cc_final: 0.7160 (tp30) REVERT: B 135 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 143 SER cc_start: 0.8202 (t) cc_final: 0.7756 (p) REVERT: B 208 ARG cc_start: 0.7407 (mtp180) cc_final: 0.7138 (ttp-110) REVERT: B 350 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7715 (pp20) REVERT: B 466 VAL cc_start: 0.6947 (OUTLIER) cc_final: 0.6702 (m) REVERT: C 22 GLN cc_start: 0.7867 (mt0) cc_final: 0.7202 (mt0) REVERT: C 26 CYS cc_start: 0.8052 (m) cc_final: 0.7678 (m) REVERT: C 28 GLN cc_start: 0.7833 (tt0) cc_final: 0.7438 (mt0) REVERT: C 54 ASP cc_start: 0.7339 (t0) cc_final: 0.6927 (t0) REVERT: C 81 ASP cc_start: 0.6775 (p0) cc_final: 0.6559 (p0) REVERT: C 87 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8103 (pt) REVERT: C 109 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6911 (mt-10) REVERT: C 118 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 153 LYS cc_start: 0.8536 (mttt) cc_final: 0.8231 (mttt) REVERT: C 182 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6700 (tm-30) REVERT: C 241 SER cc_start: 0.8500 (m) cc_final: 0.7962 (p) REVERT: C 242 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8103 (mt-10) REVERT: C 267 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: C 300 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7796 (tpp80) REVERT: C 351 GLU cc_start: 0.7610 (tm-30) cc_final: 0.6869 (tm-30) REVERT: C 355 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.6722 (p0) REVERT: C 365 LYS cc_start: 0.8434 (tttm) cc_final: 0.7765 (tttm) REVERT: C 367 TRP cc_start: 0.7583 (t-100) cc_final: 0.7364 (t-100) REVERT: C 383 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6644 (mp0) REVERT: C 430 TRP cc_start: 0.7306 (m100) cc_final: 0.5980 (m100) REVERT: D 9 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7691 (mt) REVERT: D 20 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: D 21 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6728 (tpp80) REVERT: D 25 SER cc_start: 0.7890 (p) cc_final: 0.7650 (t) REVERT: D 32 GLN cc_start: 0.7883 (tp40) cc_final: 0.7521 (tp40) REVERT: D 42 GLU cc_start: 0.6866 (tt0) cc_final: 0.6394 (tm-30) REVERT: D 44 LEU cc_start: 0.8437 (mp) cc_final: 0.7979 (mt) REVERT: D 68 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: D 73 ASP cc_start: 0.7141 (m-30) cc_final: 0.6928 (m-30) REVERT: D 79 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6939 (ttm110) REVERT: D 95 HIS cc_start: 0.7521 (m-70) cc_final: 0.7198 (m170) REVERT: D 101 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7954 (mmtt) REVERT: D 109 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6386 (mt-10) REVERT: D 132 MET cc_start: 0.7304 (mmm) cc_final: 0.6963 (mmm) REVERT: D 138 LYS cc_start: 0.8157 (mttp) cc_final: 0.7796 (mtpp) REVERT: D 142 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7524 (ptm-80) REVERT: D 164 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7915 (mt) REVERT: D 199 HIS cc_start: 0.7065 (t70) cc_final: 0.6325 (t70) REVERT: D 214 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7730 (ttmm) REVERT: D 226 GLN cc_start: 0.7513 (mt0) cc_final: 0.7232 (mt0) REVERT: D 235 LEU cc_start: 0.8510 (mt) cc_final: 0.8248 (mt) REVERT: D 276 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6433 (mm-30) REVERT: D 279 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.7215 (ptp90) REVERT: D 301 VAL cc_start: 0.5706 (OUTLIER) cc_final: 0.5472 (m) REVERT: D 331 PHE cc_start: 0.7320 (m-10) cc_final: 0.7088 (m-10) REVERT: D 348 PHE cc_start: 0.7906 (t80) cc_final: 0.7529 (t80) REVERT: D 350 GLU cc_start: 0.8587 (tp30) cc_final: 0.8169 (mm-30) REVERT: D 351 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: D 409 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.7852 (tpp-160) REVERT: D 454 TRP cc_start: 0.7795 (t60) cc_final: 0.7184 (t60) REVERT: D 458 MET cc_start: 0.7347 (mmt) cc_final: 0.6625 (mmt) outliers start: 76 outliers final: 51 residues processed: 437 average time/residue: 0.1769 time to fit residues: 109.1510 Evaluate side-chains 454 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 388 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 30 optimal weight: 30.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 195 HIS ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.187074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133212 restraints weight = 36413.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136961 restraints weight = 16488.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138412 restraints weight = 9703.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139261 restraints weight = 8354.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139390 restraints weight = 6964.269| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20302 Z= 0.271 Angle : 0.694 14.470 28362 Z= 0.386 Chirality : 0.046 0.202 3108 Planarity : 0.006 0.081 3020 Dihedral : 23.583 82.454 4303 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.80 % Allowed : 17.46 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.19), residues: 1936 helix: 1.90 (0.17), residues: 913 sheet: -0.29 (0.30), residues: 279 loop : 0.36 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 11 TYR 0.022 0.003 TYR C 216 PHE 0.027 0.002 PHE D 53 TRP 0.040 0.002 TRP D 345 HIS 0.019 0.002 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.27 (20286) covalent geometry : angle 0.68761 / 0.39 (28338) hydrogen bonds : bond 0.05322 / 3.67 ( 1053) hydrogen bonds : angle 4.07295 / 2.97 ( 2783) metal coordination : bond 0.00608 / 0.36 ( 16) metal coordination : angle 3.41689 / 2.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 385 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7179 (tp30) cc_final: 0.6626 (tp30) REVERT: A 70 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 85 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6871 (mmm-85) REVERT: A 135 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6764 (tm-30) REVERT: A 140 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.7454 (tmm-80) REVERT: A 150 ARG cc_start: 0.7324 (ttm170) cc_final: 0.7012 (mmm-85) REVERT: A 182 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 233 THR cc_start: 0.8697 (m) cc_final: 0.8458 (p) REVERT: A 235 LEU cc_start: 0.8749 (mt) cc_final: 0.8159 (mt) REVERT: A 239 MET cc_start: 0.7800 (mmm) cc_final: 0.7109 (mmm) REVERT: A 244 MET cc_start: 0.6334 (mpp) cc_final: 0.6039 (mpt) REVERT: A 250 LEU cc_start: 0.7214 (tp) cc_final: 0.6833 (tp) REVERT: A 253 LYS cc_start: 0.7771 (mptt) cc_final: 0.7394 (mptt) REVERT: A 342 MET cc_start: 0.6307 (ttp) cc_final: 0.5920 (ttp) REVERT: A 344 GLU cc_start: 0.5731 (tm-30) cc_final: 0.5265 (tm-30) REVERT: A 383 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 397 ARG cc_start: 0.0403 (OUTLIER) cc_final: -0.0784 (ttm170) REVERT: A 423 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6166 (mm) REVERT: B 20 GLU cc_start: 0.7512 (pm20) cc_final: 0.7269 (mp0) REVERT: B 109 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7466 (mt-10) REVERT: B 135 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7239 (mm-30) REVERT: B 139 GLU cc_start: 0.7562 (tp30) cc_final: 0.6394 (tp30) REVERT: B 142 ARG cc_start: 0.6961 (ttp-110) cc_final: 0.6610 (ttp-110) REVERT: B 143 SER cc_start: 0.8254 (t) cc_final: 0.7812 (p) REVERT: B 175 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 251 ASN cc_start: 0.8519 (m-40) cc_final: 0.8281 (m-40) REVERT: B 273 GLU cc_start: 0.7879 (tt0) cc_final: 0.7230 (tp30) REVERT: B 350 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7846 (pp20) REVERT: B 351 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: B 376 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8146 (mm-30) REVERT: B 466 VAL cc_start: 0.6867 (OUTLIER) cc_final: 0.6641 (m) REVERT: C 22 GLN cc_start: 0.7891 (mt0) cc_final: 0.7229 (mt0) REVERT: C 26 CYS cc_start: 0.8077 (m) cc_final: 0.7753 (m) REVERT: C 28 GLN cc_start: 0.7904 (tt0) cc_final: 0.7560 (mt0) REVERT: C 36 ASP cc_start: 0.7556 (p0) cc_final: 0.7349 (p0) REVERT: C 54 ASP cc_start: 0.7407 (t0) cc_final: 0.7055 (t0) REVERT: C 69 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: C 73 ASP cc_start: 0.7754 (m-30) cc_final: 0.7537 (m-30) REVERT: C 81 ASP cc_start: 0.6817 (p0) cc_final: 0.6592 (p0) REVERT: C 109 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6973 (mt-10) REVERT: C 118 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7253 (t80) REVERT: C 139 GLU cc_start: 0.7779 (tp30) cc_final: 0.7384 (tp30) REVERT: C 153 LYS cc_start: 0.8591 (mttt) cc_final: 0.8287 (mttt) REVERT: C 182 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6672 (tm-30) REVERT: C 186 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7357 (tp30) REVERT: C 241 SER cc_start: 0.8558 (m) cc_final: 0.8050 (p) REVERT: C 267 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: C 300 ARG cc_start: 0.8307 (mmt180) cc_final: 0.7945 (tpp80) REVERT: C 325 ARG cc_start: 0.7262 (ptt180) cc_final: 0.6780 (ptm-80) REVERT: C 351 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 365 LYS cc_start: 0.8473 (tttm) cc_final: 0.8024 (tttm) REVERT: C 367 TRP cc_start: 0.7347 (t-100) cc_final: 0.6798 (t-100) REVERT: D 9 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7721 (mt) REVERT: D 20 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: D 21 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6788 (tpp80) REVERT: D 25 SER cc_start: 0.7889 (p) cc_final: 0.7604 (t) REVERT: D 32 GLN cc_start: 0.7819 (tp40) cc_final: 0.7469 (tp40) REVERT: D 42 GLU cc_start: 0.6938 (tt0) cc_final: 0.6313 (tm-30) REVERT: D 44 LEU cc_start: 0.8462 (mp) cc_final: 0.8032 (mt) REVERT: D 73 ASP cc_start: 0.7113 (m-30) cc_final: 0.6851 (m-30) REVERT: D 79 ARG cc_start: 0.7632 (mtp-110) cc_final: 0.6981 (ttm110) REVERT: D 95 HIS cc_start: 0.7581 (m-70) cc_final: 0.7245 (m170) REVERT: D 101 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7819 (mmtt) REVERT: D 102 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7395 (mmtm) REVERT: D 109 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6362 (mt-10) REVERT: D 132 MET cc_start: 0.7394 (mmm) cc_final: 0.7047 (mmm) REVERT: D 138 LYS cc_start: 0.8164 (mttp) cc_final: 0.7843 (mtpp) REVERT: D 142 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7545 (ptm-80) REVERT: D 164 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7902 (mt) REVERT: D 173 ARG cc_start: 0.7390 (ttm110) cc_final: 0.7171 (mtp-110) REVERT: D 183 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7373 (mmp80) REVERT: D 199 HIS cc_start: 0.7330 (t70) cc_final: 0.6531 (t70) REVERT: D 214 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7815 (ttmm) REVERT: D 226 GLN cc_start: 0.7546 (mt0) cc_final: 0.7286 (mt0) REVERT: D 276 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6708 (mm-30) REVERT: D 301 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5549 (m) REVERT: D 331 PHE cc_start: 0.7446 (m-10) cc_final: 0.7140 (m-10) REVERT: D 333 LYS cc_start: 0.6520 (tttp) cc_final: 0.6231 (tttp) REVERT: D 346 ASP cc_start: 0.7983 (p0) cc_final: 0.7426 (p0) REVERT: D 348 PHE cc_start: 0.8008 (t80) cc_final: 0.7591 (t80) REVERT: D 350 GLU cc_start: 0.8789 (tp30) cc_final: 0.8418 (mm-30) REVERT: D 351 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: D 409 ARG cc_start: 0.8691 (tpp-160) cc_final: 0.7960 (tpp-160) REVERT: D 454 TRP cc_start: 0.7995 (t60) cc_final: 0.7282 (t60) REVERT: D 458 MET cc_start: 0.7665 (mmt) cc_final: 0.6920 (mmt) outliers start: 77 outliers final: 43 residues processed: 426 average time/residue: 0.1734 time to fit residues: 104.3301 Evaluate side-chains 440 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 380 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.188820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138509 restraints weight = 36326.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138573 restraints weight = 17411.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139838 restraints weight = 11090.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140954 restraints weight = 8746.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140986 restraints weight = 8298.899| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20302 Z= 0.167 Angle : 0.629 15.338 28362 Z= 0.351 Chirality : 0.042 0.230 3108 Planarity : 0.005 0.059 3020 Dihedral : 23.557 83.304 4303 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.55 % Allowed : 19.01 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.20), residues: 1936 helix: 2.08 (0.17), residues: 910 sheet: -0.21 (0.29), residues: 290 loop : 0.51 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 325 TYR 0.020 0.002 TYR C 216 PHE 0.017 0.001 PHE D 67 TRP 0.070 0.002 TRP C 430 HIS 0.020 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (20286) covalent geometry : angle 0.62191 / 0.35 (28338) hydrogen bonds : bond 0.04542 / 3.12 ( 1053) hydrogen bonds : angle 3.83848 / 2.80 ( 2783) metal coordination : bond 0.00295 / 0.19 ( 16) metal coordination : angle 3.23661 / 2.28 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 382 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7069 (tp30) cc_final: 0.6507 (tp30) REVERT: A 70 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 102 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7573 (mmtp) REVERT: A 135 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6733 (tm-30) REVERT: A 140 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7454 (ttp80) REVERT: A 150 ARG cc_start: 0.7434 (ttm170) cc_final: 0.7097 (mmm-85) REVERT: A 182 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 233 THR cc_start: 0.8667 (m) cc_final: 0.8408 (p) REVERT: A 235 LEU cc_start: 0.8730 (mt) cc_final: 0.8132 (mt) REVERT: A 239 MET cc_start: 0.7696 (mmm) cc_final: 0.6936 (mmm) REVERT: A 250 LEU cc_start: 0.7186 (tp) cc_final: 0.6863 (tp) REVERT: A 253 LYS cc_start: 0.7755 (mptt) cc_final: 0.7386 (mptt) REVERT: A 342 MET cc_start: 0.6320 (ttp) cc_final: 0.5919 (ttp) REVERT: A 344 GLU cc_start: 0.5609 (tm-30) cc_final: 0.5126 (tm-30) REVERT: A 383 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 423 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6265 (mm) REVERT: B 109 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 121 VAL cc_start: 0.8375 (t) cc_final: 0.8150 (p) REVERT: B 135 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7259 (mm-30) REVERT: B 139 GLU cc_start: 0.7541 (tp30) cc_final: 0.6525 (tp30) REVERT: B 142 ARG cc_start: 0.6977 (ttp-110) cc_final: 0.6589 (ttp-110) REVERT: B 143 SER cc_start: 0.8174 (t) cc_final: 0.7759 (p) REVERT: B 196 GLU cc_start: 0.7690 (tp30) cc_final: 0.7430 (tp30) REVERT: B 203 HIS cc_start: 0.7576 (t-90) cc_final: 0.7242 (t-90) REVERT: B 208 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7141 (ttp-110) REVERT: B 251 ASN cc_start: 0.8468 (m-40) cc_final: 0.8229 (m-40) REVERT: B 273 GLU cc_start: 0.7809 (tt0) cc_final: 0.7088 (tp30) REVERT: B 299 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 350 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: B 351 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8259 (tp30) REVERT: B 376 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8013 (mm-30) REVERT: B 466 VAL cc_start: 0.6866 (OUTLIER) cc_final: 0.6635 (m) REVERT: C 20 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7354 (mm-30) REVERT: C 26 CYS cc_start: 0.8115 (m) cc_final: 0.7710 (m) REVERT: C 28 GLN cc_start: 0.7891 (tt0) cc_final: 0.7548 (mt0) REVERT: C 57 ARG cc_start: 0.6970 (mpp80) cc_final: 0.6687 (mtm-85) REVERT: C 69 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: C 73 ASP cc_start: 0.7740 (m-30) cc_final: 0.7528 (m-30) REVERT: C 109 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7045 (mt-10) REVERT: C 118 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7154 (t80) REVERT: C 139 GLU cc_start: 0.7635 (tp30) cc_final: 0.7295 (tp30) REVERT: C 153 LYS cc_start: 0.8560 (mttt) cc_final: 0.8276 (mttt) REVERT: C 182 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 241 SER cc_start: 0.8455 (m) cc_final: 0.7945 (p) REVERT: C 267 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 300 ARG cc_start: 0.8307 (mmt180) cc_final: 0.7907 (tpp80) REVERT: C 325 ARG cc_start: 0.7234 (ptt180) cc_final: 0.6198 (ptm-80) REVERT: C 329 MET cc_start: 0.7652 (ttm) cc_final: 0.6694 (ttm) REVERT: C 351 GLU cc_start: 0.7687 (tm-30) cc_final: 0.6940 (tm-30) REVERT: C 355 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6743 (p0) REVERT: C 367 TRP cc_start: 0.7815 (t-100) cc_final: 0.7066 (t-100) REVERT: D 9 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7629 (mt) REVERT: D 20 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: D 25 SER cc_start: 0.7936 (p) cc_final: 0.7712 (t) REVERT: D 32 GLN cc_start: 0.7897 (tp40) cc_final: 0.7578 (tp40) REVERT: D 42 GLU cc_start: 0.7018 (tt0) cc_final: 0.6322 (tm-30) REVERT: D 44 LEU cc_start: 0.8434 (mp) cc_final: 0.8006 (mt) REVERT: D 73 ASP cc_start: 0.7084 (m-30) cc_final: 0.6829 (m-30) REVERT: D 74 VAL cc_start: 0.8423 (p) cc_final: 0.8093 (m) REVERT: D 79 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7077 (ttm110) REVERT: D 101 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7808 (mmtt) REVERT: D 102 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7339 (mmtm) REVERT: D 109 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6318 (mt-10) REVERT: D 132 MET cc_start: 0.7404 (mmm) cc_final: 0.7005 (mmm) REVERT: D 142 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7533 (ptm-80) REVERT: D 164 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7976 (mt) REVERT: D 173 ARG cc_start: 0.7439 (ttm110) cc_final: 0.7156 (mtp-110) REVERT: D 183 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7321 (mmp80) REVERT: D 199 HIS cc_start: 0.7119 (t70) cc_final: 0.6311 (t70) REVERT: D 214 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7717 (ttmm) REVERT: D 276 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6647 (mm-30) REVERT: D 279 ARG cc_start: 0.7514 (ptp-110) cc_final: 0.6925 (ptp90) REVERT: D 301 VAL cc_start: 0.5662 (OUTLIER) cc_final: 0.5436 (m) REVERT: D 331 PHE cc_start: 0.7469 (m-10) cc_final: 0.7150 (m-10) REVERT: D 333 LYS cc_start: 0.6529 (tttp) cc_final: 0.6232 (tttp) REVERT: D 346 ASP cc_start: 0.7987 (p0) cc_final: 0.7706 (p0) REVERT: D 348 PHE cc_start: 0.7961 (t80) cc_final: 0.7483 (t80) REVERT: D 350 GLU cc_start: 0.8765 (tp30) cc_final: 0.8365 (mm-30) REVERT: D 351 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: D 409 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.7974 (tpp-160) REVERT: D 454 TRP cc_start: 0.7895 (t60) cc_final: 0.7207 (t60) REVERT: D 458 MET cc_start: 0.7507 (mmt) cc_final: 0.6810 (mmt) outliers start: 57 outliers final: 32 residues processed: 413 average time/residue: 0.1616 time to fit residues: 93.9143 Evaluate side-chains 424 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 377 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 HIS ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN C 27 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139268 restraints weight = 36163.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138908 restraints weight = 19351.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139627 restraints weight = 11972.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140223 restraints weight = 10600.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140506 restraints weight = 9206.379| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20302 Z= 0.184 Angle : 0.642 16.340 28362 Z= 0.357 Chirality : 0.042 0.235 3108 Planarity : 0.005 0.059 3020 Dihedral : 23.586 82.226 4293 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.49 % Allowed : 19.39 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.20), residues: 1936 helix: 2.06 (0.17), residues: 910 sheet: -0.18 (0.29), residues: 290 loop : 0.49 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 279 TYR 0.020 0.002 TYR C 216 PHE 0.016 0.001 PHE D 67 TRP 0.069 0.002 TRP C 430 HIS 0.021 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (20286) covalent geometry : angle 0.63635 / 0.36 (28338) hydrogen bonds : bond 0.04658 / 3.18 ( 1053) hydrogen bonds : angle 3.86587 / 2.81 ( 2783) metal coordination : bond 0.00371 / 0.24 ( 16) metal coordination : angle 3.11192 / 2.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7019 (tp30) cc_final: 0.6462 (tp30) REVERT: A 70 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7162 (tm-30) REVERT: A 102 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7554 (mmtp) REVERT: A 135 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6742 (tm-30) REVERT: A 150 ARG cc_start: 0.7361 (ttm170) cc_final: 0.7024 (mmm-85) REVERT: A 182 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 233 THR cc_start: 0.8630 (m) cc_final: 0.8401 (p) REVERT: A 235 LEU cc_start: 0.8706 (mt) cc_final: 0.8116 (mt) REVERT: A 239 MET cc_start: 0.7491 (mmm) cc_final: 0.6872 (mmm) REVERT: A 244 MET cc_start: 0.6295 (mpp) cc_final: 0.6065 (mpt) REVERT: A 250 LEU cc_start: 0.7188 (tp) cc_final: 0.6854 (tp) REVERT: A 253 LYS cc_start: 0.7898 (mptt) cc_final: 0.7486 (mptt) REVERT: A 265 ARG cc_start: 0.6980 (ptt180) cc_final: 0.6647 (ptt180) REVERT: A 342 MET cc_start: 0.6337 (ttp) cc_final: 0.5920 (ttp) REVERT: A 344 GLU cc_start: 0.5580 (tm-30) cc_final: 0.4997 (tm-30) REVERT: A 383 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 423 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6093 (mm) REVERT: B 2 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7732 (mtp180) REVERT: B 135 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 139 GLU cc_start: 0.7577 (tp30) cc_final: 0.6548 (tp30) REVERT: B 142 ARG cc_start: 0.7024 (ttp-110) cc_final: 0.6582 (ttp-110) REVERT: B 143 SER cc_start: 0.8141 (t) cc_final: 0.7718 (p) REVERT: B 208 ARG cc_start: 0.7349 (mtp180) cc_final: 0.7116 (ttp-110) REVERT: B 251 ASN cc_start: 0.8489 (m-40) cc_final: 0.8252 (m-40) REVERT: B 273 GLU cc_start: 0.7784 (tt0) cc_final: 0.7122 (tp30) REVERT: B 299 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8268 (mt) REVERT: B 350 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7675 (pp20) REVERT: B 376 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7858 (mm-30) REVERT: B 466 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6818 (m) REVERT: C 20 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7355 (mm-30) REVERT: C 26 CYS cc_start: 0.8116 (m) cc_final: 0.7762 (m) REVERT: C 28 GLN cc_start: 0.7886 (tt0) cc_final: 0.7548 (mt0) REVERT: C 69 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: C 113 ASP cc_start: 0.7353 (t0) cc_final: 0.7017 (t0) REVERT: C 118 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7121 (t80) REVERT: C 139 GLU cc_start: 0.7621 (tp30) cc_final: 0.7367 (mm-30) REVERT: C 153 LYS cc_start: 0.8583 (mttt) cc_final: 0.8307 (mttt) REVERT: C 181 ARG cc_start: 0.8294 (mtp85) cc_final: 0.8074 (mtp85) REVERT: C 182 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6687 (tm-30) REVERT: C 186 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7297 (tp30) REVERT: C 241 SER cc_start: 0.8442 (m) cc_final: 0.8003 (p) REVERT: C 267 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: C 300 ARG cc_start: 0.8258 (mmt180) cc_final: 0.7936 (tpp80) REVERT: C 325 ARG cc_start: 0.7168 (ptt180) cc_final: 0.6155 (ptm-80) REVERT: C 329 MET cc_start: 0.7564 (ttm) cc_final: 0.6660 (ttm) REVERT: C 351 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6872 (tm-30) REVERT: C 355 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6668 (p0) REVERT: C 367 TRP cc_start: 0.7797 (t-100) cc_final: 0.7041 (t-100) REVERT: D 9 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7626 (mt) REVERT: D 25 SER cc_start: 0.7957 (p) cc_final: 0.7639 (t) REVERT: D 32 GLN cc_start: 0.7877 (tp40) cc_final: 0.7535 (tp40) REVERT: D 42 GLU cc_start: 0.6964 (tt0) cc_final: 0.6262 (tm-30) REVERT: D 44 LEU cc_start: 0.8454 (mp) cc_final: 0.8026 (mt) REVERT: D 73 ASP cc_start: 0.7066 (m-30) cc_final: 0.6851 (m-30) REVERT: D 79 ARG cc_start: 0.7520 (mtp180) cc_final: 0.7029 (ttm110) REVERT: D 86 SER cc_start: 0.8482 (t) cc_final: 0.8010 (m) REVERT: D 101 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7942 (mmtt) REVERT: D 109 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6376 (mt-10) REVERT: D 132 MET cc_start: 0.7395 (mmm) cc_final: 0.6996 (mmm) REVERT: D 138 LYS cc_start: 0.8213 (mttp) cc_final: 0.7899 (mtpp) REVERT: D 164 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7997 (mt) REVERT: D 173 ARG cc_start: 0.7408 (ttm110) cc_final: 0.7133 (mtp-110) REVERT: D 199 HIS cc_start: 0.7042 (t70) cc_final: 0.6269 (t70) REVERT: D 214 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7679 (ttmm) REVERT: D 239 MET cc_start: 0.7547 (mmm) cc_final: 0.7313 (mmm) REVERT: D 276 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6808 (mm-30) REVERT: D 331 PHE cc_start: 0.7411 (m-10) cc_final: 0.7143 (m-10) REVERT: D 333 LYS cc_start: 0.6477 (tttp) cc_final: 0.6201 (tttp) REVERT: D 346 ASP cc_start: 0.7806 (p0) cc_final: 0.7548 (p0) REVERT: D 348 PHE cc_start: 0.7860 (t80) cc_final: 0.7351 (t80) REVERT: D 350 GLU cc_start: 0.8618 (tp30) cc_final: 0.8264 (mm-30) REVERT: D 351 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: D 409 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.7860 (tpp-160) REVERT: D 454 TRP cc_start: 0.7779 (t60) cc_final: 0.7118 (t60) REVERT: D 458 MET cc_start: 0.7505 (mmt) cc_final: 0.6763 (mmt) outliers start: 56 outliers final: 38 residues processed: 405 average time/residue: 0.1704 time to fit residues: 97.3559 Evaluate side-chains 422 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 373 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 159 optimal weight: 0.1980 chunk 205 optimal weight: 10.9990 chunk 43 optimal weight: 0.1980 chunk 177 optimal weight: 7.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 95 HIS ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN C 27 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.190076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140335 restraints weight = 36246.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140539 restraints weight = 17761.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142118 restraints weight = 10939.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142748 restraints weight = 8982.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143022 restraints weight = 8411.214| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20302 Z= 0.132 Angle : 0.625 17.661 28362 Z= 0.346 Chirality : 0.041 0.232 3108 Planarity : 0.005 0.056 3020 Dihedral : 23.541 82.070 4293 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.93 % Allowed : 20.32 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.20), residues: 1936 helix: 2.18 (0.17), residues: 910 sheet: -0.26 (0.29), residues: 285 loop : 0.60 (0.25), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 256 TYR 0.019 0.002 TYR C 188 PHE 0.040 0.001 PHE B 348 TRP 0.079 0.002 TRP C 430 HIS 0.024 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (20286) covalent geometry : angle 0.61870 / 0.35 (28338) hydrogen bonds : bond 0.04135 / 2.85 ( 1053) hydrogen bonds : angle 3.72967 / 2.72 ( 2783) metal coordination : bond 0.00203 / 0.13 ( 16) metal coordination : angle 3.09068 / 2.15 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 380 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.6956 (tp30) cc_final: 0.6431 (tp30) REVERT: A 70 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 88 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6912 (tpp-160) REVERT: A 102 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7471 (mmtp) REVERT: A 113 ASP cc_start: 0.7538 (t0) cc_final: 0.7279 (t0) REVERT: A 131 GLN cc_start: 0.7655 (tp40) cc_final: 0.7363 (tt0) REVERT: A 135 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6700 (tm-30) REVERT: A 150 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7014 (mmm-85) REVERT: A 182 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 233 THR cc_start: 0.8665 (m) cc_final: 0.8418 (p) REVERT: A 235 LEU cc_start: 0.8725 (mt) cc_final: 0.8137 (mt) REVERT: A 239 MET cc_start: 0.7621 (mmm) cc_final: 0.6948 (mmm) REVERT: A 244 MET cc_start: 0.6330 (mpp) cc_final: 0.6062 (mpt) REVERT: A 250 LEU cc_start: 0.7128 (tp) cc_final: 0.6817 (tp) REVERT: A 253 LYS cc_start: 0.7822 (mptt) cc_final: 0.7408 (mptt) REVERT: A 265 ARG cc_start: 0.7023 (ptt180) cc_final: 0.6650 (ptt180) REVERT: A 342 MET cc_start: 0.6330 (ttp) cc_final: 0.5907 (ttp) REVERT: A 344 GLU cc_start: 0.5751 (tm-30) cc_final: 0.5298 (tm-30) REVERT: A 423 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6034 (mm) REVERT: B 20 GLU cc_start: 0.7566 (pm20) cc_final: 0.7199 (mp0) REVERT: B 109 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 135 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 142 ARG cc_start: 0.6980 (ttp-110) cc_final: 0.6498 (ttp-110) REVERT: B 153 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7422 (mtmp) REVERT: B 203 HIS cc_start: 0.7515 (t-90) cc_final: 0.7252 (t-90) REVERT: B 208 ARG cc_start: 0.7348 (mtp180) cc_final: 0.7111 (ttp-110) REVERT: B 244 MET cc_start: 0.8311 (mmt) cc_final: 0.7848 (mmp) REVERT: B 251 ASN cc_start: 0.8499 (m-40) cc_final: 0.8258 (m-40) REVERT: B 273 GLU cc_start: 0.7745 (tt0) cc_final: 0.7050 (tp30) REVERT: B 299 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 350 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7747 (pp20) REVERT: B 351 GLU cc_start: 0.8711 (pt0) cc_final: 0.8369 (pt0) REVERT: B 376 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7984 (mm-30) REVERT: B 466 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6805 (m) REVERT: C 20 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7303 (mm-30) REVERT: C 26 CYS cc_start: 0.8075 (m) cc_final: 0.7754 (m) REVERT: C 28 GLN cc_start: 0.7833 (tt0) cc_final: 0.7506 (mt0) REVERT: C 43 ASP cc_start: 0.7464 (m-30) cc_final: 0.7194 (m-30) REVERT: C 57 ARG cc_start: 0.6904 (mpp80) cc_final: 0.6583 (mtm-85) REVERT: C 69 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: C 109 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6826 (pt0) REVERT: C 113 ASP cc_start: 0.7256 (t0) cc_final: 0.6955 (t0) REVERT: C 118 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6988 (t80) REVERT: C 139 GLU cc_start: 0.7507 (tp30) cc_final: 0.7073 (mm-30) REVERT: C 142 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7250 (ptm-80) REVERT: C 153 LYS cc_start: 0.8540 (mttt) cc_final: 0.8257 (mttt) REVERT: C 175 VAL cc_start: 0.7639 (p) cc_final: 0.7191 (m) REVERT: C 181 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7936 (mtp85) REVERT: C 182 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6580 (tm-30) REVERT: C 186 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7187 (tp30) REVERT: C 226 GLN cc_start: 0.7350 (mp10) cc_final: 0.7084 (mp10) REVERT: C 241 SER cc_start: 0.8438 (m) cc_final: 0.7965 (p) REVERT: C 267 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: C 300 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7961 (tpp80) REVERT: C 325 ARG cc_start: 0.7159 (ptt180) cc_final: 0.6108 (ptm-80) REVERT: C 329 MET cc_start: 0.7415 (ttm) cc_final: 0.6551 (ttm) REVERT: C 351 GLU cc_start: 0.7673 (tm-30) cc_final: 0.6925 (tm-30) REVERT: C 355 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.6658 (p0) REVERT: C 367 TRP cc_start: 0.7748 (t-100) cc_final: 0.6991 (t-100) REVERT: D 9 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7577 (mt) REVERT: D 25 SER cc_start: 0.8000 (p) cc_final: 0.7746 (t) REVERT: D 32 GLN cc_start: 0.7860 (tp40) cc_final: 0.7493 (tp40) REVERT: D 42 GLU cc_start: 0.6995 (tt0) cc_final: 0.6288 (tm-30) REVERT: D 44 LEU cc_start: 0.8402 (mp) cc_final: 0.7958 (mt) REVERT: D 74 VAL cc_start: 0.8377 (p) cc_final: 0.8055 (m) REVERT: D 79 ARG cc_start: 0.7460 (mtp180) cc_final: 0.6839 (ttm110) REVERT: D 86 SER cc_start: 0.8426 (t) cc_final: 0.7941 (m) REVERT: D 101 LYS cc_start: 0.8234 (mmtt) cc_final: 0.8031 (mmtt) REVERT: D 109 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6258 (mt-10) REVERT: D 132 MET cc_start: 0.7285 (mmm) cc_final: 0.6872 (mmm) REVERT: D 164 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7929 (mt) REVERT: D 173 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7106 (mtp-110) REVERT: D 199 HIS cc_start: 0.7064 (t70) cc_final: 0.6223 (t70) REVERT: D 214 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7660 (ttmm) REVERT: D 276 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6864 (mm-30) REVERT: D 331 PHE cc_start: 0.7465 (m-10) cc_final: 0.7137 (m-10) REVERT: D 333 LYS cc_start: 0.6485 (tttp) cc_final: 0.6192 (tttp) REVERT: D 348 PHE cc_start: 0.7885 (t80) cc_final: 0.7204 (t80) REVERT: D 350 GLU cc_start: 0.8777 (tp30) cc_final: 0.8403 (mm-30) REVERT: D 351 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: D 409 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8006 (tpp-160) REVERT: D 454 TRP cc_start: 0.7889 (t60) cc_final: 0.7226 (t60) REVERT: D 458 MET cc_start: 0.7453 (mmt) cc_final: 0.6774 (mmt) outliers start: 47 outliers final: 32 residues processed: 402 average time/residue: 0.1919 time to fit residues: 108.3858 Evaluate side-chains 419 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 375 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 HIS ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN C 27 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140000 restraints weight = 36362.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140959 restraints weight = 19992.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141102 restraints weight = 13603.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142780 restraints weight = 11170.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142717 restraints weight = 9390.754| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20302 Z= 0.136 Angle : 0.635 17.258 28362 Z= 0.349 Chirality : 0.041 0.304 3108 Planarity : 0.005 0.078 3020 Dihedral : 23.526 82.466 4293 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.68 % Allowed : 20.70 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.20), residues: 1936 helix: 2.08 (0.17), residues: 911 sheet: -0.25 (0.29), residues: 289 loop : 0.60 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 397 TYR 0.018 0.002 TYR C 216 PHE 0.039 0.001 PHE B 348 TRP 0.081 0.002 TRP C 430 HIS 0.025 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (20286) covalent geometry : angle 0.62947 / 0.35 (28338) hydrogen bonds : bond 0.04142 / 2.84 ( 1053) hydrogen bonds : angle 3.78783 / 2.75 ( 2783) metal coordination : bond 0.00215 / 0.14 ( 16) metal coordination : angle 2.92798 / 2.04 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.45 seconds wall clock time: 64 minutes 24.41 seconds (3864.41 seconds total)